Max Planck Institute for Molecular Genetics

Publications

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Journal Article (10)

Journal Article

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)

MPG.PuRe

publisher-version

Journal Article

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)

MPG.PuRe

publisher-version

Journal Article

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

MPG.PuRe

publisher-version

Journal Article

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)

MPG.PuRe

publisher-version

Journal Article

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)

MPG.PuRe

publisher-version

Journal Article

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)

MPG.PuRe

publisher-version

Journal Article

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

MPG.PuRe

publisher-version

Journal Article

Phan, M. H. Q.; Zehnder, T.; Puntieri, F.; Lo, B.-W.; Lenhard, B.; Mueller, F.; Vingron, M.; Ibrahim, D. M.: Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances. bioRxiv (2024)

MPG.PuRe

Journal Article

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)

MPG.PuRe

publisher-version

Journal Article

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)

MPG.PuRe

publisher-version

Thesis - PhD (4)

Thesis - PhD

Zhao, Y.: Correspondence analysis based biclustering and joint visualization of cells and genes for single cell transcriptomic data. Dissertation (2024)

MPG.PuRe

Thesis - PhD

Thedinga, K.: Machine Learning for Cancer Survival Prediction. Dissertation (2024)

MPG.PuRe

Thesis - PhD

Wang, G.: Copy number variation characterization using nanopore sequencing. Dissertation (2024)

MPG.PuRe

Thesis - PhD

Kibar, G.: Exploring feature identification and machine learning in predicting protein-protein interactions of disordered proteins. Dissertation (2024)

MPG.PuRe

Thesis - Master (4)

Thesis - Master

Hübner, P.: Association Plots – A Method to Detect Tissue-Specific Regulatory Patterns? Master (2024)

MPG.PuRe

Thesis - Master

Kane, M.: Mathematical Modeling of High-Risk Viral Mutations. Master (2024)

MPG.PuRe

Thesis - Master

Lopez Ruiz de Vargas, S.: Adding 3D chromatin structure information to enhancer- target prediction with CENTRE. Master (2024)

MPG.PuRe

Thesis - Master

Raei, W. A.: Genotyping tandem repeats: Introducing Tandem Twister, a rapid and universal tool for long-read sequencing technologies. Master (2024)

MPG.PuRe

Preprint (3)

Preprint

Schindler, M.; Feregrino, C.; Aldrovandi, S.; Lo, B.-W.; Monaco, A. A.; Ringel, A. R.; Morales, A.; 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.; Hechavarria, J.; Fasel, P.; Hiller, M.; Lupiáñez, D.; Mundlos, S.; Real, F. M.: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development. bioRxiv: the preprint server for biology (2024)

MPG.PuRe

Preprint

Schwaemmle, T.; Noviello, G.; Kanata, E.; Froehlich, J. J.; Bothe, M.; Altay, A.; Scouarnec, J.; Feng, V.-Y.; Vingron, M.; Schulz, E. G.: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus. bioRxiv (2024)

MPG.PuRe