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 [Optiona]

Under review / accepted [Optional]

Lastname, F.
Article Title
Scientific Journal. Accepted

Preprints [Optional]

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)
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)
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)
Swanepoel, C. M.; Wang, G.; Zhang, L.; Brändl, B.; Bauer, H.; Tsaytler, P.; Müller, F.-J.; Herrmann, B. G.; Mueller , J. L.: Acquisition of ampliconic sequences marks a selfish mouse t-haplotype. bioRxiv (2025)
Jakobson, C. M.; Hartl , J.; Trébulle, P.; Mülleder, M.; Jarosz , D. F.; Ralser, M.: A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects. bioRxiv (2024)
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)
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)
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. bioRxiv (2024)
Guckelberger, P.; Doughty, B. R.; Munson, G.; Rao, S. S. P.; Tan, Y.; Cai, X. S.; Fulco, C. P.; Nasser, J.; Mualim, K. S.; Bergman, D. T. et al.; Ray, J.; Jagoda, E.; Munger, C. J.; Gschwind, A. R.; Sheth, M. U.; Tan, A. S.; Pulido, S. G.; Mitra, N.; Weisz, D.; Shamim, M. S.; Durand, N. C.; Mahajan, R.; Khan, R.; Steinmetz, L. M.; Kanemaki, M. T.; Lander, E. S.; Meissner, A.; Lieberman Aiden, E.; Engreitz, J. M.: Cohesin-mediated 3D contacts tune enhancer-promoter regulation. bioRxiv (2024)
Zagoren, E.; Dias, N.; Smith, Z. D.: A second wave of Notch signaling diversifies the intestinal secretory lineage. bioRxiv (2024)
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)
Mutzel, V.; Schwämmle, T.; Oeverdieck, S.; Librenjak, L.; Boesen, B.; Bothe, M.; Gjaltema, R. A. F.; Dunkel, I.; Noviello, G.; Schulz, E. G.: Antisense transcription can induce expression memory via stable promoter repression. bioRxiv (2024)
Kaur Aulakh, S.; Lemke, O.; Szyrwiel, L.; Kamrad, S.; Chen, Y.; Hartl, J.; Muelleder, M.; Nielsen, J.; Ralser, M.: The molecular landscape of cellular metal ion biology. bioRxiv (2024)
Kӧvér, B.; Cohen, C. E.; Ralser, M.: Genetic and environmental determinants of multicellular-like phenotypes in fission yeast. bioRxiv (2023)
Schmidt, D.; Duport, Y.; Kollan, C.; Marcus, U.; Iannuzzi, S.; von Kleist, M.: Dynamics of HIV PrEP use and coverage during and after COVID-19 in Germany. SSRN eLibrary (2023)
Basu, S.; Martínez-Cristóbal, P.; Pesarrodona, M.; Frigolé-Vivas, M.; Szulc, E.; Lewis, M.; Bañuelos, C. A.; Sánchez-Zarzalejo, C.; Bielskutė, S.; Zhu, J. et al.; Garcia-Cabau, C.; Batlle, C.; Mateos, B.; Biesaga, M.; Escobedo, A.; Bardia, L.; Verdaguer, X.; Ruffoni, A.; Mawji, N. R.; Wang, J.; Tam, T.; Brun-Heath, I.; Ventura, S.; Meierhofer, D.; García, J.; Robustelli, P.; Stracker, T. H.; Sadar, M. D.; Riera, A.; Hnisz, D.; Salvatella, X.: Androgen receptor condensates as drug targets. bioRxiv (2022)
Graziadei, A.; Schildhauer, F.; Spahn, C.; Kraushar, M.; Rappsilber, J.: SARS-CoV-2 Nsp1 N-terminal and linker regions as a platform for host translational shutoff. bioRxiv (2022)
Ambrozkiewicz, M. C.; Borisova, E.; Newman, A. G.; Kraushar, M.; Schaub, T.; Dannenberg, R.; Brockmann, M.; Rosário, M.; Turko, P.; Jahn, O. et al.; Kaplan, D. R.; Iwawaki, T.; Spahn, C. M. T.; Rosenmund, C.; Tarabykin, V.: Ire1a-Regulated mRNA Translation Rate Controls the Identity and Polarity of Upper Layer Cortical Neurons. bioRxiv (2022)
Ambrozkiewicz, M. C.; Borisova, E.; Newman, A. G.; Kraushar, M. L.; Schaub, T.; Dannenberg, R.; Brockmann, M.; Rosário, M.; Turko, P.; Jahn, O. et al.; Kaplan, D. R.; Iwawaki, T.; Spahn, C. M. T.; Rosenmund, C.; Tarabykin, V.: Ire1α-Regulated Rate of mRNA Translation is Required for Acquisition of Identity and Polarity in Upper Layer Cortical Neurons. bioRxiv (2021)
Smajić, S.; Prada-Medina, C. A.; Landoulsi​, Z.; Dietrich, C.; Jarazo, J.; Henck, J.; Balachandran, S.; Pachchek, S.; Morris, C. M.; Antony, P. et al.; Timmermann, B.; Sauer, S.; Schwamborn, J. C.; May, P.; Grünewald, A.; Spielmann, M.: Single-cell sequencing of the human midbrain reveals glial activation and a neuronal state specific to Parkinson’s disease. medRxiv (2020)
Hogan, J. D.; Keenan, J. L.; Luo, L.; Hawkins, D. Y.; Ibn-Salem, J.; Lamba, A.; Schatzberg, D.; Piacentino, M. L.; Zuch, D. T.; Core, A. B. et al.; Blumberg, C.; Timmermann, B.; Grau, J. H.; Speranza, E.; Andrade-Narravo, M. A.; Irie, N.; Poustka, A. J.; Bradham, C. A.: The Developmental Transcriptome for Lytechinus variegatus Exhibits Temporally Punctuated Gene Expression Changes. Developmental Biology 460 (2), pp. 139 - 154 (2020)
Lammel, D. R.; Meierhofer, D.; Johnston, P.; Mbedi, S.; Rillig, M. C.: The effects of arbuscular mycorrhizal fungi (AMF) and Rhizophagus irregularis on soil microorganisms assessed by metatranscriptomics and metaproteomics. bioRxiv (2019)
Despang, A.; Schöpflin, R.; Franke, M.; Ali, S.; Jerkovic, I.; Paliou, C.; Chan, W.-L.; Timmermann, B.; Wittler, L.; Vingron, M. et al.; Mundlos, S.; Ibrahim, D. M.: Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression. bioRxiv (2019)
Mutzel, V.; Okamoto, I.; Dunkel, I.; Saitou, M.; Giorgetti, L.; Heard, E.; Schulz, E. G.: Two coupled feedback loops explain random mono-allelic Xist upregulation at the onset of X-chromosome inactivation. bioRxiv: the preprint server for biology 2017, pp. 1 - 54 (2017)

Published

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

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)
Max Planck
Zur Theorie des Gesetzes der Energieverteilung im Normalspektrum.
Verhandl. Dtsch. Phys. Ges. Band 2, 1900, S. 237–245
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