List of publications

Schwämmle, T.; Noviello, G.; Kanata, E.; Froehlich, J. J.; Bothe, A. M.; Martitz, A.; Altay, A.; Scouarnec, J.; Feng, V.-Y.; Mallie, H. et al.; Vingron, M.; Schulz, E. G.: Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus. Nature Structural & Molecular Biology (2025)

Rübsam, F. N. M.; Liuwei, W.; Sun, Y.; Patel, B. I.; van der Toorn, W.; Piechotta, M.; Dieterich, C.; von Kleist, M.; Ehrenhofer-Murra, A. E.: MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers. Nucleic Acids Research (2025)

Kapmaz, M.; Keske, Ş.; Tekin, S.; Doğan, Ö.; İrkören, P.; Ataç, N.; Vatansever, C.; Albayrak, Ö.; Genç, Z.; Madran, B. et al.; Dönmez, H. E.; Özer, B.; Aksu, E. D.; Başkurt, D.; Berkkan, M.; Güldan, M.; Bakır, V. O.; Gönen, M.; Can, F.; Ergönül, Ö.: The Analysis of Missed Antibiotic De-Escalation Opportunities in Gram-Negative Bloodstream Infections. Antibiotics 14, p. 800 (2025)

Schindler, M.; Feregrino, C.; Aldrovandi, S.; Lo, B.-W.; Monaco, A. A.; Ringel, A. R.; Morales, A. E.; Zehnder, T.; Behncke, R. Y.; Glaser, J. et al.; Barclay, A.; Andrey, G.; Kragesteen, B. K.; Hägerling, R.; Haas, S.; Vingron, M.; Ulitsky, I.; Marti-Renom, M. A.; Hechavarria, J.; Fasel, N.; Hiller, M.; Lupiáñez, D. G.; Mundlos, S.; Martinez Real, F.: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development. Nature Ecology & Evolution (2025)

Glaser, J.; Cova, G.; Fauler, B.; Prada-Medina, C. A.; Stanislas, V.; Phan, M. H. Q.; Schöpflin, R.; Aktas, Y.; Franke, M.; Andrey, G. et al.; Paliou, C.; Laupert, V.; Chan, W.-L.; Wittler, L.; Mielke, T.; Mundlos, S.: Enhancer adoption by an LTR retrotransposon generates viral-like particles causing developmental limb phenotypes. Nature Genetics 57, pp. 1766 - 1776 (2025)

Rossi, F.; Magalhães, A. P.; Buschow, R.; Schubert , T.; Glaser, L. V.; Fontana, A.; Mai , J.; Staege, H.; Grimme, A.; Will, H. et al.; Schriener, .; Hnisz, D.; Vingron, M.; Chiariello, A. M.; Kinkley, S.: Differential oligomerization regulates PHF13 chromatin affinity and function. Nucleic Acids Research 53 (12) (2025)

Phan, M. H. Q.; Zehnder, T.; Puntieri, F.; Magg, A.; Majchrzycka, B.; Antonović, M.; Wieler, H. M.; Lo, B.-W.; Baranasic, D.; Lenhard, B. et al.; Müller, F.; Vingron, M.; Ibrahim, D. M.: Conservation of regulatory elements with highly diverged sequences across large evolutionary distances. Nature Genetics 57, pp. 1524 - 1534 (2025)

Bebelman, M. P.; Belicova, L.; Gralinska, E.; Jumel , T.; Lahree, A.; Sommer, S.; Shevchenko, A.; Zatsepin, T.; Kalaidzidis, Y.; Vingron, M. et al.; Zerial, M.: Hepatocyte differentiation requires anisotropic expansion of bile canaliculi. Development 151 (22), Article dev202777 (2024)

Henglin, M.; Ghareghani, M.; Harvey, W. T.; Porubsky, D.; Koren, S.; Eichler, E. E.; Ebert, P.; Marschall, T.: Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing. Genome Biology: Biology for the Post-Genomic Era 25 (1), Article 265 (2024)

Altay, A.; Vingron, M.: scATAcat: cell-type annotation for scATAC-seq data. NAR: genomics and bioinformatics 6 (4), Article lqae135 (2024)

Stötzel, M.; Cheng, C.-Y.; Ilik, I. A.; Sampath Kumar, A.; Akbari-Omgba, P.; van der Weijden, V. A.; Zhang, Y.; Vingron, M.; Meissner, A.; Aktas, T. et al.; Kretzmer, H.; Bulut-Karslioglu, A.: TET activity safeguards pluripotency throughout embryonic dormancy. Nature Structural & Molecular Biology 31 (10), pp. 1625 - 1639 (2024)

Naderi, J.; Magalhães, A. P.; Kibar, G.; Stik, G.; Zhang, Y.; Mackowiak, S.; Wieler, H. M.; Rossi, F.; Buschow, R.; Christou-Kent, M. et al.; Alcoverro-Bertran, M.; Graf, T.; Vingron, M.; Hnisz, D.: An activity-specificity trade-off encoded in human transcription factors. Nature Cell Biology 26 (8), pp. 1309 - 1321 (2024)

Zhao, Y.; Kohl, C.; Rosebrock, D.; Hu, Q.; Hu, Y.; Vingron, M.: CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics. Nucleic Acids Research 52 (13), Article e57 (2024)

Rosebrock, D.; Vingron, M.; Arndt, P. F.: Modeling gene expression cascades during cell state transitions. iScience 27 (4), Article 109386 (2024)

Yan, M.; Li, M.; Wang, Y.; Wang, X.; Moeinzadeh, H.-M.; Quispe-Huamanquispe, D. G.; Fan, W.; Fang, Y.; Wang, Y.; Nie, H. et al.; Wang, Z.; Tanaka, A.; Heider, B.; Kreuze, J. F.; Gheysen, G.; Wang, H.; Vingron, M.; Bock, R.; Yang, J.: Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato. Molecular Plant 17 (2), pp. 277 - 296 (2024)

van der Weijden, V. A.; Stötzel, M.; Iyer, D. P.; Fauler, B.; Gralinska, E.; Shahraz, M.; Meierhofer, D.; Vingron, M.; Rulands, S.; Alexandrov, T. et al.; Mielke, T.; Bulut-Karslioglu, A.: FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy. Nature Cell Biology 26 (2), pp. 181 - 193 (2024)

Rapakoulia, T.; Lopez Ruiz de Vargas, S.; Akbari-Omgba, P.; Laupert, V.; Ulitsky, I.; Vingron, M.: CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction. Bioinformatics 39 (11), btad687 (2023)

Jatzlau, J.; Mendez, P.-L.; Altay, A.; Raaz, L.; Zhang, Y.; Mähr, S.; Sesver, A.; Reichenbach, M.; Mundlos, S.; Vingron, M. et al.; Knaus, P.: Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription. iScience 26 (9), 107405 (2023)

Gralinska, E.; Vingron, M.: Association Plots: visualizing cluster-specific associations in high-dimensional correspondence analysis biplots. Journal of the Royal Statistical Society - Series C: Applied Statistics 72 (4), pp. 1023 - 1040 (2023)

Lienhard, M.; van den Beucken , T.; Timmermann, B.; Hochradel, M.; Boerno, S.; Caiment , F.; Vingron, M.; Herwig, R.: IsoTools: a flexible workflow for long-read transcriptome sequencing analysis. Bioinformatics 39 (6), btad364 (2023)