Browse by Research Area

2025

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

2024

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

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

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

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

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

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

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

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

Amplification of autoimmune organ damage by NKp46-activated ILC1.
Biniaris-Georgallis, S.I., Aschman, T., Stergioula, K., Schreiber, F., Jafari, V., Taranko, A., Karmalkar, T., Kasapi, A., Lenac Rovis, T., Jelencic, V., Bejarano, D.A., Fabry, L., Papacharalampous, M., Mattiola, I., Molgora, M., Hou, J., Hublitz, K.W., Heinrich, F., Guerra, G.M., Durek, P., Patone, G., Lindberg, E.L.H., Maatz, H., Hölsken, O., Krönke, G., Mortha, A., Voll, R.E., Clarke, A.J., Hauser, A.E., Colonna, M., Thurley, K., Schlitzer, A., Schneider, C., Stamatiades, E.G., Mashreghi, M.F., Jonjic, S., Hübner, N., Diefenbach, A., Kanda, M. and Triantafyllopoulou, A.
Nature 634 (8035): 952-960. 24 October 2024

Endothelial overexpression of TGF-β-induced protein impairs venous thrombus resolution.
Bochenek, M.L., Saar, K., Nazari-Jahantigh, M., Gogiraju, R., Wiedenroth, C.B., Münzel, T., Mayer, E., Fink, L., Schober, A., Hübner, N., Guth, S., Konstantinides, S. and Schäfer, K.
JACC: Basic to Translational Science 9 (1): 100-116. January 2024

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

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

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

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

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

Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort.
Camarena, M.E., Theunissen, P., Ruiz, M., Ruiz-Orera, J., Calvo-Serra, B., Castelo, R., Castro, C., Sarobe, P., Fortes, P., Perera-Bel, J. and Albà, M.M.
Science Advances 10 (28): eadn3628. July 2024

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

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

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

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

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

Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
Cess, C.G. and Haghverdi, L.
Bioinformatics : btae471. 25 July 2024 (In Press)

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

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

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

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

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

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch, Eric W, Kok, Leron W, Mudge, Jonathan M, Ruiz-Orera, J., Fierro-Monti, Ivo, Sun, Zhi, Abelin, Jennifer G, Alba, M Mar, Aspden, Julie L, Bazzini, Ariel A, Bruford, Elspeth, Brunet, Marie A, Calviello, L., Carr, Steven A, Carvunis, Anne-Ruxandra, Chothani, Sonia, Clauwaert, Jim, Dean, Kellie, Faridi, Pouya, Frankish, Adam, Hubner, N., Ingolia, Nicholas, Magrane, Michele, Martin, Maria Jesus, Martinez, Thomas F, Menschaert, Gerben, Ohler, U., Orchard, Sandra, Rackham, Owen, Roucou, Xavier, Slavoff, Sarah A, Valen, Eivind, Wacholder, Aaron C, Weissman, Jonathan S., Wu, Wei, Xie, Zhi, Choudhary, Jyoti, Bassani-Sternberg, Michal, Vizcaino, Juan Antonio, Ternette, Nicola, Moritz, Robert L., Prensner, John and van Heesch, S.
bioRxiv : 2024.09.09.612016. 9 September 2024

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

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

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

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

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

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

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 : 2301983. 4 September 2024 (In Press)

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

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

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

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

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

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

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

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

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

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

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

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

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 : JCO2301867. 30 September 2024 (In Press)

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

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

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

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.
Hofman, D.A., Ruiz-Orera, J., Yannuzzi, I., Murugesan, R., Brown, A., Clauser, K.R., Condurat, A.L., van Dinter, J.T., Engels, S.A.G., Goodale, A., van der Lugt, J., Abid, T., Wang, L., Zhou, K.N., Vogelzang, J., Ligon, K.L., Phoenix, T.N., Roth, J.A., Root, D.E, Hubner, N., Golub, T.R., Bandopadhayay, P., van Heesch, S. and Prensner, J.R.
Molecular Cell 84 (2): 261-276. 18 January 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)

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

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

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

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

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

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

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

Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment.
Kaiser, R., Gold, C., Joppich, M., Loew, Q., Akhalkatsi, A., Mueller, T.T., Offensperger, F., Droste Zu Senden, A., Popp, O., di Fina, L., Knottenberg, V., Martinez-Navarro, A., Eivers, L., Anjum, A., Escaig, R., Bruns, N., Briem, E., Dewender, R., Muraly, A., Akgöl, S., Ferraro, B., Hoeflinger, J.K.L., Polewka, V., Khaled, N.B., Allgeier, J., Tiedt, S., Dichgans, M., Engelmann, B., Enard, W., Mertins, P., Hubner, N., Weckbach, L., Zimmer, R., Massberg, S., Stark, K., Nicolai, L. and Pekayvaz, K.
Science Advances 10 (12): eadl1710. 22 March 2024

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

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

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

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

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

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

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

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

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

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

Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression.
Laschtowitz, A., Lindberg, E.L., Liebhoff, A.M., Liebig, L.A., Casar, C., Steinmann, S., Guillot, A., Xu, J., Schwinge, D., Trauner, M., Lohse, A.W., Bonn, S., Hübner, N. and Schramm, C.
JHEP Reports : 101267. 12 November 2024 (In Press)

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

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

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

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

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

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

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.
Malekpour, S.A., Haghverdi, L. and Sadeghi, M.
Briefings in Bioinformatics 25 (3): bbae180. May 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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 : cvae169. 12 August 2024 (In Press)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 15 November 2024 (In Press)

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Evolution and implications of de novo genes in humans.
Broeils, L.A., Ruiz-Orera, J., Snel, B., Hubner, N. and van Heesch, S.
Nature Ecology & Evolution 7 (6): 804-815. June 2023

European and multi-ancestry genome-wide association meta-analysis of atopic dermatitis highlights importance of systemic immune regulation.
Budu-Aggrey, A., Kilanowski, A., Sobczyk, M.K., Shringarpure, S.S., Mitchell, R., Reis, K., Reigo, A., Mägi, R., Nelis, M., Tanaka, N., Brumpton, B.M., Thomas, L.F., Sole-Navais, P., Flatley, C., Espuela-Ortiz, A., Herrera-Luis, E., Lominchar, J.V.T., Bork-Jensen, J., Marenholz, I., Arnau-Soler, A., Jeong, A., Fawcett, K.A., Baurecht, H., Rodriguez, E., Alves, A.C., Kumar, A., Sleiman, P.M., Chang, X., Medina-Gomez, C., Hu, C., Xu, C.J., Qi, C., El-Heis, S., Titcombe, P., Antoun, E., Fadista, J., Wang, C.A., Thiering, E., Wu, B., Kress, S., Kothalawala, D.M., Kadalayil, L., Duan, J., Zhang, H., Hadebe, S., Hoffmann, T., Jorgenson, E., Choquet, H., Risch, N., Njølstad, P., Andreassen, O.A., Johansson, S., Almqvist, C., Gong, T., Ullemar, V., Karlsson, R., Magnusson, P.K.E., Szwajda, A., Burchard, E.G., Thyssen, J.P., Hansen, T., Kårhus, L.L., Dantoft, T.M., Jeanrenaud, A.C.S.N., Ghauri, A., Arnold, A., Homuth, G., Lau, S., Nöthen, M.M., Hübner, N., Imboden, M., Visconti, A., Falchi, M., Bataille, V., Hysi, P., Ballardini, N., Boomsma, D.I., Hottenga, J.J., Müller-Nurasyid, M., Ahluwalia, T.S., Stokholm, J., Chawes, B., Schoos, A.M.M., Esplugues, A., Bustamante, M., Raby, B., Arshad, S., German, C., Esko, T., Milani, L.A., Metspalu, A., Terao, C., Abuabara, K., Løset, M., Hveem, K., Jacobsson, B., Pino-Yanes, M., Strachan, D.P., Grarup, N., Linneberg, A., Lee, Y., Probst-Hensch, N., Weidinger, S., Jarvelin, M.R., Melén, E., Hakonarson, H., Irvine, A.D., Jarvis, D., Nijsten, T., Duijts, L., Vonk, J.M., Koppelmann, G.H., Godfrey, K.M., Barton, S.J., Feenstra, B., Pennell, C.E., Sly, P.D., Holt, P.G., Williams, L.K., Bisgaard, H., Bønnelykke, K., Curtin, J., Simpson, A., Murray, C., Schikowski, T., Bunyavanich, S., Weiss, S.T., Holloway, J.W., Min, J.L., Brown, S.J., Standl, M. and Paternoster, L.
Nature Communications 14 (1): 6172. 4 October 2023

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

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

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

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

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

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

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

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.
Cui, L., Yang, B., Xiao, S., Gao, J., Baud, A., Graham, D., McBride, M., Dominiczak, A., Schafer, S., Aumatell, R.L., Mont, C., Teruel, A.F., Hübner, N., Flint, J., Mott, R. and Huang, L.
Genome Biology 24 (1): 215. 29 September 2023

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

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

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

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

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

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

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

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

Machine learning-based ozone and PM2.5 forecasting: application to multiple AQS sites in the Pacific Northwest.
Fan, K., Dhammapala, R., Harrington, K., Lamb, B. and Lee, Y.
Frontiers in Big Data 6 : 1124148. 24 February 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Spatially resolved multiomics of human cardiac niches.
Kanemaru, K., Cranley, J., Muraro, D., Miranda, A.M.A., Ho, S.Y., Wilbrey-Clark, A., Patrick Pett, J., Polanski, K., Richardson, L., Litvinukova, M., Kumasaka, R., Qin, Y., Jablonska, Z., Semprich, C.I., Mach, L., Dabrowska, M., Richoz, R., Bolt, L., Mamanova, L., Kapuge, R., Barnett, S.N., Perera, S., Talavera-López, C., Mulas, I., Mahbubani, K.T., Tuck, Liz, Wang, Lu, Huang, M.M., Prete, M., Pritchard, S., Dark, J., Saeb-Parsy, K., Patel, M., Clatworthy, M.R., Hübner, N., Chowdhury, R.A., Noseda, M. and Teichmann, S.A.
Nature 619 : 801-810. 27 July 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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Adjustments to the reference dataset design improve cell type label transfer.
Mölbert, C. and Haghverdi, L.
Frontiers in Bioinformatics 3 : 1150099. 5 April 2023

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

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

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

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

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

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 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

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

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

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 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

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

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

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

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

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

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

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

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

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

Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
Rybak-Wolf, A., Wyler, E., Pentimalli, T.M., Legnini, I., Oliveras Martinez, A., Glažar, P., Loewa, A., Kim, S.J., Kaufer, B.B., Woehler, A., Landthaler, M. and Rajewsky, N.
Nature Microbiology 8 (7): 1252-1266. July 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

Doxorubicin changes the spatial organization of the genome around active promoters.
Stefanova, M.E., Ing-Simmons, E., Stefanov, S., Flyamer, I., Dorado Garcia, H., Schöpflin, R., Henssen, A.G., Vaquerizas, J.M. and Mundlos, S.
Cells 12 (15): 2001. 4 August 2023

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

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

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

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

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

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

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

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

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

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Watkins, T.B.K., Colliver, E.C., Huska, M.R., Kaufmann, T.L., Lim, E.L., Duncan, C.B., Haase, K., Van Loo, P., Swanton, C., McGranahan, N. and Schwarz, R.F.
PLoS Computational Biology 19 (10): e1011379. 23 October 2023

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

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

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

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

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

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 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

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

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

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

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

2022

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

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

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

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

Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes.
Ansari, S.A., Dantoft, W., Ruiz-Orera, J., Syed, A.P., Blachut, S., van Heesch, S., Hübner, N. and Uhlenhaut, N.H.
Computational and Structural Biotechnology Journal 20 : 5622-5638. 3 October 2022

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R. and Jug, F.
Frontiers in Computer Science 4 : 777728. 10 February 2022

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

Ablation of lysophosphatidic acid receptor 1 attenuates hypertrophic cardiomyopathy in a mouse model.
Axelsson Raja, A., Wakimoto, H., DeLaughter, D.M., Reichart, D., Gorham, J., Conner, D.A., Lun, M., Probst, C.K., Sakai, N., Knipe, R.S., Montesi, S.B., Shea, B., Adam, L.P., Leinwand, L.A., Wan, W., Choi, E.S., Lindberg, E.L., Patone, G., Noseda, M., Hübner, N., Seidman, C.E., Tager, A.M., Seidman, J.G. and Ho, C.Y.
Proceedings of the National Academy of Sciences of the United States of America 119 (28): e2204174119. 12 July 2022

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E., Breimann, L., Zouinkhi, M., Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S., Lionnet, T. and Preibisch, S.
Nature Methods 19 (12): 1563-1567. December 2022

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

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