Publications

Max Planck Institute for Molecular Genetics

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 (112)

Journal Article

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

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

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Pardo-Palacios, F. J.; Wang, D.; Reese, F.; Diekhans, M.; Carbonell-Sala, S.; Williams, B.; Loveland, J. E.; De Maria, M.; Adams, M. S.; Balderrama-Gutierrez, G. et al.; Behera, A. K.; Gonzalez, J. M.; Hunt, T.; Lagarde, J.; Liang, C. E.; Li, H.; Jerryd Meade, M.; Moraga Amador, D. A.; Prjibelski, A. D.; Birol, I.; Bostan, H.; Brooks, A. M.; Hasan Celik, M.; Chen, Y.; Du, M. R. M.; Felton, C.; Goke, J.; Hafezqorani, S.; Herwig, R.; Kawaji, H.; Lee, J.; Liang Li, J.; Lienhard, M.; Mikheenko, A.; Mulligan, D.; Ming Nip, K.; Pertea, M.; Ritchie, M. E.; Sim, A. D.; Tang, A. D.; Kei Wan, Y.; Wang, C.; Wong, B. Y.; Yang, C.; Barnes, I.; Berry, A.; Capella, S.; Dhillon, N.; Fernandez-Gonzalez, J. M.; Ferrandez-Peral, L.; Garcia-Reyero, N.; Goetz, S.; Hernandez-Ferrer, C.; Kondratova, L.; Liu, T.; Martinez-Martin, A.; Menor, C.; Mestre-Tomas, J.; Mudge, J. M.; Panayotova, N. G.; Paniagua, A.; Repchevsky, D.; Rouchka, E.; Saint-John, B.; Sapena, E.; Sheynkman, L.; Laird Smith, M.; Suner, M. M.; Takahashi, H.; Youngworth, I. A.; Carninci, P.; Denslow, N. D.; Guigo, R.; Hunter, M. E.; Tilgner, H. U.; Wold, B. J.; Vollmers, C.; Frankish, A.; Fai Au, K.; Sheynkman, G. M.; Mortazavi, A.; Conesa, A.; Brooks, A. N.: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods 21 (7), pp. 1349 - 1363 (2024)

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Springer, C.; Binsch, C.; Weide, D.; Toska, L.; Cremer, A. L.; Backes, H.; Scheel, A. K.; Espelage, L.; Kotzka, J.; Sill, S. et al.; Kurowski, A.; Daebin, K.; Karpinski, S.; Schnurr, T. M.; Hansen, T.; Hartwig, S.; Lehr, S.; Cames, S.; Brüning, J.; Lienhard, M.; Herwig, R.; Börno, S.; Timmermann, B.; Al-Hasani, H.; Chadt, A.: Depletion of TBC1D4 improves the metabolic exercise response by overcoming genetically induced peripheral insulin resistance. Diabetes 73 (7), pp. 1058 - 1071 (2024)

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Ulicevic, J.; Shao, Z.; Jasnovidova, O.; Bressin, A.; Gajos, M.; Ng, A. H.; Annaldasula, S.; Meierhofer, D.; Church, G. M.; Busskamp, V. et al.; Mayer, A.: Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular Systems Biology 20 (7), pp. 767 - 798 (2024)

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van der Weijden, V. A.; Bulut-Karslioglu, A.: Embryos burn fat in standby. Trends in Cell Biology 34 (9), pp. 700 - 702 (2024)

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Bolondi, A.; Law, B. K.; Kretzmer, H.; Gassaloglu, S. I.; Buschow, R.; Riemenschneider, C.; Yang, D.; Walther, M.; Veenvliet, J. V.; Meissner, A. et al.; Smith, Z. D.; Chan, M. M.: Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Developmental Cell 59 (12), pp. 1489 - 1505 (2024)

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Pan, C.; Reinert, K.: Leaf: an ultrafast filter for population-scale long-read SV detection. Genome Biology: Biology for the Post-Genomic Era 25 (1), Article 155 (2024)

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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)

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Borisova, E.; Newman, A. G.; Couce Iglesias, M.; Dannenberg, R.; Schaub, T.; Qin, B.; Rusanova, A.; Brockmann, M.; Koch, J.; Daniels, M. et al.; Turko, P.; Jahn, O.; Kaplan, D. R.; Rosário, M.; Iwawaki, T.; Spahn, C. M. T.; Rosenmund, C.; Meierhofer, D.; Kraushar, M. L.; Tarabykin, V.; Ambrozkiewicz, M. C.: Protein translation rate determines neocortical neuron fate. Nature Communications 15 (1), Article 4879 (2024)

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Muenzner, J.; Trébulle, P.; Agostini, F. e. a.; Ralser, M.: Natural proteome diversity links aneuploidy tolerance to protein turnover. Nature 630 (8015), pp. 149 - 157 (2024)

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Tan, J.; Virtue, S.; Norris, D. M.; Conway, O. J.; Yang, M.; Bidault, G. ....; Vallier, L.; Fisher-Wellman, K. H.; Frezza, C.; Vidal-Puig, A. et al.; Fazakerley, D. J.: Limited oxygen in standard cell culture alters metabolism and function of differentiated cells. The EMBO Journal 43 (11), pp. 2127 - 2165 (2024)

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Andrique, C.; Bonnet, A. L.; Dang, J.; Lesieur, J.; Krautzberger, A. M.; Baroukh, B.; Torrens, C.; Sadoine, J.; Schmitt, A.; Rochefort, G. Y. et al.; Bardet, C.; Six, I.; Houillier, P.; Tharaux, P. L.; Schrewe, H.; Gaucher, C.; Chaussain, C.: Vasorin as an actor of bone turnover? Journal of Cellular Physiology 239 (6), Article e31257 (2024)

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Campana , P. A.; Prasse , P.; Lienhard, M.; Thedinga, K.; Herwig, R.; Scheffer , T.: Cancer drug sensitivity estimation using modular deep Graph Neural Networks. NAR: Genomics and Bioinformatics 6 (2), Article lqae043 (2024)

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Gribben, C.; Galanakis, V.; Calderwood, A.; Williams, E. C.; Chazarra-Gil , R.; Larraz, M.; Frau, C.; Puengel, T.; Guillot, A.; Rouhani, F. J. et al.; Mahbubani, K.; Godfrey, E.; Davies, S. E.; Athanasiadis, E.; Saeb-Parsy, K.; Tacke, F.; Allison, M.; Mohorianu, I.; Vallier, L.: Acquisition of epithelial plasticity in human chronic liver disease. Nature 630 (8015), pp. 166 - 173 (2024)

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Mölling, K.: Epigenetics and transgenerational inheritance. The Journal of Physiology 602 (11), pp. 2537 - 2545 (2024)

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Liu-Wei, W.; van der Toorn, W.; Bohn, P.; Hölzer, M.; Smyth, R. P.; von Kleist, M.: Sequencing accuracy and systematic errors of nanopore direct RNA sequencing. BMC Genomics 25 (1), Article 528 (2024)

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Oliveira, D.; Assoni, A. F.; Alves, L. M.; Sakugawa, A.; Melo, U. S.; Teles e Silva, A. L.; Sertie, A. L.; Caires, L. C.; Goulart, E.; Ghirotto, B. et al.; Carvalho, V. M.; Ferrari, M. R.; Zatz, M.: ALS-associated VRK1 R321C mutation causes proteostatic imbalance and mitochondrial defects in iPSC-derived motor neurons. Neurobiology of Disease 198, Article 106540 (2024)

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

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Auzat, I.; Ouldali, M.; Jacquet, E.; Fauler, B.; Mielke, T.; Tavares, P.: Dual function of a highly conserved bacteriophage tail completion protein essential for bacteriophage infectivity. Communications Biology 7 (1), Article 590 (2024)

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