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Nature Genetics
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Expanding the spectrum of EEF1D neurodevelopmental disorders: biallelic variants in the guanine exchange domain.
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Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage.
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RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
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Nature Genetics 54
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Multi-omics alleviates the limitations of panel sequencing for cancer drug response prediction.
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PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
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Nature Cell Biology 26
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State-of-the-art analytical methods of viral infections in human lung organoids.
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Science Signaling 17
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Investigating the role of GLUL as a survival factor in cellular adaptation to glutamine depletion via targeted stable isotope resolved metabolomics.
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Frontiers in Molecular Biosciences 9
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SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics.
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Biotechniques 73
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Robust co-immunoprecipitation with mass spectrometry for Caenorhabditis elegans using solid-phase enhanced sample preparation.
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Biotechniques 72
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Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
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Nature Methods 20
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July 2023
The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
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Nature Communications 14
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Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia.
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Cell Stem Cell 30
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4 May 2023
Using DNA sequencing data to quantify T cell fraction and therapy response.
Bentham, R., Litchfield, K., Watkins, T.B.K., Lim, E.L., Rosenthal, R., Martínez-Ruiz, C., Hiley, C.T., Bakir, M.A., Salgado, R., Moore, D.A., Jamal-Hanjani, M., Swanton, C. and McGranahan, N.
Nature 597
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23 September 2021
Amplification of autoimmune organ damage by NKp46-activated ILC1.
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Nature
13 August 2024
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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
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1 December 2023
Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation.
Blassberg, R., Patel, H., Watson, T., Gouti, M., Metzis, V., Delás, M.J. and Briscoe, J.
Nature Cell Biology 24
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Uncovering de novo gene birth in yeast using deep transcriptomics.
Blevins, W.R., Ruiz-Orera, J., Messeguer, X., Blasco-Moreno, B., Villanueva-Cañas, J.L., Espinar, L., Díez, J., Carey, L.B. and Albà, M.M.
Nature Communications 12
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27 January 2021
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
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SLM2 is a novel cardiac splicing factor involved in heart failure due to dilated cardiomyopathy.
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Genomics Proteomics & Bioinformatics 20
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A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease.
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Genome Medicine 15
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20 July 2023
Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging.
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Full-length spatial transcriptomics reveals the unexplored isoform diversity of the myocardium post-MI.
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22 July 2022
pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation.
Boix, O., Martinez, M., Vidal, S., Giménez-Alejandre, M., Palenzuela, L., Lorenzo-Sanz, L., Quevedo, L., Moscoso, O., Ruiz-Orera, J., Ximénez-Embún, P., Ciriaco, N., Nuciforo, P., Stephan-Otto Attolini, C., Albà, M.M., Muñoz, J., Tian, T.V., Varela, I., Vivancos, A., Ramón Y Cajal, S., Muñoz, P., Rivas, C. and Abad, M.
Nature Communications 13
(1): 6840.
11 November 2022
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
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17 April 2024
Transient stabilization of human cardiovascular progenitor cells from hPSCs 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
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5 June 2024
(In Press)
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
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February 2023
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
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March 2024
Claudin-10a deficiency shifts proximal tubular Cl(-) permeability to cation selectivity via claudin-2 redistribution.
Breiderhoff, T., Himmerkus, N., Meoli, L., Fromm, A., Sewerin, S., Kriuchkova, N., Nagel, O., Ladilov, Y., Krug, S., Quintanova, C., Stumpp, M., Garbe-Schönberg, D., Westernströer, U., Merkel, C., Brinkhus, M., Altmüller, J., Schweiger, M., Mueller, D., Mutig, K., Morawski, M., Halbritter, J., Milatz, S., Bleich, M. and Günzel, D.
Journal of the American Society of Nephrology 33
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April 2022
The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L., Morao, A.K., Kim, J., Jimenez, D.S., Maryn, N., Bikkasani, K., Carrozza, M.J., Albritton, S.E., Kramer, M., Street, L.A., Cerimi, K., Schumann, V.F., Bahry, E., Preibisch, S., Woehler, A. and Ercan, S.
Journal of Cell Science 135
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January 2022
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programming.
Breitenbach, T., Schmitt, M.J. and Dandekar, T.
Bioinformatics 38
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1 September 2022
Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.
Broto, M., Kaminski, M.M., Adrianus, C., Kim, N., Greensmith, R., Dissanayake-Perera, S., Schubert, A.J., Tan, X., Kim, H., Dighe, A.S., Collins, J.J. and Stevens, M.M.
Nature Nanotechnology 17
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October 2022
Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage.
Bubb, K., Holzer, T., Nolte, J.L., Krüger, M., Wilson, R., Schlötzer-Schrehardt, U., Brinckmann, J., Altmüller, J., Aszodi, A., Fleischhauer, L., Clausen-Schaumann, H., Probst, K. and Brachvogel, B.
Journal of Biological Chemistry 297
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October 2021
Systematic identification of A-to-I RNA editing in zebrafish development and adult organs.
Buchumenski, I., Holler, K., Appelbaum, L., Eisenberg, E., Junker, J.P. and Levanon, E.Y.
Nucleic Acids Research 49
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7 May 2021
European and multi-ancestry genome-wide association meta-analysis of atopic dermatitis highlights importance of systemic immune regulation.
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Nature Communications 14
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4 October 2023
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression.
Bujanic, L., Shevchuk, O., von Kügelgen, N., Kalinina, A., Ludwik, K., Koppstein, D., Zerna, N., Sickmann, A. and Chekulaeva, M.
RNA 28
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May 2022
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
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23 July 2024
WARS1 and SARS1: two tRNA synthetases implicated in autosomal recessive microcephaly.
Bögershausen, N., Krawczyk, H.E., Jamra, R.A., Lin, S.J., Yigit, G., Hüning, I., Polo, A.M., Vona, B., Huang, K., Schmidt, J., Altmüller, J., Luppe, J., Platzer, K., Dörgeloh, B.B., Busche, A., Biskup, S., Mendes, M.I., Smith, D.E.C., Salomons, G.S., Zibat, A., Bültmann, E., Nürnberg, P., Spielmann, M., Lemke, J.R., Li, Y., Zenker, M., Varshney, G.K., Hillen, H.S., Kratz, C.P. and Wollnik, B.
Human Mutation 43
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October 2022
Single cell biology - a Keystone Symposia report.
Cable, J., Elowitz, M.B., Domingos, A.I., Habib, N., Itzkovitz, S., Hamidzada, H., Balzer, M.S., Yanai, I., Liberali, P., Whited, J., Streets, A., Cai, L., Stergachis, A.B., Hong, C.K.Y., Keren, L., Guilliams, M., Alon, U., Shalek, A.K., Hamel, R., Pfau, S.J., Raj, A., Quake, S.R., Zhang, N.R., Fan, J., Trapnell, C., Wang, B., Greenwald, N.F., Vento-Tormo, R., Santos, S.D.M., Spencer, S.L., Garcia, H.G., Arekatla, G., Gaiti, F., Arbel-Goren, R., Rulands, S., Junker, J.P., Klein, A.M., Morris, S.A., Murray, J.I., Galloway, K.E., Ratz, M. and Romeike, M.
Annals of the New York Academy of Sciences 1506
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December 2021
Organoids as tools for fundamental discovery and translation - a Keystone Symposia report.
Cable, J., Lutolf, M.P., Fu, J., Park, S.E., Apostolou, A., Chen, S., Song, C.J., Spence, J.R., Liberali, P., Lancaster, M., Meier, A.B., Pek, N.M.Q., Wells, J.M., Capeling, M.M., Uzquiano, A., Musah, S., Huch, M., Gouti, M., Hombrink, P., Quadrato, G. and Urenda, J.P.
Annals of the New York Academy of Sciences 1518
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December 2022
DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
Calviello, L., Venkataramanan, S., Rogowski, K.J., Wyler, E., Wilkins, K., Tejura, M., Thai, B., Krol, J., Filipowicz, W., Landthaler, M. and Floor, S.N.
Nucleic Acids Research 49
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May 2021
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
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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
2 August 2024
(In Press)
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
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29 April 2024
Ecological factors influence balancing selection on leaf chemical profiles of a wildflower.
Carley, L.N., Mojica, J.P., Wang, B., Chen, C.Y., Lin, Y.P., Prasad, K.V.S.K, Chan, E., Hsu, C.W., Keith, R., Nuñez, C.L., Olson-Manning, C.F., Rushworth, C.A., Wagner, M.R., Wang, J., Yeh, P.M., Reichelt, M., Ghattas, K., Gershenzon, J., Lee, C.R. and Mitchell-Olds, T.
Nature Ecology & Evolution 5
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August 2021
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
22 July 2024
(In Press)
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
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15 November 2023
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
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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
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July 2024
Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
Cess, C.G. and Haghverdi, L.
Bioinformatics
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25 July 2024
(In Press)
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
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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
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10 November 2023
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
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13 May 2024
A high-resolution map of human RNA translation.
Chothani, S.P., Adami, E., Widjaja, A.A., Langley, S.R., Viswanathan, S., Pua, C.J., Zhihao, N.T., Harmston, N., D'Agostino, G., Whiffin, N., Mao, W., Ouyang, J.F., Lim, W.W., Lim, S., Lee, C.Q.E., Grubman, A., Chen, J., Kovalik, J.P., Tryggvason, K., Polo, J.M., Ho, L., Cook, S.A., Rackham, O.J.L. and Schafer, S.
Molecular Cell 82
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4 August 2022
A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome.
Cinque, L., Micale, L., Manara, E., Esposito, A., Palumbo, O., Chiariello, A.M., Bianco, S., Guerri, G., Bertelli, M., Giuffrida, M.G., Bernardini, L., Notarangelo, A., Nicodemi, M. and Castori, M.
Human Genetics 141
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February 2022
Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.
Company, C., Schmitt, M.J., Dramaretska, Y., Serresi, M., Kertalli, S., Jiang, B., Yin, J.A., Aguzzi, A., Barozzi, I. and Gargiulo, G.
Nature Communications 15
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5 February 2024
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
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2023
Dynamic and equilibrium properties of finite-size polymer models of chromosome folding.
Conte, M., Fiorillo, L., Annunziatella, C., Esposito, A., Musella, F., Abraham, A., Bianco, S. and Chiariello, A.M.
Physical Review E 104
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10 November 2021
A polymer physics model to dissect genome organization in healthy and pathological phenotypes.
Conte, M., Fiorillo, L., Bianco, S., Chiariello, A.M., Esposito, A., Musella, F., Flora, F., Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2301
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2022
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.
Conte, M., Irani, E., Chiariello, A.M., Abraham, A., Bianco, S., Esposito, A. and Nicodemi, M.
Nature Communications 13
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13 July 2022
Combining callers improves the detection of copy number variants from whole-genome sequencing.
Coutelier, M., Holtgrewe, M., Jäger, M., Flöttman, R., Mensah, M.A., Spielmann, M., Krawitz, P., Horn, D., Beule, D. and Mundlos, S.
European Journal of Human Genetics 30
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February 2022
Association of the human gut microbiota with vascular stiffness.
Cuadrat, R.R.C., Goris, T., Birukov, A., Eichelmann, F., Andrade, B.G.N., Bang, C., Franke, A., Wittenbecher, C. and Schulze, M.B.
Scientific Reports 13
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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
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June 2023
Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation.
Cuello, F., Knaust, A.E., Saleem, U., Loos, M., Raabe, J., Mosqueira, D., Laufer, S., Schweizer, M., Kraak, P., Flenner, F., Ulmer, B.M, Braren, I., Yin, X., Theofilatos, K., Ruiz-Orera, J., Patone, G., Klampe, B., Schulze, T., Piasecki, A., Pinto, Y., Vink, A., Hübner, N., Harding, S., Mayr, M., Denning, C., Eschenhagen, T. and Hansen, A.
EMBO Molecular Medicine 13
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7 June 2021
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
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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
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7 February 2023
Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension.
Dahale, S., Ruiz-Orera, J., Silhavy, J., Hübner, N., van Heesch, S., Pravenec, M. and Atanur, S.S.
Life Science Alliance 5
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April 2022
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
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30 May 2023
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
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June 2024
Activated SUMOylation restricts MHC class I antigen presentation to confer immune evasion in cancer.
Demel, U.M., Böger, M., Yousefian, S., Grunert, C., Zhang, L., Hotz, P.W., Gottschlich, A., Köse, H., Isaakidis, K., Vonficht, D., Grünschläger, F., Rohleder, E., Wagner, K., Dönig, J., Igl, V., Brzezicha, B., Baumgartner, F., Habringer, S., Löber, J., Chapuy, B., Weidinger, C., Kobold, S., Haas, S., Busse, A.B., Müller, S., Wirth, M., Schick, M. and Keller, U.
Journal of Clinical Investigation 132
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2 May 2022
A complex proinflammatory cascade mediates the activation of HSCs upon LPS exposure in vivo.
Demel, U.M., Lutz, R., Sujer, S., Demerdash, Y., Sood, S., Grünschläger, F., Kuck, A., Werner, P., Blaszkiewicz, S., Uckelmann, H.J., Haas, S. and Essers, M.
Blood Advances 6
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10 June 2022
Small molecule SUMO inhibition for biomarker-informed B-cell lymphoma therapy.
Demel, U.M., Wirth, M., Yousefian, S., Zhang, L., Isaakidis, K., Dönig, J., Böger, M., Singh, N., Köse, H., Haas, S., Müller, S., Schick, M. and Keller, U.
Haematologica 108
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February 2023
Elevated Flt3L predicts long-term survival in patients with high-grade gastroenteropancreatic neuroendocrine neoplasms.
Detjen, K.M., Otto, R., Giesecke, Y., Geisler, L., Riemer, P., Jann, H., Grötzinger, C., Sers, C., Pascher, A., Lüdde, T., Leser, U., Wiedenmann, B., Sigal, M., Tacke, F., Roderburg, C. and Hammerich, L.
Cancers 13
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1 September 2021
Molecular identity of proprioceptor subtypes innervating different muscle groups in mice.
Dietrich, S., Company, C., Song, K., Lowenstein, E.D., Riedel, L., Birchmeier, C., Gargiulo, G. and Zampieri, N.
Nature Communications 13
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11 November 2022
T- and L-type calcium channels maintain calcium oscillations in the murine zona glomerulosa.
Dinh, H.A., Volkert, M., Secener, A.K., Scholl, U.I. and Stölting, G.
Hypertension 81
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April 2024
Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
Divisato, G., Chiariello, A.M., Esposito, A., Zoppoli, P., Zambelli, F., Elia, M.A., Pesole, G., Incarnato, D., Passaro, F., Piscitelli, S., Oliviero, S., Nicodemi, M., Parisi, S. and Russo, T.
BMC Biology 20
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2 August 2022
Identifying tumor cells at the single-cell level using machine learning.
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Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.
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Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.
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Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma.
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Nature Biotechnology 40
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Truncated titin proteins and titin haploinsufficiency are targets for functional recovery in human cardiomyopathy due to TTN mutations.
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The SEQC2 epigenomics quality control (EpiQC) study.
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Advancements in pulsed stable isotope-resolved metabolomics.
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Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
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Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.
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Optimized workflow for on-line derivatization for targeted metabolomics approach by gas chromatography-mass spectrometry.
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C. elegans gene regulatory alleles and reporter bashing studies.
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Interferon regulatory factor 4 plays a pivotal role in the development of aGVHD-associated colitis.
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Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN.
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Nature Communications 14
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4 July 2023
Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice.
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Cell states in cancer: drivers, passengers, and trailers.
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The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.
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Cell Reports 38
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SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals.
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Nature Communications 12
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21 June 2021
Salt transiently inhibits mitochondrial energetics in mononuclear phagocytes.
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Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
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Rapid inflammasome activation is attenuated in post-myocardial infarction monocytes.
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Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
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Deep learning-assisted peak curation for large-scale LC-MS metabolomics.
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Expression of circ_Satb1 is decreased in mesial temporal lobe epilepsy and regulates dendritic spine morphology.
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The zinc finger antiviral protein ZAP restricts human cytomegalovirus and selectively binds and destabilizes viral UL4/UL5 transcripts.
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CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting.
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
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Nature Communications 12
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2 June 2021
Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.
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Nature Genetics 56
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Epigenetic modifier balances Mapk and Wnt signalling in differentiation of goblet and Paneth cells.
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Life Science Alliance 5
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April 2022
Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.
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Nature Communications 12
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16 November 2021
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.
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11 May 2023
How to find genomic regions relevant for gene regulation.
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14 August 2021
Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons.
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Human Molecular Genetics
24 July 2024
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Phenotypic spectrum of BLM- and RMI1-related Bloom syndrome.
Gönenc, I.I., Elcioglu, N.H., Martinez Grijalva, C., Aras, S., Großmann, N., Praulich, I., Altmüller, J., Kaulfuß, S., Li, Y., Nürnberg, P., Burfeind, P., Yigit, G. and Wollnik, B.
Clinical Genetics 101
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May 2022
Transcription factor induction of vascular blood stem cell niches in vivo.
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Developmental Cell 58
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19 June 2023
A comparative study of graph matching algorithms in computer vision.
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Lecture Notes in Computer Science 13683
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Short-term mucosal disruption enables colibactin-producing E. coli to cause long-term perturbation of colonic homeostasis.
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Gut Microbes 15
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A critical period of translational control during brain development at codon resolution.
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Nature Structural & Molecular Biology 29
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Genome-wide analysis of actively translated open reading frames using riboTaper/ORFquant.
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A comparison of nine machine learning mutagenicity models and their application for predicting pyrrolizidine alkaloids.
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Frontiers in Pharmacology 12
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22 July 2021
Antigen presentation safeguards the integrity of the hematopoietic stem cell pool.
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5 May 2022
High Yap and Mll1 promote a persistent regenerative cell state induced by Notch signaling and loss of p53.
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1 June 2021
Epithelial response to IFN-γ promotes SARS-CoV-2 infection.
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EMBO Molecular Medicine 13
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9 April 2021
Pangenome graph construction from genome alignments with Minigraph-Cactus.
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Nature Biotechnology 42
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Lung adenocarcinoma promotion by air pollutants.
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Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
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Genome Medicine 14
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Tracking by weakly-supervised learning and graph optimization for whole-embryo c. elegans lineages.
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Science Advances 10
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15 March 2024
HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness.
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Human alveolar progenitors generate dual lineage bronchioalveolar organoids.
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Communications Biology 5
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Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.
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Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance.
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Journal of the American Society of Nephrology 33
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Spatio-temporal mRNA tracking in the early zebrafish embryo.
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Nature Communications 12
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7 June 2021
A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.
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NAR Genomics and Bioinformatics 5
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March 2023
Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
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Eurosurveillance 27
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27 October 2022
REEV: review, evaluate and explain variants.
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Nucleic Acids Research 52
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5 July 2024
Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.
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STAR Protocols 3
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Origin and function of activated fibroblast states during zebrafish heart regeneration.
Hu, B., Lelek, S., Spanjaard, B., El-Sammak, H., Simões, M.G., Mintcheva, J., Aliee, H., Schäfer, R., Meyer, A.M., Theis, F., Stainier, D.Y.R., Panáková, D. and Junker, J.P.
Nature Genetics 54
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August 2022
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
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Nature Genetics 53
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July 2021
Women in the European Virus Bioinformatics Center.
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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
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10 April 2023
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
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7 May 2024
Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.
Hönzke, K., Obermayer, B., Mache, C., Fathykova, D., Kessler, M., Dökel, S., Wyler, E., Baumgardt, M., Löwa, A., Hoffmann, K., Graff, P., Schulze, J., Mieth, M., Hellwig, K., Demir, Z., Biere, B., Brunotte, L., Mecate-Zambrano, A., Bushe, J., Dohmen, M., Hinze, C., Elezkurtaj, S., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Schmidt-Ott, K.M., Busch, J., Klauschen, F., Horst, D., Radbruch, H., Radke, J., Heppner, F., Corman, V.M., Niemeyer, D., Müller, M.A., Goffinet, C., Mothes, R., Pascual-Reguant, A., Hauser, A.E., Beule, D., Landthaler, M., Ludwig, S., Suttorp, N., Witzenrath, M., Gruber, A.D., Drosten, C., Sander, L.E., Wolff, T., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal 60
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1 December 2022
Apple peel and flesh contain pro-neurogenic compounds.
Ichwan, M., Walker, T.L., Nicola, Z., Ludwig-Müller, J., Böttcher, C., Overall, R.W., Adusumilli, V.S., Bulut, M., Sykes, A.M., Hübner, N., Ramirez-Rodriguez, G., Ortiz-López, L., Lugo-Hernández, E.A. and Kempermann, G.
Stem Cell Reports 16
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9 March 2021
Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells.
Iftekhar, A., Berger, H., Bouznad, N., Heuberger, J., Boccellato, F., Dobrindt, U., Hermeking, H., Sigal, M. and Meyer, T.F.
Nature Communications 12
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12 February 2021
Defence and adaptation mechanisms of the intestinal epithelium upon infection.
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International Journal of Medical Microbiology 311
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April 2021
Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts.
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Science Advances 9
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December 2023
MACC1 regulates clathrin-mediated endocytosis and receptor recycling of transferrin receptor and EGFR in colorectal cancer.
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April 2021
Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome.
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Nature Communications 12
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26 March 2021
Dynamics of bacteria scanning a porous environment.
Irani, E., Mokhtari, Z. and Zippelius, A.
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5 April 2022
Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells.
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Pathogens 10
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21 May 2021
Immunobiotic Lactobacilli improve resistance of respiratory epithelial cells to SARS-CoV-2 infection.
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Pathogens 10
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September 2021
Increased β(2)-adrenergic signaling promotes fracture healing through callus neovascularization in mice.
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Science Translational Medicine 16
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Nature Medicine 29
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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
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14 November 2022
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1 August 2022
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Identification of drug candidates targeting monocyte reprogramming in people living with HIV.
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European Journal of Human Genetics
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Association of ultra-rare coding variants with genetic generalized epilepsy: a case-control whole exome sequencing study.
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Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study.
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European Journal of Human Genetics
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Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
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Nature Machine Intelligence 4
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Deletion in the Y chromosome of B10.BR-Y(del) mice alters transcription from MSYq genes and has moderate effect on DNA methylation.
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Disruption of stem cell niche-confined R-spondin 3 expression leads to impaired hematopoiesis.
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Health workforce response to Covid-19: What pandemic preparedness planning and action at the federal and state levels in Germany? Germany's health workforce responses to Covid-19.
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Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
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Sox9 is required for nail bed differentiation and digit tip regeneration.
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Journal of Investigative Dermatology 142
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October 2022
Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.
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Nature Genetics 55
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Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
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Nature Protocols 18
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Latent human herpesvirus 6 is reactivated in CAR T cells.
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Nature 623
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Generation of human brain organoids for mitochondrial disease modeling.
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Journal of Visualized Experiments
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21 June 2021
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
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Virus-induced senescence is driver and therapeutic target in COVID-19.
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Nature 599
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Alport syndrome and autosomal dominant tubulointerstitial kidney disease frequently underlie end stage renal disease of unknown origin - a single center analysis.
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Nature Methods 20
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Spatial single cell profiling using imaging mass cytometry: inflammatory versus penetrating Crohn's disease.
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Journal of Crohn's & Colitis
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A novel homozygous synonymous variant further expands the phenotypic spectrum of POLR3A-related pathologies.
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Stem cells, helicobacter pylori and mutational landscape: utility of preclinical models to understand carcinogenesis and to direct management of gastric cancer.
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Human model of primary carnitine deficiency cardiomyopathy reveals ferroptosis as a novel mechanism.
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Molecular characterization of nodose ganglia development reveals a novel population of Phox2b+ glial progenitors in mice.
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AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics.
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The genomic landscape across 474 surgically accessible epileptogenic human brain lesions.
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Analysis of correlation and ionization from pair distributions in many-electron systems.
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22 July 2021
A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration.
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27 March 2023
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Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.
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Satellite glia of the adult dorsal root ganglia harbor stem cells that yield glia under physiological conditions and neurons in response to injury.
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8 November 2022
GAS1 is required for Notch-dependent facilitation of SHH signaling in the ventral forebrain neuroepithelium.
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In vitro Kinase-to-Phosphosite database (iKiP-DB) predicts kinase activity in phosphoproteomic datasets.
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3 June 2022
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Nature Communications 12
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9 September 2021
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
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Bioinformatics 37
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1 October 2021
The little skate genome and the evolutionary emergence of wing-like fins.
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20 April 2023
Towards reliable quantification of cell state velocities.
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PLoS Computational Biology 18
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28 September 2022
NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.
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eLife 10
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17 August 2021
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Despite the odds: formation of the SARS-CoV-2 methylation complex.
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The relevance of the SH2 domain for c-Src functionality in triple-negative breast cancer cells.
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Identification of disease-relevant modulators of the SHH pathway in the developing brain.
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Reliable assessment of telomere maintenance mechanisms in neuroblastoma.
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A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.
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Lymphocyte access to lymphoma is impaired by high endothelial venule regression.
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A high-resolution map of small-scale inversions in the gibbon genome.
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MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.
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A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants.
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Generation of hiPSC-derived skeletal muscle cells: exploiting the potential of skeletal muscle-derived hiPSCs.
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Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart.
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Generation of an induced pluripotent stem cell line from a Huntington's disease patient with a long HTT-PolyQ sequence.
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Generation of induced pluripotent stem cells from three individuals with Huntington's disease.
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December 2022
Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
Miller, T.E., Lareau, C.A., Verga, J.A., DePasquale, E.A.K., Liu, V., Ssozi, D., Sandor, K., Yin, Y., Ludwig, L.S., El Farran, C.A., Morgan, D.M., Satpathy, A.T., Griffin, G.K., Lane, A.A., Love, J.C., Bernstein, B.E., Sankaran, V.G. and van Galen, P.
Nature Biotechnology 40
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24 February 2022
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Mimitou, E.P., Lareau, C.A., Chen, K.Y., Zorzetto-Fernandes, A.L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.S., Yeung, B.Z., Papalexi, E., Thakore, P.I., Kibayashi, T., Wing, J.B., Hata, M., Satija, R., Nazor, K.L., Sakaguchi, S., Ludwig, L.S., Sankaran, V.G., Regev, A. and Smibert, P.
Nature Biotechnology 39
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October 2021
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
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2 April 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
8 June 2024
(In Press)
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
Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R., Rautenstrauch, P., Ghanbari, M., James, A.R., Kirchler, M., Ohler, U., Konigorski, S. and Lippert, C.
Nature Communications 13
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10 September 2022
Variability of an early developmental cell population underlies stochastic laterality defects.
Moreno-Ayala, R., Olivares-Chauvet, P., Schäfer, R. and Junker, J.P.
Cell Reports 34
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12 January 2021
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N., Senel, E., Friedman, N., Rajewsky, N., Karaiskos, N. and Nitzan, M.
Nature Protocols 16
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September 2021
Impact of uORFs in mediating regulation of translation in stress conditions.
Moro, S.G., Hermans, C., Ruiz-Orera, J. and Albà, M.M.
BMC Molecular and Cell Biology 22
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16 May 2021
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
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21 March 2023
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
29 July 2024
(In Press)
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus, C., Luecken, M.D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E.D., Subramanian, A., Smillie, C., Jagadeesh, K.A., Duong, E.T., Fiskin, E., Triglia, E.T., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A.L., Chung, H., Montoro, D.T., Adams, T., Aliee, H., Allon, S.J., Andrusivova, Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L.T., Callori, S., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T.M., Cuoco, M.S., Cuomo, A.S.E., Deprez, M., Duclos, G., Fine, D., Fischer, D.S., Ghazanfar, S., Gillich, A., Giotti, B., Gould, J., Guo, M., Gutierrez, A.J., Habermann, A.C., Harvey, T., He, P., Hou, X., Hu, L., Hu, Y., Jaiswal, A., Ji, L., Jiang, P., Kapellos, T.S., Kuo, C.S., Larsson, L., Leney-Greene, M.A., Lim, K., Litviňuková, M., Ludwig, L.S., Lukassen, S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Leroy, S., Mayr, C.H., Mbano, I.M., McAdams, A.M., Nabhan, A.N., Nyquist, S.K., Penland, L., Poirion, O.B., Poli, S., Qi, C.C., Queen, R., Reichart, D., Rosas, I., Schupp, J.C., Shea, C.V., Shi, X., Sinha, R., Sit, R.V., Slowikowski, K., Slyper, M., Smith, N.P., Sountoulidis, A., Strunz, M., Sullivan, T.B., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K.J., Tucker, N.R., Vernon, K.A., Wadsworth, M.H., Waldman, J., Wang, X., Xu, K., Yan, W., Zhao, W. and Ziegler, C.G.K.
Nature Medicine 27
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2 March 2021
Adjustments to the reference dataset design improve cell type label transfer.
Mölbert, C. and Haghverdi, L.
Frontiers in Bioinformatics 3
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5 April 2023
Isolation of nuclei from mammalian cells and tissues for single-nucleus molecular profiling.
Nadelmann, E.R., Gorham, J.M., Reichart, D., Delaughter, D.M., Wakimoto, H., Lindberg, E.L., Litviňuková, M., Maatz, H., Curran, J.J., Ischiu Gutierrez, D., Hübner, N., Seidman, C.E. and Seidman, J G
Current Protocols 1
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May 2021
Deep learning is widely applicable to phenotyping embryonic development and disease.
Naert, T., Çiçek, Ö., Ogar, P., Bürgi, M., Shaidani, N.I., Kaminski, M.M., Xu, Y., Grand, K., Vujanovic, M., Prata, D., Hildebrandt, F., Brox, T., Ronneberger, O., Voigt, F.F., Helmchen, F., Loffing, J., Horb, M.E., Willsey, H.R. and Lienkamp, S.S.
Development 148
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1 November 2021
Vascular tissue specific miRNA profiles reveal novel correlations with risk factors in coronary artery disease.
Neiburga, K., Vilne, B., Bauer, S., Bongiovanni, D., Ziegler, T., Lachmann, M., Wengert, S., Hawe, J., Güldener, U., Westerlund, A., Li, L., Pang, S., Yang, C., Saar, K., Huebner, N., Maegdefessel, L., Lange, R., Krane, M., Schunkert, H. and von Scheidt, M.
Biomolecules 11
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12 November 2021
Candesartan does not activate PPAR(γ) and its target genes in early gestation trophoblasts.
Neuper, L., Kummer, D., Forstner, D., Guettler, J., Ghaffari-Tabrizi-Wizsy, N., Fischer, C., Juch, H., Nonn, O. and Gauster, M.
International Journal of Molecular Sciences 23
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October 2022
A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A., Bakina, O., Badillo Lisakowski, V., Olivares-Chauvet, P., Conrad, T., Gotthardt, M., Kettenmann, H. and Junker, J.P.
Molecular Systems Biology 19
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10 February 2023
IL11 activates pancreatic stellate cells and causes pancreatic inflammation, fibrosis and atrophy in a mouse model of pancreatitis.
Ng, B., Viswanathan, S., Widjaja, A.A., Lim, W.W., Shekeran, S.G., Goh, J.W.T., Tan, J., Kuthubudeen, F., Lim, S.Y., Xie, C., Schafer, S., Adami, E. and Cook, S.A.
International Journal of Molecular Sciences 23
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24 March 2022
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
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20 April 2023
Best practice standards for circular RNA research.
Nielsen, A.F., Bindereif, A., Bozzoni, I., Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S., Legnini, I., Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J., Preibisch, S., Rajewsky, N., Suenkel, C. and Kjems, J.
Nature Methods 19
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October 2022
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
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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
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31 March 2023
Maternal angiotensin increases placental leptin in early gestation via an alternative renin-angiotensin system pathway: suggesting a link to preeclampsia.
Nonn, O., Fischer, C., Geisberger, S., El-Heliebi, A., Kroneis, T., Forstner, D., Desoye, G., Staff, A.C., Sugulle, M., Dechend, R., Pecks, U., Kollmann, M., Stern, C., Cartwright, J.E., Whitley, G.S., Thilaganathan, B., Wadsack, C., Huppertz, B., Herse, F. and Gauster, M.
Hypertension 77
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May 2021
Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.
Norin, U., Rintisch, C., Meng, L., Forster, F., Ekman, D., Tuncel, J., Klocke, K., Bäcklund, J., Yang, M., Bonner, M.Y, Lahore, G.F., James, J., Shchetynsky, K., Bergquist, M., Gjertsson, I., Hubner, N., Bäckdahl, L. and Holmdahl, R.
Nature Communications 12
(1): 610.
27 January 2021
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
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May 2023
Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19.
Nouailles, G., Wyler, E., Pennitz, P., Postmus, D., Vladimirova, D., Kazmierski, J., Pott, F., Dietert, K., Muelleder, M., Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L.E., Suttorp, N., Ralser, M., Beule, D., Gruber, A.D., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Nature Communications 12
(1): 4869.
11 August 2021
Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens.
Numberger, D., Zoccarato, L., Woodhouse, J., Ganzert, L., Sauer, S., García Márquez, J.R., Domisch, S., Grossart, H.P. and Greenwood, A.D.
Science of the Total Environment 845
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1 November 2022
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, Friedrich and Na, I.K.
Frontiers in Immunology 14
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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
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February 2023
The C. elegans pseudogene sspt-16 (F55A3.7) is required to safeguard germ cells against reprogramming.
Ofenbauer, A., Kraus, C.M. and Tursun, B.
microPublication Biology 2021
18 May 2021
Exercise blood-drop metabolic profiling links metabolism with perceived exertion.
Opialla, T., Gollasch, B., Kuich, P.H.J.L., Klug, L., Rahn, G., Busjahn, A., Spuler, S., Boschmann, M., Kirwan, J.A., Luft, F.C. and Kempa, S.
Frontiers in Molecular Biosciences 9
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21 December 2022
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
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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
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February 2024
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
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31 January 2023
A growth factor-expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15.
Patsalos, A., Halasz, L., Medina-Serpas, M.A., Berger, W.K., Daniel, B., Tzerpos, P., Kiss, M., Nagy, G., Fischer, C., Simandi, Z., Varga, T. and Nagy, L.
Journal of Experimental Medicine 219
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3 January 2022
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
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25 June 2024
Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection.
Pekayvaz, K., Leunig, A., Kaiser, R., Joppich, M., Brambs, S., Janjic, A., Popp, O., Nixdorf, D., Fumagalli, V., Schmidt, N., Polewka, V., Anjum, A., Knottenberg, V., Eivers, L., Wange, L.E., Gold, C., Kirchner, M., Muenchhoff, M., Hellmuth, J.C., Scherer, C., Rubio-Acero, R., Eser, T., Deák, F., Puchinger, K., Kuhl, N., Linder, A., Saar, K., Tomas, L., Schulz, C., Wieser, A., Enard, W., Kroidl, I., Geldmacher, C., von Bergwelt-Baildon, M., Keppler, O.T., Munschauer, M., Iannacone, M., Zimmer, R., Mertins, P., Hubner, N., Hoelscher, M., Massberg, S., Stark, K. and Nicolai, L.
Nature Communications 13
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23 February 2022
Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes.
Pekayvaz, K., Losert, C., Knottenberg, V., Gold, C., van Blokland, I.V., Oelen, R., Groot, H.E., Benjamins, J.W., Brambs, S., Kaiser, R., Gottschlich, A., Hoffmann, G.V., Eivers, L., Martinez-Navarro, A., Bruns, N., Stiller, S., Akgöl, S., Yue, K., Polewka, V., Escaig, R., Joppich, M., Janjic, A., Popp, O., Kobold, S., Petzold, T., Zimmer, R., Enard, W., Saar, K., Mertins, P., Huebner, N., van der Harst, P., Franke, L.H., van der Wijst, M.G.P., Massberg, S., Heinig, M., Nicolai, L. and Stark, K.
Nature Medicine 30
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June 2024
Protocol to dissociate healthy and infected murine- and hamster-derived lung tissue for single-cell transcriptome analysis.
Pennitz, P., Goekeri, C., Trimpert, J., Wyler, E., Ebenig, A., Weissfuss, C., Mühlebach, M.D., Witzenrath, M. and Nouailles, G.
STAR Protocols 4
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17 March 2023
A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics.
Pennitz, P., Kirsten, H., Friedrich, V.D., Wyler, E., Goekeri, C., Obermayer, B., Heinz, G.A., Mashreghi, M.F., Büttner, M., Trimpert, J., Landthaler, M., Suttorp, N., Hocke, A.C., Hippenstiel, S., Tönnies, M., Scholz, M., Kuebler, W.M., Witzenrath, M., Hoenzke, K. and Nouailles, G.
European Respiratory Review 31
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30 September 2022
Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history.
Penter, L., Gohil, S.H., Lareau, C., Ludwig, L.S., Parry, E.M., Huang, T., Li, S., Zhang, W., Livitz, D., Leshchiner, I., Parida, L., Getz, G., Rassenti, L.Z., Kipps, T.J., Brown, J.R., Davids, M.S., Neuberg, D.S., Livak, K.J., Sankaran, V.G. and Wu, C.J.
Cancer Discovery 11
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December 2021
Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.
Penter, L., Ten Hacken, E., Southard, J., Lareau, C., Ludwig, L.S., Li, S., Neuberg, D.S., Livak, K.J. and Wu, C.J.
Cancer Research 83
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1 March 2023
Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis.
Perne, C., Peters, S., Cartolano, M., Horpaopan, S., Grimm, C., Altmüller, J., Sommer, A.K., Hillmer, A.M., Thiele, H., Odenthal, M., Möslein, G., Adam, R., Sivalingam, S., Kirfel, J., Schweiger, M.R., Peifer, M., Spier, I. and Aretz, S.
PLoS ONE 16
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29 November 2021
Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus.
Phan, Q.V., Bogdanow, B., Wyler, E., Landthaler, M., Liu, F., Hagemeier, C. and Wiebusch, L.
PLoS Pathogens 18
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4 January 2022
Tuning the 3D microenvironment of reprogrammed tubule cells enhances biomimetic modeling of polycystic kidney disease.
Pichler, R., Rizzo, L., Tröndle, K., Bühler, M., Brucker, H., Müller, A.L., Grand, K., Farè, S., Viau, A., Kaminski, M.M., Kuehn, E.W., Koch, F., Zimmermann, S., Koltay, P. and Lienkamp, S.S.
Biomaterials 291
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December 2022
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
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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
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1 July 2024
The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y., de Biase, M.S., Schwarz, R.F. and Siegal, M.L.
G3 : Genes Genomes Genetics 13
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March 2023
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
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16 July 2024
RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
Poetz, F., Corbo, J., Levdansky, Y., Spiegelhalter, A., Lindner, D., Magg, V., Lebedeva, S., Schweiggert, J., Schott, J., Valkov, E. and Stoecklin, G.
Nature Communications 12
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9 December 2021
Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
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Swarm Learning for decentralized and confidential clinical machine learning.
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Ablation of collagen XII disturbs joint extracellular matrix organization and causes patellar subluxation.
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DCGG: drug combination prediction using GNN and GAE.
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Nature Communications 13
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18 May 2022
MicroRNAs are deeply linked to the emergence of the complex octopus brain.
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Life Science Alliance 5
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Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction.
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Scientific Reports 12
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8 March 2022
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk.
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Genome Medicine 16
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8 April 2024
Altered nuclear architecture in blood cells from Huntington's disease patients.
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SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
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15 July 2021
The phenotypic and genotypic spectrum of epilepsy and intellectual disability in adults: Implications for genetic testing.
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Soluble urokinase plasminogen activator receptor levels are associated with severity of fibrosis in patients with primary sclerosing cholangitis.
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28 April 2022
Biliary microbial patterns in primary sclerosing cholangitis are linked to poorer transplant-free survival.
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Book Section
Mathematical and bioinformatic tools for cell tracking.
Hirsch, P., Epstein, L. and Guignard, L.
In:
Cell Movement in Health and Disease.
Academic Press, London, 341-361.
ISBN 978-0-323-90195-6
2022
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
Gene expression analysis and next-generation sequencing.
Lindberg, E.L. and Hübner, N.
In:
Encyclopedia of Molecular Pharmacology : Third Edition.
Springer, Cham, 684-688.
ISBN 978-3-030-57400-0
2021
Conference or Workshop Item
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
Fusion moves for graph matching.
Hutschenreiter, L., Haller, S., Feineis, L., Rother, C., Kainmüller, D. and Savchynskyy, B.
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada.
28 February 2022
Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L., Baumann, E., Hirsch, P., Janowczyk, A., Zlobec, I. and Kainmueller, D.
In: 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 28-31 March 2022, Kolkata, India.
17 August 2022
ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
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The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis.
Schneeberger, S., Kim, S.J., Eede, P., Boltengagen, A., Braeuning, C., Andreadou, M., Becher, B., Karaiskos, N., Kocks, C., Rajewsky, N. and Heppner, F.L.
bioRxiv
: 2021.04.25.441313.
27 April 2021
Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V., Ruiz-Orera, J., Hubner, N. and van Heesch, S.
bioRxiv
: 2021.04.13.439465.
13 April 2021
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
Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S., Franke, V., Drayman, N., Wyler, E., Tay, S., Landthaler, M., Akalin, A., Ensser, A. and Full, F.
bioRxiv
: 2021.03.24.436599.
24 March 2021
Other
Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
Schinke, C., Fernandez Vallone, V., Ivanov, A., Peng, Y., Körtvelyessy, P., Nolte, L., Huehnchen, P., Beule, D., Stachelscheid, H., Boehmerle, W. and Endres, M.
Elsevier.
October 2021
This list was generated on Fri Aug 16 21:10:20 2024 UTC.