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Research Areas (689)
- Topic 1: Genes, Cells and Cell-Based Medicine (689)

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Akalin, Altuna (BIMSB)

Enhancing biomarker-based oncology trial matching using large language models.
Al Khoury, N., Shaik, M., Wurmus, R. and Akalin, A.
bioRxiv : 2024.09.13.612922. 19 September 2024

The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19.
Andrade, B.G.N., Cuadrat, R.R.C., Tonetti, F.R., Kitazawa, H. and Villena, J.
Bioscience of Microbiota, Food and Health 41 (3): 94-102. 1 July 2022

Putative mobilized colistin resistance genes in the human gut microbiome.
Andrade, B.G.N., Goris, T., Afli, H., Coutinho, F.H., Dávila, A.M.R. and Cuadrat, R.R.C.
BMC Microbiology 21 : 220. 22 July 2021

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M., Franke, V., Benedum, J., Grishkovskaya, I., Strobl, X., Polyansky, A., Ammann, G., Platzer, S., Neudolt, A., Wunder, A., Walch, L., Kaiser, S., Zagrovic, B., Djinovic-Carugo, K., Akalin, A. and Slade, D.
Nature Communications 14 (1): 166. 11 January 2023

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
Appel, L.M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., Schoeberl, U.E., Puchinger, M.G., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K., Lin, G., Vlasova, A., Leeb, M., Pavri, R., Stark, A., Akalin, A., Stefl, R., Bernecky, C., Djinovic-Carugo, K. and Slade, D.
Nature Communications 12 (1): 6078. 19 October 2021

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

Multi-omics alleviates the limitations of panel sequencing for cancer drug response prediction.
Baranovskii, A., Gündüz, I.B., Franke, V., Uyar, B. and Akalin, A.
Cancers 14 (22): 5604. 15 November 2022

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
Benedum, J., Franke, V., Appel, L.M., Walch, L., Bruno, M., Schneeweiss, R., Gruber, J., Oberndorfer, H., Frank, E., Strobl, X., Polyansky, A., Zagrovic, B., Akalin, A. and Slade, D.
Nature Communications 14 (1): 7912. 30 November 2023

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L., Morao, A.K., Kim, J., Jimenez, D.S., Maryn, N., Bikkasani, K., Carrozza, M.J., Albritton, S.E., Kramer, M., Street, L.A., Cerimi, K., Schumann, V.F., Bahry, E., Preibisch, S., Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

Association of the human gut microbiota with vascular stiffness.
Cuadrat, R.R.C., Goris, T., Birukov, A., Eichelmann, F., Andrade, B.G.N., Bang, C., Franke, A., Wittenbecher, C. and Schulze, M.B.
Scientific Reports 13 (1): 13348. 16 August 2023

Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation.
Cuadrat, R.R.C., Kratzer, A., Arnal, H.G., Rathgeber, A.C., Wreczycka, K., Blume, A., Gündüz, I.B., Ebenal, V., Mauno, T., Osberg, B., Moobed, M., Hartung, J., Jakobs, K., Seppelt, C., Meteva, D., Haghikia, A., Leistner, D.M., Landmesser, Ulf and Akalin, A.
NAR Genomics and Bioinformatics 5 (2): lqad061. June 2023

Identifying tumor cells at the single-cell level using machine learning.
Dohmen, J., Baranovskii, A., Ronen, J., Uyar, B., Franke, V. and Akalin, A.
Genome Biology 23 (1): 123. 30 May 2022

The SEQC2 epigenomics quality control (EpiQC) study.
Foox, J., Nordlund, J., Lalancette, C., Gong, T., Lacey, M., Lent, S., Langhorst, B.W., Ponnaluri, V.K.C., Williams, L., Padmanabhan, K.R., Cavalcante, R., Lundmark, A., Butler, D., Mozsary, C., Gurvitch, J., Greally, J.M., Suzuki, M., Menor, M., Nasu, M., Alonso, A., Sheridan, C., Scherer, A., Bruinsma, S., Golda, G., Muszynska, A., Łabaj, P.P., Campbell, M.A., Wos, F., Raine, A., Liljedahl, U., Axelsson, T., Wang, C., Chen, Z., Yang, Z., Li, J., Yang, X., Wang, H., Melnick, A., Guo, S., Blume, A., Franke, V., Ibanez de Caceres, I., Rodriguez-Antolin, C., Rosas, R., Davis, J.W., Ishii, J., Megherbi, D.B., Xiao, W., Liao, W., Xu, J., Hong, H., Ning, B., Tong, W., Akalin, A., Wang, Y., Deng, Y. and Mason, C.E.
Genome Biology 22 (1): 332. 6 December 2021

A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency.
Fornes, O., Jia, A., Kuehn, H.S., Min, Q., Pannicke, U., Schleussner, N., Thouenon, R., Yu, Z., de Los Angeles Astbury, M., Biggs, C.M., Galicchio, M., Garcia-Campos, J.A., Gismondi, S., Gonzalez Villarreal, G., Hildebrand, K.J., Hönig, M., Hou, J., Moshous, D., Pittaluga, S., Qian, X., Rozmus, J., Schulz, A.S., Staines-Boone, A.T., Sun, B., Sun, J., Uwe, S., Venegas-Montoya, E., Wang, W., Wang, X., Ying, W., Zhai, X., Zhou, Q., Akalin, A., André, I., Barth, T.F.E., Baumann, B., Brüstle, A., Burgio, G., Bustamante, J.C., Casanova, J.L., Casarotto, M.G., Cavazzana, M., Chentout, L., Cockburn, I.A., Costanza, M., Cui, C., Daumke, O., Del Bel, K.L., Eibel, H., Feng, X., Franke, V., Gebhardt, J.C.M., Götz, A., Grunwald, S., Hoareau, B., Hughes, T.R., Jacobsen, E.M., Janz, M., Jolma, A., Lagresle-Peyrou, C., Lai, N., Li, Y., Lin, S., Lu, H.Y., Lugo-Reyes, S.O., Meng, X., Möller, P., Moreno-Corona, N., Niemela, J.E., Novakovsky, G., Perez-Caraballo, J.J., Picard, C., Poggi, L., Puig-Lombardi, M.E., Randall, K.L., Reisser, A., Schmitt, Y., Seneviratne, S., Sharma, M., Stoddard, J., Sundararaj, S., Sutton, H., Tran, L.Q., Wang, Y., Wasserman, W.W., Wen, Z., Winkler, W., Xiong, E., Yang, A.W.H., Yu, M., Zhang, L., Zhang, H., Zhao, Q., Zhen, X., Enders, A., Kracker, S., Martinez-Barricarte, R., Mathas, S., Rosenzweig, S.D., Schwarz, K., Turvey, S.E. and Wang, J.Y.
Science Immunology 8 (79): eade7953. January 2023

Parallel genetics of regulatory sequences using scalable genome editing in vivo.
Froehlich, J.J., Uyar, B., Herzog, M., Theil, K., Glažar, P., Akalin, A. and Rajewsky, N.
Cell Reports 35 (2): 108988. 13 April 2021

Evaluating large language model workflows in clinical decision support: referral, triage, and diagnosis.
Gaber, F., Shaik, M., Franke, V. and Akalin, A.
medRxiv : 2024.09.27.24314505. 28 September 2024

Rapid inflammasome activation is attenuated in post-myocardial infarction monocytes.
Giral, H., Franke, V., Moobed, M., Müller, M.F., Lübking, L., James, D.M., Hartung, J., Kuschnerus, K., Meteva, D., Seppelt, C., Jakob, P., Klingenberg, R., Kränkel, N., Leistner, D., Zeller, T., Blankenberg, S., Zimmermann, F., Haghikia, A., Lüscher, T.F., Akalin, A., Landmesser, U. and Kratzer, A.
Frontiers in Immunology 13 : 857455. 26 April 2022

Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells.
Islam, M.A., Albarracin, L., Melnikov, V., Andrade, B.G.N., Cuadrat, R.R.C., Kitazawa, H. and Villena, J.
Pathogens 10 (6): 634. 21 May 2021

Immunobiotic Lactobacilli improve resistance of respiratory epithelial cells to SARS-CoV-2 infection.
Islam, M.A., Albarracin, L., Tomokiyo, M., Valdez, J.C., Sacur, J., Vizoso-Pinto, M.G., Andrade, B.G.N., Cuadrat, R.C., Kitazawa, H. and Villena, J.
Pathogens 10 (9): 1197. September 2021

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data.
Jeong, Y., Ronen, J., Kopp, W., Lutsik, P. and Akalin, A.
BMC Bioinformatics 25 (1): 257. 6 August 2024

Cytosolic nucleic acid sensors and interferon beta-1 activation drive radiation-induced anti-tumour immune effects in human pancreatic cancer cells.
Kerschbaum-Gruber, S., Kleinwächter, A., Popova, K., Kneringer, A., Appel, L.M., Stasny, K., Röhrer, A., Dias, A.B., Benedum, J., Walch, L., Postl, A., Barna, S., Kratzer, B., Pickl, W.F., Akalin, A., Horvat, F., Franke, V., Widder, J., Georg, D. and Slade, D.
Frontiers in Immunology 15 : 1286942. 20 September 2024

Transcriptional repression of NFKBIA triggers constitutive IKK- and proteasome-independent p65/RelA activation in senescence.
Kolesnichenko, M., Mikuda, N., Höpken, U.E., Kärgel, E., Uyar, B., Tufan, A.B., Milanovic, M., Sun, W., Krahn, I., Schleich, K., von Hoff, L., Hinz, M., Willenbrock, M., Jungmann, S., Akalin, A., Lee, S., Schmidt-Ullrich, R., Schmitt, C.A. and Scheidereit, C.
EMBO Journal 40 (6): e104296. 15 March 2021

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W., Akalin, A. and Ohler, U.
Nature Machine Intelligence 4 (2): 162-168. February 2022

Spatio-temporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Rybak-Wolf, A., Kempa, S., Zinzen, R.P., Woehler, A. and Rajewsky, N.
bioRxiv : 2021.09.26.461850v3. 9 February 2022

Predicting lethal courses in critically ill COVID-19 patients using a machine learning model trained on patients with non-COVID-19 viral pneumonia.
Lichtner, G., Balzer, F., Haufe, S., Giesa, N., Schiefenhövel, F., Schmieding, M., Jurth, C., Kopp, W., Akalin, A., Schaller, S.J., Weber-Carstens, S., Spies, C. and von Dincklage, F.
Scientific Reports 11 (1): 13205. 24 June 2021

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C., Kopp, W., Vučićević, D., Mattonet, K., Kempfer, R., Hirsekorn, A., Bilić, I., Gil, M., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

Lymphocyte access to lymphoma is impaired by high endothelial venule regression.
Menzel, L., Zschummel, M., Crowley, T., Franke, V., Grau, M., Ulbricht, C., Hauser, A., Siffrin, V., Bajénoff, M., Acton, S.E., Akalin, A., Lenz, G., Willimsky, G., Höpken, U.E. and Rehm, A.
Cell Reports 37 (4): 109878. 26 October 2021

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions.
Rrustemi, T., Meyer, K., Roske, Y., Uyar, B., Akalin, A., Imami, K., Ishihama, Y., Daumke, O. and Selbach, M.
Nature Communications 15 (1): 3146. 11 April 2024

CompassDock: Comprehensive accurate assessment approach for deep learning-based molecular docking in inference and fine-tuning.
Sariguen, A., Franke, V., Uyar, B. and Akalin, A.
arXiv : 2406.06841. 1 October 2024

Transcriptional reprogramming by mutated IRF4 in lymphoma.
Schleussner, N., Cauchy, P., Franke, V., Giefing, M., Fornes, O., Vankadari, N., Assi, S.A., Costanza, M., Weniger, M.A., Akalin, A., Anagnostopoulos, I., Bukur, T., Casarotto, M.G., Damm, F., Daumke, O., Edginton-White, B., Gebhardt, J.C.M., Grau, M., Grunwald, S., Hansmann, M.L., Hartmann, S., Huber, L., Kärgel, E., Lusatis, S., Noerenberg, D., Obier, N., Pannicke, U., Fischer, A., Reisser, A., Rosenwald, A., Schwarz, K., Sundararaj, S., Weilemann, A., Winkler, W., Xu, W., Lenz, G., Rajewsky, K., Wasserman, W.W., Cockerill, P.N., Scheidereit, C., Siebert, R., Küppers, R., Grosschedl, R., Janz, M., Bonifer, C. and Mathas, S.
Nature Communications 14 (1): 6947. 7 November 2023

Oncogene inactivation-induced senescence facilitates tumor relapse.
Schmitt, P., Hönig, K., Milojkovic, A., Anders, K., Schröck, E., Sauer, S., Uyar, B., Akalin, A., Martínez-Reyes, I. and Blankenstein, T.
bioRxiv : 2024.07.13.603369. 17 July 2024

Disintegration of the NuRD complex in primary human muscle stem cells in critical illness myopathy.
Schneider, J., Sundaravinayagam, D., Blume, A., Marg, A., Grunwald, S., Metzler, E., Escobar, H., Müthel, S., Wang, H., Wollersheim, T., Weber-Carstens, S., Akalin, A., Di Virgilio, M., Tursun, B. and Spuler, S.
International Journal of Molecular Sciences 24 (3): 2772. 1 February 2023

SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Schumann, V.F., de Castro Cuadrat, R.R., Wyler, E., Wurmus, R., Deter, A., Quedenau, C., Dohmen, J., Faxel, M., Borodina, T., Blume, A., Freimuth, J., Meixner, M., Grau, J.H., Liere, K., Hackenbeck, T., Zietzschmann, F., Gnirss, R., Böckelmann, U., Uyar, B., Franke, V., Barke, N., Altmüller, J., Rajewsky, N., Landthaler, M. and Akalin, A.
Science of the Total Environment 853 : 158931. 20 December 2022

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.
Sieberts, S.K., Schaff, J., Duda, M., Pataki, B.Á., Sun, M., Snyder, P., Daneault, J.F., Parisi, F., Costante, G., Rubin, U., Banda, P., Chae, Y., Chaibub Neto, E., Dorsey, E.R., Aydın, Z., Chen, A., Elo, L.L., Espino, C., Glaab, E., Goan, E., Golabchi, F.N., Görmez, Y., Jaakkola, M.K., Jonnagaddala, J., Klén, R., Li, D., McDaniel, C., Perrin, D., Perumal, T.M., Rad, N.M., Rainaldi, E., Sapienza, S., Schwab, P., Shokhirev, N., Venäläinen, M.S., Vergara-Diaz, G., Zhang, Y., Wang, Y., Guan, Y., Brunner, D., Bonato, P., Mangravite, L.M. and Omberg, L.
NPJ Digital Medicine 4 (1): 53. 19 March 2021

A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.
Szabó, D., Franke, V., Bianco, S., Batiuk, M.Y., Paul, E.J., Kukalev, A., Pfisterer, U.G., Irastorza-Azcarate, I., Chiariello, A.M., Demharter, S., Zea-Redondo, L., Lopez-Atalaya, J.P., Nicodemi, M., Akalin, A., Khodosevich, K., Ungless, M.A., Winick-Ng, W. and Pombo, A.
bioRxiv : 2024.05.10.593308. 12 May 2024

DNA virus infections shape transposable elements activity in vitro and in vivo.
Tan, J., Franke, V., Neugebauer, E., Lagisquet, J., Kuderna, A.K., Walter, S., Landthaler, M., Ensser, A., Stamminger, T., Gramberg, T., Akalin, A., Wyler, E. and Full, F.
bioRxiv : 2024.04.18.589901. 19 April 2024

Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond.
Uyar, B., Savchyn, T., Wurmus, R., Sarigun, A., Shaik, M.M., Franke, V. and Akalin, A.
bioRxiv : 2024.07.16.603606. 18 July 2024

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S., Franke, V., Drayman, N., Wyler, E., Tay, S., Landthaler, M., Akalin, A., Ensser, A. and Full, F.
bioRxiv : 2021.03.24.436599. 24 March 2021

Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng, W., Kukalev, A., Harabula, I., Zea-Redondo, L., Szabó, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A.M., Irastorza-Azcarate, I., Thieme, C.J., Sparks, T.M., Carvalho, S., Fiorillo, L., Musella, F., Irani, E., Triglia, E.T., Kolodziejczyk, A.A., Abentung, A., Apostolova, G., Paul, E.J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S.A., Dechant, G., Ungless, M.A., Nicodemi, M., Welch, L., Castelo-Branco, G. and Pombo, A.
Nature 599 (7886): 684-691. 25 November 2021

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L.T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T.F., Müller, M.A., Niemeyer, D., Hocke, A., Selbach, M., Akalin, A., Rajewsky, N., Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

Altmüller, Janine (BIMSB/BIH)

The interleukin-11 receptor variant p.W307R results in craniosynostosis in humans.
Ahmad, I., Lokau, J., Kespohl, B., Malik, N.A., Baig, S.M., Hartig, R., Behme, D., Schwab, R., Altmüller, J., Jameel, M., Mucha, S., Thiele, H., Tariq, M., Nürnberg, P., Erdmann, J. and Garbers, C.
Scientific Reports 13 (1): 13479. 18 August 2023

Single-nucleus and spatial transcriptome reveal adrenal homeostasis in normal and tumoural adrenal glands.
Altieri, B., Secener, A.K., Sai, S., Fischer, C., Sbiera, S., Arampatzi, P., Kircher, S., Herterich, S., Landwehr, L.S., Vitcetz, S.N., Braeuning, C., Fassnacht, M., Ronchi, C.L. and Sauer, S.
Clinical and Translational Medicine 14 (8): e1798. August 2024

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19.
Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J. and Wyler, E.
Genome Biology and Evolution 14 (7): evac100. July 2022

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A., Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

De novo variants of CSNK2B cause a new intellectual disability-craniodigital syndrome by disrupting the canonical Wnt signaling pathway.
Asif, M., Kaygusuz, E., Shinawi, M., Nickelsen, A., Hsieh, T.C., Wagle, P., Budde, B., Hochscherf, J., Abdullah, U., Höning, S., Nienberg, C., Lindenblatt, D., Noegel, A.A., Altmüller, J., Thiele, H., Motameny, S., Fleischer, N., Segal, I., Pais, L., Tinschert, S., Samra, N.G., Savatt, J.M., Rudy, N.L., De Luca, C., Fortugno, P., White, S.M., Krawitz, P., Hurst, A.C.E., Niefind, K., Jose, J., Brancati, F., Nürnberg, P. and Hussain, M.S.
Human Genetics and Genomics Advances 3 (3): 100111. 14 July 2022

A novel missense variant of SCN4A co-segregates with congenital essential tremor in a consanguineous Kurdish family.
Asif, M., Mocanu, I.D., Abdullah, U., Höhne, W., Altmüller, J., Makhdoom, E.U.H., Thiele, H., Baig, S.M., Nürnberg, P., Graul-Neumann, L. and Hussain, M.S.
American Journal of Medical Genetics A 188 (4): 1251-1258. April 2022

Expanding the spectrum of EEF1D neurodevelopmental disorders: biallelic variants in the guanine exchange domain.
Averdunk, L., Al-Thihli, K., Surowy, H., Lüdecke, H.J., Drechsler, M., Yigit, G., Smorag, L., Hallak, B.A., Li, Y., Altmüller, J., Guthoff, T., Wallot, M., Nürnberg, P., Wollnik, B., Abou Jamra, R., Al-Maawali, A. and Wieczorek, D.
Clinical Genetics 103 (4): 484-491. April 2023

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia.
Bakina, O., Conrad, T., Mitic, N., Vidal, R.O., Obrusnik, T., Sai, S., Nolte, C., Semtner, M. and Kettenmann, H.
PLoS ONE 19 (7): e0302376. 11 July 2024

Activation of gp130 signaling in T cells drives T(H)17-mediated multi-organ autoimmunity.
Baumgartner, F., Bamopoulos, S.A., Faletti, L., Hsiao, H.J., Holz, M., Gonzalez-Menendez, I., Solé-Boldo, L., Horne, A., Gosavi, S., Özerdem, C., Singh, N., Liebig, S., Ramamoorthy, S., Lehmann, M., Demel, U., Kühl, A.A., Wartewig, T., Ruland, J., Wunderlich, F.T., Schick, M., Walther, W., Rose-John, S., Haas, S., Quintanilla-Martinez, L., Feske, S., Ehl, S., Glauben, R. and Keller, U.
Science Signaling 17 (824): eadc9662. 20 February 2024

A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover.
Boileau, E., Altmüller, J., Naarmann-de Vries, I.S. and Dieterich, C.
Briefings in Bioinformatics 22 (6): bbab219. November 2021

Full-length spatial transcriptomics reveals the unexplored isoform diversity of the myocardium post-MI.
Boileau, E., Li, X., Naarmann-de Vries, I.S., Becker, C., Casper, R., Altmüller, J., Leuschner, F. and Dieterich, C.
Frontiers in Genetics 13 : 912572. 22 July 2022

Claudin-10a deficiency shifts proximal tubular Cl(-) permeability to cation selectivity via claudin-2 redistribution.
Breiderhoff, T., Himmerkus, N., Meoli, L., Fromm, A., Sewerin, S., Kriuchkova, N., Nagel, O., Ladilov, Y., Krug, S., Quintanova, C., Stumpp, M., Garbe-Schönberg, D., Westernströer, U., Merkel, C., Brinkhus, M., Altmüller, J., Schweiger, M., Mueller, D., Mutig, K., Morawski, M., Halbritter, J., Milatz, S., Bleich, M. and Günzel, D.
Journal of the American Society of Nephrology 33 (4): 699-717. April 2022

Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage.
Bubb, K., Holzer, T., Nolte, J.L., Krüger, M., Wilson, R., Schlötzer-Schrehardt, U., Brinckmann, J., Altmüller, J., Aszodi, A., Fleischhauer, L., Clausen-Schaumann, H., Probst, K. and Brachvogel, B.
Journal of Biological Chemistry 297 (4): 101224. October 2021

Mutation-induced LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome.
Busley, A.V., Gutiérrez-Gutiérrez, Ó., Hammer, E., Koitka, F., Mirzaiebadizi, A., Steinegger, M., Pape, C., Böhmer, L., Schroeder, H., Kleinsorge, M., Engler, M., Cirstea, I.C., Gremer, L., Willbold, D., Altmüller, J., Marbach, F., Hasenfuss, G., Zimmermann, W.H., Ahmadian, M.R., Wollnik, B. and Cyganek, L.
Cell Reports 43 (7): 114448. 23 July 2024

WARS1 and SARS1: two tRNA synthetases implicated in autosomal recessive microcephaly.
Bögershausen, N., Krawczyk, H.E., Jamra, R.A., Lin, S.J., Yigit, G., Hüning, I., Polo, A.M., Vona, B., Huang, K., Schmidt, J., Altmüller, J., Luppe, J., Platzer, K., Dörgeloh, B.B., Busche, A., Biskup, S., Mendes, M.I., Smith, D.E.C., Salomons, G.S., Zibat, A., Bültmann, E., Nürnberg, P., Spielmann, M., Lemke, J.R., Li, Y., Zenker, M., Varshney, G.K., Hillen, H.S., Kratz, C.P. and Wollnik, B.
Human Mutation 43 (10): 1454-1471. October 2022

Intramyocardial sprouting tip cells specify coronary arterialization.
Cano, E., Schwarzkopf, J., Kanda, M., Lindberg, E.L., Hollfinger, I., Pogontke, C., Braeuning, C., Fischer, C., Hübner, N. and Gerhardt, H.
Circulation Research 135 (6): 671-684. 30 August 2024

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R., Conrad, T., Stöber, M.C., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Kasack, K., Brückner, L., van Leen, E., Helmsauer, K., Dorado Garcia, H., Stefanova, M.E., Hung, K.L., Bei, Y., Schmelz, K., Lodrini, M., Mundlos, S., Chang, H.Y., Deubzer, H.E., Sauer, S., Eggert, A., Schulte, J.H., Schwarz, R.F., Haase, K., Koche, R.P. and Henssen, A.G.
Nature Genetics 55 (5): 880-890. May 2023

XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes.
Chatzinikolaou, G., Stratigi, K., Siametis, A., Goulielmaki, E., Akalestou-Clocher, A., Tsamardinos, I., Topalis, P., Austin, C., Bouwman, B.A.M., Crosetto, N., Altmüller, J. and Garinis, G.A.
Science Advances 9 (45): eadi2095. 10 November 2023

Single cell‐ and spatial 'omics revolutionize physiology.
Conrad, T. and Altmüller, J.
Acta Physiologica 235 (4): e13848. August 2022

T- and L-type calcium channels maintain calcium oscillations in the murine zona glomerulosa.
Dinh, H.A., Volkert, M., Secener, A.K., Scholl, U.I. and Stölting, G.
Hypertension 81 (4): 811-822. April 2024

Mutant phosphodiesterase 3A protects from hypertension-induced cardiac damage.
Ercu, M., Mücke, M.B., Pallien, T., Markó, L., Sholokh, A., Schächterle, C., Aydin, A., Kidd, A., Walter, S., Esmati, Y., McMurray, B.J., Lato, D.F., Sunaga-Franze, D.Y., Dierks, P.H., Flores, B.I.M., Walker-Gray, R., Gong, M., Merticariu, C., Zühlke, K., Russwurm, M., Liu, T., Batolomaeus, T.U.P., Pautz, S., Schelenz, S., Taube, M., Napieczynska, H., Heuser, A., Eichhorst, J., Lehmann, M., Miller, D.C., Diecke, S., Qadri, F., Popova, E., Langanki, R., Movsesian, M.A., Herberg, F.W., Forslund, S.K., Müller, D.N., Borodina, T., Maass, P.G., Bähring, S., Hübner, N., Bader, M. and Klussmann, E.
Circulation 146 (23): 1758-1778. 6 December 2022

Germline C1GALT1C1 mutation causes a multisystem chaperonopathy.
Erger, F., Aryal, R.P., Reusch, B., Matsumoto, Y., Meyer, R., Zeng, J., Knopp, C., Noel, M., Muerner, L., Wenzel, A., Kohl, S., Tschernoster, N., Rappl, G., Rouvet, I., Schröder-Braunstein, J., Seibert, F.S., Thiele, H., Häusler, M.G., Weber, L.T., Büttner-Herold, M., Elbracht, M., Cummings, S.F., Altmüller, J., Habbig, S., Cummings, R.D. and Beck, B.B.
Proceedings of the National Academy of Sciences of the United States of America 120 (22): e2211087120. 30 May 2023

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging.
Freitag, K., Eede, P., Ivanov, A., Schneeberger, S., Borodina, T., Sauer, S., Beule, D. and Heppner, F.L.
bioRxiv : 2021.08.02.454573v1. 28 November 2021

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
Freitag, K., Eede, P., Ivanov, A., Sterczyk, N., Schneeberger, S., Borodina, T., Sauer, S., Beule, D. and Heppner, F.L.
Communications Biology 6 (1): 40. 13 January 2023

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.
Freitag, K., Sterczyk, N., Wendlinger, S., Obermayer, B., Schulz, J., Farztdinov, V., Mülleder, M., Ralser, M., Houtman, J., Fleck, L., Braeuning, C., Sansevrino, R., Hoffmann, C., Milovanovic, D., Sigrist, S.J., Conrad, T., Beule, D., Heppner, F.L. and Jendrach, M.
Journal of Neuroinflammation 19 (1): 172. 2 July 2022

Interferon regulatory factor 4 plays a pivotal role in the development of aGVHD-associated colitis.
Frueh, J.T., Campe, J., Sunaga-Franze, D.Y., Verheyden, N.A., Ghimire, S., Meedt, E., Haslinger, D., Harenkamp, S., Staudenraus, D., Sauer, S., Kreft, A., Schubert, R., Lohoff, M., Krueger, A., Bonig, H., Chiocchetti, A.G., Zeiser, R., Holler, E. and Ullrich, E.
OncoImmunology 13 (1): 2296712. 2024

Phenotypic spectrum of BLM- and RMI1-related Bloom syndrome.
Gönenc, I.I., Elcioglu, N.H., Martinez Grijalva, C., Aras, S., Großmann, N., Praulich, I., Altmüller, J., Kaulfuß, S., Li, Y., Nürnberg, P., Burfeind, P., Yigit, G. and Wollnik, B.
Clinical Genetics 101 (5-6): 559-564. May 2022

NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling.
Hanssen, F., Gabernet, G., Smith, N.H., Mertes, C., Neogi, A.G., Brandhoff, L., Ossowski, A., Altmueller, J., Becker, K., Petzold, A., Sturm, M., Stöcker, T., Sivalingam, S., Brand, F., Schmidt, A., Buness, A., Probst, A.J., Motameny, S. and Köster, J.
F1000Research 12 : 1125. 11 September 2023

Circulating tumor DNA sequencing for biologic classification and individualized risk stratification in patients with Hodgkin Lymphoma.
Heger, J.M., Mammadova, L., Mattlener, J., Sobesky, S., Cirillo, M., Altmüller, J., Kirst, E., Reinke, S., Klapper, W., Bröckelmann, P.J., Ferdinandus, J., Kaul, H., Schneider, G., Schneider, J., Schleifenbaum, J.K., Ullrich, R.T., Freihammer, M., Awerkiew, S., Lohmann, M., Klein, F., Nürnberg, P., Hallek, M., Rossi, D., Mauz-Körholz, C., Gattenlöhner, S., Bräuninger, A., Borchmann, P., von Tresckow, B. and Borchmann, S.
Journal of Clinical Oncology 42 (35): 4218-4230. 10 December 2024

Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4(+) T cells as predictors for response to integrin α4β7-blocking therapy in inflammatory bowel disease.
Horn, V., Cancino, C.A., Steinheuer, L.M., Obermayer, B., Fritz, K., Nguyen, A.L., Juhran, K.S., Plattner, C., Bösel, D., Oldenburg, L., Burns, M., Schulz, A.R., Saliutina, M., Mantzivi, E., Lissner, D., Conrad, T., Mashreghi, M.F., Zundler, S., Sonnenberg, E., Schumann, M., Haag, L.M., Beule, D., Flatz, L., Trjanoski, Z., D'Haens, G., Weidinger, C., Mei, H.E., Siegmund, B., Thurley, K. and Hegazy, A.N.
Gastroenterology 28 September 2024 (In Press)

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
Houwaart, Torsten, Belhaj, S., Tawalbeh, E., Nagels, D., Fröhlich, Y., Finzer, P., Ciruela, P., Sabrià, A., Herrero, M., Andrés, C., Antón, A., Benmoumene, A., Asskali, D., Haidar, H., von Dahlen, J., Nicolai, J., Stiller, M., Blum, J., Lange, C., Adelmann, C., Schroer, B., Osmers, U., Grice, C., Kirfel, P.P., Jomaa, H., Strelow, D., Hülse, L., Pigulla, M., Kreuzer, P., Tyshaieva, A., Weber, J., Wienemann, T., Kohns Vasconcelos, M., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Scholz, C.J., Jazmati, N., Göbels, K., Zotz, R., Pfeffer, K., Timm, J., Ehlkes, L., Walker, A. and Dilthey, A.T.
Eurosurveillance 27 (43): 2101089. 27 October 2022

Diagnosing recipient- vs. donor-derived posttransplant myelodysplastic neoplasm via targeted single-cell mutational profiling.
Ihlow, J., Penter, L., Vuong, L.G., Bischoff, P., Obermayer, B., Trinks, A., Blau, O., Behnke, A., Conrad, T., Morkel, M., Wu, C.J., Westermann, J., Bullinger, L., von Brünneck, A.C., Blüthgen, N., Horst, D. and Praktiknjo, S.D.
Med 6 December 2024 (In Press)

Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia.
Jiang, Q., Stachelscheid, J., Bloehdorn, J., Pacholewska, A., Aszyk, C.M., Grotenhuijs, F., Müller, T.A., Onder, O., Wagle, P., Herling, C.D., Kleppe, M., Wang, Z., Coombes, K.R., Robrecht, S., Dalvi, P.S., Plosnita, B., Mayer, P., Abruzzo, L.V., Altmüller, J., Gathof, B.S., Persigehl, T., Fischer, K., Jebaraj, B.M.C., Rienhoff, H.Y., Ecker, R.C., Zhao, Y., Bruns, C.J., Stilgenbauer, S., Elenitoba-Johnson, K.S.J., Hallek, M., Schweiger, M.R., Odenthal, M., Vasyutina, E. and Herling, M.
Blood 142 (1): 44-61. 6 July 2023

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells.
Kalnytska, O., Qvist, P., Kunz, S., Conrad, T., Willnow, T.E. and Schmidt, V.
iScience 27 (1): 108725. 19 January 2024

(RB1)-negative retinal organoids display proliferation of cone photoreceptors and loss of retinal differentiation.
Kanber, D., Woestefeld, J., Döpper, H., Bozet, M., Brenzel, A., Altmüller, J., Kilpert, F., Lohmann, D., Pommerenke, C. and Steenpass, L.
Cancers 14 (9): 2166. 26 April 2022

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., Sattler, M., Urlaub, H. and Sträßer, K.
Nucleic Acids Research 51 (2): 831-851. 25 January 2023

iPSC-derived reactive astrocytes from patients with multiple-sclerosis protect cocultured neurons in inflammatory conditions.
Kerkering, J., Muinjonov, B., Rosiewicz, K.S., Diecke, S., Biese, C., Schiweck, J., Chien, C., Zocholl, D., Conrad, T., Paul, F., Alisch, M. and Siffrin, V.
Journal of Clinical Investigation 133 (13): e164637. 3 July 2023

Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare).
Kiełbowicz-Matuk, A., Smaczniak, C., Mikołajczak, K., Kuczyńska, A., Xu, X., Braeuning, C. and Krajewski, P.
Plant Molecular Biology 114 (6): 115. 22 October 2024

Bi-allelic PRRT2 variants may predispose to Self-limited Familial Infantile Epilepsy.
Koko, M., Elseed, M.A., Mohammed, I.N., Hamed, A.A., Abd Allah, A.S.I., Yahia, A., Siddig, R.A., Altmüller, J., Toliat, M.R., Elmahdi, E.O., Amin, M., Ahmed, E. A., Eltazi, I.Z.M., Elmugadam, F.A., Abdelgadir, W.A., Eltaraifee, E., Ibrahim, M.O.M., Ali, N.M.H., Malik, H.M., Babai, A.M., Bakhit, Y.H., Nürnberg, P., Ibrahim, M.E., Salih, M.A., Schubert, J., Elsayed, L.E.O. and Lerche, H.
European Journal of Human Genetics 32 (10): 1338-1342. October 2024

Association of ultra-rare coding variants with genetic generalized epilepsy: a case-control whole exome sequencing study.
Koko, M., Motelow, J.E., Stanley, K.E., Bobbili, D.R., Dhindsa, R.S. and May, P.
Epilepsia 63 (3): 723-735. March 2022

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer, B., Knoll, R., Bonaguro, L., ToVinh, M., Raabe, J., Astaburuaga-García, R., Schulte-Schrepping, J., Kaiser, K.M., Rieke, G.J., Bischoff, J., Monin, M.B., Hoffmeister, C., Schlabe, S., De Domenico, E., Reusch, N., Händler, K., Reynolds, G., Blüthgen, N., Hack, G., Finnemann, C., Nischalke, H.D., Strassburg, C.P., Stephenson, E., Su, Y., Gardner, L., Yuan, D., Chen, D., Goldman, J., Rosenstiel, P., Schmidt, S.V., Latz, E., Hrusovsky, K., Ball, A.J., Johnson, J.M., Koenig, P.A., Schmidt, F.I., Haniffa, M., Heath, J.R., Kümmerer, B.M., Keitel, V., Jensen, B., Stubbemann, P., Kurth, F., Sander, L.E., Sawitzki, B., Aschenbrenner, A.C., Schultze, J.L. and Nattermann, J.
Immunity 54 (11): 2650-2669. 9 November 2021

Alport syndrome and autosomal dominant tubulointerstitial kidney disease frequently underlie end stage renal disease of unknown origin - a single center analysis.
Leenen, E., Erger, F., Altmüller, J., Wenzel, A., Thiele, H., Harth, A., Tschernoster, N., Lokhande, S., Joerres, A., Becker, J.U., Ekici, A., Huettel, B., Beck, B. and Weidemann, A.
Nephrology Dialysis Transplantation 37 (10): 1895-1905. 22 September 2022

Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing.
Leiz, J., Hinze, C., Boltengagen, A., Braeuning, C., Kocks, C., Rajewsky, N. and Schmidt-Ott, K.M.
Journal of Visualized Experiments (175): e62901. September 2021

A novel homozygous synonymous variant further expands the phenotypic spectrum of POLR3A-related pathologies.
Lessel, D., Rading, K., Campbell, S.E., Thiele, H., Altmüller, J., Gordon, L.B. and Kubisch, C.
American Journal of Medical Genetics A 188 (1): 216-223. January 2022

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
Lin, M., Hartl, K., Heuberger, J., Beccaceci, G., Berger, H., Li, H., Liu, L., Müllerke, S., Conrad, T., Heymann, F., Woehler, A., Tacke, F., Rajewsky, N. and Sigal, M.
Nature Communications 14 (1): 3025. 25 May 2023

Effective inhibitor removal from wastewater samples increases sensitivity of RT-dPCR and sequencing analyses and enhances the stability of wastewater-based surveillance.
Linzner, N., Bartel, A., Schumacher, V., Grau, J.H., Wyler, E., Preuß, H., Garske, S., Bitzegeio, J., Kirst, E.B., Liere, K., Hoppe, S., Borodina, T.A., Altmüller, J., Landthaler, M., Meixner, M., Sagebiel, D. and Böckelmann, U.
Microorganisms 12 (12): 2475. December 2024

Tongue immune compartment analysis reveals spatial macrophage heterogeneity.
Lyras, E.M., Zimmermann, K., Wagner, L.K., Dörr, D., Klose, C.S.N, Fischer, C., Jung, S., Yona, S., Hovav, A.H., Stenzel, W., Dommerich, S., Conrad, T., Leutz, A. and Mildner, A.
eLife 11 : 77490. 24 June 2022

Platelet-derived factors dysregulate placental sphingosine-1-phosphate receptor 2 in human trophoblasts.
Lyssy, F., Guettler, J., Brugger, B.A., Stern, C., Forstner, D., Nonn, O., Fischer, C., Herse, F., Wernitznig, S., Hirschmugl, B., Wadsack, C. and Gauster, M.
Reproductive BioMedicine Online 47 (2): 103215. August 2023

The genomic landscape across 474 surgically accessible epileptogenic human brain lesions.
López-Rivera, J.A., Leu, C., Macnee, M., Khoury, J., Hoffmann, L., Coras, R., Kobow, K., Bhattarai, N., Pérez-Palma, E., Hamer, H., Brandner, S., Rössler, K., Bien, C.G., Kalbhenn, T., Pieper, T., Hartlieb, T., Butler, E., Genovese, G., Becker, K., Altmüller, J., Niestroj, L.M., Ferguson, L., Busch, R.M., Nürnberg, P., Najm, I., Blümcke, I. and Lal, D.
Brain 146 (4): 1342-1356. April 2023

Reliable assessment of telomere maintenance mechanisms in neuroblastoma.
Meeser, A., Bartenhagen, C., Werr, L., Hellmann, A.M., Kahlert, Y., Hemstedt, N., Nürnberg, P., Altmüller, J., Ackermann, S., Hero, B., Simon, T., Peifer, M., Fischer, M. and Rosswog, C.
Cell and Bioscience 12 (1): 160. 24 September 2022

Generation of hiPSC-derived skeletal muscle cells: exploiting the potential of skeletal muscle-derived hiPSCs.
Metzler, E., Escobar, H., Sunaga-Franze, D.Y., Sauer, S., Diecke, S. and Spuler, S.
Biomedicines 10 (5): 1204. 23 May 2022

Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19.
Mothes, R., Pascual-Reguant, A., Koehler, R., Liebeskind, J., Liebheit, A., Bauherr, S., Philipsen, L., Dittmayer, C., Laue, M., von Manitius, R., Elezkurtaj, S., Durek, P., Heinrich, F., Heinz, G.A., Guerra, G.M., Obermayer, B., Meinhardt, J., Ihlow, J., Radke, J., Heppner, F.L., Enghard, P., Stockmann, H., Aschman, T., Schneider, J., Corman, V.M., Sander, L.E., Mashreghi, M.F., Conrad, T., Hocke, A.C., Niesner, R.A., Radbruch, H. and Hauser, A.E.
Nature Communications 14 (1): 791. 11 February 2023

Candesartan does not activate PPAR(γ) and its target genes in early gestation trophoblasts.
Neuper, L., Kummer, D., Forstner, D., Guettler, J., Ghaffari-Tabrizi-Wizsy, N., Fischer, C., Juch, H., Nonn, O. and Gauster, M.
International Journal of Molecular Sciences 23 (20): 12326. October 2022

A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A., Bakina, O., Badillo Lisakowski, V., Olivares-Chauvet, P., Conrad, T., Gotthardt, M., Kettenmann, H. and Junker, J.P.
Molecular Systems Biology 19 (2): e11147. 10 February 2023

Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver.
Nikopoulou, C., Kleinenkuhnen, N., Parekh, S., Sandoval, T., Ziegenhain, C., Schneider, F., Giavalisco, P., Donahue, K.F., Vesting, A.J., Kirchner, M., Bozukova, M., Vossen, C., Altmüller, J., Wunderlich, T., Sandberg, R., Kondylis, V., Tresch, A. and Tessarz, P.
Nature Aging 3 (11): 1430-1445. November 2023

Senescent syncytiotrophoblast secretion during early onset preeclampsia.
Nonn, O., Debnath, O., Valdes, D.S., Sallinger, K., Secener, A.K., Fischer, C., Tiesmeyer, S., Nimo, J., Kuenzer, T., Ulrich, J., Maxian, T., Knöfler, M., Karau, P., Bartolomaeus, H., Kroneis, T., Frolova, A., Neuper, L., Haase, N., Malt, A., Müller-Bötticher, N., Kräker, K., Kedziora, S., Forstner, D., Eils, R., Schmidt-Ullrich, R., Haider, S., Verlohren, S., Stern, C., Sugulle, M., Jones, S., Thilaganathan, B., Kaitu'u-Lino, T.J., Tong, S., Huppertz, B., El-Heliebi, A., Staff, A.C., Coscia, F., Müller, D.N., Dechend, R., Gauster, M., Ishaque, N. and Herse, F.
Hypertension 23 October 2024 (In Press)

Maternal angiotensin increases placental leptin in early gestation via an alternative renin-angiotensin system pathway: suggesting a link to preeclampsia.
Nonn, O., Fischer, C., Geisberger, S., El-Heliebi, A., Kroneis, T., Forstner, D., Desoye, G., Staff, A.C., Sugulle, M., Dechend, R., Pecks, U., Kollmann, M., Stern, C., Cartwright, J.E., Whitley, G.S., Thilaganathan, B., Wadsack, C., Huppertz, B., Herse, F. and Gauster, M.
Hypertension 77 (5): 1723-1736. May 2021

Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation.
Obermayer, B., Keilholz, L., Conrad, T., Frentsch, M., Blau, I.W., Vuong, L., Lesch, S., Movasshagi, K., Tietze-Stolley, C., Loyal, L., Henze, L., Penack, O., Stervbo, U., Babel, N., Haas, S., Beule, D., Bullinger, L., Wittenbecher, F. and Na, I.K.
Frontiers in Immunology 14 : 1114368. 10 February 2023

Modeling of ACTN4-based podocytopathy using Drosophila nephrocytes.
Odenthal, J., Dittrich, S., Ludwig, V., Merz, T., Reitmeier, K., Reusch, B., Höhne, M., Cosgun, Z.C., Hohenadel, M., Putnik, J., Göbel, H., Rinschen, M.M., Altmüller, J., Koehler, S., Schermer, B., Benzing, T., Beck, B.B., Brinkkötter, P.T., Habbig, S. and Bartram, M.P.
Kidney International Reports 8 (2): 317-329. February 2023

Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture.
Patsalos, A., Halasz, L., Oleksak, D., Wei, X., Nagy, G., Tzerpos, P., Conrad, T., Hammers, D.W., Sweeney, H.L. and Nagy, L.
Journal of Clinical Investigation 134 (20): e173858. 15 October 2024

A growth factor-expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15.
Patsalos, A., Halasz, L., Medina-Serpas, M.A., Berger, W.K., Daniel, B., Tzerpos, P., Kiss, M., Nagy, G., Fischer, C., Simandi, Z., Varga, T. and Nagy, L.
Journal of Experimental Medicine 219 (1): e20210420. 3 January 2022

Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis.
Perne, C., Peters, S., Cartolano, M., Horpaopan, S., Grimm, C., Altmüller, J., Sommer, A.K., Hillmer, A.M., Thiele, H., Odenthal, M., Möslein, G., Adam, R., Sivalingam, S., Kirfel, J., Schweiger, M.R., Peifer, M., Spier, I. and Aretz, S.
PLoS ONE 16 (11): e0259185. 29 November 2021

MAGED2 controls vasopressin-induced aquaporin-2 expression in collecting duct cells.
Reusch, B., Bartram, M.P., Dafinger, C., Palacio-Escat, N., Wenzel, A., Fenton, R.A., Saez-Rodriguez, J., Schermer, B., Benzing, T., Altmüller, J., Beck, B.B. and Rinschen, M.M.
Journal of Proteomics 252 : 104424. 10 February 2022

Prevalence of cancer predisposition germline variants in male breast cancer patients: results of the German Consortium for Hereditary Breast and Ovarian Cancer.
Rolfes, M., Borde, J., Möllenhoff, K., Kayali, M., Ernst, C., Gehrig, A., Sutter, C., Ramser, J., Niederacher, D., Horváth, J., Arnold, N., Meindl, A., Auber, B., Rump, A., Wang-Gohrke, S., Ritter, J., Hentschel, J., Thiele, H., Altmüller, J., Nürnberg, P., Rhiem, K., Engel, C., Wappenschmidt, B., Schmutzler, R.K., Hahnen, E. and Hauke, J.
Cancers 14 (13): 3292. 5 July 2022

Chromothripsis followed by circular recombination drives oncogene amplification in human cancer.
Rosswog, C., Bartenhagen, C., Welte, A., Kahlert, Y., Hemstedt, N., Lorenz, W., Cartolano, M., Ackermann, S., Perner, S., Vogel, W., Altmüller, J., Nürnberg, P., Hertwig, F., Göhring, G., Lilienweiss, E., Stütz, A.M., Korbel, J.O., Thomas, R.K., Peifer, M. and Fischer, M.
Nature Genetics 53 (12): 1673–1685. December 2021

Genomic ALK alterations in primary and relapsed neuroblastoma.
Rosswog, C., Fassunke, J., Ernst, A., Schömig-Markiefka, B., Merkelbach-Bruse, S., Bartenhagen, C., Cartolano, M., Ackermann, S., Theissen, J., Blattner-Johnson, M., Jones, B., Schramm, K., Altmüller, J., Nürnberg, P., Ortmann, M., Berthold, F., Peifer, M., Büttner, R., Westermann, F., Schulte, J.H., Simon, T., Hero, B. and Fischer, M.
British Journal of Cancer 128 (8): 1559-1571. 12 April 2023

Somatic mosaicism in STAG2-associated cohesinopathies: Expansion of the genotypic and phenotypic spectrum.
Schmidt, J., Dreha-Kulaczewski, S., Zafeiriou, M.P., Schreiber, M.K., Wilken, B., Funke, R., Neuhofer, C.M., Altmüller, J., Thiele, H., Nürnberg, P., Biskup, S., Li, Y., Zimmermann, W.H., Kaulfuß, S., Yigit, G. and Wollnik, B.
Frontiers in Cell and Developmental Biology 10 : 1025332. 16 November 2022

Biallelic variants in YRDC cause a developmental disorder with progeroid features.
Schmidt, J., Goergens, J., Pochechueva, T., Kotter, A., Schwenzer, N., Sitte, M., Werner, G., Altmueller, J., Thiele, H., Nürnberg, P., Isensee, J., Li, Y., Müller, C., Leube, B., Reinhardt, H.C., Hucho, T., Salinas, G., Helm, M., Jachimowicz, R.D., Wieczorek, D., Kohl, T., Lehnart, S.E., Yigit, G. and Wollnik, B.
Human Genetics 140 (12): 1679-1693. December 2021

Familial cleft tongue caused by a unique translation initiation codon variant in TP63.
Schmidt, J., Schreiber, G., Altmüller, J., Thiele, H., Nürnberg, P., Li, Y., Kaulfuß, S., Funke, R., Wilken, B., Yigit, G. and Wollnik, B.
European Journal of Human Genetics 30 (2): 211-218. February 2022

Homozygous loss-of-function variants in FILIP1 cause autosomal recessive arthrogryposis multiplex congenita with microcephaly.
Schnabel, F., Schuler, E., Al-Maawali, A., Chaurasia, A., Syrbe, S., Al-Kindi, A., Bhavani, G.S., Shukla, A., Altmüller, J., Nürnberg, P., Banka, S., Girisha, K.M., Li, Y., Wollnik, B. and Yigit, G.
Human Genetics 142 (4): 543-552. April 2023

The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis.
Schneeberger, S., Kim, S.J., Eede, P., Boltengagen, A., Braeuning, C., Andreadou, M., Becher, B., Karaiskos, N., Kocks, C., Rajewsky, N. and Heppner, F.L.
bioRxiv : 2021.04.25.441313. 27 April 2021

Mutant phosphodiesterase 3A protects the kidney from hypertension-induced damage.
Sholokh, A., Walter, S., Markó, L., McMurray, B.J., Sunaga-Franze, D.Y., Xu, M., Zühlke, K., Russwurm, M., Bartolomaeus, T.U.P., Langanki, R., Qadri, F., Heuser, A., Patzak, A., Forslund, S.K., Bähring, S., Borodina, T., Persson, P.B., Maass, P.G., Bader, M. and Klussmann, E.
Kidney International 104 (2): 388-393. August 2023

Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity.
Stöber, M.C., Chamorro González, R., Brückner, L., Conrad, T., Wittstruck, N., Szymansky, A., Eggert, A., Schulte, J.H., Koche, R.P., Henssen, A.G., Schwarz, R.F. and Haase, K.
Cell Reports 43 (9): 114711. 24 September 2024

Male carriers of HLA-C*04:01 have increased risk of cardiac injury in COVID-19.
Suwalski, P., Violano, M., Müller, M., Patriki, D., Thibeault, C., Quedenau, C., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J.M., Hübner, R.H., Hinzmann, B., Beer, H.J., Wiggli, B., Siemann, S., Suttorp, N., Witzenrath, M., Hippenstiel, S., Skurk, C., Poller, W., Sander, L.E., Kurth, F., Borodina, T., Guettouche, T., Landmesser, U. and Heidecker, B.
Journal of Cardiovascular Aging 2 (3): 33. 27 June 2022

Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions.
Tschernoster, N., Erger, F., Kohl, S., Reusch, B., Wenzel, A., Walsh, S., Thiele, H., Becker, C., Franitza, M., Bartram, M.P., Kömhoff, M., Schumacher, L., Kukat, C., Borodina, T., Quedenau, C., Nürnberg, P., Rinschen, M.M., Driller, J.H., Pedersen, B.P., Schlingmann, K.P., Hüttel, B., Bockenhauer, D., Beck, B. and Altmüller, J.
Genome Medicine 15 (1): 62. 23 August 2023

Unraveling structural rearrangements of the CFH gene cluster in atypical hemolytic uremic syndrome patients using molecular combing and long-fragment targeted sequencing.
Tschernoster, N., Erger, F., Walsh, P.R., McNicholas, B., Fistrek, M., Habbig, S., Schumacher, L., Folz-Donahue, K., Kukat, C., Toliat, M.R., Becker, C., Thiele, H., Kavanagh, D., Nürnberg, P., Beck, B. and Altmüller, J.
Journal of Molecular Diagnostics 24 (6): 619-631. June 2022

A local subset of mesenchymal cells expressing the transcription factor Osr1 orchestrates lymph node initiation.
Vallecillo-García, P., Orgeur, M., Comai, G., Poehle-Kronnawitter, S., Fischer, C., Gloger, M., Dumas, C.E., Giesecke-Thiel, C., Sauer, S., Tajbakhsh, S., Höpken, U.E. and Stricker, S.
Immunity 56 (6): 1204-1219. 13 June 2023

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker, A., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., Tamayo, T., Kohns Vasconcelos, M., Hülse, L., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Däumer, M.P., Thielen, A., Kolbe-Busch, S., Göbels, K., Zotz, R., Pfeffer, K., Timm, J. and Dilthey, A.T.
Clinical Infectious Diseases 74 (6): 1039-1046. 15 March 2022

Swarm Learning for decentralized and confidential clinical machine learning.
Warnat-Herresthal, S., Schultze, H., Shastry, K.L., Manamohan, S., Mukherjee, S., Garg, V., Sarveswara, R., Händler, K., Pickkers, P., Aziz, N.A., Ktena, S., Tran, F., Bitzer, M., Ossowski, S., Casadei, N., Herr, C., Petersheim, D., Behrends, U., Kern, F., Fehlmann, T., Schommers, P., Lehmann, C., Augustin, M., Rybniker, J., Altmüller, J., Mishra, N., Bernardes, J.P., Krämer, B., Bonaguro, L., Schulte-Schrepping, J., De Domenico, E., Siever, C., Kraut, M., Desai, M., Monnet, B., Saridaki, M., Siegel, C.M., Drews, A., Nuesch-Germano, M., Theis, H., Heyckendorf, J., Schreiber, S., Kim-Hellmuth, S., Nattermann, J., Skowasch, D., Kurth, I., Keller, A., Bals, R., Nürnberg, P., Rieß, O., Rosenstiel, P., Netea, M.G., Theis, F., Mukherjee, S., Backes, M., Aschenbrenner, A.C., Ulas, T., Breteler, M.M.B., Giamarellos-Bourboulis, E.J., Kox, M., Becker, M., Cheran, S., Woodacre, M.S., Goh, E.L. and Schultze, J.L.
Nature 594 (7862): 265-270. 10 June 2021

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.
Weiner, J., Suwalski, P., Holtgrewe, M., Rakitko, A., Thibeault, C., Müller, M., Patriki, D., Quedenau, C., Krüger, U., Ilinsky, V., Popov, I., Balnis, J., Jaitovich, A., Helbig, E.T., Lippert, L.J., Stubbemann, P., Real, L.M., Macías, J., Pineda, J.A., Fernandez-Fuertes, M., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J.M., Hübner, R.H., Hinzmann, B., Salvo, M., Blueher, A., Siemann, S., Jurisic, S., Beer, J.H., Rutishauser, J., Wiggli, B., Schmid, H., Danninger, K., Binder, R., Corman, V.M., Mühlemann, B., Arjun Arkal, R., Fragiadakis, G.K., Mick, E., Calfee, C.S., Erle, D.J., Hendrickson, C.M., Kangelaris, K.N., Krummel, M.F., Woodruff, P.G., Langelier, C.R., Venkataramani, U., García, F., Zyla, J., Drosten, C., Braun, A., Jones, T.C., Suttorp, N., Witzenrath, M., Hippenstiel, S., Zemojtel, T., Skurk, C., Wolfgang, P., Borodina, T., Ripke, S., Sander, L.E., Beule, D., Landmesser, U., Guettouche, T., Kurth, F. and Heidecker, B.
EClinicalMedicine 40 : 101099. October 2021

Mutations in TAF8 cause a neurodegenerative disorder.
Wong, K.M., Jepsen, W.M., Efthymiou, S., Salpietro, V., Sanchez-Castillo, M., Yip, J., Kriouile, Y., Diegmann, S., Dreha-Kulaczewski, S., Altmüller, J., Thiele, H., Nürnberg, P., Toosi, M.B., Akhondian, J., Ghayoor Karimiani, E., Hummel-Abmeier, H., Huppke, B., Houlden, H., Gärtner, J., Maroofian, R. and Huppke, P.
Brain 145 (9): 3022-3034. September 2022

Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater.
Wyler, E., Lauber, C., Manukyan, A., Deter, A., Quedenau, C., Teixeira Alves, L.G., Wylezich, C., Borodina, T., Seitz, S., Altmüller, J. and Landthaler, M.
Environment International 190 : 108875. August 2024

Ablation of collagen XII disturbs joint extracellular matrix organization and causes patellar subluxation.
Zhu, M., Metzen, F., Hopkinson, M., Betz, J., Heilig, J., Sodhi, J., Imhof, T., Niehoff, A., Birk, D.E., Izu, Y., Krüger, M., Pitsillides, A. A., Altmüller, J., van Osch, G.J.V.M., Straub, V., Schreiber, G., Paulsson, M., Koch, M. and Brachvogel, B.
iScience 26 (7): 107225. 21 July 2023

The phenotypic and genotypic spectrum of epilepsy and intellectual disability in adults: Implications for genetic testing.
von Brauchitsch, S., Haslinger, D., Lindlar, S., Thiele, H., Bernsen, N., Zahnert, F., Reif, P.S., Balcik, Y., Au, P.Y.B., Josephson, C., Altmüller, J., Strzelczyk, A., Knake, S., Rosenow, F., Chiocchetti, A. and Klein, K.M.
Epilepsia Open 8 (2): 497-508. June 2023

Bader, Michael

Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage.
Avery, E.G., Bartolomaeus, H., Rauch, A., Chen, C.Y., N'Diaye, G., Löber, U., Bartolomaeus, T.U.P., Fritsche-Guenther, R., Rodrigues, A.F., Yarritu, A., Zhong, C., Fei, L., Tsvetkov, D., Todiras, M., Park, J.K., Markó, L., Maifeld, A., Patzak, A., Bader, M., Kempa, S., Kirwan, J.A., Forslund, S.K., Müller, D.N. and Wilck, N.
Cardiovascular Research 119 (6): 1441-1452. May 2023

Elevated sortilin expression discriminates functional from non-functional neuroendocrine tumors and enables therapeutic targeting.
Bolduan, F., Wetzel, A., Giesecke, Y., Eichhorn, I., Alenina, N., Bader, M., Willnow, T.E., Wiedenmann, B. and Sigal, M.
Frontiers in Endocrinology 15 : 1331231. 17 April 2024

Ethanol deprivation and central 5-HT deficiency differentially affect the mRNA editing of the 5-HT(2C) receptor in the mouse brain.
Zaniewska, M., Alenina, N., Fröhler, S., Chen, W. and Bader, M.
Pharmacological Reports 75 (6): 1502-1521. December 2023

Beule, Dieter (MDC/BIH)

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.
Al-Diab, O., Sünkel, C., Blanc, E., Catar, R.A., Ashraf, M.I., Zhao, H., Wang, P., Rinschen, M.M., Fritsche-Guenther, R., Grahammer, F., Bachmann, S., Beule, D., Kirwan, J.A., Rajewsky, N., Huber, T.B., Gürgen, D. and Kusch, A.
Biology of Sex Differences 15 (1): 72. 15 September 2024

State-of-the-art analytical methods of viral infections in human lung organoids.
Baumgardt, M., Hülsemann, M., Löwa, A., Fatykhova, D., Hoffmann, K., Kessler, M., Mieth, M., Hellwig, K., Frey, D., Langenhagen, A., Voss, A., Obermayer, B., Wyler, E., Dökel, S., Gruber, A.D., Tölch, U., Hippenstiel, S., Hocke, A.C. and Hönzke, K.
PLoS ONE 17 (12): e0276115. 20 December 2022

A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease.
Boeddrich, A., Haenig, C., Neuendorf, N., Blanc, E., Ivanov, A., Kirchner, M., Schleumann, P., Bayraktaroğlu, I., Richter, M., Molenda, C.M., Sporbert, A., Zenkner, M., Schnoegl, S., Suenkel, C., Schneider, L.S., Rybak-Wolf, A., Kochnowsky, B., Byrne, L.M., Wild, E.J., Nielsen, J.E., Dittmar, G., Peters, O., Beule, D. and Wanker, E.E.
Genome Medicine 15 (1): 50. 20 July 2023

Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma.
Burkert, M., Blanc, E., Thiessen, N., Weber, C., Toedling, J., Monti, R., Dombrowe, V.M., de Biase, M.S., Kaufmann, T.L., Haase, K., Waszak, S.M., Eggert, A., Beule, D., Schulte, J.H., Ohler, U. and Schwarz, R.F.
iScience 27 (10): 110918. 18 October 2024

Combining callers improves the detection of copy number variants from whole-genome sequencing.
Coutelier, M., Holtgrewe, M., Jäger, M., Flöttman, R., Mensah, M.A., Spielmann, M., Krawitz, P., Horn, D., Beule, D. and Mundlos, S.
European Journal of Human Genetics 30 (2): 178-186. February 2022

C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.
Dörr, D., Obermayer, B., Weiner, J.M., Zimmermann, K., Anania, C., Wagner, L.K., Lyras, E.M., Sapozhnikova, V., Lara-Astiaso, D., Prósper, F., Lang, R., Lupiáñez, D.G., Beule, D., Höpken, U.E., Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.
Essex, M., Millet Pascual-Leone, B.L., Löber, U., Kuhring, M., Zhang, B., Brüning, U., Fritsche-Guenther, R., Krzanowski, M., Fiocca Vernengo, F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thibeault, C., Corman, V.M., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
NPJ Biofilms and Microbiomes 10 (1): 66. 1 August 2024

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M., Pascual-Leone, B.M., Löber, U., Kuhring, M., Zhang, B., Bruening, U., Fritsche-Guenther, R., Krzanowski, M., Vernengo, F.F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thiebeault, C., Corman, V., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 December 2022

Microenvironmental acidification by pneumococcal sugar consumption fosters barrier disruption and immune suppression in the human alveolus.
Fatykhova, D., Fritsch, V.N., Siebert, K., Methling, K., Lalk, M., Busche, T., Kalinowski, J., Weiner, J., Beule, D., Bertrams, W., Kohler, T.P., Hammerschmidt, S., Löwa, A., Fischer, M., Mieth, M., Hellwig, K., Frey, D., Neudecker, J., Rueckert, J.C., Toennies, M., Bauer, T.T., Graff, M., Tran, H.L., Eggeling, S., Gruber, A.D., Antelmann, H., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal 64 (6): 2301983. December 2024

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P., Astaburuaga-García, R., Bonaguro, L., Brumhard, S., Michalick, L., Lippert, L.J., Kostevc, T., Gäbel, C., Schneider, M., Streitz, M., Demichev, V., Gemünd, I., Barone, M., Tober-Lau, P., Helbig, E.T., Hillus, D., Petrov, L., Stein, J., Dey, H.P., Paclik, D., Iwert, C., Mülleder, M., Aulakh, S.K., Djudjaj, S., Bülow, R.D., Mei, H.E., Schulz, A.R., Thiel, A., Hippenstiel, S., Saliba, A.E., Eils, R., Lehmann, I., Mall, M.A., Stricker, S., Röhmel, J., Corman, V.M., Beule, D., Wyler, E., Landthaler, M., Obermayer, B., von Stillfried, S., Boor, P., Demir, M., Wesselmann, H., Suttorp, N., Uhrig, A., Müller-Redetzky, H., Nattermann, J., Kuebler, W.M., Meisel, C., Ralser, M., Schultze, J.L., Aschenbrenner, A.C., Thibeault, C., Kurth, F., Sander, L.E., Blüthgen, N. and Sawitzki, B.
Cell 185 (3): 493-512. 3 February 2022

Deep learning-assisted peak curation for large-scale LC-MS metabolomics.
Gloaguen, Y., Kirwan, J.A. and Beule, D.
Analytical Chemistry 94 (12): 4930-4937. 29 March 2022

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C., Kocks, C., Leiz, J., Karaiskos, N., Boltengagen, A., Cao, S., Skopnik, C.M., Klocke, J., Hardenberg, J.H., Stockmann, H., Gotthardt, I., Obermayer, B., Haghverdi, L., Wyler, E., Landthaler, M., Bachmann, S., Hocke, A.C., Corman, V., Busch, J., Schneider, W., Himmerkus, N., Bleich, M., Eckardt, K.U., Enghard, P., Rajewsky, N. and Schmidt-Ott, K.M.
Genome Medicine 14 (1): 103. 9 September 2022

Human alveolar progenitors generate dual lineage bronchioalveolar organoids.
Hoffmann, K., Obermayer, B., Hönzke, K., Fatykhova, D., Demir, Z., Löwa, A., Teixeira Alves, L.G., Wyler, E., Lopez-Rodriguez, E., Mieth, M., Baumgardt, M., Hoppe, J., Firsching, T.C., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Gruber, A.D., Ochs, M., Landthaler, M., Beule, D., Suttorp, N., Hippenstiel, S., Hocke, A.C. and Kessler, M.
Communications Biology 5 (1): 875. 25 August 2022

Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance.
Holle, J., Bartolomaeus, H., Löber, U., Behrens, F., Bartolomaeus, T.U.P., Anandakumar, H., Wimmer, M., Vu, D.L., Kuhring, M., Brüning, U., Maifeld, A., Geisberger, S., Kempa, S., Schumacher, F., Kleuser, B., Bufler, P., Querfeld, U., Kitschke, S., Engler, D., Kuhrt, L.D., Drechsel, O., Eckardt, K.U., Forslund, S., Thürmer, A., McParland, V., Kirwan, J., Wilck, N. and Mueller, D.
Journal of the American Society of Nephrology 33 (12): 2259-2275. December 2022

REEV: review, evaluate and explain variants.
Hramyka, D., Sczakiel, H.L., Zhao, M.X., Stolpe, O., Nieminen, M., Adam, R., Danyel, M., Einicke, L., Hägerling, R., Knaus, A., Mundlos, S., Schwartzmann, S., Seelow, D., Ehmke, N., Mensah, M.A., Boschann, F., Beule, D. and Holtgrewe, M.
Nucleic Acids Research 52 (W1): W148-W158. 5 July 2024

Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.
Hönzke, K., Obermayer, B., Mache, C., Fathykova, D., Kessler, M., Dökel, S., Wyler, E., Baumgardt, M., Löwa, A., Hoffmann, K., Graff, P., Schulze, J., Mieth, M., Hellwig, K., Demir, Z., Biere, B., Brunotte, L., Mecate-Zambrano, A., Bushe, J., Dohmen, M., Hinze, C., Elezkurtaj, S., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Schmidt-Ott, K.M., Busch, J., Klauschen, F., Horst, D., Radbruch, H., Radke, J., Heppner, F., Corman, V.M., Niemeyer, D., Müller, M.A., Goffinet, C., Mothes, R., Pascual-Reguant, A., Hauser, A.E., Beule, D., Landthaler, M., Ludwig, S., Suttorp, N., Witzenrath, M., Gruber, A.D., Drosten, C., Sander, L.E., Wolff, T., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal 60 (6): 2102725. 1 December 2022

Increased β(2)-adrenergic signaling promotes fracture healing through callus neovascularization in mice.
Jahn, D., Knapstein, P.R., Otto, E., Köhli, P., Sevecke, J., Graef, F., Graffmann, C., Fuchs, M., Jiang, S., Rickert, M., Erdmann, C., Appelt, J., Revend, L., Küttner, Q., Witte, J., Rahmani, A., Duda, G., Xie, W., Donat, A., Schinke, T., Ivanov, A., Tchouto, M.N., Beule, D., Frosch, K.H., Baranowsky, A., Tsitsilonis, S. and Keller, J.
Science Translational Medicine 16 (743): eadk9129. 17 April 2024

Intestinal retinol saturase is implicated in the development of obesity and epithelial homeostasis upon injury.
Kiefer, M.F., Meng, Y., Yang, N., Vahrenbrink, M., Wulff, S., Li, C., Wowro, S.J., Petricek, K.M., Sommerfeld, M., Flores, R.E., Obermayer, B., Piepelow, K., Klaus, S., Hartl, K., Guillot, A., Tacke, F., Sigal, M. and Schupp, M.
American Journal of Physiology Endocrinology and Metabolism 327 (2): E203-E216. August 2024

Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J., Theisen, S., Dartsch, J., Fritsche-Guenther, R., Kirchner, M., Obermayer, B., Bauer, A., Kahlert, A.K., Rothe, M., Beule, D., Heuser, A., Mertins, P., Kirwan, J.A., Berndt, N., MacRae, C.A., Hubner, N. and Klaassen, S.
Cardiovascular Research 119 (18): 2902-2916. December 2023

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V., Beneyto-Calabuig, S., Obermayer, B., Velten, L., Beule, D. and Haghverdi, L.
Bioinformatics 40 (9): btae512. September 2024

Microglia undergo molecular and functional adaptations to dark and light phases in male laboratory mice.
Mattei, D., Ivanov, A., Hammer, J., Ugursu, B., Schalbetter, S., Richetto, J., Weber-Stadlbauer, U., Mueller, F., Scarborough, J., Wolf, S.A., Kettenmann, H., Wollscheid, B., Beule, D. and Meyer, U.
Brain, Behavior and Immunity 210 : 571-583. August 2024

Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19.
Nouailles, G., Wyler, E., Pennitz, P., Postmus, D., Vladimirova, D., Kazmierski, J., Pott, F., Dietert, K., Muelleder, M., Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L.E., Suttorp, N., Ralser, M., Beule, D., Gruber, A.D., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Nature Communications 12 (1): 4869. 11 August 2021

Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19.
Nouailles, Geraldine, Wyler, E., Pennitz, P., Postmus, D., Vladrimirova, D., Kazmierski, J., Pott, F., Dietert, K., Mülleder, M.l, Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L., Suttorp, N., Ralser, M., Beule, D., Gruber, A., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Research Square : rs-148392/v1. 28 January 2021

Harnessing transcriptomic signals for amyotrophic lateral sclerosis to identify novel drugs and enhance risk prediction.
Pain, O., Jones, A., Al Khleifat, A., Agarwal, D., Hramyka, D., Karoui, H., Kubica, J., Llewellyn, D.J., Ranson, J.M., Yao, Z., Iacoangeli, A. and Al-Chalabi, A.
Heliyon 10 (15): e35342. 15 August 2024

A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics.
Pennitz, P., Kirsten, H., Friedrich, V.D., Wyler, E., Goekeri, C., Obermayer, B., Heinz, G.A., Mashreghi, M.F., Büttner, M., Trimpert, J., Landthaler, M., Suttorp, N., Hocke, A.C., Hippenstiel, S., Tönnies, M., Scholz, M., Kuebler, W.M., Witzenrath, M., Hoenzke, K. and Nouailles, G.
European Respiratory Review 31 (165): 220056. 30 September 2022

Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses.
Rajasekaran, S., Siddiqui, J., Rakijas, J., Nicolay, B., Lin, C., Khan, E., Patel, R., Morris, R., Wyler, E., Boukhali, M., Balasubramanyam, J., Ranjith Kumar, R., Van Rechem, C., Vogel, C., Elchuri, S.V., Landthaler, M., Obermayer, B., Haas, W., Dyson, N. and Miles, W.
Communications Biology 4 (1): 977. 17 August 2021

The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities.
Ramberger, E., Sapozhnikova, V., Ng, Y.L.D., Dolnik, A., Ziehm, M., Popp, O., Sträng, E., Kull, M., Grünschläger, F., Krüger, J., Benary, M., Müller, S., Gao, X., Murgai, A., Haji, M., Schmidt, A., Lutz, R., Nogai, A., Braune, J., Laue, D., Langer, C., Khandanpour, C., Bassermann, F., Döhner, H., Engelhardt, M., Straka, C., Hundemer, M., Beule, D., Haas, S., Keller, U., Einsele, H., Bullinger, L., Knop, S., Mertins, P. and Krönke, J.
Nature Cancer 5 (8): 1267-1284. August 2024

Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E., Planas-Fèlix, M., Burkert, M., Puiggròs, M., Toedling, J., Thiessen, N., Blanc, E., Szymansky, A., Hertwig, F., Ishaque, N., Beule, D., Torrents, D., Eggert, A., Koche, R.P., Schwarz, R.F., Haase, K., Schulte, J.H. and Henssen, A.G.
Cell Genomics 3 (10): 100402. 11 October 2023

Adolescence is a sensitive period for prefrontal microglia to act on cognitive development.
Schalbetter, S.M., von Arx, A.S., Cruz-Ochoa, N., Dawson, K., Ivanov, A., Mueller, F.S., Lin, H.Y., Amport, R., Mildenberger, W., Mattei, D., Beule, D., Földy, C., Greter, M., Notter, T. and Meyer, U.
Science Advances 8 (9): eabi6672. 4 March 2022

Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
Schinke, C., Fernandez Vallone, V., Ivanov, A., Peng, Y., Körtvelyessy, P., Nolte, L., Huehnchen, P., Beule, D., Stachelscheid, H., Boehmerle, W. and Endres, M.
Elsevier. October 2021

Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
Schinke, C., Vallone, V.F., Ivanov, A., Peng, Y., Körtvelyessy, P., Nolte, L., Huehnchen, P., Beule, D., Stachelscheid, H., Boehmerle, W. and Endres, M.
Neurobiology of Disease 155 : 105391. July 2021

Pathogenic variants associated with dilated cardiomyopathy predict outcome in pediatric myocarditis.
Seidel, F., Holtgrewe, M., Al-Wakeel-Marquard, N., Opgen-Rhein, B., Dartsch, J., Herbst, C., Beule, D., Pickardt, T., Klingel, K., Messroghli, D., Berger, F., Schubert, S., Kühnisch, J. and Klaassen, S.
Circulation Genomic and Precision Medicine 14 (4): e003250. 4 August 2021

Pathogenic variants in cardiomyopathy disorder genes underlie pediatric myocarditis - Further impact of heterozygous immune disorder gene variants?
Seidel, F., Laser, K.T., Klingel, K., Dartsch, J., Theisen, S., Pickardt, T., Holtgrewe, M., Gärtner, A., Berger, F., Beule, D., Milting, H., Schubert, S., Klaassen, S. and Kühnisch, J.
Journal of Cardiovascular Development and Disease 9 (7): 216. 5 July 2022

Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
Uhlitz, F., Bischoff, P., Peidli, S., Sieber, A., Trinks, A., Lüthen, M., Obermayer, B., Blanc, E., Ruchiy, Y., Sell, T., Mamlouk, S., Arsie, R., Wei, T.T., Klotz-Noack, K., Schwarz, R.F., Sawitzki, B., Kamphues, C., Beule, D., Landthaler, M., Sers, C., Horst, D., Blüthgen, N. and Morkel, M.
EMBO Molecular Medicine 13 (10): e14123. 7 October 2021

Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations.
Zieger, H.K., Weinhold, L., Schmidt, A., Holtgrewe, M., Juranek, S.A., Siewert, A., Scheer, A.B., Thieme, F., Mangold, E., Ishorst, N., Brand, F.U., Welzenbach, J., Beule, D., Paeschke, K., Krawitz, P.M. and Ludwig, K.U.
Human Genetics and Genomics Advances 4 (1): 100166. 12 January 2023

Birchmeier, Walter

Epigenetic modifier balances Mapk and Wnt signalling in differentiation of goblet and Paneth cells.
Grinat, J., Kosel, F., Goveas, N., Kranz, A., Alexopoulou, D., Rajewsky, K., Sigal, M., Stewart, A.F. and Heuberger, J.
Life Science Alliance 5 (4): e202101187. April 2022

High Yap and Mll1 promote a persistent regenerative cell state induced by Notch signaling and loss of p53.
Heuberger, J., Grinat, J., Kosel, F., Liu, L., Kunz, S., Vidal, R.O., Keil, M., Haybaeck, J., Robine, S., Louvard, D., Regenbrecht, C., Sporbert, A., Sauer, S., von Eyss, B., Sigal, M. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 118 (22): e2019699118. 1 June 2021

Birchmeier-Kohler, Carmen

Molecular identity of proprioceptor subtypes innervating different muscle groups in mice.
Dietrich, S., Company, C., Song, K., Lowenstein, E.D., Riedel, L., Birchmeier, C., Gargiulo, G. and Zampieri, N.
Nature Communications 13 (1): 6867. 11 November 2022

Molecular characterization of nodose ganglia development reveals a novel population of Phox2b+ glial progenitors in mice.
Lowenstein, E.D., Misios, A., Buchert, S. and Ruffault, P.L.
Journal of Neuroscience 44 (28): e1441232024. 10 July 2024

Prox2 and Runx3 vagal sensory neurons regulate esophageal motility.
Lowenstein, E.D., Ruffault, P.L., Misios, A., Osman, K.L., Li, H., Greenberg, R.S., Thompson, R., Song, K., Dietrich, S., Li, X., Vladimirov, N., Woehler, A., Brunet, J.F., Zampieri, N., Kühn, R., Liberles, S.D., Jia, S., Lewin, G.R., Rajewsky, N., Lever, T.E. and Birchmeier, C.
Neuron 111 (14): 2184-2200.e7. 19 July 2023

Birol, Melissa (BIMSB)

The C-terminus of α-synuclein regulates its dynamic cellular internalization by neurexin 1β.
Birol, M., Douzoglou Muñoz, I.I. and Rhoades, E.
Molecular Biology of the Cell 34 (13): br21. 1 December 2023

Routing of Kv7.1 to endoplasmic reticulum plasma membrane junctions.
Serrano-Novillo, C., Estadella, I., Navarro-Pérez, M., Oliveras, A., de Benito-Bueno, A., Socuéllamos, P.G., Bosch, M., Coronado, M.J., Sastre, D., Valenzuela, C., Soeller, C. and Felipe, A.
Acta Physiologica 240 (3): e14106. March 2024

Enzyme self-label-bound ATTO700 in single-molecule and super-resolution microscopy.
Trumpp, M., Oliveras, A., Gonschior, H., Ast, J., Hodson, D.J., Knaus, P., Lehmann, M., Birol, M. and Broichhagen, J.
Chemical Communications 58 (99): 13724-13727. 13 December 2022

Blankenstein, Thomas

Boschmann, Michael (ECRC)

Exercise blood-drop metabolic profiling links metabolism with perceived exertion.
Opialla, T., Gollasch, B., Kuich, P.H.J.L., Klug, L., Rahn, G., Busjahn, A., Spuler, S., Boschmann, M., Kirwan, J.A., Luft, F.C. and Kempa, S.
Frontiers in Molecular Biosciences 9 : 1042231. 21 December 2022

Bullinger, Lars

Cell fate determinant Llgl1 is required for propagation of acute myeloid leukemia.
Eifert, T., Hsu, C.J., Becker, A.L., Graessle, S., Horne, A., Bemmann, F., Zhang, Q., Heuser, M., Vasioukhin, V., Scholl, S., Hochhaus, A., Siegerist, F., Endlich, N., Bullinger, L., Lane, S.W., Haas, S., Schnoeder, T.M and Heidel, F.H.
Leukemia 37 (10): 2027-2035. October 2023

Antigen presentation safeguards the integrity of the hematopoietic stem cell pool.
Hernández-Malmierca, P., Vonficht, D., Schnell, A., Uckelmann, H.J., Bollhagen, A., Mahmoud, M.A.A., Landua, S.L., van der Salm, E., Trautmann, C., Raffel, S., Grünschläger, F., Lutz, R., Ghosh, M., Renders, S., Correia, N., Donato, E., Dixon, K.O., Hirche, C., Andresen, C., Robens, Cl., Werner, P.S., Boch, T., Eisel, D., Osen, W., Pilz, F., Przybylla, A., Klein, C., Buchholz, F., Milsom, M.D., Essers, M.A.G., Eichmüller, S.B., Hofmann, W.K., Nowak, D., Hübschmann, D., Hundemer, M., Thiede, C., Bullinger, L., Müller-Tidow, C., Armstrong, S.A., Trumpp, A., Kuchroo, V.K. and Haas, S.
Cell Stem Cell 29 (5): 760-775. 5 May 2022

Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype.
Leppä, A.M., Grimes, K., Jeong, H., Huang, F.Y., Andrades, A., Waclawiczek, A., Boch, T., Jauch, A., Renders, S., Stelmach, P., Müller-Tidow, C., Karpova, D., Sohn, M., Grünschläger, F., Hasenfeld, P., Benito Garagorri, E., Thiel, V., Dolnik, A., Rodriguez-Martin, B., Bullinger, L., Mrózek, K., Eisfeld, A.K., Krämer, A., Sanders, A.D., Korbel, J.O. and Trumpp, A.
Nature Genetics 56 (12): 2790-2803. December 2024

Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations.
Penter, L., Cieri, N., Maurer, K., Kwok, M., Lyu, H., Lu, W.S., Oliveira, G., Gohil, S.H., Leshchiner, I., Lareau, C.A., Ludwig, L.S., Neuberg, D.S., Kim, H.T., Li, S., Bullinger, L., Ritz, J., Getz, G., Garcia, J.S., Soiffer, R.J., Livak, K.J. and Wu, C.J.
Blood Cancer Discovery 5 (6): 442-459. 1 November 2024

Böttcher, Chotima (ECRC)

Store-operated calcium entry controls innate and adaptive immune cell function in inflammatory bowel disease.
Letizia, M., Wang, Y.H., Kaufmann, U., Gerbeth, L., Sand, A., Brunkhorst, M., Weidner, P., Ziegler, J.F., Böttcher, C., Schlickeiser, S., Fernández, C., Yamashita, M., Stauderman, K., Sun, K., Kunkel, D., Prakriya, M., Sanders, A.D., Siegmund, B., Feske, S. and Weidinger, C.
EMBO Molecular Medicine 14 (9): e15687. 7 September 2022

Proteomic and transcriptomic profiling of brainstem, cerebellum and olfactory tissues in early- and late-phase COVID-19.
Radke, J., Meinhardt, J., Aschman, T., Chua, R.L., Farztdinov, V., Lukassen, S., Ten, F.W., Friebel, E., Ishaque, N., Franz, J., Huhle, V.H., Mothes, R., Peters, K., Thomas, C., Schneeberger, S., Schumann, E., Kawelke, L., Jünger, J., Horst, V., Streit, S., von Manitius, R., Körtvélyessy, P., Vielhaber, S., Reinhold, D., Hauser, A.E., Osterloh, A., Enghard, P., Ihlow, J., Elezkurtaj, S., Horst, D., Kurth, F., Müller, M.A., Gassen, N.C., Melchert, J., Jechow, K., Timmermann, B., Fernandez-Zapata, C., Böttcher, C., Stenzel, W., Krüger, E., Landthaler, M., Wyler, E., Corman, V., Stadelmann, C., Ralser, M., Eils, R., Heppner, F.L., Mülleder, M., Conrad, C. and Radbruch, H.
Nature Neuroscience 27 (3): 409-420. March 2024

Chekulaeva, Marina (BIMSB)

Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs.
Baranovsky, A., Ivanov, T., Granovskaya, M., Papatsenko, D. and Pervouchine, D.D.
PLoS ONE 17 (5): e0268626. 19 May 2022

The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression.
Bujanic, L., Shevchuk, O., von Kügelgen, N., Kalinina, A., Ludwik, K., Koppstein, D., Zerna, N., Sickmann, A. and Chekulaeva, M.
RNA 28 (5): 766-779. May 2022

Mechanistic insights into the basis of widespread RNA localization.
Chekulaeva, M.
Nature Cell Biology 26 (7): 1037-1046. July 2024

First demonstration of miRNA-dependent mRNA decay.
Chekulaeva, M.
Nature Reviews Molecular Cell Biology 24 (3): 164. March 2023

Concurrent profiling of localized transcriptome and RNA dynamics in neurons by spatial SLAMseq.
Dantsuji, S. and Chekulaeva, M.
Methods in Molecular Biology 2863 : 297-317. 2025

Identifying tumor cells at the single-cell level using machine learning.
Dohmen, J., Baranovskii, A., Ronen, J., Uyar, B., Franke, V. and Akalin, A.
Genome Biology 23 (1): 123. 30 May 2022

MACC1 regulates clathrin-mediated endocytosis and receptor recycling of transferrin receptor and EGFR in colorectal cancer.
Imbastari, F., Dahlmann, M., Sporbert, A., Ciolli Mattioli, C., Mari, T., Scholz, F., Timm, L., Twamley, S., Migotti, R., Walther, W., Dittmar, G., Rehm, A. and Stein, U.
Cellular and Molecular Life Sciences 78 (7): 3525-3542. April 2021

mRNA stability and m(6)A are major determinants of subcellular mRNA localization in neurons.
Loedige, I., Baranovskii, A., Mendonsa, S., Dantsuji, S., Popitsch, N., Breimann, L., Zerna, N., Cherepanov, V., Milek, M., Ameres, S. and Chekulaeva, M.
Molecular Cell 83 (15): 2709-2725. 3 August 2023

Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
Mendonsa, S., von Kuegelgen, N., Bujanic, L. and Chekulaeva, M.
Nucleic Acids Research 49 (17): 10007-10017. 27 September 2021

Massively parallel identification of mRNA localization elements in primary cortical neurons.
Mendonsa, S., von Kügelgen, N., Dantsuji, S., Ron, M., Breimann, L., Baranovskii, A., Lödige, I., Kirchner, M., Fischer, M., Zerna, N., Bujanic, L., Mertins, P., Ulitsky, I. and Chekulaeva, M.
Nature Neuroscience 26 (3): 394-405. March 2023

Viruses and endogenous retroviruses as roots for neuroinflammation and neurodegenerative diseases.
Römer, C.
Frontiers in Neuroscience 15 : 648629. 12 March 2021

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.
Witte, F., Ruiz-Orera, J., Ciolli Mattioli, C., Blachut, S., Adami, E., Schulz, J.F., Schneider-Lunitz, V., Hummel, O., Patone, G., Mücke, M.B., Šilhavý, Jan, Heinig, M., Bottolo, L., Sanchis, D., Vingron, M., Chekulaeva, M., Pravenec, M., Hubner, N. and van Heesch, S.
Genome Biology 22 (1): 191. 28 June 2021

Novel targets, treatments, and advanced models for intracerebral haemorrhage.
Zille, M., Farr, T.D., Keep, R.F., Römer, C., Xi, G. and Boltze, J.
EBioMedicine 76 : 103880. 12 February 2022

Neuromuscular dysfunction in patient-derived FUS(R244RR)-ALS iPSC model via axonal downregulation of neuromuscular junction proteins.
von Kuegelgen, N., Ludwik, K., Mendonsa, S., Roemer, C., Becher, E., Breimann, L., Strauch, M., Mari, T., Mongellaz, S., Zuckerman, B., Grexa, N., Oliveras-Martinez, A., Woehler, A., Selbach, M., La Bella, V., Ulitsky, I. and Chekulaeva, M.
bioRxiv : 2024.08.17.607965. 17 August 2024

Chen, Wei (BIMSB/BIH)

Profiling of sub-lethal in vitro effects of multi-walled carbon nanotubes reveals changes in chemokines and chemokine receptors.
Keshavan, S., Andón, F.T., Gallud, A., Chen, W., Reinert, K., Tran, L. and Fadeel, B.
Nanomaterials 11 (4): 883. 30 March 2021

Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex.
Weigt, M., Gao, Q., Ban, H., He, H., Mastrobuoni, G., Kempa, S., Chen, W. and Li, F.
Epigenetics & Chromatin 14 (1): 8. 19 January 2021

Coscia, Fabian

Daumke, Oliver

Sociality shapes mitochondrial adaptations supporting hypoxia tolerance.
Rossi, A., Ruwolt, M., Kakouri, P., Kosten, T., Kunz, S., Puchkov, D., Reznick, J., Purfürst, B., Omerbašić, D., Méndez Aranda, D., Carai, G., Mastrobuoni, G., Hart, D.W., Carraro, M., Tommasin, L., Bennett, N.C., Bégay, V., Faelber, K., Daumke, O., Bernardi, P., Park, T.J., Kempa, S., Liu, F. and Lewin, G.R.
bioRxiv : 2024.09.30.615914. 2 October 2024

Deubzer, Hedwig (ECRC)

Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect.
Arlt, B., Mastrobuoni, G., Wuenschel, J., Astrahantseff, K., Eggert, A., Kempa, S. and Deubzer, H.E.
Journal of Enzyme Inhibition and Medicinal Chemistry 36 (1): 1282-1289. 30 June 2021

L-glyceraldehyde inhibits neuroblastoma cell growth via a multi-modal mechanism on metabolism and Signaling.
Forbes, M., Kempa, R., Mastrobuoni, G., Rayman, L., Pietzke, M., Bayram, S., Arlt, B., Spruessel, A., Deubzer, H.E. and Kempa, S.
Cancers 16 (9): 1664. May 2024

Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN.
Fuchs, S., Danßmann, C., Klironomos, F., Winkler, A., Fallmann, J., Kruetzfeldt, L.M., Szymansky, A., Naderi, J., Bernhart, S.H., Grunewald, L., Helmsauer, K., Rodriguez-Fos, E., Kirchner, M., Mertins, P., Astrahantseff, K., Suenkel, C., Toedling, J., Meggetto, F., Remke, M., Stadler, P.F., Hundsdoerfer, P., Deubzer, H.E., Künkele, A., Lang, P., Fuchs, J., Henssen, A.G., Eggert, A., Rajewsky, N., Hertwig, F. and Schulte, J.H.
Nature Communications 14 (1): 3936. 4 July 2023

Di Virgilio, Michela

Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome.
Inak, G., Rybak-Wolf, A., Lisowski, P., Pentimalli, T.M., Jüttner, R., Glažar, P., Uppal, K., Bottani, E., Brunetti, D., Secker, C., Zink, A., Meierhofer, D., Henke, M.T., Dey, M., Ciptasari, U., Mlody, B., Hahn, T., Berruezo-Llacuna, M., Karaiskos, N., Di Virgilio, M., Mayr, J.A., Wortmann, S.B., Priller, J., Gotthardt, M., Jones, D.P., Mayatepek, E., Stenzel, W., Diecke, S., Kühn, R., Wanker, E.E., Rajewsky, N., Schuelke, M. and Prigione, A.
Nature Communications 12 (1): 1929. 26 March 2021

Diecke, Sebastian (MDC/BIH)

SRRM2 splicing factor modulates cell fate in early development.
Carvalho, S., Zea-Redondo, L., Tang, T.C.C., Stachel-Braum, P., Miller, D., Caldas, P., Kukalev, A., Diecke, S., Grosswendt, S., Grosso, A.R. and Pombo, A.
Biology Open 13 (4): bio060415. April 2024

Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure.
Lisowski, P., Lickfett, S., Rybak-Wolf, A., Menacho, C., Le, S., Pentimalli, T.M., Notopoulou, S., Dykstra, W., Oehler, D., López-Calcerrada, S., Mlody, B., Otto, M., Wu, H., Richter, Y., Roth, P., Anand, R., Kulka, L.A.M., Meierhofer, D., Glazar, P., Legnini, I., Telugu, N.S., Hahn, T., Neuendorf, N., Miller, D.C., Böddrich, A., Polzin, A., Mayatepek, E., Diecke, S., Olzscha, H., Kirstein, J., Ugalde, C., Petrakis, S., Cambridge, S., Rajewsky, N., Kühn, R., Wanker, E.E., Priller, J., Metzger, J.J. and Prigione, A.
Nature Communications 15 (1): 7027. 22 August 2024

Generation of an induced pluripotent stem cell line from a Huntington's disease patient with a long HTT-PolyQ sequence.
Miller, D.C., Lisowski, P., Genehr, C., Wanker, E.E., Priller, J., Prigione, A. and Diecke, S.
Stem Cell Research 68 : 103056. April 2023

Generation of induced pluripotent stem cells from three individuals with Huntington's disease.
Miller, D.C., Lisowski, P., Lickfett, S., Mlody, B., Bünning, M., Genehr, C., Ulrich, C., Wanker, E.E., Diecke, S., Priller, J. and Prigione, A.
Stem Cell Research 65 : 102976. December 2022

Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts.
Ruiz-Orera, J., Miller, D.C., Greiner, J., Genehr, C., Grammatikaki, A., Blachut, S., Mbebi, J., Patone, G., Myronova, A., Adami, E., Dewani, N., Liang, N., Hummel, O., Mücke, M.B., Hildebrandt, T.B., Fritsch, G., Schrade, L., Zimmermann, W.H., Kondova, I., Diecke, S., van Heesch, S. and Hübner, N.
Nature Cardiovascular Research 3 (10): 1217-1235. October 2024

Efficient generation of a self-organizing neuromuscular junction model from human pluripotent stem cells.
Urzi, A., Lahmann, I., Nguyen, L.V.N., Rost, B.R., García-Pérez, A., Lelievre, N., Merritt-Garza, M.E., Phan, H.C, Bassell, G.J., Rossoll, W., Diecke, S., Kunz, S., Schmitz, D. and Gouti, M.
Nature Communications 14 (1): 8043. 19 December 2023

Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction.
Zywitza, V., Rusha, E., Shaposhnikov, D., Ruiz-Orera, J., Telugu, N., Rishko, V., Hayashi, M., Michel, G., Wittler, L., Stejskal, J., Holtze, S., Göritz, F., Hermes, R., Wang, J., Izsvák, Z., Colleoni, S., Lazzari, G., Galli, C., Hildebrandt, T.B., Hayashi, K., Diecke, S. and Drukker, M.
Scientific Reports 12 (1): 3100. 8 March 2022

Falcke, Martin

Visualizing sarcomere and cellular dynamics in skeletal muscle to improve cell therapies.
Hüttemeister, J., Rudolph, F., Radke, M.H., Fink, C., Friedrich, D., Preibisch, S., Falcke, M., Wagner, E., Lehnart, S.E. and Gotthardt, M.
bioRxiv : 2024.02.01.578471. 7 February 2024

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Liu, H., Arsiè, R., Schwabe, D., Schilling, M., Minia, I., Alles, J., Boltengagen, A., Kocks, C., Falcke, M., Friedman, N., Landthaler, M. and Rajewsky, N.
Molecular Systems Biology 19 (10): e11427. 12 October 2023

Fielitz, Jens (ECRC)

The transcription factor EB (TFEB) sensitizes the heart to chronic pressure overload.
Wundersitz, S., Pablo Tortola, C., Schmidt, S., Oliveira Vidal, R., Kny, M., Hahn, A., Zanders, L., Katus, H.A., Sauer, S., Butter, C., Luft, F.C., Müller, O.J. and Fielitz, J.
International Journal of Molecular Sciences 23 (11): 5943. 25 May 2022

Forslund, Sofia (MDC/ECRC)

Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface.
Avery, E.G., Haag, L.M., McParland, V., Kedziora, S.M., Zigra, G.J., Valdes, D.S., Kirchner, M., Popp, O., Geisberger, S., Nonn, O., Karlsen, T.V., N'Diaye, G., Yarritu, A., Bartolomaeus, H., Bartolomaeus, T.U.P., Wimmer, M.I., Haase, N., Wilhelm, A., Grütz, G., Tenstad, O., Wilck, N., Forslund, S.K., Klopfleisch, R., Kühl, A.A., Atreya, R., Kempa, S., Mertins, P., Siegmund, B., Wiig, H. and Müller, D.N.
bioRxiv : 2024.01.11.574524. 11 January 2024

Ecological factors influence balancing selection on leaf chemical profiles of a wildflower.
Carley, L.N., Mojica, J.P., Wang, B., Chen, C.Y., Lin, Y.P., Prasad, K.V.S.K, Chan, E., Hsu, C.W., Keith, R., Nuñez, C.L., Olson-Manning, C.F., Rushworth, C.A., Wagner, M.R., Wang, J., Yeh, P.M., Reichelt, M., Ghattas, K., Gershenzon, J., Lee, C.R. and Mitchell-Olds, T.
Nature Ecology & Evolution 5 : 1135-1144. August 2021

Salt transiently inhibits mitochondrial energetics in mononuclear phagocytes.
Geisberger, S., Bartolomaeus, H., Neubert, P., Willebrand, R., Zasada, C., Bartolomaeus, T., McParland, V., Swinnen, D., Geuzens, A., Maifeld, A., Krampert, L., Vogl, M., Mähler, A., Wilck, N., Marko, L., Tilic, E., Forslund, S.K., Binger, K.J., Stegbauer, J., Dechend, R., Kleinewietfeld, M., Jantsch, J., Kempa, S. and Müller, D.N.
Circulation 144 (2): 144-158. 13 July 2021

Gargiulo, Gaetano

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programming.
Breitenbach, T., Schmitt, M.J. and Dandekar, T.
Bioinformatics 38 (17): 4162-4171. 1 September 2022

Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.
Company, C., Schmitt, M.J., Dramaretska, Y., Serresi, M., Kertalli, S., Jiang, B., Yin, J.A., Aguzzi, A., Barozzi, I. and Gargiulo, G.
Nature Communications 15 (1): 897. 5 February 2024

Cell states in cancer: drivers, passengers, and trailers.
Gargiulo, G., Serresi, M. and Marine, J.C.
Cancer Discovery 14 (4): 610-614. 4 April 2024

Clonal dominance defines metastatic dissemination in pancreatic cancer.
Ho, I.L., Li, C.Y., Wang, F., Zhao, L., Liu, J., Yen, E.Y., Dyke, C.A., Shah, R., Liu, Z., Çetin, A.O., Chu, Y., Citron, F., Attanasio, S., Corti, D., Darbaniyan, F., Del Poggetto, E., Loponte, S., Liu, J., Soeung, M., Chen, Z., Jiang, S., Jiang, H., Inoue, A., Gao, S., Deem, A., Feng, N., Ying, H., Kim, M., Giuliani, V., Genovese, G., Zhang, J., Futreal, A., Maitra, A., Heffernan, T., Wang, L., Do, K.A., Gargiulo, G., Draetta, G., Carugo, A., Lin, R. and Viale, A.
Science Advances 10 (11): eadd9342. 15 March 2024

HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness.
Ho, J.S., Di Tullio, F., Schwarz, M., Low, D., Incarnato, D., Gay, F., Tabaglio, T., Zhang, J.X., Wollmann, H., Chen, L., An, O., Chan, T.H.M., Hall Hickman, A., Zheng, S., Roudko, V., Chen, S., Karz, A., Ahmed, M., He, H.H., Greenbaum, B.D., Oliviero, S., Serresi, M., Gargiulo, G., Mann, K.M., Hernando, E., Mulholland, D., Marazzi, I., Wee, D.K.B. and Guccione, E.
eLife 10 : e59654. 2 June 2021

Pharmacological modulators of epithelial immunity uncovered by synthetic genetic tracing of SARS-CoV-2 infection responses.
Jiang, B., Schmitt, M.J., Rand, U., Company, C., Dramaretska, Y., Grossmann, M., Serresi, M., Cicin-Sain, L. and Gargiulo, G.
Science Advances 9 (25): eadf4975. 23 June 2023

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.
Marques, C., Unterkircher, T., Kroon, P., Oldrini, B., Izzo, A., Dramaretska, Y., Ferrarese, R., Kling, E., Schnell, O., Nelander, S., Wagner, E.F., Bakiri, L., Gargiulo, G., Carro, M.S. and Squatrito, M.
eLife 10 : e64846. 17 August 2021

The relevance of the SH2 domain for c-Src functionality in triple-negative breast cancer cells.
Mayoral-Varo, V., Sánchez-Bailón, M.P., Calcabrini, A., García-Hernández, M., Frezza, V., Martín, M.E., González, V.M. and Martín-Pérez, J.
Cancers 13 (3): 462. 26 January 2021

Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition.
Serresi, M., Kertalli, S., Li, L., Schmitt, M.J., Dramaretska, Y., Wierikx, J., Hulsman, D. and Gargiulo, G.
Science Advances 7 (9): eabd7974. 24 February 2021

Cannabidiol converts NF(κ)B into a tumor suppressor in glioblastoma with defined antioxidative properties.
Volmar, M.N.M., Cheng, J., Alenezi, H., Richter, S., Haug, A., Hassan, Z., Goldberg, M., Li, Y., Hou, M., Herold-Mende, C., Maire, C.L., Lamszus, K., Flüh, C., Held-Feindt, J., Gargiulo, G., Topping, G.J., Schilling, F., Saur, D., Schneider, G., Synowitz, M., Schick, J.A., Kälin, R.E. and Glass, R.
Neuro-Oncology 23 (11): 1898-1910. November 2021

Gerhardt, Holger

Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma.
Finotto, L., Cole, B., Giese, W., Baumann, E., Claeys, A., Vanmechelen, M., Decraene, B., Derweduwe, M., Dubroja Lakic, N., Shankar, G., Nagathihalli Kantharaju, M., Albrecht, J.P., Geudens, I., Stanchi, F., Ligon, K.L., Boeckx, B., Lambrechts, D., Harrington, K., Van Den Bosch, L., De Vleeschouwer, S., De Smet, F. and Gerhardt, H.
EMBO Molecular Medicine 15 (11): e18144. 8 November 2023

Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification.
Giese, W., Albrecht, J.P., Oppenheim, O., Akmeriç, E.B., Kraxner, J., Schmidt, D., Harrington, K.I. and Gerhardt, H.
bioRxiv : 2024.01.24.577027v2. 27 April 2024

Converting PROMIS®-29 v2.0 profile data to SF-36 physical and mental component summary scores in patients with cardiovascular disorders.
Liegl, G., Fischer, F.H., Martin, C.N., Rönnefarth, M., Blumrich, A., Ahmadi, M., Boldt, L.H., Eckardt, K.U., Endres, M., Edelmann, F., Gerhardt, H., Grittner, U., Haghikia, A., Hübner, N., Landmesser, U., Leistner, D., Mai, K., Kollmus-Heege, J., Müller, D.N., Nolte, C.H., Piper, S.K., Schmidt-Ott, K.M., Pischon, T., Rattan, S., Rohrpasser-Napierkowski, Ira, Schönrath, K., Schulz-Menger, J., Schweizerhof, O., Spranger, J., Weber, J.E., Witzenrath, M., Schmidt, S. and Rose, M.
Health and Quality of Life Outcomes 22 (1): 64. 15 August 2024

Protocol of the Berlin Long-term Observation of Vascular Events (BeLOVE): a prospective cohort study with deep phenotyping and long-term follow up of cardiovascular high-risk patients.
Weber, J.E., Ahmadi, M., Boldt, L.H., Eckardt, K.U., Edelmann, F., Gerhardt, H., Grittner, U., Haubold, K., Hübner, N., Kollmus-Heege, J., Landmesser, U., Leistner, D.M., Mai, K., Müller, D.N., Nolte, C.H., Pieske, B., Piper, S.K., Rattan, S., Rauch, G., Schmidt, S., Schmidt-Ott, K.M., Schönrath, K., Schulz-Menger, J., Schweizerhof, O., Siegerink, B., Spranger, J., Ramachandran, V.S., Witzenrath, M., Endres, M. and Pischon, T.
BMJ Open 13 (10): e076415. 31 October 2023

Gotthardt, Michael

SLM2 is a novel cardiac splicing factor involved in heart failure due to dilated cardiomyopathy.
Boeckel, J.N., Möbius-Winkler, M., Müller, M., Rebs, S., Eger, N., Schoppe, L., Tappu, R., Kokot, K.E., Kneuer, J.M., Gaul, S., Bordalo, D.M., Lai, A., Haas, J., Ghanbari, M., Drewe-Boss, P., Liss, M., Katus, H.A., Ohler, U., Gotthardt, M., Laufs, U., Streckfuss-Bömeke, K. and Meder, B.
Genomics Proteomics & Bioinformatics 20 (1): 129-146. February 2022

Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.
Sandmann, C.L., Schulz, J.F., Ruiz-Orera, J., Kirchner, M., Ziehm, M., Adami, E., Marczenke, M., Christ, A., Liebe, N., Greiner, J., Schoenenberger, A., Mücke, M.B., Liang, N., Moritz, R.L., Sun, Z., Deutsch, E.W., Gotthardt, M., Mudge, J.M., Prensner, J.R., Willnow, T.E., Mertins, P., van Heesch, S. and Hubner, N.
Molecular Cell 83 (6): 994-1011.e18. 16 March 2023

Gouti, Mina

Sensor macrophages derived from human induced pluripotent stem cells to assess pyrogenic contaminations in parenteral drugs.
Abdin, S.M., Mansel, F., Rafiei Hashtchin, A., Ackermann, M., Hansen, G., Becker, B., Kick, B., Pham, N., Dietz, H., Schaniel, C., Martin, U., Spreitzer, I. and Lachmann, N.
Biofabrication 16 (3): 035017. July 2024

Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation.
Blassberg, R., Patel, H., Watson, T., Gouti, M., Metzis, V., Delás, M.J. and Briscoe, J.
Nature Cell Biology 24 (5): 633-644. May 2022

Organoids as tools for fundamental discovery and translation - a Keystone Symposia report.
Cable, J., Lutolf, M.P., Fu, J., Park, S.E., Apostolou, A., Chen, S., Song, C.J., Spence, J.R., Liberali, P., Lancaster, M., Meier, A.B., Pek, N.M.Q., Wells, J.M., Capeling, M.M., Uzquiano, A., Musah, S., Huch, M., Gouti, M., Hombrink, P., Quadrato, G. and Urenda, J.P.
Annals of the New York Academy of Sciences 1518 (1): 196-208. December 2022

Humane neuromuskuläre Organoide - Anwendung und Perspektive [Human neuromuscular organoids - Application and perspective].
Faustino Martins, J.M., Nguyen, L.V.N. and Gouti, M.
BIOspektrum 27 (2): 135-138. March 2021

Once upon a dish: the next frontier in engineering multicellular systems.
Huch, M. and Gouti, M.
Development 149 (20): dev200744. 15 October 2022

Canonical and non-canonical integrin-based adhesions dynamically interconvert.
Lukas, F., Matthaeus, C., López-Hernández, T., Lahmann, I., Schultz, N., Lehmann, M., Puchkov, D., Pielage, J., Haucke, V. and Maritzen, T.
Nature Communications 15 (1): 2093. 7 March 2024

A new era in neuromuscular junction research: current advances in self-organized and assembled in vitro models.
Nebol, A. and Gouti, M.
Current Opinion in Genetics & Development 87 : 102229. August 2024

Großwendt, Stefanie (MDC/BIH)

Extraembryonic gut endoderm cells undergo programmed cell death during development.
Batki, J., Hetzel, S., Schifferl, D., Bolondi, A., Walther, M., Wittler, L., Grosswendt, S., Herrmann, B.G. and Meissner, A.
Nature Cell Biology 26 (6): 868-877. June 2024

Basal delamination during mouse gastrulation primes pluripotent cells for differentiation.
Sato, N., Rosa, V.S., Makhlouf, A., Kretzmer, H., Sampath Kumar, A., Grosswendt, S., Mattei, A.L., Courbot, O., Wolf, S., Boulanger, J., Langevin, F., Wiacek, M., Karpinski, D., Elosegui-Artola, A., Meissner, A., Zernicka-Goetz, M. and Shahbazi, M.N.
Developmental Cell 59 (10): 1252-1268. 20 May 2024

Haas, Simon (MDC/BIMSB/BIH)

Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia.
Beneyto-Calabuig, S., Merbach, A.K., Kniffka, J.A., Antes, M., Szu-Tu, C., Rohde, C., Waclawiczek, A., Stelmach, P., Gräßle, S., Pervan, P., Janssen, M., Landry, J.J.M., Benes, V., Jauch, A., Brough, M., Bauer, M., Besenbeck, B., Felden, J., Bäumer, S., Hundemer, M., Sauer, T., Pabst, C., Wickenhauser, C., Angenendt, L., Schliemann, C., Trumpp, A., Haas, S., Scherer, M., Raffel, S., Müller-Tidow, C. and Velten, L.
Cell Stem Cell 30 (5): 706-721. 4 May 2023

Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging.
Bogeska, R., Mikecin, A.M., Kaschutnig, P., Fawaz, M., Büchler-Schäff, M., Le, D., Ganuza, M., Vollmer, A., Paffenholz, S.V., Asada, N., Rodriguez-Correa, E., Frauhammer, F., Buettner, F., Ball, M., Knoch, J., Stäble, S., Walter, D., Petri, A., Carreño-Gonzalez, M.J., Wagner, V., Brors, B., Haas, S., Lipka, D.B., Essers, M.A.G., Weru, V., Holland-Letz, T., Mallm, J.P., Rippe, K., Krämer, S., Schlesner, M., McKinney Freeman, S., Florian, M.C., King, K.Y., Frenette, P.S., Rieger, M.A. and Milsom, M.D.
Cell Stem Cell 29 (8): 1273-1284. 4 August 2022

Single-cell time series analysis reveals the dynamics of HSPC response to inflammation.
Bouman, B.J., Demerdash, Y., Sood, S., Grünschläger, F., Pilz, F., Itani, A.R., Kuck, A., Marot-Lassauzaie, V., Haas, S., Haghverdi, L. and Essers, M.A.
Life Science Alliance 7 (3): e202302309. March 2024

Proteomic signatures improve risk prediction for common and rare diseases.
Carrasco-Zanini, J., Pietzner, M., Davitte, J., Surendran, P., Croteau-Chonka, D.C., Robins, C., Torralbo, A., Tomlinson, C., Grünschläger, F., Fitzpatrick, N., Ytsma, C., Kanno, T., Gade, S., Freitag, D., Ziebell, F., Haas, S., Denaxas, S., Betts, J.C., Wareham, N.J., Hemingway, H., Scott, R.A. and Langenberg, C.
Nature Medicine 30 (9): 2489-2498. September 2024

Activated SUMOylation restricts MHC class I antigen presentation to confer immune evasion in cancer.
Demel, U.M., Böger, M., Yousefian, S., Grunert, C., Zhang, L., Hotz, P.W., Gottschlich, A., Köse, H., Isaakidis, K., Vonficht, D., Grünschläger, F., Rohleder, E., Wagner, K., Dönig, J., Igl, V., Brzezicha, B., Baumgartner, F., Habringer, S., Löber, J., Chapuy, B., Weidinger, C., Kobold, S., Haas, S., Busse, A.B., Müller, S., Wirth, M., Schick, M. and Keller, U.
Journal of Clinical Investigation 132 (9): e152383. 2 May 2022

A complex proinflammatory cascade mediates the activation of HSCs upon LPS exposure in vivo.
Demel, U.M., Lutz, R., Sujer, S., Demerdash, Y., Sood, S., Grünschläger, F., Kuck, A., Werner, P., Blaszkiewicz, S., Uckelmann, H.J., Haas, S. and Essers, M.
Blood Advances 6 (11): 3513-3528. 10 June 2022

Small molecule SUMO inhibition for biomarker-informed B-cell lymphoma therapy.
Demel, U.M., Wirth, M., Yousefian, S., Zhang, L., Isaakidis, K., Dönig, J., Böger, M., Singh, N., Köse, H., Haas, S., Müller, S., Schick, M. and Keller, U.
Haematologica 108 (2): 555-567. February 2023

Third-generation anti-CD19 CAR T cells for relapsed/refractory chronic lymphocytic leukemia: a phase 1/2 study.
Derigs, P., Schubert, M.L., Dreger, P., Schmitt, A., Yousefian, S., Haas, S., Röthemeier, C., Neuber, B., Hückelhoven-Krauss, A., Brüggemann, M., Bernhard, H., Kobbe, G., Lindemann, A., Rummel, M., Michels, B., Korell, F., Ho, A.D., Müller-Tidow, C. and Schmitt, M.
Leukemia 38 (11): 2419-2428. November 2024

Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice.
Funk, M.C., Gleixner, J.G., Heigwer, F., Vonficht, D., Valentini, E., Aydin, Z., Tonin, E., Del Prete, S., Mahara, S., Throm, Y., Hetzer, J., Heide, D., Stegle, O., Odom, D.T., Feldmann, A., Haas, S., Heikenwalder, M. and Boutros, M.
Developmental Cell 58 (24): 2914-2929. 18 December 2023

Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level.
John, L., Poos, A.M., Brobeil, A., Schinke, C., Huhn, S., Prokoph, N., Lutz, R., Wagner, B., Zangari, M., Tirier, S.M., Mallm, J.P., Schumacher, S., Vonficht, D., Solé-Boldo, L., Quick, S., Steiger, S., Przybilla, M.J., Bauer, K., Baumann, A., Hemmer, S., Rehnitz, C., Lückerath, C., Sachpekidis, C., Mechtersheimer, G., Haberkorn, U., Dimitrakopoulou-Strauss, A., Reichert, P., Barlogie, B., Müller-Tidow, C., Goldschmidt, H., Hillengass, J., Rasche, L., Haas, S.F., van Rhee, F., Rippe, K., Raab, M.S., Sauer, S. and Weinhold, N.
Nature Communications 14 (1): 5011. 17 August 2023

Identification of drug candidates targeting monocyte reprogramming in people living with HIV.
Knoll, R., Bonaguro, L., Dos Santos, J.C., Warnat-Herresthal, S., Jacobs-Cleophas, M.C.P., Blümel, E., Reusch, N., Horne, A., Herbert, M., Nuesch-Germano, M., Otten, T., van der Heijden, W.A., van de Wijer, L., Shalek, A.K., Händler, K., Becker, M., Beyer, M.D., Netea, M.G., Joosten, L.A.B., van der Ven, A.J.A.M., Schultze, J.L. and Aschenbrenner, A.C.
Frontiers in Immunology 14 : 1275136. 20 November 2023

Aggressive lymphoma after CD19 CAR T-cell therapy.
Kobbe, G., Brüggemann, M., Baermann, B.N., Wiegand, L., Trautmann, H., Yousefian, S., Libertini, S., Menssen, H.D., Maier, H.J., Ulrich, P., Gao, J., Bruch, P.M., Liebers, N., Radujkovic, A., Seifert, M., Schniederjohann, C., Paramasivam, N., Fitzgerald, D., Seidel, M., Esposito, I., Germing, U., Cadeddu, R.P., Nachtkamp, K., Jäger, P., Ulrych, T., Fischer, J.C., Rox, J.M., Giesel, F., Koch, R., Antoch, G., Distler, J.H.W., Meuth, S.G., Jacobsen, M., Hübschmann, D., Lu, J., Iaccarino, I., Haas, S., Damm, F. and Dietrich, S.
New England Journal of Medicine 391 (13): 1217-1226. 3 October 2024

Disruption of stem cell niche-confined R-spondin 3 expression leads to impaired hematopoiesis.
Kurtova, A.V., Heinlein, M., Haas, S., Velten, L., Dijkgraaf, G.J.P., Storm, E.E., Kljavin, N.M., Boumahdi, S., Himmels, P., Herault, A., Mancini, A.G., Koeppen, H., Dail, M., Yan, M., Zhang, J., Koch, U., Radtke, F., Modrusan, Z., Metcalfe, C., Piskol, R. and de Sauvage, F.J.
Blood Advances 7 (4): 491-507. 28 February 2023

Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy.
Lutz, R., Grünschläger, F., Simon, M., Awwad, M.H.S., Bauer, M., Yousefian, S., Beumer, N., Jopp-Saile, L., Sedlmeier, A., Solé-Boldo, L., Avanesyan, B., Vonficht, D., Stelmach, P., Steinbuss, G., Boch, T., Steiger, S., Baertsch, M.A., Prokoph, N., Rippe, K., Durie, B.G.M., Wickenhauser, C., Trumpp, A., Müller-Tidow, C., Hübschmann, D., Weinhold, N., Raab, M.S., Brors, B., Goldschmidt, H., Imbusch, C.D., Hundemer, M. and Haas, S.
Nature Communications 15 (1): 10396. 29 November 2024

ATACing single cells with phages.
Maschmeyer, P. and Haas, S.
Molecular Cell 82 (2): 234-236. 20 January 2022

Cellular hierarchies predict drug response in acute myeloid leukemia.
Raffel, S., Velten, L. and Haas, S.
Cancer Cell 40 (9): 917-919. 12 September 2022

Resistance to mesenchymal reprogramming sustains clonal propagation in metastatic breast cancer.
Saini, M., Schmidleitner, L., Moreno, H.D., Donato, E., Falcone, M., Bartsch, J.M., Vogel, V., Würth, R., Pfarr, N., Espinet, E., Lehmann, M., Königshoff, M., Reitberger, M., Haas, S., Graf, E., Schwarzmayr, T., Strom, T.M., Spaich, S., Sütterlin, M., Schneeweiss, A., Weichert, W., Schotta, G., Reichert, M., Aceto, N., Sprick, M.R., Trumpp, A., Scheel, C.H. and Klein, C.
Cell Reports 42 (6): 112533. 27 June 2023

Treatment of adult ALL patients with third-generation CD19-directed CAR T cells: results of a pivotal trial.
Schubert, M.L., Schmitt, A., Hückelhoven-Krauss, A., Neuber, B., Kunz, A., Waldhoff, P., Vonficht, D., Yousefian, S., Jopp-Saile, L., Wang, L., Korell, F., Keib, A., Michels, B., Haas, D., Sauer, T., Derigs, P., Kulozik, A., Kunz, J., Pavel, P., Laier, S., Wuchter, P., Schmier, J., Bug, G., Lang, F., Gökbuget, N., Casper, J., Görner, M., Finke, J., Neubauer, A., Ringhoffer, M., Wolleschak, D., Brüggemann, M., Haas, S., Ho, A.D., Müller-Tidow, C., Dreger, P. and Schmitt, M.
Journal of Hematology & Oncology 16 (1): 79. 22 July 2023

Systematic perturbation of chromatin factors identifies regulatory networks during healthy and malignant hematopoiesis.
Solé-Boldo, L. and Haas, S.
Nature Genetics 55 (9): 1430-1431. September 2023

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.
Triana, S., Vonficht, D., Jopp-Saile, L., Raffel, S., Lutz, R., Leonce, D., Antes, M., Hernández-Malmierca, P., Ordoñez-Rueda, D., Ramasz, B., Boch, T., Jann, J.C., Nowak, D., Hofmann, W.K., Müller-Tidow, C., Hübschmann, D., Alexandrov, T., Benes, V., Trumpp, A., Paulsen, M., Velten, L. and Haas, S.
Nature Immunology 22 (12): 1577-1589. December 2021

Cancer stem cells: The adventurous journey from hematopoietic to leukemic stem cells.
Trumpp, A. and Haas, S.
Cell 185 (8): 1266-1270. 14 April 2022

Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics.
Velten, L., Story, B.A., Hernández-Malmierca, P., Raffel, S., Leonce, D.R., Milbank, J., Paulsen, M., Demir, A., Szu-Tu, C., Frömel, R., Lutz, C., Nowak, D., Jann, J.C., Pabst, C., Boch, T., Hofmann, W.K., Müller-Tidow, C., Trumpp, A., Haas, S. and Steinmetz, L.M.
Nature Communications 12 (1): 1366. 1 March 2021

The cycling and aging mouse female reproductive tract at single-cell resolution.
Winkler, I., Tolkachov, A., Lammers, F., Lacour, P., Daugelaite, K., Schneider, N., Koch, M.L., Panten, J., Grünschläger, F., Poth, T., Ávila, B.M.d., Schneider, A., Haas, S., Odom, D.T. and Gonçalves, Â.
Cell 187 (4): 981-998. 15 February 2024

Cellular atlases are unlocking the mysteries of the human body.
Yanai, I., Haas, S., Lippert, C. and Kretzmer, H.
Nature 635 (8039): 553-555. November 2024

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Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
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Single-cell multi-omics and lineage tracing to dissect cell fate decision-making.
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Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.
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Towards reliable quantification of cell state velocities.
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Adjustments to the reference dataset design improve cell type label transfer.
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KDD Health Day/DSHealth 2021: Joint KDD 2021 Health Day and 2021 KDD Workshop on Applied Data Science for Healthcare: state of XAI and trustworthiness in health.
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Identification of disease-relevant modulators of the SHH pathway in the developing brain.
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SNT: a unifying toolbox for quantification of neuronal anatomy.
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LABKIT: labeling and segmentation toolkit for big image data.
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RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
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PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
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Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
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Development of a machine learning approach for local-scale ozone forecasting: application to Kennewick, WA.
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Machine learning-based ozone and PM2.5 forecasting: application to multiple AQS sites in the Pacific Northwest.
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Mathematical and bioinformatic tools for cell tracking.
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Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
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Nature Microbiology 8 (7): 1252-1266. July 2023

Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China).
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Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions.
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Doxorubicin changes the spatial organization of the genome around active promoters.
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Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
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Heuser, Arnd

Hoepken, Uta

EBAG9 controls CD8(+) T cell memory formation responding to tumor challenge in mice.
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Huebner, Norbert

Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes.
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Ablation of lysophosphatidic acid receptor 1 attenuates hypertrophic cardiomyopathy in a mouse model.
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Extracellular matrix in heart Failure: role of ADAMTS5 in proteoglycan remodeling.
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Amplification of autoimmune organ damage by NKp46-activated ILC1.
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Uncovering de novo gene birth in yeast using deep transcriptomics.
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Nature Communications 12 (1): 604. 27 January 2021

Endothelial overexpression of TGF-β-induced protein impairs venous thrombus resolution.
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pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation.
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Evolution and implications of de novo genes in humans.
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European and multi-ancestry genome-wide association meta-analysis of atopic dermatitis highlights importance of systemic immune regulation.
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Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort.
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Science Advances 10 (28): eadn3628. July 2024

A high-resolution map of human RNA translation.
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Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation.
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EMBO Molecular Medicine 13 (6): e13074. 7 June 2021

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.
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Genome Biology 24 (1): 215. 29 September 2023

Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension.
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Life Science Alliance 5 (4): e202101234. April 2022

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
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Insulin secretion defect in children and adolescents with obesity: clinical and molecular genetic characterization.
Enders-Seidlitz, H., Raile, K., Gong, M., Galler, A., Kuehnen, P. and Wiegand, S.
Journal of Diabetes Research 2024 : 5558634. 20 March 2024

Truncated titin proteins and titin haploinsufficiency are targets for functional recovery in human cardiomyopathy due to TTN mutations.
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Science Translational Medicine 13 (618): eabd3079. 3 November 2021

Aging-regulated TUG1 is dispensable for endothelial cell function.
Gimbel, A.T., Koziarek, S., Theodorou, K., Schulz, J.F., Stanicek, L., Kremer, V., Ali, T., Günther, S., Kumar, S., Jo, H., Hübner, N., Maegdefessel, L., Dimmeler, S., van Heesch, S. and Boon, R.A.
PLoS ONE 17 (9): e0265160. 29 September 2022

Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.
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Nature Communications 12 (1): 6618. 16 November 2021

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.
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Molecular Cell 84 (2): 261-276. 18 January 2024

Apple peel and flesh contain pro-neurogenic compounds.
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Stem Cell Reports 16 (3): 548-565. 9 March 2021

Expression of cardiovascular-related microRNAs is altered in L-arginine:glycine amidinotransferase deficient mice.
Jensen, M., Müller, C., Huebner, N., Patone, G., Saar, K., Choe, C.U., Schwedhelm, E. and Zeller, T.
Scientific Reports 12 (1): 5108. 24 March 2022

Functional analysis of a gene-edited mouse model to gain insights into the disease mechanisms of a titin missense variant.
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Basic Research in Cardiology 116 (1): 14. 26 February 2021

Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment.
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Science Advances 10 (12): eadl1710. 22 March 2024

Self-sustaining interleukin-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19.
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JCI Insight 6 (18): e150862. 22 September 2021

Spatially resolved multiomics of human cardiac niches.
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Nature 619 : 801-810. 27 July 2023

Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study.
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European Journal of Human Genetics 32 (9): 1127-1135. September 2022

Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression.
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Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function.
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Gene expression analysis and next-generation sequencing.
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Human model of primary carnitine deficiency cardiomyopathy reveals ferroptosis as a novel mechanism.
Loos, M., Klampe, B., Schulze, T., Yin, X., Theofilatos, K., Ulmer, B.M., Schulz, C., Behrens, C.S., van Bergen, T.D., Adami, E., Maatz, H., Schweizer, M., Brodesser, S., Skryabin, B.V., Rozhdestvensky, T.S., Bodbin, S., Stathopoulou, K., Christ, T., Denning, C., Hübner, N., Mayr, M., Cuello, F., Eschenhagen, T. and Hansen, A.
Stem Cell Reports 18 (11): 2123-2137. 14 November 2023

AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics.
Lund, J.B., Lindberg, E.L., Maatz, H., Pottbaecker, F., Hübner, N. and Lippert, C.
NAR Genomics and Bioinformatics 4 (4): lqac073. December 2022

SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA.
Maharana, S., Kretschmer, S., Hunger, S., Yan, X., Kuster, D., Traikov, S., Zillinger, T., Gentzel, M., Elangovan, S., Dasgupta, P., Chappidi, N., Lucas, N., Maser, K.I., Maatz, H., Rapp, A., Marchand, V., Chang, Y.T., Motorin, Y., Hubner, N., Hartmann, G., Hyman, A.A., Alberti, S. and Lee-Kirsch, M.A.
Molecular Cell 82 (19): 3712-3728.e10. 6 October 2022

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart.
Milenkovic, I., Santos Vieira, H.G., Lucas, M.C., Ruiz-Orera, J., Patone, G., Kesteven, S., Wu, J., Feneley, M., Espadas, G., Sabidó, E., Hübner, N., van Heesch, S., Völkers, M. and Novoa, E.M.
Nucleic Acids Research 51 (11): 5301-5324. 23 June 2023

Single-cell transcriptomics for the assessment of cardiac disease.
Miranda, A.M.A., Janbandhu, V., Maatz, H., Kanemaru, K., Cranley, J., Teichmann, S.A., Huebner, N., Schneider, M.D., Harvey, R.P. and Noseda, M.
Nature Reviews Cardiology 20 (5): 289-308. May 2023

Impact of uORFs in mediating regulation of translation in stress conditions.
Moro, S.G., Hermans, C., Ruiz-Orera, J. and Albà, M.M.
BMC Molecular and Cell Biology 22 (1): 29. 16 May 2021

Standardized annotation of translated open reading frames.
Mudge, J.M., Ruiz-Orera, J., Prensner, J.R., Brunet, M.A., Calvet, F., Jungreis, I., Gonzalez, Jo.M., Magrane, M., Martinez, T.F., Schulz, J.F., Yang, Y.T., Albà, M.M., Aspden, J.L., Baranov, P.V., Bazzini, A.A., Bruford, E., Martin, M.J., Calviello, L., Carvunis, A.R., Chen, J., Couso, J.P., Deutsch, E.W., Flicek, P., Frankish, A., Gerstein, M., Hubner, N., Ingolia, N.T., Kellis, M., Menschaert, G., Moritz, R.L., Ohler, U., Roucou, X., Saghatelian, A., Weissman, J.S. and van Heesch, S.
Nature Biotechnology 40 (7): 994–999. July 2022

Targeting the tissue factor coagulation initiation complex prevents antiphospholipid antibody development.
Mueller-Calleja, N., Grunz, K., Nguyen, T.S., Posma, J., Pedrosa, D., Meineck, M., Hollerbach, A., Braun, J., Muth, S., Schild, H., Saar, K., Hübner, N., Krishnaswamy, S., Royce, J., Teyton, L., Lemmermann, N.A., Weinmann-Menke, J., Lackner, K.J. and Ruf, W.
Blood 143 (12): 1167-1180. 21 March 2023

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus, C., Luecken, M.D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E.D., Subramanian, A., Smillie, C., Jagadeesh, K.A., Duong, E.T., Fiskin, E., Triglia, E.T., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A.L., Chung, H., Montoro, D.T., Adams, T., Aliee, H., Allon, S.J., Andrusivova, Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L.T., Callori, S., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T.M., Cuoco, M.S., Cuomo, A.S.E., Deprez, M., Duclos, G., Fine, D., Fischer, D.S., Ghazanfar, S., Gillich, A., Giotti, B., Gould, J., Guo, M., Gutierrez, A.J., Habermann, A.C., Harvey, T., He, P., Hou, X., Hu, L., Hu, Y., Jaiswal, A., Ji, L., Jiang, P., Kapellos, T.S., Kuo, C.S., Larsson, L., Leney-Greene, M.A., Lim, K., Litviňuková, M., Ludwig, L.S., Lukassen, S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Leroy, S., Mayr, C.H., Mbano, I.M., McAdams, A.M., Nabhan, A.N., Nyquist, S.K., Penland, L., Poirion, O.B., Poli, S., Qi, C.C., Queen, R., Reichart, D., Rosas, I., Schupp, J.C., Shea, C.V., Shi, X., Sinha, R., Sit, R.V., Slowikowski, K., Slyper, M., Smith, N.P., Sountoulidis, A., Strunz, M., Sullivan, T.B., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K.J., Tucker, N.R., Vernon, K.A., Wadsworth, M.H., Waldman, J., Wang, X., Xu, K., Yan, W., Zhao, W. and Ziegler, C.G.K.
Nature Medicine 27 (3): 546-559. 2 March 2021

Isolation of nuclei from mammalian cells and tissues for single-nucleus molecular profiling.
Nadelmann, E.R., Gorham, J.M., Reichart, D., Delaughter, D.M., Wakimoto, H., Lindberg, E.L., Litviňuková, M., Maatz, H., Curran, J.J., Ischiu Gutierrez, D., Hübner, N., Seidman, C.E. and Seidman, J G
Current Protocols 1 (5): e132. May 2021

Vascular tissue specific miRNA profiles reveal novel correlations with risk factors in coronary artery disease.
Neiburga, K., Vilne, B., Bauer, S., Bongiovanni, D., Ziegler, T., Lachmann, M., Wengert, S., Hawe, J., Güldener, U., Westerlund, A., Li, L., Pang, S., Yang, C., Saar, K., Huebner, N., Maegdefessel, L., Lange, R., Krane, M., Schunkert, H. and von Scheidt, M.
Biomolecules 11 (11): 1683. 12 November 2021

IL11 activates pancreatic stellate cells and causes pancreatic inflammation, fibrosis and atrophy in a mouse model of pancreatitis.
Ng, B., Viswanathan, S., Widjaja, A.A., Lim, W.W., Shekeran, S.G., Goh, J.W.T., Tan, J., Kuthubudeen, F., Lim, S.Y., Xie, C., Schafer, S., Adami, E. and Cook, S.A.
International Journal of Molecular Sciences 23 (7): 3549. 24 March 2022

Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.
Norin, U., Rintisch, C., Meng, L., Forster, F., Ekman, D., Tuncel, J., Klocke, K., Bäcklund, J., Yang, M., Bonner, M.Y, Lahore, G.F., James, J., Shchetynsky, K., Bergquist, M., Gjertsson, I., Hubner, N., Bäckdahl, L. and Holmdahl, R.
Nature Communications 12 (1): 610. 27 January 2021

Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection.
Pekayvaz, K., Leunig, A., Kaiser, R., Joppich, M., Brambs, S., Janjic, A., Popp, O., Nixdorf, D., Fumagalli, V., Schmidt, N., Polewka, V., Anjum, A., Knottenberg, V., Eivers, L., Wange, L.E., Gold, C., Kirchner, M., Muenchhoff, M., Hellmuth, J.C., Scherer, C., Rubio-Acero, R., Eser, T., Deák, F., Puchinger, K., Kuhl, N., Linder, A., Saar, K., Tomas, L., Schulz, C., Wieser, A., Enard, W., Kroidl, I., Geldmacher, C., von Bergwelt-Baildon, M., Keppler, O.T., Munschauer, M., Iannacone, M., Zimmer, R., Mertins, P., Hubner, N., Hoelscher, M., Massberg, S., Stark, K. and Nicolai, L.
Nature Communications 13 (1): 1018. 23 February 2022

Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes.
Pekayvaz, K., Losert, C., Knottenberg, V., Gold, C., van Blokland, I.V., Oelen, R., Groot, H.E., Benjamins, J.W., Brambs, S., Kaiser, R., Gottschlich, A., Hoffmann, G.V., Eivers, L., Martinez-Navarro, A., Bruns, N., Stiller, S., Akgöl, S., Yue, K., Polewka, V., Escaig, R., Joppich, M., Janjic, A., Popp, O., Kobold, S., Petzold, T., Zimmer, R., Enard, W., Saar, K., Mertins, P., Huebner, N., van der Harst, P., Franke, L.H., van der Wijst, M.G.P., Massberg, S., Heinig, M., Nicolai, L. and Stark, K.
Nature Medicine 30 (6): 1696-1710. June 2024

Intergenic risk variant rs56258221 skews the fate of naive CD4(+) T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis.
Poch, T., Bahn, J., Casar, C., Krause, J., Evangelakos, I., Gilladi, H., Kunzmann, L.K., Laschtowitz, A., Iuso, N., Schäfer, A.M., Liebig, L.A., Steinmann, S., Sebode, M., Folseraas, T., Engesæter, L.K., Karlsen, T.H., Franke, A., Hubner, N., Schlein, C., Galun, E., Huber, S., Lohse, A.W., Gagliani, N., Schwinge, D. and Schramm, C.
Cell Reports Medicine 5 (7): 101620. 16 July 2024

What can Ribo-seq, immunopeptidomics, and proteomics tell us about the non-canonical proteome?
Prensner, J.R., Abelin, J.G., Kok, L.W., Clauser, K.R., Mudge, J.M., Ruiz-Orera, J., Bassani-Sternberg, M., Moritz, R.L., Deutsch, E.W. and van Heesch, S.
Molecular & Cellular Proteomics 22 (9): 100631. September 2023

LINC01013 is a determinant of fibroblast activation and encodes a novel fibroblast-activating micropeptide.
Quaife, N.M., Chothani, S., Schulz, J.F., Lindberg, E.L., Vanezis, K., Adami, E., O'Fee, K., Greiner, J., Litviňuková, M., van Heesch, S., Whiffin, N., Hubner, N., Schafer, S., Rackham, O., Cook, S.A. and Barton, P.J.R.
Journal of cardiovascular translational research 16 (1): 77-85. February 2023

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.
Reichart, D., Lindberg, E.L., Maatz, H., Miranda, A.M.A., Viveiros, A., Shvetsov, N., Gärtner, A., Nadelmann, E.R., Lee, M., Kanemaru, K., Ruiz-Orera, J., Strohmenger, V., DeLaughter, D.M., Patone, G., Zhang, H., Woehler, A., Lippert, C., Kim, Y., Adami, E., Gorham, J.M., Barnett, S.N., Brown, K., Buchan, R.J., Chowdhury, R.A., Constantinou, C., Cranley, J., Felkin, L.E., Fox, H., Ghauri, A., Gummert, J., Kanda, M., Li, R., Mach, L., McDonough, B., Samari, S., Shahriaran, F., Yapp, C., Stanasiuk, C., Theotokis, P.I., Theis, F.J., van den Bogaerdt, A., Wakimoto, H., Ware, J.S., Worth, C.L., Barton, P.J.R., Lee, Y.A., Teichmann, S.A., Milting, H., Noseda, M., Oudit, G.Y., Heinig, M., Seidman, J.G., Hubner, N. and Seidman, C.E.
Science 377 (6606): eabo1984. 5 August 2022

PITX2 deficiency leads to atrial mitochondrial dysfunction.
Reyat, J.S., Sommerfeld, L.C., O'Reilly, M., Cardoso, V.R., Thiemann, E., Khan, A.O., O'Shea, C., Harder, S., Müller, C., Barlow, J., Stapley, R.J., Chua, W., Kabir, S.N., Grech, O., Hummel, O., Hübner, N., Kääb, S., Mont, Ll., Hatem, S.N., Winters, J., Zeemering, S., Morgan, N.V., Rayes, J., Gehmlich, K., Stoll, M., Brand, T., Schweizer, M., Piasecki, A., Schotten, U., Gkoutos, G.V., Lorenz, K., Cuello, F., Kirchhof, P. and Fabritz, L.
Cardiovascular Research 120 (15): 1907-1923. November 2024

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V., Ruiz-Orera, J., Hubner, N. and van Heesch, S.
PLoS Computational Biology 17 (12): e1009658. 8 December 2021

Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V., Ruiz-Orera, J., Hubner, N. and van Heesch, S.
bioRxiv : 2021.04.13.439465. 13 April 2021

In prostate cancer cells cytokines are early responders to gravitational changes occurring in parabolic flights.
Schulz, H., Dietrichs, D., Wehland, M., Corydon, T.J., Hemmersbach, R., Liemersdorf, C., Melnik, D., Hübner, N., Saar, K., Infanger, M. and Grimm, D.
International Journal of Molecular Sciences 23 (14): 7876. 17 July 2022

TUNAR lncRNA encodes a microprotein that regulates neural differentiation and neurite formation by modulating calcium dynamics.
Senís, E., Esgleas, M., Najas, S., Jiménez-Sábado, V., Bertani, C., Giménez-Alejandre, M., Escriche, A., Ruiz-Orera, J., Hergueta-Redondo, M., Jiménez, M., Giralt, A., Nuciforo, P., Albà, M.M., Peinado, H., Del Toro, D., Hove-Madsen, L., Götz, M. and Abad, M.
Frontiers in Cell and Developmental Biology 9 : 747667. 31 December 2021

The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary.
Steffens, S., Schröder, K., Krüger, M., Maack, C., Streckfuss-Bömeke, K., Backs, J., Backofen, R., Baeßler, B., Devaux, Y., Gilsbach, R., Heijman, J., Knaus, J., Kramann, R., Linz, D., Lister, A.L., Maatz, H., Maegdefessel, L., Mayr, M., Meder, B., Nussbeck, S.Y., Rog-Zielinska, E.A., Schulz, M.H., Sickmann, A., Yigit, G. and Kohl, P.
Clinical Research in Cardiology 113 (5): 672-679. May 2024

Macrocephaly and digital anomalies expand the phenotypic spectrum of PGAP2 variants in hyperphosphatasia with impaired intellectual development syndrome 3 (HPMRS3).
Susgun, S., Ben-Mahmoud, A., Rüschendorf, F., Ku, B., Hussain, S.I., Schulz, S., Puk, O., Biskup, S., Labonne, J.D.J., Don, D.W., Gupta, V., Choi, T.I., Khan, S., Wasif, N., Lacassie, Y., Layman, L.C., Ugur Iseri, S.A., Kim, C.H. and Kim, H.G.
Human Mutation 2024 : 1-13. 5 January 2024

Interleukin 11 therapy causes acute left ventricular dysfunction.
Sweeney, M., O’Fee, K., Villanueva-Hayes, C., Rahman, E., Lee, M., Tam, C.N., Pascual-Navarro, E., Maatz, H., Lindberg, E.L., Vanezis, K., Ramachandra, C.J., Andrew, Iv., Jennings, E.R., Lim, W.W., Widjaja, A.A., Carling, D., Hausenloy, D.J., Hubner, N., Barton, P.J.R. and Cook, S.A.
Cardiovascular Research : cvae224. 9 October 2024 (In Press)

A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans.
Vona, B., Mazaheri, N., Lin, S.J., Dunbar, L.A., Maroofian, R., Azaiez, H., Booth, K.T., Vitry, S., Rad, A., Rüschendorf, F., Varshney, P., Fowler, B., Beetz, C., Alagramam, K.N., Murphy, D., Shariati, G., Sedaghat, A., Houlden, H., Petree, C., VijayKumar, S., Smith, R.J.H., Haaf, T., El-Amraoui, A., Bowl, M.R., Varshney, G.K. and Galehdari, H.
Human Genetics 140 (6): 915-931. June 2021

Inhibition of IL-11 signalling extends mammalian healthspan and lifespan.
Widjaja, A.A., Lim, W.W., Viswanathan, S., Chothani, S., Corden, B., Dasan, C.M., Goh, J.W.T., Lim, R., Singh, B.K., Tan, J., Pua, C.J., Lim, S.Y., Adami, E., Schafer, S., George, B.L., Sweeney, M., Xie, C., Tripathi, M., Sims, N.A., Hübner, N., Petretto, E., Withers, D.J., Ho, L., Gil, J., Carling, D. and Cook, S.A.
Nature 632 (8023): 157-165. 1 August 2024

A neutralizing IL-11 antibody improves renal function and increases lifespan in a mouse model of alport syndrome.
Widjaja, A.A., Shekeran, S., Adami, E., Goh, J., Tan, J., Viswanathan, S., Lim, S.Y., Tan, P.H., Hübner, N., Coffman, T. and Cook, S.
Journal of the American Society of Nephrology 33 (4): 718-730. April 2022

Targeting endogenous kidney regeneration using anti-IL11 therapy in acute and chronic models of kidney disease.
Widjaja, A.A., Viswanathan, S., Shekeran, S.G., Adami, E., Lim, W.W., Chothani, S., Tan, J., Goh, J.W.T., Chen, H.M., Lim, S.Y., Boustany-Kari, C.M., Hawkins, J., Petretto, E., Hübner, N., Schafer, S., Coffman, T.M. and Cook, S.A.
Nature Communications 13 (1): 7497. 5 December 2022

Izsvak, Zsuzsanna

Atypical KCNQ1/Kv7 channel function in a neonatal diabetes patient: hypersecretion preceded the failure of pancreatic β-cells.
Zhou, Z., Gong, M., Pande, A., Margineanu, A., Lisewski, U., Purfürst, B., Zhu, H., Liang, L., Jia, S., Froehler, S., Zeng, C., Kühnen, P., Khodaverdi, S., Krill, W., Röpke, T., Chen, W., Raile, K., Sander, M. and Izsvák, Z.
iScience 27 (7): 110291. 19 July 2024

Janz, Martin / Mathas, Stephan (MDC/ECRC)

Jentsch, Thomas

Renal deletion of LRRC8/VRAC channels induces proximal tubulopathy.
López-Cayuqueo, K.I., Planells-Cases, R., Pietzke, M., Oliveras, A., Kempa, S., Bachmann, S. and Jentsch, T.J.
Journal of the American Society of Nephrology 33 (8): 1528-1545. August 2022

Junker, Jan Philipp (BIMSB)

Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy.
Boogerd, C.J., Lacraz, G.P.A., Vértesy, Á., van Kampen, S.J., Perini, I., de Ruiter, H., Versteeg, D., Brodehl, A., van der Kraak, P., Giacca, M., de Jonge, N., Junker, J.P., van Oudenaarden, A., Vink, A. and van Rooij, E.
Cardiovascular Research 119 (2): 477-491. February 2023

Systematic identification of A-to-I RNA editing in zebrafish development and adult organs.
Buchumenski, I., Holler, K., Appelbaum, L., Eisenberg, E., Junker, J.P. and Levanon, E.Y.
Nucleic Acids Research 49 (8): 4325-4337. 7 May 2021

Single cell biology - a Keystone Symposia report.
Cable, J., Elowitz, M.B., Domingos, A.I., Habib, N., Itzkovitz, S., Hamidzada, H., Balzer, M.S., Yanai, I., Liberali, P., Whited, J., Streets, A., Cai, L., Stergachis, A.B., Hong, C.K.Y., Keren, L., Guilliams, M., Alon, U., Shalek, A.K., Hamel, R., Pfau, S.J., Raj, A., Quake, S.R., Zhang, N.R., Fan, J., Trapnell, C., Wang, B., Greenwald, N.F., Vento-Tormo, R., Santos, S.D.M., Spencer, S.L., Garcia, H.G., Arekatla, G., Gaiti, F., Arbel-Goren, R., Rulands, S., Junker, J.P., Klein, A.M., Morris, S.A., Murray, J.I., Galloway, K.E., Ratz, M. and Romeike, M.
Annals of the New York Academy of Sciences 1506 (1): 74-97. December 2021

Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish.
Cardeira-da-Silva, J., Wang, Q., Sagvekar, P., Mintcheva, J., Latting, S., Günther, S., Ramadass, R., Yekelchyk, M., Preussner, J., Looso, M., Junker, J.P. and Stainier, D.Y.R.
Nature Communications 15 (1): 3637. 29 April 2024

Transcription factor induction of vascular blood stem cell niches in vivo.
Hagedorn, E.J., Perlin, J.R., Freeman, R.J., Wattrus, S.J., Han, T., Mao, C., Kim, J.W., Fernández-Maestre, I., Daily, M.L., D'Amato, C., Fairchild, M.J., Riquelme, R., Li, B., Ragoonanan, D.A.V.E., Enkhbayar, K., Henault, E.L., Wang, H.G., Redfield, S.E., Collins, S.H., Lichtig, A., Yang, S., Zhou, Y., Kunar, B., Gomez-Salinero, J.M., Dinh, T.T., Pan, J., Holler, K., Feldman, H.A., Butcher, E.C., van Oudenaarden, A., Rafii, S., Junker, J.P. and Zon, L.I.
Developmental Cell 58 (12): 1037-1051. 19 June 2023

Spatio-temporal mRNA tracking in the early zebrafish embryo.
Holler, K., Neuschulz, A., Drewe-Boß, P., Mintcheva, J., Spanjaard, B., Arsiè, R., Ohler, U., Landthaler, M. and Junker, J.P.
Nature Communications 12 : 3358. 7 June 2021

Mit Einzelzell-Genomik die Entscheidungen von Zellen verfolgen [Deciphering cell fate decisions using single cell genomics].
Hu, B. and Junker, J.P.
BIOspektrum 27 (1): 25-27. February 2021

Origin and function of activated fibroblast states during zebrafish heart regeneration.
Hu, B., Lelek, S., Spanjaard, B., El-Sammak, H., Simões, M.G., Mintcheva, J., Aliee, H., Schäfer, R., Meyer, A.M., Theis, F., Stainier, D.Y.R., Panáková, D. and Junker, J.P.
Nature Genetics 54 (8): 1227-1237. August 2022

Inference of differentiation trajectories by transfer learning across biological processes.
Jumde, G., Spanjaard, B. and Junker, J.P.
Cell Systems 15 (1): 75-82.e5. 17 January 2024

Transient activated fibroblasts contribute to zebrafish heart regeneration.
Junker, J.P. and Panáková, D.
Nature Genetics 54 (8): 1076-1077. August 2022

Mapping lineage-traced cells across time points with moslin.
Lange, M., Piran, Z., Klein, M., Spanjaard, B., Klein, D., Junker, J.P., Theis, F.J. and Nitzan, M.
Genome Biology 25 (1): 277. 21 October 2024

Dissecting the spatiotemporal diversity of adult neural stem cells.
Mitic, N., Neuschulz, A., Spanjaard, B., Schneider, J., Fresmann, N., Novoselc, K.T., Strunk, T., Münster, L., Olivares-Chauvet, P., Ninkovic, J. and Junker, J.P.
Molecular Systems Biology 20 (4): 321-337. 2 April 2024

Single-cell genomics to study developmental cell fate decisions in zebrafish.
Moreno-Ayala, R. and Junker, J.P.
Briefings in Functional Genomics 20 (6): 420–426. November 2021

Variability of an early developmental cell population underlies stochastic laterality defects.
Moreno-Ayala, R., Olivares-Chauvet, P., Schäfer, R. and Junker, J.P.
Cell Reports 34 (2): 108606. 12 January 2021

MDC1 maintains active elongation complexes of RNA polymerase II.
Pappas, G., Munk, S.H.N., Watanabe, K., Thomas, Q., Gál, Z., Gram, H.H., Lee, M.H., Gómez-Cabello, D., Kanellis, D.C., Olivares-Chauvet, P., Larsen, D.H., Gregersen, L.H., Maya-Mendoza, A., Galanos, P. and Bartek, J.
Cell Reports 42 (1): 111979. 31 January 2023

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F., Neuschulz, A., Junker, J.P., Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ-cells to diabetes recovery in zebrafish.
Singh, S.P., Chawla, P., Hnatiuk, A., Kamel, M., Silva, L.D., Spanjaard, B., Eski, S.E., Janjuha, S., Olivares-Chauvet, P., Kayisoglu, O., Rost, F., Bläsche, J., Kränkel, A., Petzold, A., Kurth, T., Reinhardt, S., Junker, J.P. and Ninov, N.
Development 149 (2): dev199853. January 2022

Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C., Maghsudi, S. and Ohler, U.
Nucleic Acids Research 50 (18): e107. 14 October 2022

Kainmüller, Dagmar

Towards hierarchical regional transformer-based multiple instance learning.
Cersovsky, J., Mohammadi, S., Kainmueller, D. and Hoehne, J.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

Simultaneous lung cell and nucleus segmentation from labelled versus unlabelled human lung DIC images.
Dohmen, M., Mittermaier, M., Rumberger, J.L., Yang, L.L., Gruber, A.D., Toennies, M., Hippenstiel, S., Kainmueller, D. and Hocke, A.C.
In: 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 27-30 May 2024, Athens, Greece. 22 August 2024

Arctique: an artificial histopathological dataset unifying realism and controllability for uncertainty quantification.
Franzen, J., Winklmayr, C., Guarino, V.E., Karg, C., Yu, X., Koreuber, N., Albrecht, J.P., Bischoff, P. and Kainmueller, D.
arXiv : 2411.0709. 11 November 2024

CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting.
Graham, S., Vu, Q.D., Jahanifar, M., Weigert, M., Schmidt, U., Zhang, W., Zhang, J., Yang, S., Xiang, J., Wang, X., Rumberger, J.L., Baumann, E., Hirsch, P., Liu, L., Hong, C., Aviles-Rivero, A.I., Jain, A., Ahn, H., Hong, Y., Azzuni, H., Xu, M., Yaqub, M., Blache, M.C., Piégu, B., Vernay, B., Scherr, T., Böhland, M., Löffler, K., Li, J., Ying, W., Wang, C., Snead, D., Raza, S.E.A., Minhas, F. and Rajpoot, N.M.
Medical Image Analysis 92 : 103047. February 2024

A comparative study of graph matching algorithms in computer vision.
Haller, S., Feineis, L., Hutschenreiter, L., Bernard, F., Rother, C., Kainmüller, D., Swoboda, P. and Savchynskyy, B.
Lecture Notes in Computer Science 13683 : 636-653. 2022

Tracking by weakly-supervised learning and graph optimization for whole-embryo c. elegans lineages.
Hirsch, P., Malin-Mayor, C., Santella, A., Preibisch, S., Kainmueller, D. and Funke, J.
Lecture Notes in Computer Science 13434 : 25-35. 16 September 2022

Fusion moves for graph matching.
Hutschenreiter, L., Haller, S., Feineis, L., Rother, C., Kainmüller, D. and Savchynskyy, B.
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada. 28 February 2022

The Collaborative Research Center FONDA.
Leser, U., Hilbrich, M., Draxl, C., Eisert, P., Grunske, L., Hostert, P., Kainmüller, D., Kao, O., Kehr, B., Kehrer, T., Koch, C., Markl, V., Meyerhenke, H., Rabl, T., Reinefeld, A., Reinert, K., Ritter, K., Scheuermann, B., Schintke, F., Schweikardt, N. and Weidlich, M.
Datenbank-Spektrum 21 : 255-260. November 2021

Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering.
Liu, C.C., Greenwald, N.F., Kong, A., McCaffrey, E.F., Leow, K.X., Mrdjen, D., Cannon, B.J., Rumberger, J.L., Varra, S.R. and Angelo, M.
Nature Communications 14 (1): 4618. 1 August 2023

Metrics reloaded: recommendations for image analysis validation.
Maier-Hein, L., Reinke, A., Godau, P., Tizabi, M.D., Buettner, F., Christodoulou, E., Glocker, B., Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M.A., Wiesenfarth, M., Kavur, A.E., Sudre, C.H., Baumgartner, M., Eisenmann, M., Heckmann-Nötzel, D., Rädsch, T., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Blaschko, M.B., Cardoso, M.J., Cheplygina, V., Cimini, B.A., Collins, G.S., Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Haase, R., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Karthikesalingam, A., Kofler, F., Kopp-Schneider, A., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G., Madani, A., Maier-Hein, K., Martel, A.L., Mattson, P., Meijering, E., Menze, B., Moons, K.G.M., Müller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rajpoot, N., Rieke, N., Saez-Rodriguez, J., Sánchez, C.I., Shetty, S., van Smeden, M., Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Van Calster, B., Varoquaux, G. and Jäger, P.F.
Nature Methods 21 (2): 195-212. 12 February 2024

FISBe: a real-world benchmark dataset for instance segmentation of long-range thin filamentous structures.
Mais, L., Hirsch, P., Managan, Claire, Kandarpa, Ramya, Rumberger, J.L., Reinke, Annika, Maier-Hein, Lena, Ihrke, Gudrun and Kainmueller, D.
In: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 16-22 June 2024, Seattle, WA, USA. 16 September 2024

PatchPerPixMatch for automated 3d search of neuronal morphologies in light microscopy.
Mais, L., Hirsch, P., Managan, C., Wang, K., Rokicki, K., Svirskas, R.R., Dickson, B.J., Korff, W., Rubin, G.M., Ihrke, G., Meissner, G.W. and Kainmueller, D.
bioRxiv : 2021.07.23.453511. 26 July 2021

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C., Hirsch, P., Guignard, L., McDole, K., Wan, Y., Lemon, W.C., Kainmueller, D., Keller, P.J., Preibisch, S. and Funke, J.
Nature Biotechnology 44 (1): 44-49. January 2023

A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.
Meissner, G.W., Nern, A., Dorman, Z., DePasquale, G.M., Forster, K., Gibney, T., Hausenfluck, J.H., He, Y., Iyer, N.A., Jeter, J., Johnson, L., Johnston, R.M., Lee, K., Melton, B., Yarbrough, B., Zugates, C.T., Clements, Jody, Goina, C., Otsuna, H., Rokicki, K., Svirskas, R.R., Aso, Y., Card, G.M., Dickson, B.J., Ehrhardt, E., Goldammer, J., Ito, M., Kainmueller, D., Korff, W., Mais, L., Minegishi, R., Namiki, S., Rubin, G.M., Sterne, G.R., Wolff, T. and Malkesman, O.
eLife 12 : e80660. 23 February 2023

Understanding metric-related pitfalls in image analysis validation.
Reinke, A., Tizabi, M.D., Baumgartner, M., Eisenmann, M., Heckmann-Nötzel, D., Kavur, A.E., Rädsch, T., Sudre, C.H., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Buettner, F., Cardoso, M.J., Cheplygina, V., Chen, J., Christodoulou, E., Cimini, B.A., Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Glocker, B., Godau, P., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Isensee, F., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Kleesiek, J., Kofler, F., Kooi, T., Kopp-Schneider, A., Kozubek, M., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G., Madani, A., Maier-Hein, K., Martel, A.L., Meijering, E., Menze, B., Moons, K.G.M., Müller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rafelski, S.M., Rajpoot, N., Reyes, M., Riegler, M.A., Rieke, N., Saez-Rodriguez, J., Sánchez, C.I., Shetty, S., Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Van Calster, B., Varoquaux, G., Yaniv, Z.R., Jäger, P.F. and Maier-Hein, L.
Nature Methods 21 (2): 182–194. February 2024

Automated classification of cellular expression in multiplexed imaging data with Nimbus.
Rumberger, J.L., Greenwald, N.F., Ranek, J.S., Boonrat, P., Walker, C., Franzen, J., Varra, S.R., Kong, A., Sowers, C., Liu, C.C., Averbukh, I., Piyadasa, H., Vanguri, R., Nederlof, I., Wang, X.J., Van Valen, D., Kok, M., Hollmann, T.J., Kainmueller, D. and Angelo, M.
bioRxiv : 2024.06.02.597062. 3 June 2024

Content-based image retrieval assists radiologists in diagnosing eye and orbital mass lesions in MRI.
Rumberger, J.L., Lim, W., Wildfeuer, B., Sodemann, E.B., Lecler, A., Stemplinger, S., Issever, A.S., Sepahdari, A.R., Langner, S., Kainmueller, D., Hamm, B. and Erg-Eigner, K.
medRxiv : 2024.07.24.24310920. 24 July 2024

Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L., Baumann, E., Hirsch, P., Janowczyk, A., Zlobec, I. and Kainmueller, D.
In: 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 28-31 March 2022, Kolkata, India. 17 August 2022

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L., Franzen, J., Hirsch, P., Albrecht, J.P. and Kainmueller, D.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

Probabilistic deep learning for instance segmentation.
Rumberger, J.L., Mais, L. and Kainmueller, D.
Lecture Notes in Computer Science 12535 : 445-457. 2021

How shift equivariance impacts metric learning for instance segmentation.
Rumberger, J.L., Yu, X., Hirsch, P., Dohmen, M., Guarino, V.E., Mokarian, A., Mais, L., Funke, J. and Kainmueller, D.
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada. 28 February 2022

Validity constraints for data analysis workflows.
Schintke, F., Belhajjame, K., De Mecquenem, N., Frantz, D., Guarino, V.E., Hilbrich, M., Lehmann, F., Missier, P., Sattler, R., Sparka, J.A., Speckhard, D.T., Stolte, H., Vu, A.D. and Leser, U.
Future Generation Computer Systems 157 : 82-97. August 2024

TLIMB - a transfer learning framework for image analysis of the brain.
Schulz, M.A., Albrecht, J.P., Yilmaz, A., Koch, A., Kainmüller, D., Leser, U. and Ritter, K.
In: Workshops of the EDBT/ICDT 2024 Joint Conference, EDBT/ICDT-WS 2024, 25-28 March 2024, Paestum, Italy. 25 March 2024

Data augmentation via partial nonlinear registration for brain-age prediction.
Schulz, M.A., Koch, A., Guarino, V.E., Kainmueller, D. and Ritter, K.
Lecture Notes in Computer Science 13596 : 169-178. 2022

Do transformers and CNNs learn different concepts of brain age?
Siegel, N.T., Kainmueller, D., Deniz, F., Ritter, K. and Schulz, M.A.
bioRxiv : 2024.08.09.607321. 9 August 2024

Heat in Germany: Health risks and preventive measures.
Winklmayr, C., Matthies-Wiesler, F., Muthers, S., Buchien, S., Kuch, B., An der Heiden, M. and Mücke, H.G.
Journal of Health Monitoring 8 (S4): 3-32. 6 September 2023

Model guidance via explanations turns image classifiers into segmentation models.
Yu, X., Franzen, J., Samek, W., Höhne, M.M.C. and Kainmueller, D.
In: Second World Conference, xAI 2024, July 17–19, 2024, Valletta, Malta. 10 July 2024

Kaminski, Michael (BIMSB)

Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.
Broto, M., Kaminski, M.M., Adrianus, C., Kim, N., Greensmith, R., Dissanayake-Perera, S., Schubert, A.J., Tan, X., Kim, H., Dighe, A.S., Collins, J.J. and Stevens, M.M.
Nature Nanotechnology 17 (10): 1120-1126. October 2022

HNF1B alters an evolutionarily conserved nephrogenic program of target genes.
Grand, K., Stoltz, M., Rizzo, L., Röck, R., Kaminski, M.M., Salinas, G., Getwan, M., Naert, T., Pichler, R. and Lienkamp, S.S.
Journal of the American Society of Nephrology 34 (3): 412-432. March 2023

CRISPR-enabled point-of-care genotyping for APOL1 genetic risk assessment.
Greensmith, R., Lape, I.T., Riella, C.V., Schubert, A.J., Metzger, J.J., Dighe, A.S., Tan, X., Hemmer, B., Rau, J., Wendlinger, S., Diederich, N., Schütz, A., Riella, L.V. and Kaminski, M.M.
EMBO Molecular Medicine 16 (10): 2619-2637. 14 October 2024

Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts.
Ilia, K., Shakiba, N., Bingham, T., Jones, R.D., Kaminski, M.M., Aravera, E., Bruno, S., Palacios, S., Weiss, R., Collins, J.J., Del Vecchio, D. and Schlaeger, T.M.
Science Advances 9 (48): eadg8495. December 2023

CRISPR-based diagnostics.
Kaminski, M.M., Abudayyeh, O.O., Gootenberg, J.S., Zhang, F. and Collins, J.J.
Nature Biomedical Engineering 5 (7): 643-656. July 2021

Deep learning is widely applicable to phenotyping embryonic development and disease.
Naert, T., Çiçek, Ö., Ogar, P., Bürgi, M., Shaidani, N.I., Kaminski, M.M., Xu, Y., Grand, K., Vujanovic, M., Prata, D., Hildebrandt, F., Brox, T., Ronneberger, O., Voigt, F.F., Helmchen, F., Loffing, J., Horb, M.E., Willsey, H.R. and Lienkamp, S.S.
Development 148 (21): dev199664. 1 November 2021

Single-stranded HDR templates with truncated Cas12a binding sequences improve knock-in efficiencies in primary human T cells.
Nitulescu, A.M., Du, W., Glaser, V., Kath, J., Greensmith, R., Mikkelsen, N.S., Stein, M., Bak, R., Kaminski, M.M. and Wagner, D.L.
bioRxiv : 2024.09.11.608426. 11 September 2024

Tuning the 3D microenvironment of reprogrammed tubule cells enhances biomimetic modeling of polycystic kidney disease.
Pichler, R., Rizzo, L., Tröndle, K., Bühler, M., Brucker, H., Müller, A.L., Grand, K., Farè, S., Viau, A., Kaminski, M.M., Kuehn, E.W., Koch, F., Zimmermann, S., Koltay, P. and Lienkamp, S.S.
Biomaterials 291 : 121910. December 2022

Keller, Ulrich

Kempa, Stefan (BIMSB)

Investigating the role of GLUL as a survival factor in cellular adaptation to glutamine depletion via targeted stable isotope resolved metabolomics.
Bayram, S., Razzaque, Y.S., Geisberger, S., Pietzke, M., Fürst, S., Vechiatto, C., Forbes, M., Mastrobuoni, G. and Kempa, S.
Frontiers in Molecular Biosciences 9 : 859787. 12 August 2022

Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs.
Côrte-Real, B.F., Hamad, I., Arroyo Hornero, R., Geisberger, S., Roels, J., Van Zeebroeck, L., Dyczko, A., van Gisbergen, M.W., Kurniawan, H., Wagner, A., Yosef, N., Weiss, S.N.Y., Schmetterer, K.G., Schröder, A., Krampert, L., Haase, S., Bartolomaeus, H., Hellings, N., Saeys, Y., Dubois, L.J., Brenner, D., Kempa, S., Hafler, D.A., Stegbauer, J., Linker, R.A., Jantsch, J., Müller, D.N. and Kleinewietfeld, M.
Cell Metabolism 35 (2): 299-315. 7 February 2023

Advancements in pulsed stable isotope-resolved metabolomics.
Forbes, M., Geisberger, S., Pietzke, M., Mastrobuoni, G. and Kempa, S.
Handbook of Experimental Pharmacology 277 : 165-180. 3 March 2023

Optimized workflow for on-line derivatization for targeted metabolomics approach by gas chromatography-mass spectrometry.
Fritsche-Guenther, R., Gloaguen, Y., Bauer, A., Opialla, T., Kempa, S., Fleming, C.A., Redmond, H.P. and Kirwan, J.A.
Metabolites 11 (12): 888. 18 December 2021

Wie Kochsalz Mitochondrien beeinflusst.
Geisberger, S.
BIOspektrum 28 (4): 387-389. June 2022

p53 terminates the regenerative fetal-like state after colitis-associated injury.
Hartl, K., Bayram, Ş., Wetzel, A., Harnack, C., Lin, M., Fischer, A.S., Liu, L., Beccacec, G., Mastrobuoni, G., Geisberger, S., Forbes, M., Monteiro, B.J.E., Macino, M., Flores, R.E., Engelmann, C., Mollenkopf, H.J., Schupp, M., Tacke, F., Sanders, A.D., Kempa, S., Berger, H. and Sigal, M.
Science Advances 10 (43): eadp8783. 25 October 2024

The effects of hypoxia on the immune-metabolic interplay in liver cancer.
He, Y., Xu, H., Liu, Y., Kempa, S., Vechiatto, C., Schmidt, R., Yilmaz, E.Y., Heidemann, L., Schnorr, J., Metzkow, S., Schellenberger, E., Häckel, A., Patzak, A., Müller, D.N. and Savic, L.J.
Biomolecules 14 (8): 1024. 17 August 2024

Extensive folding variability between homologous chromosomes in mammalian cells.
Irastorza-Azcarate, I., Kukalev, A., Kempfer, R., Thieme, C.J., Mastrobuoni, G., Markowski, J., Loof, G., Sparks, T.M., Brookes, E., Natarajan, K.N., Sauer, S., Fisher, A.G., Nicodemi, M., Ren, B., Schwarz, R.F., Kempa, S. and Pombo, A.
bioRxiv : 2024.05.08.591087. 10 May 2024

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Rybak-Wolf, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Kempa, S., Zinzen, R., Woehler, A. and Rajewsky, N.
Nature Methods 20 (10): 1544-1552. October 2023

A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration.
Löffler, J., Noom, A., Ellinghaus, A., Dienelt, A., Kempa, S. and Duda, G.N.
Communications Biology 6 (1): 327. 27 March 2023

Sodium as an important regulator of immunometabolism.
Miyauchi, H., Geisberger, S., Luft, F.C., Wilck, N., Stegbauer, J., Wiig, H., Dechend, R., Jantsch, J., Kleinewietfeld, M., Kempa, S. and Mueller, D.N.
Hypertension 81 (3): 426-435. March 2024

Proteomic profiling reveals ACSS2 facilitating metabolic support in acute myeloid leukemia.
Mochmann, L.H., Treue, D., Bockmayr, M., Silva, P., Zasada, C., Mastrobuoni, G., Bayram, S., Forbes, M., Jurmeister, P., Liebig, S., Blau, O., Schleich, K., Splettstoesser, B., Nordmann, T.M., von der Heide, E.K., Isaakidis, K., Schulze, V., Busch, C., Siddiq, H., Schlee, C., Hester, S., Fransecky, L., Neumann, M., Kempa, S., Klauschen, F. and Baldus, C.D.
Cancer Gene Therapy 31 (9): 1344-1356. September 2024

Salt sensitivity includes effects on immune cell signalling and metabolism.
Müller, D.N., Geisberger, S., Kleinewietfeld, M. and Jantsch, J.
Nature Reviews Immunology 23 (6): 341-342. June 2023

Multilayer nanocarrier for the codelivery of interferons: a promising strategy for biocompatible and long-acting antiviral treatment.
Ramos, T.I., Villacis-Aguirre, C.A., Sandoval, F.S., Martin-Solano, S., Manrique-Suárez, V., Rodríguez, H., Santiago-Padilla, L., Debut, A., Gómez-Gaete, C., Arias, M.T., Montesino, R., Lamazares, E., Cabezas, I., Hugues, F., Parra, N.C., Altamirano, C., Ramos, O.S., Santiago-Vispo, N. and Toledo, J.R.
Pharmaceutics 16 (11): 1349. 22 October 2024

Targeting HFpEF: unlocking the potential of glucagon receptor blockade.
Santiago Padilla, L. and Schiattarella, G.G.
Circulation Research 135 (5): 629-631. 16 August 2024

Protective role of the HSP90 inhibitor, STA-9090, in lungs of SARS-CoV-2-infected Syrian golden hamsters.
Teixeira Alves, L.G., Baumgardt, M., Langner, C., Fischer, M., Maria Adler, J., Bushe, J., Firsching, T.C., Mastrobuoni, G., Grobe, J., Hoenzke, K., Kempa, S., Gruber, A.D., Hocke, A.C., Trimpert, J., Wyler, E. and Landthaler, M.
BMJ Open Respiratory Research 11 (1) 29 February 2024

HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins.
Zinnall, U., Milek, M., Minia, I., Vieira-Vieira, C.H., Müller, S., Mastrobuoni, G., Hazapis, O.G., Del Giudice, S., Schwefel, D., Bley, N., Voigt, F., Chao, J.A., Kempa, S., Hüttelmaier, S., Selbach, M. and Landthaler, M.
Nature Communications 13 (1): 2727. 18 May 2022

Kettenmann, Helmut

Kirwan, Jennifer (MDC/BIH)

Deep learning-assisted peak curation for large-scale LC-MS metabolomics.
Gloaguen, Y., Kirwan, J.A. and Beule, D.
Analytical Chemistry 94 (12): 4930-4937. 29 March 2022

Klaassen, Sabine (ECRC)

Klussmann, Enno

Kuehn, Ralf (MDC/BIH)

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C., Acemel, R.D., Jedamzick, J., Bolondi, A., Cova, G., Brieske, N., Kühn, R., Wittler, L., Real, F.M. and Lupiáñez, D.G.
Nature Genetics 54 (7): 1026-1036. July 2022

Novel human neurodevelopmental and neurodegenerative disease associated with IRF2BPL gene variants-mechanisms and therapeutic avenues.
Bauersachs, D., Bomholtz, L., Del Ray Mateos, S., Kühn, R. and Lisowski, P.
Frontiers in Neuroscience 18 : 1426177. 6 June 2024

Kunz, Severine

Virus-induced senescence is driver and therapeutic target in COVID-19.
Lee, S., Yu, Y., Trimpert, J., Benthani, F., Mairhofer, M., Richter-Pechanska, P., Wyler, E., Belenki, D., Kaltenbrunner, S., Pammer, M., Kausche, L., Firsching, T.C., Dietert, K., Schotsaert, M., Martínez-Romero, C., Singh, G., Kunz, S., Niemeyer, D., Ghanem, R., Salzer, H.J.F., Paar, C., Mülleder, M., Uccellini, M., Michaelis, E.G., Khan, A., Lau, A., Schönlein, M., Habringer, A., Tomasits, J., Adler, J.M., Kimeswenger, S., Gruber, A.D., Hoetzenecker, W., Steinkellner, H., Purfuerst, B., Motz, R., Di Pierro, F., Lamprecht, B., Osterrieder, N., Landthaler, M., Drosten, C., García-Sastre, A., Langer, R., Ralser, M., Eils, R., Reimann, M., Fan, D.N.Y. and Schmitt, C.A.
Nature 599 : 283-289. 11 November 2021

Lacadie, Scott

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation.
Vučićević, D., Hsu, C.W., Lopez Zepeda, L.S., Burkert, M., Hirsekorn, A., Bilić, I., Kastelić, N., Landthaler, M., Lacadie, S.A. and Ohler, U.
bioRxiv : 2024.09.12.612198. 12 September 2024

PDGFRA is a conserved HAND2 effector during early cardiac development.
Xu, Y., Gehlot, R., Capon, S.J., Albu, M., Gretz, J., Bloomekatz, J., Mattonet, K., Vucicevic, D., Talyan, S., Kikhi, K., Günther, S., Looso, M., Firulli, B.A., Sanda, M., Firulli, A.B., Lacadie, S.A., Yelon, D. and Stainier, D.Y.R.
Nature Cardiovascular Research 3 (12): 1531-1548. December 2024

Landthaler, Markus (BIMSB)

Post-COVID exercise intolerance is associated with capillary alterations and immune dysregulations in skeletal muscles.
Aschman, T., Wyler, E., Baum, O., Hentschel, A., Rust, R., Legler, F., Preusse, C., Meyer-Arndt, L., Büttnerova, I., Förster, A., Cengiz, D., Teixeira Alves, L.G., Schneider, J., Kedor, C., Bellmann-Strobl, J., Sanchin, A., Goebel, H.H., Landthaler, M., Corman, V., Roos, A., Heppner, F.L., Radbruch, H., Paul, F., Scheibenbogen, C., Dengler, N.F. and Stenzel, W.
Acta Neuropathologica Communications 11 (1): 193. 8 December 2023

SARS-CoV-2 in humans.
Binder, M. and Wyler, E.
Berliner und Munchener Tierarztliche Wochenschrift 134 : 1-13. 30 April 2021

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated transcriptome in human cells.
Boehm, V., Wallmeroth, D., Wulf, P.O., Teixeira Alves, L.G., Popp, O., Riedel, M., Wyler, E., Franitza, M., Gerbracht, J.V., Becker, K., Polkovnychenko, K., Del Giudice, S., Benlasfer, N., Mertins, P., Landthaler, M. and Gehring, N.H.
bioRxiv : 2024.03.04.583328. 8 March 2024

DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
Calviello, L., Venkataramanan, S., Rogowski, K.J., Wyler, E., Wilkins, K., Tejura, M., Thai, B., Krol, J., Filipowicz, W., Landthaler, M. and Floor, S.N.
Nucleic Acids Research 49 (9): 5336-5350. May 2021

The matrix metalloproteinase ADAM10 supports hepatitis C virus entry and cell-to-cell spread via its sheddase activity.
Carriquí-Madroñal, B., Sheldon, J., Duven, M., Stegmann, C., Cirksena, K., Wyler, E., Zapatero-Belinchón, F.J., Vondran, F.W.R. and Gerold, G.
PLoS Pathogens 19 (11): e1011759. 15 November 2023

Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture.
Dasgupta, S., Dayagi, D.Y., Haimovich, G., Wyler, E., Olender, T., Singer, R.H., Landthaler, M. and Gerst, J.E.
eLife 12 : e83584. 30 May 2023

Vaccine-associated enhanced respiratory pathology in COVID-19 hamsters after T(H)2-biased immunization.
Ebenig, A., Muraleedharan, S., Kazmierski, J., Todt, D., Auste, A., Anzaghe, M., Gömer, A., Postmus, D., Gogesch, P., Niles, M., Plesker, R., Miskey, C., Gellhorn Serra, M., Breithaupt, A., Hörner, C., Kruip, C., Ehmann, R., Ivics, Z., Waibler, Z., Pfaender, S., Wyler, E., Landthaler, M., Kupke, A., Nouailles, G., Goffinet, C., Brown, R.J.P and Mühlebach, M.D.
Cell Reports 40 (7): 111214. 16 August 2022

IGF1R is protective in pneumococcal pneumonia.
Felten, M., Teixeira Alves, L.G., Letsiou, E., Arnedo, E.A., Piñeiro-Hermida, S., López, I.P., Dietert, K., Firsching, T., Gruber, A.D., Fatykhova, D., Hocke, A., Lingscheid, T., Lienau, J., Rohde, G., Pichel, J.G. and Witzenrath, M.
bioRxiv : 2024.09.11.612370. 11 September 2024

Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease.
Friedrich, V.D., Pennitz, P., Wyler, E., Adler, J.M., Postmus, D., Müller, K., Teixeira Alves, L.G., Prigann, J., Pott, F., Vladimirova, D., Hoefler, T., Goekeri, C., Landthaler, M., Goffinet, C., Saliba, A.E., Scholz, M., Witzenrath, M., Trimpert, J., Kirsten, H. and Nouailles, G.
EBioMedicine 108 : 105312. October 2024

SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals.
Gassen, N.C., Papies, J., Bajaj, T., Emanuel, J., Dethloff, F., Chua, R.L., Trimpert, J., Heinemann, N., Niemeyer, C., Weege, F., Hönzke, K., Aschman, T., Heinz, D.E., Weckmann, K., Ebert, T., Zellner, A., Lennarz, M., Wyler, E., Schroeder, S., Richter, A., Niemeyer, D., Hoffmann, K., Meyer, T.F., Heppner, F.L., Corman, V.M., Landthaler, M., Hocke, A.C., Morkel, M., Osterrieder, N., Conrad, C., Eils, R., Radbruch, H., Giavalisco, P., Drosten, C. and Müller, M.A.
Nature Communications 12 (1): 3818. 21 June 2021

The zinc finger antiviral protein ZAP restricts human cytomegalovirus and selectively binds and destabilizes viral UL4/UL5 transcripts.
Gonzalez-Perez, A.C., Stempel, M., Wyler, E., Urban, C., Piras, A., Hennig, T., Ganskih, S., Wei, Y., Heim, A., Landthaler, M., Pichlmair, A., Dölken, L., Munschauer, M., Erhard, F. and Brinkmann, M.M.
mBio 12 (3): e02683-20. 4 May 2021

Timed global reorganization of protein synthesis during neocortex neurogenesis at codon resolution.
Harnett, D., Ambrozkiewicz, M.C., Zinnall, U., Borisova, E., Rusanova, A., Dannenberg, R., Imami, K., Münster-Wandowski, A., Fauler, B., Mielke, T., Selbach, M., Landthaler, M., Spahn, C.M.T., Tarabykin, V., Ohler, U. and Kraushar, M.L.
bioRxiv : 2021.06.23.449626. 24 June 2021

A critical period of translational control during brain development at codon resolution.
Harnett, D., Ambrozkiewicz, M.C., Zinnall, U., Rusanova, A., Borisova, E., Drescher, A.N., Couce-Iglesias, M., Villamil, G., Dannenberg, R., Imami, K., Münster-Wandowski, A., Fauler, B., Mielke, T., Selbach, M., Landthaler, M., Spahn, C.M.T., Tarabykin, V., Ohler, U. and Kraushar, M.L.
Nature Structural & Molecular Biology 29 (12): 1277-1290. December 2022

Rat cytomegalovirus efficiently replicates in dendritic cells and induces changes in their transcriptional profile.
Madela-Mönchinger, J.C., Wolf, S.A., Wyler, E., Bauer, A., Mischke, M., Möller, L., Juranić Lisnić, V., Landthaler, M., Malyshkina, A. and Voigt, S.
Frontiers in Immunology 14 : 1192057. 23 November 2023

In vitro Kinase-to-Phosphosite database (iKiP-DB) predicts kinase activity in phosphoproteomic datasets.
Mari, T., Mösbauer, K., Wyler, E., Landthaler, M., Drosten, C. and Selbach, M.
Journal of Proteome Research 21 (6): 1575-1587. 3 June 2022

Despite the odds: formation of the SARS-CoV-2 methylation complex.
Matsuda, A., Plewka, J., Rawski, M., Mourão, A., Zajko, W., Siebenmorgen, T., Kresik, L., Lis, K., Jones, A.N., Pachota, M., Karim, A., Hartman, K., Nirwal, S., Sonani, R., Chykunova, Y., Minia, I., Mak, P., Landthaler, M., Nowotny, M., Dubin, G., Sattler, M., Suder, P., Popowicz, G.M., Pyrć, K. and Czarna, A.
Nucleic Acids Research 52 (11): 6441-6458. 24 June 2024

A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants.
Metzdorf, K., Jacobsen, H., Kim, Y., Teixeira Alves, L.G., Kulkarni, U., Brdovčak, M.C., Materljan, J., Eschke, K., Chaudhry, M.Z., Hoffmann, M., Bertoglio, F., Ruschig, M., Hust, M., Šustić, M., Krmpotić, A., Jonjić, S., Widera, M., Ciesek, S., Pöhlmann, S., Landthaler, M. and Čičin-Šain, L.
Frontiers in Immunology 15 : 1383086. 25 July 2024

Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters.
Nouailles, G., Adler, J.M., Pennitz, P., Peidli, S., Teixeira Alves, L.G., Baumgardt, M., Bushe, J., Voss, A., Langenhagen, A., Langner, C., Martin Vidal, R., Pott, F., Kazmierski, J., Ebenig, A., Lange, M.V., Mühlebach, M.D., Goekeri, C., Simmons, S., Xing, N., Abdelgawad, A., Herwig, S., Cichon, G., Niemeyer, D., Drosten, C., Goffinet, C., Landthaler, M., Blüthgen, N., Wu, H., Witzenrath, M., Gruber, A.D., Praktiknjo, S.D., Osterrieder, N., Wyler, E., Kunec, D. and Trimpert, J.
Nature Microbiology 8 (5): 860-874. May 2023

Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19.
Peidli, S., Nouailles, G., Wyler, E., Adler, J.M., Kunder, S., Voß, A., Kazmierski, J., Pott, F., Pennitz, P., Postmus, D., Teixeira Alves, L.G., Goffinet, C., Gruber, A.D., Blüthgen, N., Witzenrath, M., Trimpert, J., Landthaler, M. and Praktiknjo, S.D.
Cell Reports 43 (6): 114328. 25 June 2024

Protocol to dissociate healthy and infected murine- and hamster-derived lung tissue for single-cell transcriptome analysis.
Pennitz, P., Goekeri, C., Trimpert, J., Wyler, E., Ebenig, A., Weissfuss, C., Mühlebach, M.D., Witzenrath, M. and Nouailles, G.
STAR Protocols 4 (1): 101957. 17 March 2023

Rewired type I IFN signaling is linked to age-dependent differences in COVID-19.
Petrov, L., Brumhard, S., Wisniewski, S., Georg, P., Hillus, D., Hiller, A., Astaburuaga-García, R., Blüthgen, N., Wyler, E., Vogt, K., Dey, H.P., von Stillfried, S., Iwert, C., Bülow, R.D., Märkl, B., Maas, L., Langner, C., Meyer, T., Loske, J., Eils, R., Lehmann, I., Ondruschka, B., Ralser, M., Trimpert, J., Boor, P., Bedoui, S., Meisel, C., Mall, M.A., Corman, V.M., Sander, L.E., Röhmel, J. and Sawitzki, B.
bioRxiv : 2024.10.23.619479. 23 October 2024

Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus.
Phan, Q.V., Bogdanow, B., Wyler, E., Landthaler, M., Liu, F., Hagemeier, C. and Wiebusch, L.
PLoS Pathogens 18 (1): e1010193. 4 January 2022

Single-cell analysis of arthritogenic alphavirus-infected human synovial fibroblasts links low abundance of viral RNA to induction of innate immunity and arthralgia-associated gene expression.
Pott, F., Postmus, D., Brown, R.J.P., Wyler, E., Neumann, E., Landthaler, M. and Goffinet, C.
Emerging Microbes & Infections 10 (1): 2151-2168. 16 November 2021

Single-cell transcriptomic analysis of antiviral responses and viral antagonism in Chikungunya virus-infected synovial fibroblasts.
Pott, F., Postmus, D., Brown, R.J.P., Wyler, E., Neumann, E., Landthaler, M. and Goffinet, C.
bioRxiv : 2020.06.07.138610. 11 June 2021

The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants.
Rothenberger, S., Hurdiss, D.L., Walser, M., Malvezzi, F., Mayor, J., Ryter, S., Moreno, H., Liechti, N., Bosshart, A., Iss, C., Calabro, V., Cornelius, A., Hospodarsch, T., Neculcea, A., Looser, T., Schlegel, A., Fontaine, S., Villemagne, D., Paladino, M., Schiegg, D., Mangold, S., Reichen, C., Radom, F., Kaufmann, Y., Schaible, D., Schlegel, I., Zitt, C., Sigrist, G., Straumann, M., Wolter, J., Comby, M., Sacarcelik, F., Drulyte, I., Lyoo, H., Wang, C., Li, W., Du, W., Binz, H.K., Herrup, R., Lusvarghi, S., Neerukonda, S.N., Vassell, R., Wang, W., Adler, J.M., Eschke, K., Nascimento, M., Abdelgawad, A., Gruber, A.D., Bushe, J., Kershaw, O., Knutson, C.G., Balavenkatraman, K.K., Ramanathan, K., Wyler, E., Teixeira Alves, L.G., Lewis, S., Watson, R., Haeuptle, M.A., Zürcher, A., Dawson, K.M., Steiner, D., Weiss, C.D., Amstutz, P., van Kuppeveld, F.J.M., Stumpp, M.T., Bosch, B.J., Engler, O. and Trimpert, J.
Nature Biotechnology 40 (12): 1845-1854. December 2022

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1.
Rybak-Wolf, A., Wyler, E., Legnini, I., Loewa, A., Glažar, P., Kim, S.J., Pentimalli, T.M., Oliveras Martinez, A., Beyersdorf, B., Woehler, A., Landthaler, M. and Rajewsky, N.
bioRxiv : 2021.03.05.434122. 7 March 2021

The cytomegalovirus M35 protein directly binds to the interferon-β enhancer and modulates transcription of (Ifnb1) and other IRF3-driven genes.
Schwanke, H., Gonçalves Magalhães, V., Schmelz, S., Wyler, E., Hennig, T., Günther, T., Grundhoff, A., Dölken, L., Landthaler, M., van Ham, M., Jänsch, L., Büssow, K., van den Heuvel, J., Blankenfeldt, W., Friedel, C.C., Erhard, F. and Brinkmann, M.M.
Journal of Virology 97 (6): e0040023. 29 June 2023

The interactive complex between cytomegalovirus kinase vCDK/pUL97 and host factors CDK7-cyclin H determines individual patterns of transcription in infected cells.
Schütz, M., Cordsmeier, A., Wangen, C., Horn, A.H.C., Wyler, E., Ensser, A., Sticht, H. and Marschall, M.
International Journal of Molecular Sciences 24 (24): 17421. 13 December 2023

Highly conserved interaction profiles between clinically relevant mutants of the cytomegalovirus CDK-like kinase pUL97 and human cyclins: functional significance of cyclin H.
Schütz, M., Müller, R., Socher, E., Wangen, C., Full, F., Wyler, E., Wong, D., Scherer, M., Stamminger, T., Chou, S., Rawlinson, W.D., Hamilton, S.T., Sticht, H. and Marschall, M.
International Journal of Molecular Sciences 23 (19): 11814. 5 October 2022

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.
Singh, Y., Trautwein, C., Fendel, R., Krickeberg, N., Berezhnoy, G., Bissinger, R., Ossowski, S., Salker, M.S., Casadei, N. and Riess, O.
Heliyon 7 (6): e07147. June 2021

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.
Steinbrecht, D., Minia, I., Milek, M., Meisig, J., Blüthgen, N. and Landthaler, M.
Molecular Systems Biology 20 (12): 1346-1371. 2 December 2024

Herpes simplex virus type 1 modifies the protein composition of extracellular vesicles to promote neurite outgrowth and neuroinfection.
Sun, G., Kropp, K.A., Kirchner, M., Plückebaum, N., Selich, A., Serrero, M., Dhingra, A., Cabrera, J.R., Ritter, B., Bauerfeind, R., Wyler, E., Landthaler, M., Schambach, A., Sodeik, B., Mertins, P. and Viejo-Borbolla, A.
mBio 15 (2): e0330823. 14 February 2024

AI-guided pipeline for protein-protein interaction drug discovery identifies an SARS-CoV-2 inhibitor.
Trepte, P., Secker, C., Olivet, J., Blavier, J., Kostova, S., Maseko, S.B., Minia, I., Silva Ramos, E., Cassonnet, P., Golusik, S., Zenkner, M., Beetz, S., Liebich, M.J., Scharek, N., Schutz, A., Sperling, M., Lisurek, M., Wang, Y., Spirohn, K., Hao, T., Calderwood, M.A., Hill, D.E., Landthaler, M., Choi, S.G., Twizere, J.C., Vidal, M. and Wanker, E.E.
Molecular Systems Biology 20 (4): 428-457. 2 April 2024

Regulation of lymphoid-myeloid lineage bias through Regnase-1/3-mediated control of Nfkbiz.
Uehata, T., Yamada, S., Ori, D., Vandenbon, A., Giladi, A., Jelinski, A., Murakawa, Y., Watanabe, H., Takeuchi, K., Toratani, K., Mino, T., Kiryu, H., Standley, D.M., Tsujimura, T., Ikawa, T., Kondoh, G., Landthaler, M., Kawamoto, H., Rodewald, H.R., Amit, I., Yamamoto, R., Miyazaki, M. and Takeuchi, O.
Blood 143 (3): 243-257. 18 January 2024

Poxviruses induce a nuclear environment in the cytoplasm to promote viral replication.
Veratti, P., Wyler, E., Read, C., Scherer, M., Tan, J., Walther, P., Wider, S., Weidl, D. and Full, F.
bioRxiv : 2024.11.21.624458. 22 November 2024

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis.
Wendisch, D., Dietrich, O., Mari, T., von Stillfried, S., Ibarra, I.L., Mittermaier, M., Mache, C., Chua, R.L., Knoll, R., Timm, S., Brumhard, S., Krammer, T., Zauber, H., Hiller, A.L., Pascual-Reguant, A., Mothes, R., Bülow, R.D., Schulze, J., Leipold, A.M., Djudjaj, S., Erhard, F., Geffers, R., Pott, F., Kazmierski, J., Radke, J., Pergantis, P., Baßler, K., Conrad, C., Aschenbrenner, A.C., Sawitzki, B., Landthaler, M., Wyler, E., Horst, D., Hippenstiel, S., Hocke, A., Heppner, F.L., Uhrig, A., Garcia, C., Machleidt, F., Herold, S., Elezkurtaj, S., Thibeault, C., Witzenrath, M., Cochain, C., Suttorp, N., Drosten, C., Goffinet, C., Kurth, F., Schultze, J.L., Radbruch, H., Ochs, M., Eils, R., Müller-Redetzky, H., Hauser, A.E., Luecken, M.D., Theis, F.J., Conrad, C., Wolff, T., Boor, P., Selbach, M., Saliba, A.E. and Sander, L.E.
Cell 184 (26): 6243-6261. 22 December 2021

Single-cell RNA-sequencing of RVFV infection.
Wyler, E.
Methods in Molecular Biology 2824 : 361-372. August 2024

Key benefits of dexamethasone and antibody treatment in COVID-19 hamster models revealed by single cell transcriptomics.
Wyler, E., Adler, J.M., Eschke, K., Teixeira Alves, G., Peidli, S., Pott, F., Kazmierski, J., Michalick, L., Kershaw, O., Bushe, J., Andreotti, S., Pennitz, P., Abdelgawad, A., Postmus, D., Goffinet, C., Kreye, J., Reincke, S.M., Prüss, H., Blüthgen, N., Gruber, A.D., Kuebler, W.M., Witzenrath, M., Landthaler, M., Nouailles, G. and Trimpert, J.
Molecular Therapy 30 (5): 1952-1965. 4 May 2022

Prävention von Infektionskrankheiten mit Abwasser [Prevention of Infectious Diseases with Wastewater].
Wyler, E. and Landthaler, M.
Arbeitsmedizin Sozialmedizin Umweltmedizin 58 (6): 381-384. June 2023

CRNKL1 is a highly selective regulator of intron-retaining HIV-1 and cellular mRNAs.
Xiao, H., Wyler, E., Milek, M., Grewe, B., Kirchner, P., Ekici, A., Silva, A.B.O.V., Jungnickl, D., Full, F., Thomas, M., Landthaler, M., Ensser, A. and Überla, K.
mBio 12 (1): e02525-20. 19 January 2021

Grainyhead-like 2 deficiency and kidney cyst growth in a mouse model.
Yurtdas, Z.Y., Kilic, E., Boor, P., Wyler, E., Landthaler, M., Jung, K. and Schmidt-Ott, K.M.
Journal of the American Society of Nephrology 35 (7): 838-853. July 2024

Lee, Young-Ae (MDC/ECRC)

Leutz, Achim

Lewin, Gary

Ludwig, Leif (MDC/BIMSB/BIH)

Transcript-specific enrichment enables profiling rare cell states via scRNA-seq.
Abay, T., Stickels, R.R., Takizawa, M.T., Nalbant, B.N., Hsieh, Y.H., Hwang, S., Snopkowski, C., Yu, K.K.H., Abou-Mrad, Z., Tabar, V., Ludwig, L.S., Chaligne, R., Satpathy, A.T. and Lareau, C.A.
bioRxiv : 2024.03.27.587039. 27 March 2024

Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop, F.V., Hulselmans, G., Flerin, C., Soler-Vila, P., Rafels, A., Christiaens, V., González-Blas, C.B., Marchese, D., Caratù, G., Poovathingal, S., Rozenblatt-Rosen, O., Slyper, M., Luo, W., Muus, C., Duarte, F., Shrestha, R., Bagdatli, S.T., Corces, M.R., Mamanova, L., Knights, A., Meyer, K.B., Mulqueen, R., Taherinasab, A., Maschmeyer, P., Pezoldt, J., Lambert, C.L.G., Iglesias, M., Najle, S.R., Dossani, Z.Y., Martelotto, L.G., Burkett, Z., Lebofsky, R., Martin-Subero, J.I., Pillai, S., Sebé-Pedrós, A., Deplancke, B., Teichmann, S.A., Ludwig, L.S., Braun, T.P., Adey, A.C., Greenleaf, W.J., Buenrostro, J.D., Regev, A., Aerts, S. and Heyn, H.
Nature Biotechnology 42 (6): 916-926. June 2024

Detection of Bombali virus in a Mops condylurus bat in Kyela, Tanzania.
Düx, A., Lwitiho, S.E., Ayouba, A., Röthemeier, C., Merkel, K., Weiss, S., Thaurignac, G., Lander, A., Kouadio, L., Nowak, K., Corman, V., Drosten, C., Couacy-Hymann, E., Krüger, D.H., Kurth, A., Calvignac-Spencer, S., Peeters, M., Ntinginya, N.E., Leendertz, F.H. and Mangu, C.
Viruses 16 (8): 1227. August 2024

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Fiskin, E., Lareau, C.A., Ludwig, L.S., Eraslan, G., Liu, F., Ring, A.M., Xavier, R.J. and Regev, A.
Nature Biotechnology 40 (3): 374-381. March 2022

Single-cell multi-omics and lineage tracing to dissect cell fate decision-making.
Haghverdi, L. and Ludwig, L.S.
Stem Cell Reports 18 (1): 13-25. 10 January 2023

Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference.
Lareau, C.A., Chapman, M.S., Penter, L., Nawy, T., Pe’er, D. and Ludwig, L.S.
bioRxiv : 2024.07.28.605517v2. 5 October 2024

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.
Lareau, C.A., Dubois, S.M., Buquicchio, F.A., Hsieh, Y.H., Garg, K., Kautz, P., Nitsch, L., Praktiknjo, S.D., Maschmeyer, P., Verboon, J.M., Gutierrez, J.C., Yin, Y., Fiskin, E., Luo, W., Mimitou, E.P., Muus, C., Malhotra, R., Parikh, S., Fleming, M.D., Oevermann, L., Schulte, J., Eckert, C., Kundaje, A., Smibert, P., Vardhana, S.A., Satpathy, A.T., Regev, A., Sankaran, V.G., Agarwal, S. and Ludwig, L.S.
Nature Genetics 55 (7): 1198-1209. July 2023

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
Lareau, C.A., Liu, V., Muus, C., Praktiknjo, S.D., Nitsch, L., Kautz, P., Sandor, K., Yin, Y., Gutierrez, J.C., Pelka, K., Satpathy, A.T., Regev, A., Sankaran, V.G. and Ludwig, L.S.
Nature Protocols 18 (5): 1416-1440. May 2023

Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics.
Lareau, C.A., Romagnani, C. and Ludwig, L.S.
Frontiers in Immunology 13 : 1062415. 18 October 2022

Latent human herpesvirus 6 is reactivated in CAR T cells.
Lareau, C.A., Yin, Y., Maurer, K., Sandor, K.D., Daniel, B., Yagnik, G., Peña, J., Crawford, J.C., Spanjaart, A.M., Gutierrez, J.C., Haradhvala, N.J., Riberdy, J.M., Abay, T., Stickels, R.R., Verboon, J.M., Liu, V., Buquicchio, F.A., Wang, F., Southard, J., Song, R., Li, W., Shrestha, A., Parida, L., Getz, G., Maus, M.V., Li, S., Moore, A., Roberts, Z.J., Ludwig, L.S., Talleur, A.C., Thomas, P.G., Dehghani, H., Pertel, T., Kundaje, A., Gottschalk, S., Roth, T.L., Kersten, M.J., Wu, C.J., Majzner, R.G. and Satpathy, A.T.
Nature 623 : 608-615. 16 November 2023

Spatial single cell profiling using imaging mass cytometry: inflammatory versus penetrating Crohn's disease.
Lehmann, M., Weixler, B., Elezkurtaj, S., Loddenkemper, C., Kühl, A.A. and Siegmund, B.
Journal of Crohn's & Colitis 18 (8): 1305-1318. August 2024

Concomitant sequencing of accessible chromatin and mitochondrial genomes in single cells using mtscATAC-seq.
Ludwig, L.S. and Lareau, C.A.
Methods in Molecular Biology 2611 : 269-282. 2023

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1.
Ludwig, L.S., Lareau, C.A., Bao, E.L., Liu, N., Utsugisawa, T., Tseng, A.M., Myers, S.A., Verboon, J.M., Ulirsch, J.C., Luo, W., Muus, C., Fiorini, C., Olive, M.E., Vockley, C.M., Munschauer, M., Hunter, A., Ogura, H., Yamamoto, T., Inada, H., Nakagawa, S., Ozono, S., Subramanian, V., Chiarle, R., Glader, B., Carr, S.A., Aryee, M.J., Kundaje, A., Orkin, S., Regev, A., McCavit, T., Kanno, H. and Sankaran, V.G.
Blood 139 (16): 2534-2546. 21 April 2022

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
Miller, T.E., Lareau, C.A., Verga, J.A., DePasquale, E.A.K., Liu, V., Ssozi, D., Sandor, K., Yin, Y., Ludwig, L.S., El Farran, C.A., Morgan, D.M., Satpathy, A.T., Griffin, G.K., Lane, A.A., Love, J.C., Bernstein, B.E., Sankaran, V.G. and van Galen, P.
Nature Biotechnology 40 (7): 1030-1034. 24 February 2022

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Mimitou, E.P., Lareau, C.A., Chen, K.Y., Zorzetto-Fernandes, A.L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.S., Yeung, B.Z., Papalexi, E., Thakore, P.I., Kibayashi, T., Wing, J.B., Hata, M., Satija, R., Nazor, K.L., Sakaguchi, S., Ludwig, L.S., Sankaran, V.G., Regev, A. and Smibert, P.
Nature Biotechnology 39 (10): 1246-1258. October 2021

Mitochondrial genetics through the lens of single-cell multi-omics.
Nitsch, L., Lareau, C.A. and Ludwig, L.S.
Nature Genetics 56 (7): 1355-1365. July 2024

Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history.
Penter, L., Gohil, S.H., Lareau, C., Ludwig, L.S., Parry, E.M., Huang, T., Li, S., Zhang, W., Livitz, D., Leshchiner, I., Parida, L., Getz, G., Rassenti, L.Z., Kipps, T.J., Brown, J.R., Davids, M.S., Neuberg, D.S., Livak, K.J., Sankaran, V.G. and Wu, C.J.
Cancer Discovery 11 (12): 3048-3063. December 2021

Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.
Penter, L., Ten Hacken, E., Southard, J., Lareau, C., Ludwig, L.S., Li, S., Neuberg, D.S., Livak, K.J. and Wu, C.J.
Cancer Research 83 (5): 667-672. 1 March 2023

Single-cell genomics-based immune and disease monitoring in blood malignancies.
Rathgeber, A.C., Ludwig, L.S. and Penter, L.
Clinical Hematology International 6 (2): 62-84. 14 June 2024

Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.
Rückert, T., Lareau, C.A., Mashreghi, M.F., Ludwig, L.S. and Romagnani, C.
Nature Immunology 23 (11): 1551-1563. November 2022

Clonally expanded PD-1-expressing T cells are enriched in synovial fluid of juvenile idiopathic arthritis patients.
Vanni, A., Mazzoni, A., Semeraro, R., Capone, M., Maschmeyer, P., Lamacchia, G., Salvati, L., Carnasciali, A., Farahvachi, P., Giani, T., Simonini, G., Filocamo, G., Romano, M., Liotta, F., Mashreghi, M.F., Cosmi, L., Cimaz, R., Magi, A., Maggi, L. and Annunziato, F.
European Journal of Immunology 53 (7): 2250162. July 2023

Luft, Friedrich C. (MDC/ECRC)

Lupianez, Dario (BIMSB)

Evolution of 3D chromatin organization at different scales.
Acemel, R.D. and Lupianez, D.G.
Current Opinion in Genetics & Development 78 : 102019. February 2023

Non-coding RNAs: lncRNAs, miRNAs, and piRNAs in sexual development.
Burgos, M., Hurtado, A., Jiménez, R. and Barrionuevo, F.J.
Sexual Development 15 (5-6): 335-350. December 2021

Cancer evolution: a multifaceted affair.
Ciriello, G., Magnani, L., Aitken, S.J., Akkari, L., Behjati, S., Hanahan, D., Landau, D.A., Lopez-Bigas, N., Lupiáñez, D.G., Marine, J.C., Martin-Villalba, A., Natoli, G., Obenauf, A.C., Oricchio, E., Scaffidi, P., Sottoriva, A., Swarbrick, A., Tonon, G., Vanharanta, S. and Zuber, J.
Cancer Discovery 14 : 1-13. January 2024

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.
Feregrino, C. and Tschopp, P.
Developmental Dynamics 251 (9): 1472-1489. September 2022

Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster.
Hurtado, A., Mota-Gómez, I., Lao, M., Real, F.M., Jedamzick, J., Burgos, M., Lupiáñez, D.G., Jiménez, R. and Barrionuevo, F.J.
Nature Communications 15 (1): 3809. 7 May 2024

Sox9 is required for nail bed differentiation and digit tip regeneration.
Lao, M., Hurtado, A., de Castro, A.C., Burgos, M., Jiménez, R. and Barrionuevo, F.J.
Journal of Investigative Dermatology 142 (10): 2613-2622. October 2022

The little skate genome and the evolutionary emergence of wing-like fin appendages.
Marletaz, F., de la Calle-Mustienes, E., Acemel, R.D., Nakamura, T., Paliou, C., Naranjo, S., Martinez-Garcia, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., Gonzalez-Rajal, A., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldon, T., Tena, J.J., Lupianez, D.G., Rokhsar, D.S. and Gomez-Skarmeta, J.L.
bioRxiv : 2022.03.21.485123. 22 March 2022

The little skate genome and the evolutionary emergence of wing-like fins.
Marlétaz, F., de la Calle-Mustienes, E., Acemel, R.D., Paliou, C., Naranjo, S., Martínez-García, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.Ed., González-Rajal, Á., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldón, T., Nakamura, T., Tena, J.J., Lupianez, D.G., Rokhsar, D.S. and Gómez-Skarmeta, J.L.
Nature 616 (7957): 495-503. 20 April 2023

Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species.
Real, F.M., Lao-Pérez, M., Burgos, M., Mundlos, S., Lupiáñez, D.G., Jiménez, R. and Barrionuevo, F.J.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 340 (3): 231-244. May 2023

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development.
Schindler, M., Feregrino, C., Aldrovandi, S., Lo, B.W., Monaco, A.A., Ringel, A.R., Morales, A., Zehnder, T., Behncke, R.Y., Glaser, J., Barclay, A., Andrey, G., Kragesteen, B.K., Hägerling, R., Haas, S., Vingron, M., Ulitsky, I., Marti-Renom, M., Hechavarria, J., Fasel, N., Hiller, M., Lupianez, D.G., Mundlos, S. and Real, F.M.
bioRxiv : 2024.10.10.617585. 13 October 2024

Dynamic antagonism between key repressive pathways maintains the placental epigenome.
Weigert, R., Hetzel, S., Bailly, N., Haggerty, C., Ilik, I.A., Yung, P.Y.K., Navarro, C., Bolondi, A., Kumar, A.S., Anania, C., Brändl, B., Meierhofer, D., Lupianez, D.G., Müller, F.J., Aktas, T., Elsässer, S.J., Kretzmer, H., Smith, Z.D. and Meissner, A.
Nature Cell Biology 25 : 579–591. April 2023

Analysis of copy number variation in men with non-obstructive azoospermia.
Wyrwoll, M.J., Wabschke, R., Röpke, A., Wöste, M., Ruckert, C., Perrey, S., Rotte, N., Hardy, J., Astica, L., Lupianez, D.G., Wistuba, J., Westernströer, B., Schlatt, S., Berman, A.J., Müller, A.M., Kliesch, S., Yatsenko, A.N., Tüttelmann, F. and Friedrich, C.
Andrology 10 (8): 1593-1604. November 2022

Mertins, Philipp (MDC/BIH)

SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics.
Baytek, G., Blume, A., Demirel, F.G., Bulut, S., Popp, O., Mertins, P. and Tursun, B.
Biotechniques 73 (1): 5-17. June 2022

Robust co-immunoprecipitation with mass spectrometry for Caenorhabditis elegans using solid-phase enhanced sample preparation.
Baytek, G., Popp, O., Mertins, P. and Tursun, B.
Biotechniques 72 (5): 175-184. May 2022

Human ADA2 deficiency is characterized by the absence of an intracellular hypoglycosylated form of adenosine deaminase 2.
Ehlers, L., Hombrouck, A., Wouters, M., Pillay, B., Delafontaine, S., Bucciol, G., Baggio, M., Dzhus, M., Ebstein, F., Jacquemyn, M., De Somer, L., Schrijvers, R., Vanderschueren, S., Cassiman, D., Kirchner, M., Mertins, P., Mashreghi, M.F., Kallinich, T., Daelemans, D., Agostinis, P., Moens, L. and Meyts, I.
bioRxiv : 2023.10.25.564037v3. 8 October 2024

GAS1 is required for Notch-dependent facilitation of SHH signaling in the ventral forebrain neuroepithelium.
Marczenke, M., Sunaga, D., Popp, O., Althaus, I.W., Sauer, S., Mertins, P., Christ, A., Allen, B.L. and Willnow, T.E.
Development 148 (21): dev200080. 11 November 2021

Metzger, Jakob (BIMSB)

Evaluation of aggression and fearfulness in domestic dog (Canis familiaris).
Dyjak, M., Boruta, A., Adamkiewicz, E., Walasek, A., Bury-Burzymski, P. and Lisowski, P.
Animal Science Papers and Reports 39 (4): 407-418. 2021

Genome-engineering technologies for modeling and treatment of cystic fibrosis.
Dębczyński, M., Mojsak, D., Minarowski, Ł., Maciejewska, M., Lisowski, P. and Mróz, R.M.
Advances in Medical Sciences 68 (1): 111-120. March 2023

Deletion in the Y chromosome of B10.BR-Y(del) mice alters transcription from MSYq genes and has moderate effect on DNA methylation.
Kotarska, K., Doniec, A., Korostyński, M., Piechota, M., Gołas, A., Lisowski, P. and Styrna, J.
Reproductive Biology 22 (2): 100614. June 2022

Deep learning-driven neuromorphogenesis screenings identify repurposable drugs for mitochondrial disease.
Menacho, C., Okawa, S., Alvarez-Merz, I., Wittich, A., Muñoz-Oreja, M., Lisowski, P., Pentimalli, T.M., Rybak-Wolf, A., Inak, G., Zakin, S., Thevandavakkam, M., Petersilie, L., Zaliani, A., Mlody, B., Seibt, A., Donnelly, J., Woleben, K., Fernandez-Checa, J., Herebian, D., Mayatepek, E., Rajewsky, N., Spinazzola, A., Schuelke, M., Perlstein, E., Rossi, A., Distelmaier, F., Holt, I.J., Pless, O., Rose, C., Del Sol, A. and Prigione, A.
bioRxiv : 2024.07.08.602501. 12 July 2024

Mechanisms of IRF2BPL-related disorders and identification of a potential therapeutic strategy.
Sinha Ray, S., Dutta, D., Dennys, C., Powers, S., Roussel, F., Lisowski, P., Glažar, P., Zhang, X., Biswas, P., Caporale, J.R., Rajewsky, N., Bickle, M., Wein, N., Bellen, H.J., Likhite, S., Marcogliese, P.C. and Meyer, K.C.
Cell Reports 41 (10): 111751. 6 December 2022

Meyer, Irmtraud (BIMSB)

Women in the European Virus Bioinformatics Center.
Hufsky, F., Abecasis, A., Agudelo-Romero, P., Bletsa, M., Brown, K., Claus, C., Deinhardt-Emmer, S., Deng, L., Friedel, C.C., Gismondi, M.I., Kostaki, E.G., Kühnert, D., Kulkarni-Kale, U., Metzner, K.J., Meyer, I.M., Miozzi, L., Nishimura, L., Paraskevopoulou, S., Pérez-Cataluña, A., Rahlff, J., Thomson, E., Tumescheit, C., van der Hoek, L., Van Espen, L., Vandamme, A.M., Zaheri, M., Zuckerman, N. and Marz, M.
Viruses 14 (7): 1522. 12 July 2022

Analysis of correlation and ionization from pair distributions in many-electron systems.
López-Rosa, S., Angulo, J. C., Martín, A. L. and Antolín, J.
European Physical Journal Plus 136 (7): 763. 22 July 2021

Investigating the concept of accessibility for predicting novel RNA-RNA interactions.
Reißer, S. and Meyer, I.M.
bioRxiv : 2021.06.03.446902. 3 June 2021

CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
Nucleic Acids Research 51 (2): e10. 25 January 2023

ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.
Tsybulskyi, V. and Meyer, I.M.
Nucleic Acids Research 50 (15): e85. 26 August 2022

e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Tsybulskyi, V., Semenchenko, E. and Meyer, I.M.
Nucleic Acids Research 51 (W1): W160-W167. 5 July 2023

Mittnenzweig, Markus

Mueller, Dominik N. / Dechend, Ralph (MDC/ECRC)

Salt sensitivity includes effects on immune cell signalling and metabolism.
Müller, D.N., Geisberger, S., Kleinewietfeld, M. and Jantsch, J.
Nature Reviews Immunology 23 (6): 341-342. June 2023

Mähler, Anja (ECRC)

Na, Il-Kang (ECRC)

Ohler, Uwe (BIMSB)

Modeling Structure-Activity Relationship of AMPK Activation.
Drewe, J., Küsters, E., Hammann, F., Kreuter, M., Boss, P. and Schöning, V.
Molecules 26 (21): 6508. 1 November 2021

Deep learning for prediction of population health costs.
Drewe-Boss, P., Enders, D., Walker, J. and Ohler, U.
BMC Medical Informatics and Decision Making 22 (1): 32. 3 February 2022

RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells.
Fu, R., Wellman, K., Baldwin, A., Rege, J., Walters, K., Hirsekorn, A., Riemondy, K., Rainey, W.E and Mukherjee, N.
RNA 27 (8): 933-945. August 2021

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.
Garipler, G., Lu, C., Morrissey, Al., Lopez-Zepeda, L.S., Pei, Y., Vidal, S.E., Zen Petisco Fiore, A.P., Aydin, B., Stadtfeld, M., Ohler, U., Mahony, S., Sanjana, N.E. and Mazzoni, E.O.
Cell Reports 38 (11): 110524. 15 March 2022

How to find genomic regions relevant for gene regulation.
Guo, X., Ohler, U. and Yildirim, F.
Medizinische Genetik 33 (2): 157-165. 14 August 2021

Genome-wide analysis of actively translated open reading frames using riboTaper/ORFquant.
Harnett, D., Meerdink, E., Calviello, L., Sydow, D. and Ohler, U.
Methods in Molecular Biology 2252 : 331-346. 2021

A comparison of nine machine learning mutagenicity models and their application for predicting pyrrolizidine alkaloids.
Helma, C., Schöning, V., Drewe, J. and Boss, P.
Frontiers in Pharmacology 12 : 708050. 22 July 2021

Insights, opportunities and challenges provided by large cell atlases.
Hemberg, M., Marini, F., Ghazanfar, S., Al Ajami, A., Abassi, N., Anchang, B., Benayoun, B.A., Cao, Y., Chen, K., Cuesta-Astroz, Y., DeBruine, Z., Dendrou, K.A., De Vlaminck, I., Imkeller, K., Korsunsky, I., Lederer, A.R., Meysman, P., Miller, C., Mullan, K., Ohler, U., Patikas, N., Schuck, N., Siu, J.H.Y., Triche, T.J., Tsankov, A., van der Laan, S.W., Yajima, M., Yang, J., Zanini, F. and Jelic, I.
arXiv : 2408.06563. 13 August 2024

Lung adenocarcinoma promotion by air pollutants.
Hill, W., Lim, E.L., Weeden, C.E., Lee, C., Augustine, M., Chen, K., Kuan, F.C., Marongiu, F., Evans, E.J., Moore, D.A., Rodrigues, F.S., Pich, O., Bakker, B., Cha, H., Myers, R., van Maldegem, F., Boumelha, J., Veeriah, S., Rowan, A., Naceur-Lombardelli, C., Karasaki, T., Sivakumar, M., De, S., Caswell, D.R., Nagano, A., Black, J.R.M., Martínez-Ruiz, C., Ryu, M.H., Huff, R.D., Li, S., Favé, M.J., Magness, A., Suárez-Bonnet, A., Priestnall, S.L., Lüchtenborg, M., Lavelle, K., Pethick, J., Hardy, S., McRonald, F.E., Lin, M.H., Troccoli, C.I., Ghosh, M., Miller, Y.E., Merrick, D.T., Keith, R.L., Al Bakir, M., Bailey, C., Hill, M.S., Saal, L.H., Chen, Y., George, A.M., Abbosh, C., Kanu, N., Lee, S.H., McGranahan, N., Berg, C.D., Sasieni, P., Houlston, R., Turnbull, C., Lam, S., Awadalla, P., Grönroos, E., Downward, J., Jacks, T., Carlsten, C., Malanchi, I., Hackshaw, A., Litchfield, K., DeGregori, J., Jamal-Hanjani, M. and Swanton, C.
Nature 616 (7955): 159-167. 6 April 2023

A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.
Horlacher, M., Oleshko, S., Hu, Y., Ghanbari, M., Cantini, G., Schinke, P., Vergara, E.E., Bittner, F., Mueller, N.S, Ohler, U., Moyon, L. and Marsico, A.
NAR Genomics and Bioinformatics 5 (1): lqad010. March 2023

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.
Hsu, C.W., Shahan, R., Nolan, T.M., Benfey, P.N. and Ohler, U.
STAR Protocols 3 (4): 101729. 16 December 2022

Interpreting deep neural networks for the prediction of translation rates.
Korbel, F., Eroshok, E. and Ohler, U.
BMC Genomics 25 (1): 1061. 9 November 2024

Genomic–transcriptomic evolution in lung cancer and metastasis.
Martínez-Ruiz, C., Black, J.R.M., Puttick, C., Hill, M.S., Demeulemeester, J., Larose Cadieux, E., Thol, K., Jones, T.P., Veeriah, S., Naceur-Lombardelli, C., Toncheva, A., Prymas, P., Rowan, A., Ward, S., Cubitt, L., Athanasopoulou, F., Pich, O., Karasaki, T., Moore, D.A., Salgado, R., Colliver, E., Castignani, C., Dietzen, M., Huebner, A., Al Bakir, M., Tanić, M., Watkins, T.B.K., Lim, E.L., Al-Rashed, A.M., Lang, D., Clements, J., Cook, D.E., Rosenthal, R., Wilson, G. A., Frankell, A.M., de Carné Trécesson, S., East, P., Kanu, N., Litchfield, K., Birkbak, N.J., Hackshaw, A., Beck, S., Van Loo, P., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616 (7957): 543-552. 20 April 2023

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer.
McPherson, A.W., Vázquez-Garcia, I., Myers, M.A., Zatzman, M., Al-Rawi, D.H., Weiner, A.C., Freeman, S.S., Mohibullah, N., Satas, G., Williams, M.J., Ceglia, N., Zhang, A.W., Li, J., Lim, J.L.P., Wu, M., Choi, S., Havasov, E., Grewal, D., Shi, H., Kim, M., Schwarz, R.F., Kaufmann (Ohler), T.L., Dinh, K.N., Uhlitz, F., Tran, J., Wu, Y., Patel, R., Ramakrishnan, S., Kim, D., Clarke, J., Green, H., Ali, E., DiBona, M., Varice, N., Kundra, R., Broach, V., Gardner, G.J., Long Roche, K., Sonoda, Y., Zivanovic, O., Kim, S.H., Grisham, R.N., Liu, Y.L., Viale, A., Rusk, N., Lakhman, Y., Ellenson, L.H., Tavare, S., Aparicio, S.A.J.R., Chi, D.S., Aghajanian, C., Abu-Rustum, N.R., Friedman, C.F., Bakhoum, S.F., Zamarin, D., Weigelt, B. and Shah, S.P.
bioRxiv : 2024.07.11.602772v2. 15 July 2024

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
Miko, H., Qiu, Y., Gaertner, B., Sander, M. and Ohler, U.
BMC Genomics 22 (1): 84. 28 January 2021

Evaluation of polygenic scoring methods in five biobanks shows larger variation between biobanks than methods and finds benefits of ensemble learning.
Monti, R., Eick, L., Hudjashov, G., Läll, K., Kanoni, S., Wolford, B.N., Wingfield, B., Pain, O., Wharrie, S., Jermy, B., McMahon, A., Hartonen, T., Heyne, H., Mars, N., Lambert, S., Hveem, K., Inouye, M., van Heel, D.A., Mägi, R., Marttinen, P., Ripatti, S., Ganna, A. and Lippert, C.
American Journal of Human Genetics 111 (7): 1431-1447. 11 July 2024

Toward identification of functional sequences and variants in noncoding DNA.
Monti, R. and Ohler, U.
Annual Review of Biomedical Data Science 6 : 191-210. August 2023

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R., Rautenstrauch, P., Ghanbari, M., James, A.R., Kirchler, M., Ohler, U., Konigorski, S. and Lippert, C.
Nature Communications 13 (1): 5332. 10 September 2022

MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance.
Muino, J.M., Ruwe, H., Qu, Y., Maschmann, S., Chen, W., Zoschke, R., Ohler, U., Kaufmann, K. and Schmitz-Linneweber, C.
Plant Journal 119 (6): 2737-2752. September 2024

Antibodies against endogenous retroviruses promote lung cancer immunotherapy.
Ng, K.W., Boumelha, J., Enfield, K.S.S., Almagro, J., Cha, H., Pich, O., Karasaki, T., Moore, D.A., Salgado, R., Sivakumar, M., Young, G., Molina-Arcas, M., de Carné Trécesson, S., Anastasiou, P., Fendler, A., Au, L., Shepherd, S.T.C., Martínez-Ruiz, C., Puttick, C., Black, J.R.M., Watkins, T.B.K., Kim, H., Shim, S., Faulkner, N., Attig, J., Veeriah, S., Magno, N., Ward, S., Frankell, A.M., Al Bakir, M., Lim, E.L., Hill, M.S., Wilson, G.A., Cook, D.E., Birkbak, N.J., Behrens, A., Yousaf, N., Popat, S., Hackshaw, A., Hiley, C.T., Litchfield, K., McGranahan, N., Jamal-Hanjani, M., Larkin, J., Lee, S.H., Turajlic, S., Swanton, C., Downward, J. and Kassiotis, G.
Nature 616 (7957): 563-573. 20 April 2023

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.
Nolan, T.M., Vukašinović, N., Hsu, C.W., Zhang, J., Vanhoutte, I., Shahan, R., Taylor, I.W., Greenstreet, L., Heitz, M., Afanassiev, A., Wang, P., Szekely, P., Brosnan, A., Yin, Y., Schiebinger, G., Ohler, U., Russinova, E. and Benfey, P.N.
Science 379 (6639): eadf4721. 31 March 2023

The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma.
Pan, X., AbdulJabbar, K., Coelho-Lima, J., Grapa, A.I., Zhang, H., Cheung, A.H.K., Baena, J., Karasaki, T., Wilson, C.R., Sereno, M., Veeriah, S., Aitken, S.J., Hackshaw, A., Nicholson, A.G., Jamal-Hanjani, M., Swanton, C., Yuan, Y., Le Quesne, J. and Moore, D.A.
Nature Cancer 5 (2): 347-363. February 2024

RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
Poetz, F., Corbo, J., Levdansky, Y., Spiegelhalter, A., Lindner, D., Magg, V., Lebedeva, S., Schweiggert, J., Schott, J., Valkov, E. and Stoecklin, G.
Nature Communications 12 (1): 7175. 9 December 2021

Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
Poetz, F., Lebedeva, S., Schott, J., Lindner, D., Ohler, U. and Stoecklin, G.
Genome Biology 23 (1): 193. 12 September 2022

MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution.
Puttick, C., Jones, T.P., Leung, M.M., Galvez-Cancino, F., Liu, J., Varas-Godoy, M., Rowan, A., Pich, O., Martinez-Ruiz, C., Bentham, R., Dijkstra, K.K., Black, J.R.M., Rosenthal, R., Kanu, N., Litchfield, K., Salgado, R., Moore, D.A., Van Loo, P., Jamal-Hanjani, M., Quezada, S.A., Swanton, C. and McGranahan, N.
Nature Genetics 56 (10): 2121-2131. October 2024

Metadata-guided feature disentanglement for functional genomics.
Rakowski, A., Monti, R., Huryn, V., Lemanczyk, M., Ohler, U. and Lippert, C.
Bioinformatics 40 (Suppl 2): ii4-ii10. September 2024

TransferGWAS of T1-weighted brain MRI data from UK Biobank.
Rakowski, A., Monti, R. and Lippert, C.
PLoS Genetics 20 (12): e1011332. 13 December 2024 (In Press)

Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
Nucleic Acids Research 52 (12): e52. 8 July 2024

Intricacies of single-cell multi-omics data integration.
Rautenstrauch, P., Vlot, A.H.C., Saran, S. and Ohler, U.
Trends in Genetics 38 (2): 128-139. February 2022

Cell-type specific prediction of RNA stability from RNA-protein interactions.
Saran, S., Lebedeva, S., Hirsekorn, A. and Ohler, U.
bioRxiv : 2024.11.19.624283. 19 November 2024

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
Shahan, R., Hsu, C.W., Nolan, T.M., Cole, B.J., Taylor, I.W., Greenstreet, L., Zhang, S., Afanassiev, A., Vlot, A.H.C., Schiebinger, G., Benfey, P.N. and Ohler, U.
Developmental Cell 57 (4): 543-560. 28 February 2022

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A., Kaufmann, T.L. and Schwarz, R.F.
Bioinformatics 39 (3): btad102. March 2023

Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing.
Sung, H.M., Schott, J., Boss, P., Lehmann, J.A., Hardt, M.R., Lindner, D., Messens, J., Bogeski, I., Ohler, U. and Stoecklin, G.
Journal of Cell Biology 222 (12): e202111151. 4 December 2023

Arabidopsis uses a molecular grounding mechanism and a biophysical circuit breaker to limit floral abscission signaling.
Taylor, I.W., Patharkar, O.R., Mijar, M., Hsu, C.W., Baer, J., Niederhuth, C.E., Ohler, U., Benfey, P.N. and Walker, J.C.
Proceedings of the National Academy of Sciences of the United States of America 121 (44): e2405806121. 29 October 2024

Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation.
Tiniakou, I., Hsu, P.F., Lopez-Zepeda, L.S., Garipler, G., Esteva, E., Adams, N.M., Jang, G., Soni, C., Lau, C.M., Liu, F., Khodadadi-Jamayran, A., Rodrick, T.C., Jones, D., Tsirigos, A., Ohler, U., Bedford, M.T., Nimer, S.D., Kaartinen, V., Mazzoni, E.O. and Reizis, B.
Science Immunology 9 (94): eadi1023. 12 April 2024

Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C., Maghsudi, S. and Ohler, U.
Nucleic Acids Research 50 (18): e107. 14 October 2022

Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
Worpenberg, L., Paolantoni, C., Longhi, S., Mulorz, M.M., Lence, T., Wessels, H.H., Dassi, E., Aiello, G., Sutandy, F.X.R., Scheibe, M., Edupuganti, R.R., Busch, A., Möckel, M.M., Vermeulen, M., Butter, F., König, J., Notarangelo, M., Ohler, U., Dieterich, C., Quattrone, A., Soldano, A. and Roignant, J.Y.
EMBO Journal 40 (4): e104975. 15 February 2021

Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19.
Zhang, B., Zhang, Z., Koeken, V.A.C.M., Kumar, S., Aillaud, M., Tsay, H.C., Liu, Z., Kraft, A.R.M., Soon, C.F., Odak, I., Bošnjak, B., Vlot, A., Swertz, M.A., Ohler, U., Geffers, R., Illig, T., Huehn, J., Saliba, A.E., Sander, L.E., Förster, R., Xu, C.J., Cornberg, M., Schulte, L.N. and Li, Y.
Cell Genomics 3 (2): 100232. 8 February 2023

DCGG: drug combination prediction using GNN and GAE.
Ziaee, S.S., Rahmani, H., Tabatabaei, M., Vlot, A.H.C. and Bender, A.
Progress in Artificial Intelligence 13 : 17-30. March 2024

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
de Melo Costa, V.R., Pfeuffer, J., Louloupi, A., Ørom, U.A.V. and Piro, R.M.
BMC Bioinformatics 22 (1): 368. 15 July 2021

Panakova, Daniela

Transient activated fibroblasts contribute to zebrafish heart regeneration.
Junker, J.P. and Panáková, D.
Nature Genetics 54 (8): 1076-1077. August 2022

Paul, Friedemann (ECRC)

Pischon, Tobias

Pombo, Ana (BIMSB)

Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice.
Alcalá-Vida, R., Seguin, J., Lotz, C., Molitor, A.M., Irastorza-Azcarate, I., Awada, A., Karasu, N., Bombardier, A., Cosquer, B., Skarmeta, J.L.G., Cassel, J.C., Boutillier, A.L., Sexton, T. and Merienne, K.
Nature Communications 12 (1): 364. 13 January 2021

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie, R.A., Thieme, C.J., Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A., Kempfer, R., Chiariello, A.M., Bianco, S., Li, Y., Davis, T., Scialdone, A., Welch, L.R., Nicodemi, M. and Pombo, A.
Nature Methods 20 (7): 1037-1047. July 2023

Transient stabilization of human cardiovascular progenitor cells from human pluripotent stem cells in vitro reflects stage-specific heart development in vivo.
Bolesani, E., Bornhorst, D., Iyer, L.I., Zawada, D., Friese, N., Morgan, M., Lange, L., Gonzalez, D., Schrode, N., Leffler, A., Wunder, J., Franke, A., Drakhlis, L., Sebra, R., Schambach, A., Goedel, A., Dubois, N., Dobreva, G., Moretti, A., Zelarayán, L.C., Abdelilah-Seyfried, S. and Zweigerdt, R.
Cardiovascular Research 120 (11): 1295-1311. July 2024

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells.
Chiariello, A.M., Abraham, Alex, Bianco, S., Esposito, A., Fontana, A., Vercellone, F., Conte, M. and Nicodemi, M.
Nature Communications 15 (1): 4014. 13 May 2024

Physical mechanisms of chromatin spatial organization.
Chiariello, A.M., Bianco, S., Esposito, A., Fiorillo, L., Conte, M., Irani, E., Musella, F., Abraham, A., Prisco, A. and Nicodemi, M.
FEBS Journal 289 (5): 1180-1190. March 2022

A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome.
Cinque, L., Micale, L., Manara, E., Esposito, A., Palumbo, O., Chiariello, A.M., Bianco, S., Guerri, G., Bertelli, M., Giuffrida, M.G., Bernardini, L., Notarangelo, A., Nicodemi, M. and Castori, M.
Human Genetics 141 (2): 217-227. February 2022

Physics-based polymer models to probe chromosome structure in single molecules.
Conte, M., Chiariello, A.M., Bianco, S., Esposito, A., Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2655 : 57-66. 2023

Polymer models of chromatin imaging data in single cells.
Conte, M., Chiariello, A.M., Abraham, A., Bianco, S., Esposito, A., Nicodemi, M., Matteuzzi, T. and Vercellone, F.
Algorithms 15 (9): 330. 16 September 2022

Dynamic and equilibrium properties of finite-size polymer models of chromosome folding.
Conte, M., Fiorillo, L., Annunziatella, C., Esposito, A., Musella, F., Abraham, A., Bianco, S. and Chiariello, A.M.
Physical Review E 104 (5): 054402. 10 November 2021

A polymer physics model to dissect genome organization in healthy and pathological phenotypes.
Conte, M., Fiorillo, L., Bianco, S., Chiariello, A.M., Esposito, A., Musella, F., Flora, F., Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2301 : 307-316. 2022

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.
Conte, M., Irani, E., Chiariello, A.M., Abraham, A., Bianco, S., Esposito, A. and Nicodemi, M.
Nature Communications 13 (1): 4070. 13 July 2022

An integrated view of the structure and function of the human 4D nucleome.
Dekker, J., Oksuz, B.A., Zhang, Y., Wang, Y., Minsk, M.K., Kuang, S., Yang, L., Gibcus, J.H., Krietenstein, N., Rando, O., Xu, J., Janssens, D.H., Henikoff, S., Kukalev, A., Willemin, A., Winick-Ng, W., Kempfer, R., Pombo, A., Yu, M., Kumar, P., Zhang, L., Belmont, A.S., Sasaki, T., van Schaik, T., Brueckner, L., Peric-Hupkes, D., van Steensel, B., Wang, P., Chai, H., Kim, M., Ruan, Y., Zhang, R., Quinodoz, S.A., Bhat, P., Guttman, M., Zhao, W., Chien, S., Liu, Y., Venev, S.V., Plewczynski, D., Irastorza Azcarate, I., Szabo, D., Thieme, C.J., Szczepinska, T., Chilinski, M., Sengupta, K., Conte, M., Esposito, A., Abraham, A., Zhang, R., Wang, Y., Wen, X., Wu, Q., Yang, Y., Liu, J., Boninsegna, L., Yildirim, A., Zhan, Y., Chiariello, A.M., Bianco, S., Lee, L., Hu, M., Li, Y., Barnett, R.., Cook, A.L., Emerson, D.J., Marchal, C., Zhao, P., Park, P., Alver, B.H., Schroeder, A., Navelkar, R., Bakker, C., Ronchetti, W., Ehmsen, S., Veit, A., Gehlenborg, N., Wang, T., Li, D., Wang, X., Nicodemi, M., Ren, B., Zhong, S., Phillips-Cremins, J.E., Gilbert, D.M., Pollard, K.S., Alber, F., Ma, J., Noble, W.S. and Yue, F.
bioRxiv : 2024.09.17.613111v2. 27 October 2024

Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
Divisato, G., Chiariello, A.M., Esposito, A., Zoppoli, P., Zambelli, F., Elia, M.A., Pesole, G., Incarnato, D., Passaro, F., Piscitelli, S., Oliviero, S., Nicodemi, M., Parisi, S. and Russo, T.
BMC Biology 20 (1): 171. 2 August 2022

The physics of DNA folding: polymer models and phase-separation.
Esposito, A., Abraham, A., Conte, M., Vercellone, F., Prisco, A., Bianco, S. and Chiariello, A.M.
Polymers 14 (9): 1918. 9 May 2022

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.
Esposito, A., Bianco, S., Chiariello, A.M., Abraham, A., Fiorillo, L., Conte, M., Campanile, R. and Nicodemi, M.
Cell Reports 38 (13): 110601. 29 March 2022

Polymer models are a versatile tool to study chromatin 3D organization.
Esposito, A., Bianco, S., Fiorillo, L., Conte, M., Abraham, A., Musella, F., Nicodemi, M., Prisco, A. and Chiariello, A.M.
Biochemical Society Transactions 49 (4): 1675-1684. August 2021

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo, L., Musella, F., Conte, M., Kempfer, R., Chiariello, A.M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Abraham, A., Prisco, A., Pombo, A. and Nicodemi, M.
Nature Methods 18 (5): 482-490. May 2021

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression.
Franke, M., De la Calle-Mustienes, E., Neto, A., Almuedo-Castillo, M., Irastorza-Azcarate, I., Acemel, R.D., Tena, J.J., Santos-Pereira, J.M. and Gómez-Skarmeta, J.L.
Nature Communications 12 (1): 5415. 13 September 2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J.A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M.C., Chatelain, C., Carninci, P., de Hoon, M.J.L., Wasserman, W.W., Bréhélin, L. and Lecellier, C.H.
Nature Communications 12 (1): 3297. 2 June 2021

The dynamics of chromatin architecture in brain development and function.
Harabula, I. and Pombo, A.
Current Opinion in Genetics & Development 67 : 84-93. April 2021

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A.M., Yu, M., Hu, R., Tastemel, M., Juric, I., Hu, M., Nicodemi, M., Zhuang, X. and Ren, B.
Nature Genetics 53 (7): 1064-1074. July 2021

Dynamics of bacteria scanning a porous environment.
Irani, E., Mokhtari, Z. and Zippelius, A.
Physical Review Letters 128 (14): 144501. 5 April 2022

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H. and Ren, B.
Nature Structural & Molecular Biology 28 (2): 152-161. February 2021

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Kehr, B., Pombo, A., Rahmann, S. and Schwarz, R.F.
Bioinformatics 37 (19): 3128–3135. 1 October 2021

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
Ringel, A.R., Szabo, Q., Chiariello, A.M., Chudzik, K., Schöpflin, R., Rothe, P., Mattei, A.L., Zehnder, To., Harnett, D., Laupert, V., Bianco, S., Hetzel, S., Glaser, J., Phan, M.H.Q., Schindler, M., Ibrahim, D.M., Paliou, C., Esposito, A., Prada-Medina, C.A., Haas, S.A., Giere, P., Vingron, M., Wittler, L., Meissner, A., Nicodemi, M., Cavalli, G., Bantignies, F., Mundlos, S. and Robson, M.I.
Cell 185 (20): 3689-3704. 29 September 2022

Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes.
Schindler, M., Osterwalder, M., Harabula, I., Wittler, L., Tzika, A.C., Dechmann, D.K.N., Vingron, M., Visel, A., Haas, S. and Real, F.M.
Development 150 (17): dev201562. 1 September 2023

Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level.
Stein, J., Ericsson, M., Nofal, M., Magni, L., Aufmkolk, S., McMillan, R.B., Breimann, L., Herlihy, C.P., Lee, S.D., Willemin, A., Wohlmann, J., Arguedas-Jimenez, L., Yin, P., Pombo, A., Church, G.M. and Wu, C.T.
bioRxiv : 2024.02.05.576943. 5 February 2024

Genome architecture mapping detects transcriptionally active, multiway chromatin contacts.
Thieme, C.J. and Pombo, A.
Nature Methods 20 (7): 993-994. July 2023

Epigenetic regulatory layers in the 3D nucleus.
Willemin, A., Szabo, D. and Pombo, A.
Molecular Cell 84 (3): 415-428. 1 February 2024

A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
Yanchus, C., Drucker, K.L., Kollmeyer, T.M., Tsai, R., Winick-Ng, W., Liang, M., Malik, A., Pawling, J., De Lorenzo, S.B., Ali, A., Decker, P.A., Kosel, M.L., Panda, A., Al-Zahrani, K.N., Jiang, L., Browning, J.W.L., Lowden, C., Geuenich, M., Hernandez, J.J., Gosio, J.T., Ahmed, M., Loganathan, S.K., Berman, J., Trcka, D., Michealraj, K.A., Fortin, J., Carson, B., Hollingsworth, E.W., Jacinto, S., Mazrooei, P., Zhou, L., Elia, A., Lupien, M., He, H.H., Murphy, D.J., Wang, L., Abyzov, A., Dennis, J.W., Maass, P.G., Campbell, K., Wilson, M.D., Lachance, D.H., Wrensch, M., Wiencke, J., Mak, T., Pennacchio, L.A., Dickel, D.E., Visel, A., Wrana, J., Taylor, M.D., Zadeh, G., Dirks, P., Eckel-Passow, J.E., Attisano, L., Pombo, A., Ida, C.M., Kvon, E.Z., Jenkins, R.B. and Schramek, D.
Science 378 (6615): 68-78. 7 October 2022

Mechanisms of enhancer function in neuronal systems in health and disease.
Zea Redondo, L. and Pombo, A.
Current Opinion in Systems Biology 32-33 : 100443. March 2023

Altered nuclear architecture in blood cells from Huntington's disease patients.
de Castro, I.J., Toner, B., Xie, S.Q., Swingland, J., Hodges, A., Tabrizi, S.J., Turkheimer, F., Pombo, A. and Khalil, A.
Neurological Sciences 43 (1): 379-385. January 2022

Preibisch, Stephan (BIMSB)

Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos.
Breimann, L., Bahry, E., Zouinkhi, M., Kolyvanov, K., Street, L.A., Preibisch, S. and Ercan, S.
bioRxiv : 2024.05.15.594414. 16 May 2024

Image processing and analysis of light sheet microscopy data.
Jain, A., Ulman, V., Krumnikl, M., Pietzsch, T., Preibisch, S. and Tomančák, P.
In: Light Sheet Fluorescence Microscopy. Wiley‐VCH GmbH, Weinheim, Germany, 203-229. ISBN 9783527341351 18 March 2024

Best practice standards for circular RNA research.
Nielsen, A.F., Bindereif, A., Bozzoni, I., Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S., Legnini, I., Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J., Preibisch, S., Rajewsky, N., Suenkel, C. and Kjems, J.
Nature Methods 19 (10): 1208-1220. October 2022

Scalable image-based visualization and alignment of spatial transcriptomics datasets.
Preibisch, S., Innerberger, M., León-Periñán, D., Karaiskos, N. and Rajewsky, N.
bioRxiv : 2021.12.07.471629v3. 7 October 2024

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
Preusser, F., Dos Santos, N., Contzen, J., Stachelscheid, H., Costa, E.T., Mergenthaler, P. and Preibisch, S.
Bioinformatics 37 (18): 3088-3090. 15 September 2021

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F., Neuschulz, A., Junker, J.P., Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Light sheet fluorescence microscopy.
Stelzer, E.H.K., Strobl, F., Chang, B.J., Preusser, F., Preibisch, S., McDole, K. and Fiolka, R.
Nature Reviews Methods Primers 1 (1): 73. 3 November 2021

Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.
Vladimirov, N., Preusser, F., Wisniewski, J., Yaniv, Z., Desai, R.A., Woehler, A. and Preibisch, S.
Biomedical Optics Express 12 (4): 2186-2203. 1 April 2021

Prigione, Alessandro

Generation of human brain organoids for mitochondrial disease modeling.
Le, S., Petersilie, L., Inak, G., Menacho-Pando, C., Kafitz, K.W., Rybak-Wolf, A., Rajewsky, N., Rose, C.R. and Prigione, A.
Journal of Visualized Experiments (172): e62756. 21 June 2021

Purfuerst, Bettina

Rajewsky, Klaus

Rajewsky, Nikolaus (BIMSB)

Sites of transcription initiation drive mRNA isoform selection.
Alfonso-Gonzalez, C., Legnini, I., Holec, S., Arrigoni, L., Ozbulut, H.C., Mateos, F., Koppstein, D., Rybak-Wolf, A., Bönisch, U., Rajewsky, N. and Hilgers, V.
Cell 186 (11): 2438-2455. 25 May 2023

Rapid nuclear deadenylation of mammalian messenger RNA.
Alles, J., Legnini, I., Pacelli, M. and Rajewsky, N.
iScience 26 (1): 105878. 20 January 2023

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner.
Cerda Jara, C.A., Kim, S.J., Thomas, G., Farsi, Z., Zolotarov, G., Dube, G., Deter, A., Bahry, E., Georgii, E., Woehler, A., Piwecka, M. and Rajewsky, N.
EMBO Reports 25 (7): 3039. July 2024

A guide to naming eukaryotic circular RNAs.
Chen, L.L., Bindereif, A., Bozzoni, I., Chang, H.Y., Matera, A.G., Gorospe, M., Hansen, T.B., Kjems, J., Ma, X.K., Pek, J.W., Rajewsky, N., Salzman, J., Wilusz, J.E., Yang, L. and Zhao, F.
Nature Cell Biology 25 (1): 1-5. January 2023

C. elegans gene regulatory alleles and reporter bashing studies.
Froehlich, J.J. and Rajewsky, N.
microPublication Biology 2023 20 January 2023

Estimation of C. elegans cell- and tissue volumes.
Froehlich, J.J., Rajewsky, N. and Ewald, C.Y.
microPublication Biology : 000345. 4 January 2021

Expression of circ_Satb1 is decreased in mesial temporal lobe epilepsy and regulates dendritic spine morphology.
Gomes-Duarte, A., Venø, M.T., de Wit, M., Senthilkumar, K., Broekhoven, M.H., van den Herik, J., Heeres, F.R., van Rossum, D., Rybiczka-Tesulov, M., Legnini, I., van Rijen, P.C., van Eijsden, P., Gosselaar, P.H., Rajewsky, N., Kjems, J., Vangoor, V.R. and Pasterkamp, R.J.
Frontiers in Molecular Neuroscience 15 : 832133. 3 March 2022

Microglia from patients with multiple sclerosis display a cell-autonomous immune activation state.
Hyvärinen, T., Lotila, J., Giudice, L., Tujula, I., Nylund, M., Ohtonen, S., Scoyni, F., Jäntti, H., Pihlava, S., Skottman, H., Narkilahti, S., Airas, L., Malm, T. and Hagman, S.
bioRxiv : 2024.12.10.627477. 11 December 2024

SetQuence & SetOmic: deep set transformers for whole genome and exome tumour analysis.
Jurenaite, N., León-Periñán, D., Donath, V., Torge, S. and Jäkel, R.
Biosystems 235 : 105095. January 2024

Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury.
Klocke, J., Kim, S.J., Skopnik, C.M., Hinze, C., Boltengagen, A., Metzke, D., Grothgar, E., Prskalo, L., Wagner, L., Freund, P., Görlich, N., Muench, F., Schmidt-Ott, K.M., Mashreghi, M.F., Kocks, C., Eckardt, K.U., Rajewsky, N. and Enghard, P.
Kidney International 102 (6): 1359-1370. December 2022

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N., Senel, E., Friedman, N., Rajewsky, N., Karaiskos, N. and Nitzan, M.
Nature Protocols 16 (9): 4177-4200. September 2021

Challenges and opportunities in the clinical translation of high-resolution spatial transcriptomics.
Pentimalli, T.M., Karaiskos, N. and Rajewsky, N.
Annual Review of Pathology : Mechanisms of Disease 30 October 2024 (In Press)

Identifying chromosome movement patterns during meiosis using ChroMo.
Pinto-Cruz, J., Correas, M., Mendoza-Madrigal, R., León-Periñán, D. and Fernández-Álvarez, A.
Methods in Molecular Biology 2818 : 271-288. 2024

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.
Piwecka, M., Rajewsky, N. and Rybak-Wolf, A.
Nature Reviews Neurology 19 (6): 346–362. June 2023

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F., Neuschulz, A., Junker, J.P., Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.
Pulvirenti, F., Giufrè, M., Pentimalli, T.M., Camilli, R., Milito, C., Villa, A., Sculco, E., Cerquetti, M., Pantosti, A. and Quinti, I.
Frontiers in Immunology 15 : 1371118. 30 May 2024

Epigenetic targeting of transposon relics: beating the dead horses of the genome?
Sammarco, I., Pieters, J., Salony, S., Toman, I., Zolotarov, G. and Lafon Placette, C.
Epigenetics 17 (11): 1331-1344. November 2022

Twisted-plywood-like tissue formation in vitro. Does curvature do the twist?
Schamberger, B., Ehrig, S., Dechat, T., Spitzer, S., Bidan, C.M., Fratzl, P., Dunlop, J.W.C. and Roschger, A.
PNAS Nexus 3 (4): pgae121. April 2024

Curvature in biological systems: its quantification, emergence and implications across the scales.
Schamberger, B., Roschger, A., Ziege, R., Anselme, K., Amar, M.B., Bykowski, M., Castro, A.P.G., Cipitria, A., Coles, R., Dimova, R., Eder, M., Ehrig, S., Escudero, L.M., Evans, M.E., Fernandes, P.R., Fratzl, P., Geris, L., Gierlinger, N., Hannezo, E., Iglič, A., Kirkensgaard, J.J.K., Kollmannsberger, P., Kowalewska, Ł., Kurniawan, N.A., Papantoniou, I., Pieuchot, L., Pires, T.H.V., Renner, L., Sageman-Furnas, A., Schröder-Turk, G.E., Sengupta, A., Sharma, V.R., Tagua, A., Tomba, C., Trepat, X., Waters, S.L., Yeo, E., Bidan, C.M. and Dunlop, J.W.C.
Advanced Materials 35 (13): e2206110. 15 March 2023

Open-ST: high-resolution spatial transcriptomics in 3D.
Schott, M., León-Periñán, D., Splendiani, E., Strenger, L., Licha, J.R., Pentimalli, T.M., Schallenberg, S., Alles, J., Samut Tagliaferro, S., Boltengagen, A., Ehrig, S., Abbiati, S., Dommerich, S., Pagani, M., Ferretti, E., Macino, G., Karaiskos, N. and Rajewsky, N.
Cell 187 (15): 3953-3972.e26. 25 July 2024

ciRS-7 and miR-7 regulate ischemia-induced neuronal death via glutamatergic signaling.
Scoyni, F., Sitnikova, V., Giudice, L., Korhonen, P., Trevisan, D.M., Hernandez de Sande, A., Gomez-Budia, M., Giniatullina, R., Ugidos, I.F., Dhungana, H., Pistono, C., Korvenlaita, N., Välimäki, N.N., Kangas, S.M., Hiltunen, A.E., Gribchenko, E., Kaikkonen-Määttä, M.U., Koistinaho, J., Ylä-Herttuala, S., Hinttala, R., Venø, M.T., Su, J., Stoffel, M., Schaefer, A., Rajewsky, N., Kjems, J., LaPierre, M.P., Piwecka, M., Jolkkonen, J., Giniatullin, R., Hansen, T.B. and Malm, T.
Cell Reports 43 (3): 113862. 26 March 2024

A circular RNA expressed from the FAT3 locus regulates neural development.
Seeler, S., Andersen, M.S., Sztanka-Toth, T., Rybiczka-Tešulov, M., van den Munkhof, M.H., Chang, C.C., Maimaitili, M., Venø, M.T., Hansen, T.B., Pasterkamp, R.J., Rybak-Wolf, A., Denham, M., Rajewsky, N., Kristensen, L.S. and Kjems, J.
Molecular Neurobiology 60 (6): 3239–3260. June 2023

Optocoder: computational decoding of spatially indexed bead arrays.
Senel, E., Rajewsky, N. and Karaiskos, N.
NAR Genomics and Bioinformatics 4 (2): lqac042. June 2022

Cell type diversity in a developing octopus brain.
Styfhals, R., Zolotarov, G., Hulselmans, G., Spanier, K.I., Poovathingal, S., Elagoz, A.M., De Winter, S., Deryckere, A., Rajewsky, N., Ponte, G., Fiorito, G., Aerts, S. and Seuntjens, E.
Nature Communications 13 (1): 7392. 30 November 2022

Spacemake: processing and analysis of large-scale spatial transcriptomics data.
Sztanka-Toth, T.R., Jens, M., Karaiskos, N. and Rajewsky, N.
GigaScience 11 : giac064. 19 July 2022

Generation and downstream analysis of single-cell and single-nuclei transcriptomes in brain organoids.
Wandres, M., Aigner, D., Kastelic, N., Boltengagen, A., Rybak-Wolf, A. and Rajewsky, N.
Journal of Visualized Experiments (205): e66225. 29 March 2024

MicroRNAs are deeply linked to the emergence of the complex octopus brain.
Zolotarov, G., Fromm, B., Legnini, I., Ayoub, S., Polese, G., Maselli, V., Chabot, P.J., Vinther, J., Styfhals, R., Seuntjens, E., Di Cosmo, A., Peterson, K.J. and Rajewsky, N.
Science Advances 8 (47): eadd9938. 25 November 2022

Rehm, Armin

Robson, Michael (BIMSB)

Roepke, Torsten Kai (ECRC)

Rybak-Wolf, Agnieszka (BIMSB)

3D spheroid and organoid models to study neuroinfection of RNA viruses.
Dos Reis, V.P., Cirksena, K., Rybak-Wolf, A., Seeger, B., Herker, E. and Gerold, G.
Methods in Molecular Biology 2824 : 409-424. August 2024

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.
Piwecka, M., Rajewsky, N. and Rybak-Wolf, A.
Nature Reviews Neurology 19 (6): 346–362. June 2023

RNA dynamics in Alzheimer’s disease.
Rybak-Wolf, A. and Plass, M.
Molecules 26 (17): 5113. 1 September 2021

Sander, Maike

Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons.
Gutierrez Fugón, O.J., Sharifi, O., Heath, N., Soto, D.C., Gomez, J.A., Yasui, D.H., Mendiola, A.J.P., O'Geen, He., Beitnere, U., Tomkova, M., Haghani, V., Dillon, G., Segal, D.J. and LaSalle, J.M.
Human Molecular Genetics 33 (19): 1711-1725. 1 October 2024

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
Miko, H., Qiu, Y., Gaertner, B., Sander, M. and Ohler, U.
BMC Genomics 22 (1): 84. 28 January 2021

EU-LIFE charter of independent life science research institutes.
Superti-Furga, G., Agostinho, M., Bury, J., Cook, S., Durinx, C., Ender, A., van Luenen, H., Lund, A.H., Medema, R.H., Miączyńska, M., Nickel, D., Pelicci, P.G., Puisieux, A., Ripatti, S., Sander, M., Schubeler, D., Serrano, L., Sommer, T., Sonne-Hansen, K., Tomančák, P., Vives, J., Vontas, J. and Bettencourt-Dias, M.
FEBS Letters 598 (7): 719-724. April 2024

The IsletTester mouse: an immunodeficient model with stable hyperglycemia for the study of human islets.
Waite, E.L., Tigue, M., Yu, M., Lahori, D., Kelly, K., May, C.L., Naji, A., Roman, J., Doliba, N., Avrahami, D., Nguyen-Ngoc, K.V., Sander, M., Glaser, B. and Kaestner, K.H.
Diabetes : db230887. 21 November 2024 (In Press)

Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes.
Wang, G., Chiou, J., Zeng, C., Miller, M., Matta, I., Han, J.Y., Kadakia, N., Okino, M.L., Beebe, E., Mallick, M., Camunas-Soler, J., Dos Santos, T., Dai, X.Q., Ellis, C., Hang, Y., Kim, S.K., MacDonald, P.E., Kandeel, F.R., Preissl, S., Gaulton, K.J. and Sander, M.
Nature Genetics 55 (6): 984-994. June 2023

Metabolic control of adaptive β-cell proliferation by the protein deacetylase SIRT2.
Wortham, M., Ramms, B., Zeng, C., Benthuysen, J.R., Sai, S., Pollow, D.P., Liu, F., Schlichting, M., Harrington, A.R., Liu, B., Prakash, T.P., Pirie, E.C., Zhu, H., Baghdasarian, S., Auwerx, J., Shirihai, O.S. and Sander, M.
bioRxiv : 2024.02.24.581864. 28 February 2024

Sanders, Ashley (MDC/BIMSB/BIH)

Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.
Grimes, K., Jeong, H., Amoah, A., Xu, N., Niemann, J., Raeder, B., Hasenfeld, P., Stober, C., Rausch, T., Benito, E., Jann, J.C., Nowak, D., Emini, R., Hoenicka, M., Liebold, A., Ho, A., Shuai, S., Geiger, H., Sanders, A.D. and Korbel, J.O.
Nature Genetics 56 (6): 1134-1146. June 2024

Recombination between heterologous human acrocentric chromosomes.
Guarracino, A., Buonaiuto, S., de Lima, L.G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Gerton, J.L., Phillippy, A.M., Colonna, V. and Garrison, E.
Nature 617 (7960): 335-343. 11 May 2023

Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey, G., Monlong, J., Ebler, J., Novak, A.M., Eizenga, J.M., Gao, Y., Marschall, T., Li, H. and Paten, B.
Nature Biotechnology 42 (4): 663-673. April 2024

Semi-automated assembly of high-quality diploid human reference genomes.
Jarvis, E.D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M.R., Porubsky, D., Cheng, H., Asri, M., Logsdon, G.A., Carnevali, P., Chaisson, M.J.P., Chin, C.S., Cody, S., Collins, J., Ebert, P., Escalona, M., Fedrigo, O., Fulton, R.S., Fulton, L.L., Garg, S., Gerton, J.L., Ghurye, J., Granat, A., Green, R.E., Harvey, W., Hasenfeld, P., Hastie, A., Haukness, M., Jaeger, E.B., Jain, M., Kirsche, M., Kolmogorov, M., Korbel, J.O., Koren, S., Korlach, J., Lee, J., Li, D., Lindsay, T., Lucas, J., Luo, F., Marschall, T., Mitchell, M.W., McDaniel, J., Nie, F., Olsen, H.E., Olson, N.D., Pesout, T., Potapova, T., Puiu, D., Regier, A., Ruan, J., Salzberg, S.L., Sanders, A.D., Schatz, M.C., Schmitt, A., Schneider, V.A., Selvaraj, S., Shafin, K., Shumate, A., Stitziel, N.O., Stober, C., Torrance, J., Wagner, J., Wang, J., Wenger, A., Xiao, C., Zimin, A.V., Zhang, G., Wang, T., Li, H., Garrison, E., Haussler, D., Hall, I., Zook, J.M., Eichler, E.E., Phillippy, A.M., Paten, B., Howe, K. and Miga, K.H.
Nature 611 (7936): 519-531. 17 November 2022

Functional analysis of structural variants in single cells using Strand-seq.
Jeong, H., Grimes, K., Rauwolf, K.K., Bruch, P.M., Rausch, T., Hasenfeld, P., Benito, E., Roider, T., Sabarinathan, R., Porubsky, D., Herbst, S.A., Erarslan-Uysal, B., Jann, J.C., Marschall, T., Nowak, D., Bourquin, J.P., Kulozik, A.E., Dietrich, S., Bornhauser, B., Sanders, A.D. and Korbel, J.O.
Nature Biotechnology 41 (6): 832-844. June 2023

Unlocking the secrets of structural variants in a healthy tissue.
Korbel, J.O. and Sanders, A.D.
Nature Genetics 56 (6): 1047-1048. June 2024

Single-cell multi-omics allows functional characterization of structural variants.
Korbel, J.O. and Sanders, A.D.
Nature Biotechnology 24 November 2022

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
Lee, H., Greer, S.U., Pavlichin, D.S., Zhou, B., Urban, A.E., Weissman, T. and Ji, H.P.
Cell Reports Methods 3 (8): 100543. 28 August 2023

A draft human pangenome reference.
Liao, W.W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J.K., Monlong, J., Abel, H.J., Buonaiuto, S., Chang, X.H., Cheng, H., Chu, J., Colonna, V., Eizenga, J.M., Feng, X., Fischer, C., Fulton, R.S., Garg, S., Groza, C., Guarracino, A., Harvey, W.T., Heumos, S., Howe, K., Jain, M., Lu, T.Y., Markello, C., Martin, F.J., Mitchell, M.W., Munson, K.M., Mwaniki, M.N., Novak, A.M., Olsen, H.E., Pesout, T., Porubsky, D., Prins, P., Sibbesen, J.A., Sirén, J., Tomlinson, C., Villani, F., Vollger, M.R., Antonacci-Fulton, L.L., Baid, G., Baker, C.A., Belyaeva, A., Billis, K., Carroll, A., Chang, P.C., Cody, S., Cook, D.E., Cook-Deegan, R.M., Cornejo, O.E., Diekhans, M., Ebert, P., Fairley, S., Fedrigo, O., Felsenfeld, A.L., Formenti, G., Frankish, A., Gao, Yan, Garrison, N.A., Giron, C.G., Green, R.E., Haggerty, L., Hoekzema, K., Hourlier, T., Ji, H.P., Kenny, E.E., Koenig, B.A., Kolesnikov, A., Korbel, J.O., Kordosky, J., Koren, S., Lee, H.J., Lewis, A.P., Magalhães, H., Marco-Sola, S., Marijon, P., McCartney, A., McDaniel, J., Mountcastle, J., Nattestad, M., Nurk, S., Olson, N.D., Popejoy, A.B., Puiu, D., Rautiainen, M., Regier, A.A., Rhie, A., Sacco, S., Sanders, A.D., Schneider, V.A., Schultz, B.I., Shafin, K., Smith, M.W., Sofia, H.J., Abou Tayoun, A.N., Thibaud-Nissen, F., Tricomi, F.F., Wagner, J., Walenz, B., Wood, J.M.D., Zimin, A.V., Bourque, G., Chaisson, M.J P, Flicek, Paul, Phillippy, A.M., Zook, J.M., Eichler, E.E., Haussler, D., Wang, T., Jarvis, E.D., Miga, K.H., Garrison, E., Marschall, T., Hall, I.M., Li, H. and Paten, B.
Nature 617 (7960): 312-324. 11 May 2023

A high-resolution map of small-scale inversions in the gibbon genome.
Mercuri, L., Palmisano, D., L'Abbate, A., D'Addabbo, P., Montinaro, F., Catacchio, C.R., Hasenfeld, P., Ventura, M., Korbel, J.O., Sanders, A.D., Maggiolini, F.A.M. and Antonacci, F.
Genome Research 32 (10): 1941-1951. October 2022

Inversion polymorphism in a complete human genome assembly.
Porubsky, D., Harvey, W.T., Rozanski, A.N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A.D., Marschall, T., Korbel, J.O. and Eichler, E.E.
Genome Biology 24 (1): 100. 30 April 2023

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders.
Porubsky, D., Höps, W., Ashraf, H., Hsieh, P.H., Rodriguez-Martin, B., Yilmaz, F., Ebler, J., Hallast, P., Maggiolini, F.A.M., Harvey, W.T., Henning, B., Audano, P.A., Gordon, D.S., Ebert, P., Hasenfeld, P., Benito, E., Zhu, Q., Lee, C., Antonacci, F., Steinrücken, M., Beck, C.R., Sanders, A.D., Marschall, T., Eichler, E.E. and Korbel, J.O.
Cell 185 (11): 1986-2005. 26 May 2022

Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky, D., Vollger, M.R., Harvey, W.T., Rozanski, A.N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A.D., Stober, C., Korbel, J.O., Paten, B., Marschall, T. and Eichler, E.E.
Genome Research 33 (4): 496-510. April 2023

Mapping DHPS evolvability: identification of novel evolutionarily critical sub-structure through evolutionary and structural analyses of DHPS.
Sanyal, D., Shivram, A., Banerjee, S., Uversky, V.N., Chivukula, A., Chattopadhyay, K. and Chowdhury, S.
bioRxiv : 2024.10.16.618629. 18 October 2024

Increased mutation and gene conversion within human segmental duplications.
Vollger, M.R., Dishuck, P.C., Harvey, W.T., DeWitt, W.S., Guitart, X., Goldberg, M.E., Rozanski, A.N., Lucas, J., Asri, M., Munson, K.M., Lewis, A.P., Hoekzema, K., Logsdon, G.A., Porubsky, D., Paten, B., Harris, K., Hsieh, P.H. and Eichler, E.E.
Nature 617 (7960): 325-334. 11 May 2023

Sauer, Sascha (BIMSB/BIH)

BMP feed-forward loop promotes terminal differentiation in gastric glands and is interrupted by H. pylori-driven inflammation.
Kapalczynska, M., Lin, M., Maertzdorf, J., Heuberger, J., Muellerke, S., Zuo, X., Vidal, R., Shureiqi, I., Fischer, A.S., Sauer, S., Berger, H., Kidess, E., Mollenkopf, H.J., Tacke, F., Meyer, T.F. and Sigal, M.
Nature Communications 13 (1): 1577. 24 March 2022

Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses.
Kazmierski, J., Friedmann, K., Postmus, D., Emanuel, J., Fischer, C., Jansen, J., Richter, A., Bosquillon de Jarcy, L., Schüler, C., Sohn, M., Sauer, S., Drosten, C., Saliba, A.E., Sander, L.E., Müller, M.A., Niemeyer, D. and Goffinet, C.
Molecular Systems Biology 18 (8): e10961. 1 August 2022

Regional gene expression patterns are associated with task-specific brain activation during reward and emotion processing measured with functional MRI.
Komorowski, A., Murgaš, M., Vidal, R., Singh, A., Gryglewski, G., Kasper, S., Wiltfang, J., Lanzenberger, R. and Goya-Maldonado, R.
Human Brain Mapping 43 (17): 5266-5280. 1 December 2022

Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens.
Numberger, D., Zoccarato, L., Woodhouse, J., Ganzert, L., Sauer, S., García Márquez, J.R., Domisch, S., Grossart, H.P. and Greenwood, A.D.
Science of the Total Environment 845 : 157321. 1 November 2022

Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state.
Smajić, S., Prada-Medina, C.A., Landoulsi, Z., Ghelfi, J., Delcambre, S., Dietrich, C., Jarazo, J., Henck, J., Balachandran, S., Pachchek, S., Morris, C.M., Antony, P., Timmermann, B., Sauer, S., Pereira, S.L., Schwamborn, J.C., May, P., Grünewald, A. and Spielmann, M.
Brain 145 (3): 964-978. March 2022

Single-nuclei RNA-sequencing of plant tissues using a nanowell-based system.
Sunaga-Franze, D., Muino, J.M., Braeuning, C., Xu, X., Zong, M., Smaczniak, C., Yan, W., Fischer, C., Vidal, R., Kliem, M., Kaufmann, K. and Sauer, S.
Plant Journal 108 (3): 859-869. 5 November 2021

Cellular landscape of adrenocortical carcinoma at single-nuclei resolution.
Tourigny, D.S., Altieri, B., Secener, A.K., Sbiera, S., Schauer, M.P., Arampatzi, P., Herterich, S., Sauer, S., Fassnacht, M. and Ronchi, C.L.
Molecular and Cellular Endocrinology 590 : 112272. 1 September 2024

Transcriptome analysis reveals putative genes involved in the lipid metabolism of chaulmoogra oil biosynthesis in Carpotroche brasiliensis (Raddi) A.Gray, a tropical tree species.
Vasconcelos, L.M., Bittencourt, F., Vidal, R.O., Silva, E.M.A., Costa, E.A., Micheli, F., Kirst, M., Pirovani, C.P. and Gaiotto, F.A
Forests 13 (11): 1806. 29 October 2022

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law.
Zou, X., Schaefke, B., Li, Y., Jia, F., Sun, W., Li, G., Liang, W., Reif, T., Heyd, F., Gao, Q., Tian, S., Li, Y., Tang, Y., Fang, L., Hu, Y. and Chen, W.
Life Science Alliance 5 (4): e202101333. April 2022

Scheidereit, Claus

Schiattarella, Gabriele G.

Targeting HFpEF: unlocking the potential of glucagon receptor blockade.
Santiago Padilla, L. and Schiattarella, G.G.
Circulation Research 135 (5): 629-631. 16 August 2024

Schmidt, Deborah

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L., Dubois, Z., Smith, J., Lee, Y. and Harrington, K.
Biosystems 208 : 104483. October 2021

Structure, interaction and nervous connectivity of beta cell primary cilia.
Müller, A., Klena, N., Pang, S., Garcia, L.E.G., Topcheva, O., Aurrecoechea Duran, S., Sulaymankhil, D., Seliskar, M., Mziaut, H., Schöniger, E., Friedland, D., Kipke, N., Kretschmar, S., Münster, C., Weitz, J., Distler, M., Kurth, T., Schmidt, D., Hess, H.F., Xu, C.S., Pigino, G. and Solimena, M.
Nature Communications 15 (1): 9168. 24 October 2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A., Schmidt, D., Albrecht, J.P., Rieckert, L., Otto, M., Galicia Garcia, L.E., Fabig, G., Solimena, M. and Weigert, M.
Nature Protocols 19 (5): 1436-1466. May 2024

Schmidt-Ott, Kai

Schmitt, Clemens

Schmitz, Dietmar

Schuetz, Anja

Schulz-Menger, Jeanette (ECRC)

Schwarz, Roland (BIMSB)

Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.
Abbosh, C., Frankell, A.M., Harrison, T., Kisistok, J., Garnett, A., Johnson, L., Veeriah, S., Moreau, M., Chesh, A., Chaunzwa, T.L., Weiss, J., Schroeder, M.R., Ward, S., Grigoriadis, K., Shahpurwalla, A., Litchfield, K., Puttick, C., Biswas, D., Karasaki, T., Black, J.R.M., Martínez-Ruiz, C., Bakir, M.A.l., Pich, O., Watkins, T.B.K., Lim, E.L., Huebner, A., Moore, D.A., Godin-Heymann, N., L'Hernault, A., Bye, H., Odell, A., Roberts, P., Gomes, F., Patel, A.J., Manzano, E., Hiley, C.T., Carey, N., Riley, J., Cook, D.E., Hodgson, D., Stetson, D., Barrett, J.C., Kortlever, R.M., Evan, G.I., Hackshaw, A., Daber, R.D., Shaw, J.A., Aerts, H.J.W.L., Licon, A., Stahl, J., Jamal-Hanjani, M., Birkbak, N.J., McGranahan, N. and Swanton, C.
Nature 616 (7957): 553-562. 20 April 2023

The evolution of non-small cell lung cancer metastases in TRACERx.
Al Bakir, M., Huebner, A., Martínez-Ruiz, C., Grigoriadis, K., Watkins, T.B.K., Pich, O., Moore, D.A., Veeriah, S., Ward, S., Laycock, J., Johnson, D., Rowan, A., Razaq, M., Akther, M., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Hessey, S., Dietzen, M., Colliver, E., Frankell, A.M., Bunkum, A., Lim, E.L., Karasaki, T., Abbosh, C., Hiley, C.T., Hill, M.S., Cook, D.E., Wilson, G.A., Salgado, R., Nye, E., Stone, R.K., Fennell, D.A., Price, G., Kerr, K.M., Naidu, B., Middleton, G., Summers, Y., Lindsay, C.R., Blackhall, F.H., Cave, J., Blyth, K.G., Nair, A., Ahmed, A., Taylor, M.N., Procter, A.J., Falzon, M., Lawrence, D., Navani, N., Thakrar, R.M., Janes, S.M., Papadatos-Pastos, D., Forster, M.D., Lee, S.M., Ahmad, T., Quezada, S.A., Peggs, K.S., Van Loo, P., Dive, C., Hackshaw, A., Birkbak, N.J., Zaccaria, S., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616 (7957): 534-542. April 2023

Body composition and lung cancer-associated cachexia in TRACERx.
Al-Sawaf, O., Weiss, J., Skrzypski, M., Lam, J.M., Karasaki, T., Zambrana, F., Kidd, A.C., Frankell, A.M., Watkins, T.B.K., Martínez-Ruiz, C., Puttick, C., Black, J.R.M., Huebner, A., Bakir, M.A., Sokač, M., Collins, S., Veeriah, S., Magno, N., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Ward, S., Jayanth, N., Salgado, R., Bridge, C.P., Christiani, D.C., Mak, R.H., Bay, C., Rosenthal, M., Sattar, N., Welsh, P., Liu, Y., Perrimon, N., Popuri, K., Beg, M.F., McGranahan, N., Hackshaw, A., Breen, D.M., O'Rahilly, S., Birkbak, N.J., Aerts, H.J.W.L., Jamal-Hanjani, M. and Swanton, C.
Nature Medicine 29 (4): 846-858. April 2023

Determinants of expression of SARS-CoV-2 entry related genes in upper and lower airways.
Aliee, H., Massip, F., Qi, C., de Biase, M.S., van Nijnatten, J., Kersten, E.T.G., Kermani, N.Z., Khuder, B., Vonk, J.M., Vermeulen, R.C.H., Neighbors, M., Tew, G.W., Grimbaldeston, M.A., Ten Hacken, N.H.T., Hu, S., Guo, Y., Zhang, X., Sun, K., Hiemstra, P.S., Ponder, B.A., Mäkelä, M.J., Malmström, K., Rintoul, R.C., Reyfman, P.A., Theis, F.J., Brandsma, C.A., Adcock, I.M., Timens, W., Xu, C.J., van den Berge, M., Schwarz, R.F., Koppelman, G.H., Nawijn, M.C. and Faiz, A.
Allergy 77 (2): 690-694. February 2022

Using DNA sequencing data to quantify T cell fraction and therapy response.
Bentham, R., Litchfield, K., Watkins, T.B.K., Lim, E.L., Rosenthal, R., Martínez-Ruiz, C., Hiley, C.T., Bakir, M.A., Salgado, R., Moore, D.A., Jamal-Hanjani, M., Swanton, C. and McGranahan, N.
Nature 597 (7877): 555-560. 23 September 2021

IL-33 expression is lower in current smokers at both transcriptomic and protein level.
Faiz, A., Mahbub, R.M., Boedijono, F.S., Tomassen, M.I., Kooistra, W., Timens, W., Nawijn, M., Hansbro, P.M., Johansen, M.D., Pouwels, S.D., Heijink, I.H., Massip, F., de Biase, M.S., Schwarz, R.F., Adcock, I.M., Chung, K.F., van der Does, A., Hiemstra, P.S., Goulaouic, H., Xing, H., Abdulai, R., de Rinaldis, E., Cunoosamy, D., Harel, S., Lederer, D., Nivens, M.C., Wark, P.A., Kerstjens, H.A.M., Hylkema, M.N., Brandsma, C.A. and van den Berge, M.
American Journal of Respiratory and Critical Care Medicine 208 (10): 1075-1087. 15 November 2023

The evolution of lung cancer and impact of subclonal selection in TRACERx.
Frankell, A.M., Dietzen, M., Al Bakir, M., Lim, E.L., Karasaki, T., Ward, S., Veeriah, S., Colliver, E., Huebner, A., Bunkum, A., Hill, M.S., Grigoriadis, K., Moore, D.A., Black, J.R.M., Liu, W.K., Thol, K., Pich, O., Watkins, T.B.K., Naceur-Lombardelli, C., Cook, D.E., Salgado, R., Wilson, G.A., Bailey, C., Angelova, M., Bentham, R., Martínez-Ruiz, C., Abbosh, C., Nicholson, A.G., Le Quesne, J., Biswas, D., Rosenthal, R., Puttick, C., Hessey, S., Lee, C., Prymas, P., Toncheva, A., Smith, J., Xing, W., Nicod, J., Price, G., Kerr, K.M., Naidu, B., Middleton, G., Blyth, K.G., Fennell, D.A., Forster, M.D., Lee, S.M., Falzon, M., Hewish, M., Shackcloth, M.J., Lim, E., Benafif, S., Russell, P., Boleti, E., Krebs, M.G., Lester, J.F., Papadatos-Pastos, D., Ahmad, T., Thakrar, R.M., Lawrence, D., Navani, N., Janes, S.M., Dive, C., Blackhall, F.H, Summers, Y., Cave, J., Marafioti, T., Herrero, J., Quezada, S.A., Peggs, K.S., Schwarz, R.F., Van Loo, P., Miedema, D.M., Birkbak, N.J., Hiley, C.T., Hackshaw, A., Zaccaria, S., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616 (7957): 525-533. 20 April 2023

Evolutionary characterization of lung adenocarcinoma morphology in TRACERx.
Karasaki, T., Moore, D.A., Veeriah, S., Naceur-Lombardelli, C., Toncheva, A., Magno, N., Ward, S., Bakir, M.A., Watkins, T.B.K., Grigoriadis, K., Huebner, A., Hill, M.S., Frankell, A.M., Abbosh, C., Puttick, C., Zhai, H., Gimeno-Valiente, F., Saghafinia, S., Kanu, N., Dietzen, M., Pich, O., Lim, E.., Martínez-Ruiz, C., Black, J.R.M., Biswas, D., Campbell, B.B., Lee, C., Colliver, E., Enfield, K.S.S., Hessey, S., Hiley, C.T., Zaccaria, S., Litchfield, K., Birkbak, N.J., Cadieux, E.L., Demeulemeester, J., Van Loo, P., Adusumilli, P.S., Tan, K.S., Cheema, W., Sanchez-Vega, F., Jones, D.R., Rekhtman, N., Travis, W.D., Hackshaw, A., Marafioti, T., Salgado, R., Le Quesne, J., Nicholson, A.G., McGranahan, N., Swanton, C. and Jamal-Hanjani, M.
Nature Medicine 29 (4): 833-845. April 2023

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L., Petkovic, M., Watkins, T.B.K., Colliver, E.C., Laskina, S., Thapa, N., Minussi, D.C., Navin, N., Swanton, C., Van Loo, P., Haase, K., Tarabichi, M. and Schwarz, R.F.
Genome Biology 23 (1): 241. 14 November 2022

Locus specific epigenetic modalities of random allelic expression imbalance.
Marion-Poll, L., Forêt, B., Zielinski, D., Massip, F., Attia, M., Carter, A.C., Syx, L., Chang, H.Y., Gendrel, A.V. and Heard, E.
Nature Communications 12 (1): 5330. 9 September 2021

Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects.
Plavskin, Y., de Biase, M.S., Ziv, N., Janská, L., Zhu, Y.O., Hall, D.W., Schwarz, R.F., Tranchina, D. and Siegal, M.L.
PLoS Biology 22 (7): e3002698. 1 July 2024

The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y., de Biase, M.S., Schwarz, R.F. and Siegal, M.L.
G3 : Genes Genomes Genetics 13 (3): jkac330. March 2023

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.
Sheinman, M., Arkhipova, K., Arndt, P.F., Dutilh, B.E., Hermsen, R. and Massip, F.
eLife 10 : e62719. 9 July 2021

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A., Kaufmann, T.L. and Schwarz, R.F.
Bioinformatics 39 (3): btad102. March 2023

A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer.
Wu, Y., Biswas, D., Usaite, I., Angelova, M., Boeing, S., Karasaki, T., Veeriah, S., Czyzewska-Khan, J., Morton, C., Joseph, M., Hessey, S., Reading, J., Georgiou, A., Al-Bakir, M., McGranahan, N., Jamal-Hanjani, M., Hackshaw, A., Quezada, S.A., Hayday, A.C. and Swanton, C.
Nature Cancer 3 (6): 696-709. June 2022

Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk.
de Biase, M.S., Massip, F., Wei, T.T., Giorgi, F.M., Stark, R., Stone, A., Gladwell, A., O'Reilly, M., Schütte, D., de Santiago, I., Meyer, K.B., Markowetz, F., Ponder, B.A.J., Rintoul, R.C. and Schwarz, R.F.
Genome Medicine 16 (1): 54. 8 April 2024

Selbach, Matthias

Siffrin, Volker (ECRC)

Sigal, Michael (BIMSB)

Unwelcome guests – the role of gland-associated Helicobacter pylori infection in gastric carcinogenesis.
Beccaceci, G. and Sigal, M.
Frontiers in Oncology 13 : 1171003. 21 April 2023

Mucosa-associated microbiota alterations in primary sclerosing cholangitis (PSC) before and after liver transplantation—who is calling the shots?
Demir, M. and Sigal, M.
Hepatobiliary Surgery and Nutrition 12 (5): 795-797. 1 October 2023

Elevated Flt3L predicts long-term survival in patients with high-grade gastroenteropancreatic neuroendocrine neoplasms.
Detjen, K.M., Otto, R., Giesecke, Y., Geisler, L., Riemer, P., Jann, H., Grötzinger, C., Sers, C., Pascher, A., Lüdde, T., Leser, U., Wiedenmann, B., Sigal, M., Tacke, F., Roderburg, C. and Hammerich, L.
Cancers 13 (17): 4463. 1 September 2021

R-spondin-YAP axis promotes gastric oxyntic gland regeneration and Helicobacter pylori-associated metaplasia in mice.
Fischer, A.S., Müllerke, S., Arnold, A., Heuberger, J., Berger, H., Lin, M., Mollenkopf, H.J., Wizenty, J., Horst, D., Tacke, F. and Sigal, M.
Journal of Clinical Investigation 132 (21): e151363. 1 November 2022

Short-term mucosal disruption enables colibactin-producing E. coli to cause long-term perturbation of colonic homeostasis.
Harnack, C., Berger, H., Liu, L., Mollenkopf, H.J., Strowig, T. and Sigal, M.
Gut Microbes 15 (1): 2233689. 10 July 2023

Epithelial response to IFN-γ promotes SARS-CoV-2 infection.
Heuberger, J., Trimpert, J., Vladimirova, D., Goosmann, C., Lin, M., Schmuck, R., Mollenkopf, H.J., Brinkmann, V., Tacke, F., Osterrieder, N. and Sigal, M.
EMBO Molecular Medicine 13 (4): e13191. 9 April 2021

Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells.
Iftekhar, A., Berger, H., Bouznad, N., Heuberger, J., Boccellato, F., Dobrindt, U., Hermeking, H., Sigal, M. and Meyer, T.F.
Nature Communications 12 (1): 1003. 12 February 2021

Defence and adaptation mechanisms of the intestinal epithelium upon infection.
Iftekhar, A. and Sigal, M.
International Journal of Medical Microbiology 311 (3): 151486. April 2021

Health workforce response to Covid-19: What pandemic preparedness planning and action at the federal and state levels in Germany? Germany's health workforce responses to Covid-19.
Köppen, J., Hartl, K. and Maier, C.B.
International Journal of Health Planning and Management 36 (S1): 71-91. May 2021

Stem cells, helicobacter pylori and mutational landscape: utility of preclinical models to understand carcinogenesis and to direct management of gastric cancer.
Liabeuf, D., Oshima, M., Stange, D.E. and Sigal, M.
Gastroenterology 162 (4): 1067-1087. April 2022

Human embryo models: unveiling sophisticated self-organization of stem cells during post-implantation stages.
Lin, M. and Sigal, M.
Signal Transduction and Targeted Therapy 8 (1): 419. 6 November 2023

Wie das Immunsystem SARS-CoV-2 den Weg ebnet [How the immune system paves the way for SARS-CoV-2].
Sigal, M.
Hygiene und Medizin 46 (3): 22-23. 2021

S100A4 is a strong negative prognostic marker and potential therapeutic target in adenocarcinoma of the stomach and esophagus.
Treese, C., Hartl, K., Pötzsch, M., Dahlmann, M., von Winterfeld, M., Berg, E., Hummel, M., Timm, L., Rau, B., Walther, W., Daum, S., Kobelt, D. and Stein, U.
Cells 11 (6): 1056. 21 March 2022

Gastric stem cells promote inflammation and gland remodeling in response to Helicobacter pylori via Rspo3-Lgr4 axis.
Wizenty, J., Müllerke, S., Kolesnichenko, M., Heuberger, J., Lin, M., Fischer, A.S., Mollenkopf, H.J., Berger, H., Tacke, F. and Sigal, M.
EMBO Journal 41 (13): e109996. 4 July 2022

Long-term impact of scheduled regular endoscopic interventions for patients with primary sclerosing cholangitis.
Özdirik, B., Veltzke-Schlieker, W., Nicklaus, J.M., Berger, H., Schmidt, D., Leonhardt, S., Penndorf, V., Adler, A., Müller, T., Wree, A., Tacke, F. and Sigal, M.
Hepatology Communications 8 (9): e0494. September 2024

Soluble urokinase plasminogen activator receptor levels are associated with severity of fibrosis in patients with primary sclerosing cholangitis.
Özdirik, B., Maibier, M., Scherf, M., Nicklaus, J.M., Frohme, J., Puengel, T., Meyer Zum Büschenfelde, D., Tacke, F., Mueller, T. and Sigal, M.
Journal of Clinical Medicine 11 (9): 2479. 28 April 2022

Biliary microbial patterns in primary sclerosing cholangitis are linked to poorer transplant-free survival.
Özdirik, B., Scherf, M., Brumercek, A., Nicklaus, J.M., Kruis, T., Haber, P.K., Pratschke, J., Tacke, F. and Sigal, M.
Hepatology Communications 7 (6): e0156. June 2023

Sommer, Thomas

Sporbert, Anje

Spuler, Simone (ECRC)

Stein, Ulrike (MDC/ECRC)

Tursun, Baris (BIMSB)

Induced neurons from germ cells in Caenorhabditis elegans.
Marchal, I. and Tursun, B.
Frontiers in Neuroscience 15 : 771687. 3 December 2021

The C. elegans pseudogene sspt-16 (F55A3.7) is required to safeguard germ cells against reprogramming.
Ofenbauer, A., Kraus, C.M. and Tursun, B.
microPublication Biology 2021 18 May 2021

Wanker, Erich

Wilck, Nicola (ECRC)

Willnow, Thomas E.

Woehler, Andrew (BIMSB)

A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish.
Huljev, K., Shamipour, S., Pinheiro, D., Preusser, F., Steccari, I., Sommer, C.M., Naik, S. and Heisenberg, C.P.
Developmental Cell 58 (7): 582-596.e7. 10 April 2023

MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.
Mertens, T.F., Liebheit, A.T., Ehl, J., Köhler, R., Rakhymzhan, A., Woehler, A., Katthän, L., Ebel, G., Liublin, W., Kasapi, A., Triantafyllopoulou, A., Schulz, T.J., Niesner, R.A. and Hauser, A.E.
Nature Communications 15 (1): 1764. 26 February 2024

Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice.
Schepanski, S., Chini, M., Sternemann, V., Urbschat, C., Thiele, K., Sun, T., Zhao, Y., Poburski, M., Woestemeier, A., Thieme, M.T., Zazara, D.E., Alawi, M., Fischer, N., Heeren, J., Vladimirov, N., Woehler, A., Puelles, V.G., Bonn, S., Gagliani, N., Hanganu-Opatz, I.L. and Arck, P.C.
Nature Communications 13 (1): 4571. 5 August 2022

Wolf, Susanne

Zampieri, Niccolo

Zinzen, Robert (BIMSB)

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V., Steiger, M., Fuchs, A., van Bömmel, A., Einfeldt, E., Chung, H.R., Vingron, M. and Meijsing, S.H.
Nucleic Acids Research 49 (21): 12178-12195. 2 December 2021

Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early Drosophila embryo.
Gomez, J.M., Nolte, H., Vogelsang, E., Dey, B., Takeda, M., Giudice, G., Faxel, M., Haunold, T., Cepraga, A., Zinzen, R.P., Krüger, M., Petsalaki, E., Wang, Y.C. and Leptin, M.
eLife 13 : e99263. 3 October 2024

Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly.
Li, H., Janssens, J., De Waegeneer, M., Kolluru, S.S., Davie, K., Gardeux, V., Saelens, W., David, F.P.A., Brbić, M., Spanier, K., Leskovec, J., McLaughlin, C.N., Xie, Q., Jones, R.C., Brueckner, K., Shim, J., Tattikota, S.G., Schnorrer, F., Rust, K., Nystul, T.G., Carvalho-Santos, Zi., Ribeiro, C., Pal, S., Mahadevaraju, S., Przytycka, T.M., Allen, A.M., Goodwin, S.F., Berry, C.W., Fuller, M.T., White-Cooper, H., Matunis, E.L., DiNardo, S., Galenza, A., O'Brien, L.E., Dow, J.A.T., Jasper, H., Oliver, B., Perrimon, N., Deplancke, B., Quake, S.R., Luo, L. and Aerts, S.
Science 375 (6584): eabk2432. 4 March 2022

RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.
Moro, G., Mallona, I., Maillard, J., Brügger, M.D., Fazilaty, H., Szabo, Q., Valenta, T., Handler, K., Kerlin, F., Moor, A.E., Zinzen, R., Robinson, M.D., Brunner, E. and Basler, K.
bioRxiv : 2024.05.18.594120v2. 3 June 2024

Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.
Race, A.M., Fuchs, A. and Chung, H.R.
Scientific Reports 13 (1): 22020. 12 December 2023

This list was generated on Sat Dec 21 03:26:49 2024 UTC.