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 Vallier Lab

Preprints

If preprints are available, they will be listed here.

2025

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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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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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

Corridori, C.; Romeike, M.; Nicoletti, G.; Buecker, C.; Suweis, S.; Azaele, S.; Martello, G.: Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data. PLOS Computational Biology 22, p. e1014067 (2026)

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Heß, A.; Kovacsovics, A.; Bachinger, F.; Vallier, L.; Kretzmer, H.; Meissner, A.: Non-disruptive in vitro monitoring of cellular states with cell-free DNA methylation. Genome Biology 27, 59 (2026)

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Kollyfas, R.; Cagna, M.; Nicaise, A. M.; Vallier, L.; Mohorianu, I.: Unveiling Gene Regulatory Network Dynamics using Fuzzy Clustering. bioRxiv: the preprint server for biology (2026)

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2025

Hakomäki, H.; Pitkänen, S.; Levonen, A.-L.; Honkakoski, P.; Greco, D.; D'Alessandro, N.; Saarimäki, L. A.; Viegas, S.; Godinho, C.; Fyhrquist, N. et al.; Wincent, E.; Lauschke, V. M.; Hukkanen, J.; Hakkola, J.; Vallier, L.; Fortino, V.; Afantitis, A.; Sawatani, T.; Guzman, T. J.; Cnop, M.; Nawrot, T.; Harlid, S.; Vinnars, M.-T.; Tardon, A.; Grimalt, J. O.; Küblbeck, J.; Rysä, J.: Unmasking metabolic disruptors: The NEMESIS project's quest for Novel Biomarkers, Evidence on Adverse Effects, and Efficient Methodologies. Open Research Europe 4, p. 194 (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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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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Wang, L.; Riediger, L.; Rao, Q.; Xu, X.; Nie, Y.; Zhou, Y.; Zhang, J.; Tang, P.; Wang, W.; Tacke, F. et al.; Guillot, A.; Vallier, L.; Talon, I.; Li, W.; Yang, Y.; Haag, R.; Ma, N.: Tunable Synthetic Hydrogel Modulates Hepatic Lineage Specification of Human Liver Organoid. Advanced Functional Materials (2025)

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Petrus-Reurer , S.; Lei, W.; Tysoe, O.; Mairesse , M.; Baez-Ortega , A.; Jones , J.; Tan , T.; Rehakova , S.; Mahbubani , K. T.; Brodie, C. et al.; Han , N.; Martincorena , I.; Betts , C.; Vallier, L.; Saeb-Parsy , K.: Immunogenicity of autologous and allogeneic human primary cholangiocyte organoid cellular therapies. Cell Reports Medicine 6 (7) (2025)

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Miller, A.; Biga, V.; Rowntree, A.; Chhatriwala, M.; Woods, F.; Noble, B.; Marinopoulou, E.; Kamath, A.; Vallier, L.; Papalopulu, .: NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation. Developmental Cell (2025)

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Traba, S. A.; Bacigalupo, L.; Fradin, D.; Talon, I.; Heidenreich, A. C.; Muraro, D.; Garcia-Bernardo, J.; Gribben , C.; Lugtu, F.; Burgos, J. I. et al.; Romero, A.; Chhatriwala, M.; Pecci, A.; Vallier, L.; Rodríguez-Seguí, S. A.: Endogenous glucocorticoid receptor activation modulates early-stage cell differentiation in pancreatic progenitors of mice and humans. Development, Article dev.204361 (2025)

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Ortuño-Costela, M. C.; Pinzani, M.; Vallier, L.: Cell therapy for liver disorders: past, present and future. Nature Reviews Gastroenterology & Hepatology 22 (5), pp. 329 - 342 (2025)

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Liu, H.; Yin, G.; Leonardi, B. F.; Lan, T.; Ahmed, Y. A.; Berger, H.; Kohlhepp, M. S.; Amiridze, N.; Martagón Calderón, N.; Frau, C. et al.; Vallier, L.; Rezvani, M.; Tacke, F.; Guillot, A.: Reactive cholangiocyte-derived ORM2 drives a pathogenic modulation of the injured biliary niche through macrophage reprogramming. Gut, Article gutjnl-2024-334425 (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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Brumm, A. S.; McCarthy, A.; Gerri, C.; Fallesen, T.; Woods, L.; McMahon, R.; Papathanasiou, A.; Elder, K.; Snell, P.; Christie, L. et al.; Garcia, P.; Shaikly, V.; Taranissi, M.; Serhal, P.; Odia, R. A.; Vasilic, M.; Osnato, A.; Rugg-Gunn, P. J.; Vallier, L.; Hill, C. S.; Niakan, K. K.: Initiation and maintenance of the pluripotent epiblast in pre-implantation human development is independent of NODAL signaling. Developmental Cell 60 (2), pp. 174 - 185 (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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Zacharis, E. D.; Morell, C. M.; Tomaz, R. A.; Shahsavari, A.; Grey-Wilson, C.; Pesic, M.; Galanakis, V.; Williams, E. C.; Mohorianu, I.; Talon, I. et al.; Vallier, L.: Wnt signalling maintains self-renewal of human hepatoblasts without blocking their differentiation. Development 152 (2025)

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2024

Frank , A. K.; Chung, B. K.; De Novales, M. L. L.; Engesæter, L. K.; Hoyle , H. W.; Øgaard, J.; Heslop, J.; Karlsen, T. H.; Tysoe, O.; Brevini , T. et al.; Tchorz, J. S.; Vallier, L.; Mohorianu, I.; Sampaziotis, F.; Melum, E.: Single-Cell Transcriptomic Profiling of Cholangiocyte Organoids Derived from Bile Ducts of Primary Sclerosing Cholangitis Patients. Digestive Diseases and Sciences 69 (10), pp. 3810 - 3823 (2024)

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Frau, C.; Vallier, L.: Exploiting the plasticity of cholangiocytes to repair the biliary tree. Current Opinion in Genetics & Development 89, Article 102257 (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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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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Pesic, M.; Narayanareddy, G. C.; Rettig, A.; Pfau, M.; Kovacsovics, A.; Eckert, C.; Yaspo, M. L.: The testicular niche – heterogeneity in leukemic cell adaptation to the new immunemicroenvironment. 35. Jahrestagung der Kind-Philipp-Stiftung für pädiatrisch onkologische Forschung, Wilsede, June 05, 2024 - June 08, 2024. Klinische Pädiatrie 236 (03), Article 211, (2024)

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Vilà-González, M.; Pinte, L.; Fradique, R.; Causa, E.; Kool, H.; Rodrat, M. ....; Vallier, L.: In vitro platform to model the function of ionocytes in the human airway epithelium. Respiratory Research 25 (1), Article 38664797 (2024)

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Nakanoh, S.; Sham, K.; Ghimire, S.; Mohorianu, I.; Rayon, T.; Vallier, L.: Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density. Science Advances 10 (9), Article eadh7748 (2024)

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2023

Fradique , R.; Causa, E.; Delahousse, C.; Kotar, J.; Pinte, L.; Vallier, L.; Vila-Gonzalez, M.; Cicuta , P.: Assessing motile cilia coverage and beat frequency in mammalian in vitro cell culture tissues. Royal Society Open Science 10 (8), Article 230185 (2023)

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Rezvani, M.; Vallier, L.; Guillot, A.: Modeling Nonalcoholic Fatty Liver Disease in the Dish Using Human-Specific Platforms: Strategies and Limitations. Cellular and Molecular Gastroenterology and Hepatology 15 (5), pp. 1135 - 1145 (2023)

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Brevini, T.; Maes, M.; Webb, G. J.; Fuchs, C. D.; Buescher, G.; Wang, L.; Griffiths, C.; Brown, M. L.; Scott III, W. E.; Pereyra-Gerber, P. et al.; Gelson, W. T. H.; ...; Vallier, L.; Sampaziotis, F.: FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature 615 (7950), pp. 134 - 142 (2023)

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2022

Knight-Schrijver, V. R.; Davaapil, H.; Bayraktar, S.; Ross, A. D. B.; Kanemaru, K.; Cranley, J.; Dabrowska, M.; Patel, M.; Polanski, K.; He, X. et al.; Vallier, L.; Teichmann, S.; Gambardella, L.; Sinha, S.: A single-cell comparison of adult and fetal humen epicardium defines the age-associated changes in epicardial activity. Nature Cardiovascular Research 1, pp. 1215 - 1229 (2022)

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Nakanoh, S.; Kadiwala, J.; Pinte, L.; Morell, C. M.; Lenaerts, A.-S.; Vallier, L.: Simultaneous depletion of RB, RBL1 and RBL2 affects endoderm differentiation of human embryonic stem cells. PLOS ONE 17 (11), Article e0269122 (2022)

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Al-Akkad, W.; Acedo, P.; Vilia, M.-G. ....; Vallier, L.; Pinzani, M.; Rombouts , K.; Mazza, G.: Tissue-Specific Human Extracellular Matrix Scaffolds Promote Pancreatic Tumour Progression and Chemotherapy Resistance. Cells 11 (22), Article 3652 (2022)

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Speicher, A. M.; Korn, L.; Csatári, J.; Gonzalez-Cano, L.; Heming, M.; Thomas, C.; Schroeter, C. B.; Schafflick, D.; Li, X.; Gola, L. et al.; Engler, A.; Kaehne, T.; Vallier, L.; Meuth , S. G.; Meyer Zu Hörste, G.; Kovac, S.; Wiendl, H.; Schöler, H. R.; Pawlowski , M.: Deterministic programming of human pluripotent stem cells into microglia facilitates studying their role in health and disease. Proceedings of the National Academy of Sciences of the United States of America 119 (43), Article e2123476119 (2022)

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Wesley, B. T.; Ross, A. D. B.; Muraro, D.; Miao, Z.; Saxton, S.; Tomaz, R. A.; Morell, C. M.; Ridley, K.; Zacharis, E. D.; Petrus-Reurer, S. et al.; ...; Vallier, L.: Single-cell atlas of human liver development reveals pathways directing hepatic cell fates. Nature Cell Biology 24 (10), pp. 1487 - 1498 (2022)

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Jowett, G. M.; Read, E.; Roberts, L. B.; Coman, D.; Vilà González, M.; Zabinski, T.; Niazi, U.; Reis, R.; Trieu, T.-J.; Danovi, D. et al.; Gentleman, E.; Vallier, L.; Curtis, M. A.; Lord , G. M.; Neves, J. F.: Organoids capture tissue-specific innate lymphoid cell development in mice and humans. Cell Reports 40 (9), Article 111281 (2022)

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Tomaz, R. A.; Zacharis, E. D.; Bachinger, F.; Wurmser, A. ....; Vallier, L.: Generation of functional hepatocytes by forward programming with nuclear receptors. eLife 11, Article e71591 (2022)

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Roos, F. J. M.; van Tienderen, G. S.; Wu, H. ....; Vallier, L.; IJzermans, J. N. M.; Bartfai, R.; Marks, H.; Simons, B. D.; van Royen , M. E.; Verstegen, M. M. A. et al.; van der Laan, L. J. W.: Human branching cholangiocyte organoids recapitulate functional bile duct formation. Cell Stem Cell 29 (5), pp. 776 - 794 (2022)

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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