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.

Publications by the Lastname Lab [Optional]

Under review / accepted [Optional]

Lastname, F.

Article Title

Scientific Journal. Accepted

Preprints [Optional]

If preprints are available, they will be listed here.

Dingfelder, A.; Blank, F.; Quinson, N.; Holley, C.; Mayr, J.; Thieck, O.; Meierhofer, D.; Taylor, M. J.; Majer, O.: Microbial Priming Enhances TLR7-Driven Myddosome Assembly Dynamics. bioRxiv: the preprint server for biology (2025)

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Graeve, M. D.; Hantikainen, E.; Louail, P.; Hernandes, V. V.; Pattaro, C.; Domingues, F. S.; Pramstaller, P. P.; Tilg, H.; Ralser, M.; Grander, C. et al.; Rainer, J.: Molecular characterization of liver steatosis through circulating proteins, metabolites and lipids. medRxiv: the preprint server for health sciences (2025)

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Khaveh, N.; Berghöfer, J.; Ralph, B.; Buschow, R.; Cirksena, K.; Drögemüller, C.; Fatima, A.; Grabert, G.; Gerold, G.; Grahofer, A. et al.; Herwig, R.; Jung, K.; Kacprowski, T.; Lo, B.-W.; Sardoabi, R. S.; Vingron, M.; Mundlos, S.; Metzger, J.: Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs. Research Square (2025)

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Dinter, T.; Mackowiak, S. D.; Rogers, Z. J.; Bhandarkar, V.; Carney, M. Y.; Zhang, Y. J.; Morgan, D.; Pop, L.; Chatterjee, F.; Lutz, E. et al.; Jain, Y.; Radhakrishnan, A.; Lander, E.; Wittrup, K. D.; Love, J. C.; Meissner, A.; Spranger, S.: PD-1 blockade during T cell priming enhances long-term protection against metastatic tumors by epigenetically tuning T cell exhaustion. bioRxiv: the preprint server for biology (2025)

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Stylianou, P.; Adoni, K.; Nyon, M. P.; Cryar, A.; Haq, I.; Dickens, J. A.; Segeritz, C.-P.; Smith, G. C.; Ordonez, A.; Irving, J. A. et al.; Lomas, D. A.; Leighton, K.-M.; Beasley, J.; Jones, A. W.E.; Rashid, S. T.; Vallier, L.; Thalassinos, K.; Gooptu, B.: Both terminal misfolding and polymerisation contribute to disease-relevant responses in cell models of α1-antitrypsin deficiency-associated liver disease. bioRxiv: the preprint server for biology (2025)

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Stark, H.; Faltings, F.; Choi, M.; Xie, Y.; Hur, E.; O’Donnell, T.; Bushuiev, A.; Uçar, T.; Passaro, S.; Mao, W. et al.; Reveiz, M.; Bushuiev, R.; Pluskal, T.; Sivic, J.; Kreis, K.; Vahdat, A.; Ray, S.; Goldstein, J. T.; Savinov, A.; Hambalek, J. A.; Gupta, A.; Taquiri-Diaz, D. A.; Zhang, Y.; Hatstat, A. K.; Arada, A.; Kim, N. H.; Tackie-Yarboi, E.; Boselli, D.; Schnaider, L.; Liu, C. C.; Li, G.-W.; Hnisz, D.; Sabatini, D. M.; DeGrado, W. F.; Wohlwend, J.; Corso, G.; Barzilay, R.; Jaakkola, T.: BoltzGen: Toward Universal Binder Design. bioRxiv: the preprint server for biology (2025)

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Sheinman, M.; Stentella, T.; Etheimer, P.; Massip, F.; Arndt, P. F.: Reconstructing the network of horizontal gene exchange in bacteria to differentiate direct and indirect transfers. bioRxiv: the preprint server for biology (2025)

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van der Sanden, B.; Betz, C.; Herzog, K.; Schamschula, E.; Wimmer, K.; Vater, I.; Balachandran, S.; Chen, X.; Galbany, J. C.; Timmermans, R. et al.; Derks, R.; Consortium, H. S. E.; Spielmann, M.; Eberle, M. A.; Gilissen, C.; Vissers, L. E.L.M.; Zschocke, J.; Bolz, H. J.; Hoischen, A.: HiFi sequencing accurately identifies clinically relevant variants in paralogous genes. medRxiv: the preprint server for health sciences (2025)

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Aksu, E. D.; Vingron, M.: Context-aware sequence-to-function model of human gene regulation. (2025)

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Majchrzycka, B.; Mundlos, S.; Krebs, A. R.; Ibrahim, D. M.: Enhancer-promoter compatibility is mediated by the promoter-proximal region. bioRxiv: the preprint server for biology (2025)

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Taylor, S. A.; Bader, G. D.; MacParland, S.; Mullen, A. C.; Andrews, T.; Cuenca, A. G.; DasGupta, R.; Gehring, A. J.; Grün, D.; Guilliams, M. et al.; Gulamhusein, A.; Henderson, N. C.; Hirschfield, G.; Huppert, S. S.; Itzkovitz, S.; Jiang, Z. G.; Lauer, G. M.; McGilvray, I.; Mysore, K. R.; Pirola, C. J.; Quon, G.; Rahbari, M.; Regev, A.; Ricciuto, A.; Scott, C. L.; Sharma, A.; Sookoian, S.; Tana, M. M.; Teichmann, S. A.; Vallier, L.; Vlachos, I. S.; Wang, B.; Zhen, M.: Towards a reference cell atlas of liver diversity over the human lifespan. Nature Reviews Gastroenterology & Hepatology (2025)

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D'Angiolo, M.; Barré, B. P.; Khaiwal, S.; Muenzner, J.; Hallin, J.; De Chiara, M.; Tellini, N.; Warringer, J.; Ralser, M.; Gilson, E. et al.; Liti, G.: The adaptive molecular landscape of reprogrammed telomeric sequences. bioRxiv: the preprint server for biology (2025)

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Faravelli, I.; Antón-Bolaños, N.; Wei, A.; Faits, T.; Kumar, S. A.; Andreadis, S.; Kastli, R.; Crespo, M. M.; Steiger, M.; Daniel, L. et al.; Zhang, E.; An, B.; Meirovitch, Y.; Silwal, S.; Yang, S. M.; Kovacsovics, A.; Adiconis, X.; Kretzmer, H.; Levin, J. Z.; Boyden, E. S.; Lichtman, J.; Regev, A.; Meissner, A.; Arlotta, P.: Human brain organoids record the passage of time over multiple years in culture. bioRxiv: the preprint server for biology (2025)

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Kollert, M. R.; Qazi, T. H.; Phan, M. H. Q.; Majchrzycka, B.; Thünemann, A. F.; Ibrahim, D. M.; Vogel, V.; Mooney, D. J.; Duda, G. N.: Osmotic niche changes as multifaceted trigger of cellular regenerative processes in organ injury. bioRxiv: the preprint server for biology (2025)

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Kassing, I.; Kath, J.; Nitulescu, A.-M.; Glaser, V.; Hartmann, L. M.; Pu, Y.; Huth, L.; Kārkliņš, R.; Shaji, S.; Ringel, A. R. et al.; Pouzolles, M.; Stein, M.; Ibrahim, D. M.; Wagner, D. L.: Versatile and efficient non-viral integration of large transgenes in human T cells via CRISPR knock-in and engineered integrases. bioRxiv: the preprint server for biology (2025)

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Savill, R. G.; Villaronga-Luque, A.; Bustos, M. T.; Maroudas-Sacks, Y.; Batki, J.; Meissner, A.; Ryan, A. Q.; Modes, C. D.; Campàs, O.; Veenvliet, J. V.: SpinePy enables automated 3D spatiotemporal quantification of multicellular in vitro systems. bioRxiv: the preprint server for biology (2025)

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Varisco, M.; Rodrigues Cavalheiro, G.; Viales, R. R.; Schaub, C.; Girardot, C.; Forneris, M.; Comeault, A.; Furlong, E. E.M.: Heterotypic directional motifs contribute to TAD boundary function in Drosophila. bioRxiv: the preprint server for biology (2025)

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Sen, N.-E.; von Bernhardi, J. E.; Adeyemi, J. O.; Arsović, A.; Canet-Pons, J.; Miralles, A. J.; Key, J.; Bina, L.; Romano, V.; Fellenz, M. et al.; Pietzke, M.; Halbach, M.; Seidel, K.; Fidan, E.; Kaya-Güleç, Z.-E.; Almaguer-Mederos, L. E.; Becker, L. A.; Gispert, S.; Gitler, A. D.; Deller, T.; Bosman, L. W. J.; Zeeuw, C. I. D.; Meierhofer, D.; Dimou, L.; Auburger, G.: ATXN2 polyglutamine expansion impairs QKI-dependent alternative splicing and oligodendrocyte maintenance. bioRxiv: the preprint server for biology (2025)

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Bang, J. M. V.; Fagerberg, C. R.; Doktor, T. K.; Rosenlund, M. M.; Lumbreras, S. M.; Burton, M.; Brusgaard, K.; Guerra-Moreno, Á.; Høi, S.; Skovstrøm, L. W. et al.; Nielsen, N. A.; Hao, Q.; Alves, C.; Hansen, L. K.; Lees, M.; Suwannarat, P.; Stumpel, C.; Sinnema, M.; Stegmann, A. P.A.; Esch, H. V.; Luca, C. D.; Mol, C. V.; Green, A.; Wieczorek, D.; Rodgers, J.; McGaughran, J.; Duboc, V.; Zaafrane-Khachnaoui, K.; Madden, J.; Agrawal, P.; Rump, P.; Gener, B.; Martínez-González, M. J.; Good, J.-M.; Vitiello, G.; Passaretti, F.; Lolascon, A.; Field, M.; Martin, E. M.; Keren, B.; Doco-Fenzy, M.; Yammine, T.; Steindl, K.; Rauch, A.; Begemann, A.; Costain, G.; Shao, Z.; Carli, D.; Ferrero, G. B.; Valenzuela, I.; Codina-Solà, M.; Masotto, B.; Trujillano, L.; Kumps, C.; Vanakker, O.; Vasudevan, A.; Passos-Bueno, M. R.; Casella, E.; Colomé, F. B.; Faivre, L.; Philippe, C.; Touma, M.; Wang, L.-K.; Nelson, S. F.; Scala, M.; Nigro, V.; Capra, V.; Truxal, K.; Caceres, V.; Levy, J.; Kalscheuer, V. M.; Delahaye-Duriez, A.; Valcárcel, J.; Sattler, M.; Andresen, B. S.: Genotype-Phenotype Correlation in RBM10-Associated Syndromes – How Variant Function Shapes a Broad Phenotypic Landscape. medRxiv: the preprint server for health sciences (2025)

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Gerletti, P.; Gubela, N.; Escudié, J.-B.; Kühnert, D.; Kleist, M. V.: SIMPLICITY: an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution. bioRxiv: the preprint server for biology (2025)

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Weihs, J.; Baldo, F.; Cardinali, A.; Youssef, G.; Ludwik, K.; Haep, N.; Tang, P.; Kumar, P.; Engelmann, C.; Quach, S. et al.; Meindl, M.; Kucklick, M.; Engelmann, S.; Chillian, B.; Rothe, M.; Meierhofer, D.; Lurje, I.; Hammerich, L.; Ramachandran, P.; Kendall, T. J.; Fallowfield, J. A.; Stachelscheid, H.; Sauer, I.; Tacke, F.; Bufler, P.; Hudert, C.; Han, N.; Rezvani, M.: Combined stem cell and predictive models reveal flavin cofactors as targets in metabolic liver dysfunction. bioRxiv: the preprint server for biology (2025)

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Bauer, H.; Koch, F.; Lipkowitz, B.; Willert, J.; Bläß, G.; Scholze, M.; Währisch, S.; Wittler, L.; Herrmann, B. G.: Targeted sex ratio distortion in the mouse. bioRxiv: the preprint server for biology (2025)

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Balaskas, A.; Kraus, I.; Özgüldez, H. Ö.; Akbari-Omgba, P.; Buschow, R.; Berlad, I.; Hanna, J. H.; Kretzmer, H.; Bulut-Karslioglu, A.; Bolondi, A.: An advanced head-to-tail mouse embryo model with hypoxia-mediated neural patterning. bioRxiv (2025)

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Llombart, V.; O’Connor, D.; Demeulemeester, J.; Bhamra, A.; Surinova, S.; Turna, A.; Fung, K.; Wang, L.; Li, Y.; Rapoz-D’Silva, T. et al.; Ahmed, F.; Niskanen, H.; Stöppelkamp, I.; Hnisz, D.; Bottaro, S.; Fisicaro, C.; He, S.; Look, A. T.; Mansour, M. R.: MYC-induced oncogenesis is dependent on acidic patches within its N-terminal intrinsically disordered domain. bioRxiv: the preprint server for biology (2025)

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Alavi, N.; Moeinzadeh, H.; Hertzberg, J.; Melo, U. S.; Al Raei, L.; Infantino, P.; Ghareghani, M.; Savarese, M.; Mundlos, S.; Vingron, M.: Accurate detection of pathogenic structural variants guided by multi-platform comparison. bioRxiv: the preprint server for biology (2025)

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Zink, A.; Dai, D.-F.; Wittich, A.; Henke, M.-T.; Pedrotti, G.; Heiduschka, S.; Aguilar, G. S.; Pentimalli, T. M.; Brueser, C.; Notopoulou, S. et al.; Zhaivoron, A.; Umar, A. R.; Petersilie, L.; Jerred, C.; Bergmans, J.; Schumacher, F.; Keller-Findeisen, J.; Rybak-Wolf, A.; Stach, D.; Reinshagen, J.; Zaliani, A.; Haferkamp, U.; Euro, L.; Donfrancesco, A. D.; Santanatoglia, C.; Cappellozza, E.; Cubero, M. S.; Pavez-Giani, M.; Bakumenko, O.; Meierhofer, D.; Foley, A.; Morales-Gonzalez, S.; Tolle, I.; Herebian, D.; Bonesso, D.; Szabo, I.; Cecchetto, G.; Wong, S.; Moresco, M.; Maresca, A.; Decimo, I.; Adjobo-Hermans, M. J.W.; Kleuser, B.; Cyganek, L.; Mühlhausen, C.; Schlotawa, L.; Tiranti, V.; Rossi, A.; Mayatepek, E.; La Morgia, C.; Carelli, V.; Klopstock, T.; Distelmaier, F.; Ullah, G.; Jakobs, S.; Rajewsky, N.; Rose, C. R.; Petrakis, S.; Edenhofer, F.; Koopmann, W.; Brunetti, D.; Lisowski, P.; Suomalainen, A.; Sol, A. d.; Bottani, E.; Pless, O.; Schuelke, M.; Prigione, A.: Pluripotent stem cell-based drug discovery uncovers sildenafil as a treatment for mitochondrial disease. medRxiv: the preprint server for health sciences (2025)

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Kamrad, S.; Mozzachiodi, S.; Blasche, S.; Aulakh, S. K.; Scheidweiler, D.; Basile, A.; Guan, R.; Bradley, R.; van den Berg, N. I.; Mülleder, M. et al.; Ralser, M.; Patil, K. R.: Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism. bioRxiv: the preprint server for biology (2025)

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Chudzik, K.; Guerreiro, I.; Kefalopoulou, S.; Abraham, A.; Schindler, M.; Ringel, A. R.; Nicodemi, M.; Chiariello, A. M.; Mundlos, S.; Kind, J. et al.; Robson, M. I.: Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates. bioRxiv (2025)

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Chudzik, K.; Sato, Y.; Yan, X.; Ullrich, S.; Trakarnphornsombat, W.; Schermelleh, L.; Fudenberg, G.; Kimura, H.; Robson, M. I.; Solovei, I.: Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics. bioRxiv: the preprint server for biology (2025)

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Bielskutė, S.; Mateos, B.; Awawdy, M.; Garcia-Cabau, C.; Niskanen, H.; Sánchez-Zarzalejo, C.; Bracaglia, L.; Pierattelli, R.; Felli, I. C.; Frigolé-Vivas, M. et al.; García, J.; Riera, A.; Hnisz, D.; Salvatella, X.: Oligomerization enables the selective targeting of intrinsically disordered regions by small molecules. bioRxiv: the preprint server for biology (2025)

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Kohl, C.; Vingron, M.: CAdir: Fast Clustering and Visualization of Single-Cell Transcriptomics Data by Direction in CA Space. bioRxiv: the preprint server for biology (2025)

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Thelwall, I. G.; Morell, C. M.; Dziedzicka, D.; Cabriales, L.; Hodgson, A.; Roos, F. J.M.; Elfari, L.; Vallier, L.; Chalut, K. J.: Mechanical signalling through collagen I regulates cholangiocyte specification and tubulogenesis during liver development. bioRxiv: the preprint server for biology (2025)

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Galanakis, V.; Gribben, C.; Munteanu, A.; Cagna, M.; Roos, F. J.M.; Bulgaru, C.; Ciortuz, L.; Allison, M.; Mohorianu, I.; Vallier, L.: Transcriptomic and epigenetic mechanisms controlling cholangiocytes transdifferentiation into hepatocytes. Journal of Hepatology (2025)

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Published

2026

Journal Article

Malszycki, M.; Martina, L.; Ilik, I. A.; Salgado Figueroa, D.; Dasgupta, N.; Çoşar, M. F.; Kim, K.-T.; Carraco, G.; Fauler, B.; Meierhofer, D. et al.; Mielke, T.; Imai, H.; Alev, C.; Ay, F.; Aktas, T.: Nuclear speckles enable processing of RNA from GC-rich isochores. Cell (2026)

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2025

Review Article

Ilik, I. A.; Yang, X.; Zhang, Z. Z.; Aktas, T.: Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease. Nature Reviews Molecular Cell Biology (2025)

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Journal Article

Zhang, Y.; Stöppelkamp, I.; Fernandez-Pernas, P.; Allram, M.; Charman, M.; Magalhães, A. P.; Piedavent-Salomon, M.; Sommer, G.; Sung, Y.-C.; Meyer, K. et al.; Grams, N.; Halko, E.; Dongre, S.; Meierhofer, D.; Malszycki, M.; Ilik, I. A.; Aktas, T.; Kraushar, M. L.; Vastenhouw, N.; Weitzman, M. D.; Grebien, F.; Niskanen, H.; Hnisz, D.: Probing condensate microenvironments with a micropeptide killswitch. Nature (2025)

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publisher-version

Journal Article

Martina, L.; Malszycki, M.; Aktas, T.: Distinct states of Nuclear Speckles emerge as new predictors of cancer prognosis. Cancer Research 85 (8), pp. 1352 - 1353 (2025)

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publisher-version

2024

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)

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publisher-version

Journal Article

Kellner, M.; Hörmann, J.; Fackler, S.; Yuanyu, H.; Tielin, Z.; Lin, L.; Ilik, I.; Aktas, T.; Feederle, R.; Hauck, S. M. et al.; Gires, O.; Gärtner, K.; Lietao, L.; Zeidler, R.: The Nuclear Speckles Protein SRRM2 Is Exposed on the Surface of Cancer Cells. Cells 13 (18), Article 1563 (2024)

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publisher-version

Journal Article

Lisowski, P.; Lickfett, S.; Rybak-Wolf, A.; Menacho, C.; Le, S.; Pentimalli, T. M.; Notopoulou, S.; Dykstra, W.; Oehler, D.; López-Calcerrada, S. et al.; Mlody, B.; Otto, M.; Wu, H.; Richter, Y.; Roth, P.; Anand, R.; Kulka, L. A. M.; Meierhofer, D.; Glazar, P.; Legnini, I.; Telugu, N. S.; Hahn, T.; Neuendorf, N.; Miller, D. C.; Böddrich, A.; Polzin, A.; Mayatepek, E.; Diecke, S.; Olzscha, H.; Kirstein, J.; Ugalde, C.; Petrakis, S.; Cambridge, S.; Rajewsky, N.; Kühn, R.; Wanker, E. E.; Priller, J.; Metzger, J. J.; Prigione, A.: Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure. Nature Communications 15 (1), Article 7027 (2024)

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publisher-version

Journal Article

Ilik, I. A.; Glažar, P.; Tse, K.; Brändl, B.; Meierhofer, D.; Müller, F.-J.; Smith, Z. D.; Aktas, T.: Autonomous transposons tune their sequences to ensure somatic suppression. Nature 626 (8001), pp. 1116 - 1124 (2024)

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publisher-version

2023

Journal Article

Weigert, R.; Hetzel, S.; Bailly, N.; Haggerty, C.; Ilik, I. A.; Kwong Yung, P. Y.; Navarro, C.; Bolondi, A.; Sampath Kumar, A.; Anania, C. et al.; Brändl, B.; Meierhofer, D.; Lupiáñez, D. G.; Müller, F.-J.; Aktas, T.; Elsässer, S. J.; Kretzmer, H.; Smith, Z. D.; Meissner, A.: Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nature Cell Biology 25 (4), pp. 579 - 591 (2023)

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publisher-version

2022

Review Article

Ilik, I. A.; Aktas, T.: Nuclear speckles: dynamic hubs of gene expression regulation. The FEBS Journal 289 (22), pp. 7234 - 7245 (2022)

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publisher-version

Journal Article

Bergfort, A.; Hilal, T.; Kuropka, B.; Ilik, I. A.; Weber, G.; Aktas, T.; Freund, C.; Wahl, M. C.: The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling. Nucleic Acids Research (London) 50 (5), pp. 2938 - 2958 (2022)

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publisher-version

Journal Article

Aktas, T.: Transposons: catch them if you can. Nature Reviews Molecular Cell Biology 23 (5), 306 (2022)

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publisher-version

Journal Article

Bergfort, A.; Preußner, M.; Kuropka, B.; Ilik, I. A.; Hilal, T.; Weber, G.; Freund, C.; Aktas, T.; Heyd, F.; Wahl, M. C.: A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing. Nature Communications 13 (1), Article 1132 (2022)

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publisher-version

2020

Journal Article

Ilik, I. A.; Malszycki, M.; Lübke, A. K.; Schade, C.; Meierhofer, D.; Aktas, T.: SON and SRRM2 are essential for nuclear speckle formation. eLife 9, Article e60579 (2020)

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publisher-version

Journal Article

Ilik, I. A.; Aktas, T.; Maticzka, D.; Backofen, R.; Akhtar, A.: FLASH: ultra-fast protocol to identify RNA-protein interactions in cells. Nucelic Acids Research 48 (3), Article e15 (2020)

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publisher-version

Publications by Firstname Lastname before 20nm [year before MPIMG affiliation]

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)

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Max Planck

Zur Theorie des Gesetzes der Energieverteilung im Normalspektrum.

Verhandl. Dtsch. Phys. Ges. Band 2, 1900, S. 237–245