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Fabian J. Theis

Helmholtz Center Munich

125H-index
1.1KPaper Count
8.2WCitation Count
Published Papers 327
Publication Date
Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
err2026-08-11
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PREAI
errDonghoon Lee; James M. Vicari; Christian Porras; Collin Spencer; Milos Pjanic; Xinyi Wang; Seon Kinrot; Philipp Weiler; Roman Kosoy; Jaroslav Bendl; Prashant N M; Konstantina Psychogyiou; Periklis Malakates; Evelyn Hennigan; Jennifer Monteiro Fortes; Shiwei Zheng; Karen Therrien; Deepika Mathur; Steven P. Kleopoulos; Zhiping Shao; Stathis Argyriou; Marcela Alvia; Clara Casey; Aram Hong; Kristin G. Beaumont; Robert Sebra; Christopher P. Kellner; David A. Bennett; Guo-Cheng Yuan; Georgios Voloudakis; Fabian J. Theis; Vahram Haroutunian; Gabriel E. Hoffman; John F. Fullard; Panos Roussos
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Type 2 diabetes prevention across the life course
err2026-08-10
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PREAI
errYiying Wang; Jennifer L. Sargent; Chantal Mathieu; Elsa Vazquez-Arreola; Leigh Perreault; Ruth J. F. Loos; Lee-Ling Lim; Leontine Sandforth; Robert L. Hanson; Stephanie Kullmann; Julia Sbierski-Kind; Sara Y. Brucker; Martin Hrabé de Angelis; Fabian Theiss; Andrea Icks; Damon Mohebbi; Norbert Stefan; Viswanathan Mohan; Tiange Wang; Hubert Preissl; Michael Bergman; Jaakko Tuomilehto; Marie-France Hivert; Paul W. Franks; Andreas L. Birkenfeld
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Clifti-GPT: privacy-preserving federated fine-tuning and transferable inference of foundation models on clinical single-cell data
err2026-08-05
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errOAAI
errMohammad Bakhtiari; Maria Louise Elkjaer; Ali Oğuz Can; Fabian Theis; Mhaned Oubounyt; Jan Baumbach
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Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance
err2026-06-26
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errYiling Li (李怡灵); Anthi C. Krontira; Franziska Vierl; Maria L. Richter; Weixu Wang (汪伟旭); Juliane Merl-Pham; Fabian J. Theis; Stefanie M. Hauck; Magdalena Götz
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RegVelo: Gene-regulatory-informed dynamics of single cells
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IF42.5
err2026-05-12
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errOAAI
errWeixu Wang; Zhiyuan Hu; Philipp Weiler; Sarah Mayes; Marius Lange; Daniel M. Fountain; Julianna O. Haug; Jingye Wang; Zhengyuan Xue; Tatjana Sauka-Spengler; Fabian J. Theis
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Non-destructive transcriptomics via vesicular export
err2026-04-25
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errOAAI
errNiklas Armbrust; Martin Grosshauser; Julian Geilenkeuser; Luisa Stroppel; Mattea Jozinovic; Hella Levermann; Tobias Panne; Jannick Wißmann; Lukas Goelitz; Sebastian Schmidt; Tanja Orschmann; Ejona Rusha; Emily Steinmaßl; Florenc Widenmeyer; Niklas Warsing; Melike Sabry; Asina Sultanbai; Tobias Santl; Arie Geerlof; Oleksandr Berezin; Silviu-Vasile Bodea; Alessandra Moretti; Steffen Schneider; Fabian Theis; Julien Gagneur; Dong-Jiunn Jeffery Truong; Gil Gregor Westmeyer
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TarDis: Achieving robust and structured disentanglement of multiple covariates
err2026-04-08
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errOAAI
errKemal Inecik; Aleyna Kara; Antony Rose; Muzlifah Haniffa; Fabian J. Theis
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Generative models of cell dynamics: from Neural ODEs to flow matching
err2026-02-27
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errOAAI
errTill Richter; Weixu Wang; Alessandro Palma; Fabian J. Theis
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From modality-specific to compositional foundation models for cell biology
err2026-02-18
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PREAI
errMojtaba Bahrami; Till Richter; Niklas A. Schmacke; Aitana Egea Lavandera; Fabian J. Theis
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Author Correction: Single-cell atlas of the transcriptome and chromatin accessibility in the human retina
err2026-02-18
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PREAI
errJin Li; Jun Wang; Ignacio L. Ibarra; Xuesen Cheng; Malte D. Luecken; Jiaxiong Lu; Aboozar Monavarfeshani; Wenjun Yan; Yiqiao Zheng; Zhen Zuo; Samantha Lynn Zayas Colborn; Berenice Sarahi Cortez; Leah A. Owen; Brittney Wick; Xuan Bao; Jongsu Choi; Maximilian Haeussler; Nicholas M. Tran; Karthik Shekhar; Joshua R. Sanes; J. Timothy Stout; Shiming Chen; Yumei Li; Margaret M. DeAngelis; Fabian J. Theis; Rui Chen
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Single-cell atlas of the transcriptome and chromatin accessibility in the human retina
err2026-01-23
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PREAI
errJin Li; Jun Wang; Ignacio L. Ibarra; Xuesen Cheng; Malte D. Luecken; Jiaxiong Lu; Aboozar Monavarfeshani; Wenjun Yan; Yiqiao Zheng; Zhen Zuo; Samantha Lynn Zayas Colborn; Berenice Sarahi Cortez; Leah A. Owen; Brittney Wick; Xuan Bao; Maximilian Haeussler; Nicholas M. Tran; Karthik Shekhar; Joshua R. Sanes; J. Timothy Stout; Shiming Chen; Yumei Li; Margaret M. DeAngelis; Fabian J. Theis; Rui Chen
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Single-cell characterization of the adult male hippocampus suggests a prominent, and cell-type specific, role for Nrgn and Sgk1 in response to a social stressor
err2026-01-19
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errOAAI
errCarlo De Donno; Juan Pablo Lopez; Malte D. Luecken; Aron Kos; Elena Brivio; Joeri Bordes; Huanqing Yang; Jan M. Deussing; Mathias V. Schmidt; Fabian J. Theis; Alon Chen
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Pertpy: an end-to-end framework for perturbation analysis
err2025-12-31
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errLukas Heumos; Yuge Ji; Lilly May; Tessa D. Green; Stefan Peidli; Xinyue Zhang; Xichen Wu; Johannes Ostner; Antonia Schumacher; Karin Hrovatin; Michaela Müller; Faye Chong; Gregor Sturm; Alejandro Tejada; Emma Dann; Mingze Dong; Gonçalo Pinto; Mojtaba Bahrami; Ilan Gold; Sergei Rybakov; Altana Namsaraeva; Amir Ali Moinfar; Zihe Zheng; Eljas Roellin; Isra Mekki; Chris Sander; Mohammad Lotfollahi; Herbert B. Schiller; Fabian J. Theis
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QuiCAT: a scalable and flexible framework for mapping synthetic sequences
err2025-12-01
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errOAAI
errLucarelli, Daniele; Kos, Tina; Shull, Caylie; Jimenez, Sara; Oellinger, Rupert; Rad, Roland; Saur, Dieter; Theis, Fabian J.
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Spatial single-cell atlas reveals regional variations in healthy and diseased human lung
err2025-11-05
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errOAAI
errAlexandra B. Firsova; Sergio Marco Salas; Louis B. Kuemmerle; Xesús M. Abalo; Alexandros Sountoulidis; Ludvig Larsson; Krishnaa T. Mahbubani; Jonas Theelke; Zaneta Andrusivova; Leire Alonso Galicia; Andreas Liontos; Tamás Balassa; Ferenc Kovacs; Peter Horvath; Yuexin Chen; Janine Gote-Schniering; Mircea-Gabriel Stoleriu; Jürgen Behr; Kerstin B. Meyer; Wim Timens; Herbert B. Schiller; Malte D. Luecken; Fabian J. Theis; Joakim Lundeberg; Mats Nilsson; Martijn C. Nawijn; Christos Samakovlis
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Toward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Sequencing Reveals Initiating Cell Circuits in Pulmonary Inflammation
err2025-11-03
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errOAAI
errCarola Voss; Lianyong Han; Meshal Ansari; Maximilian Strunz; Verena Haefner; Ilias Angelidis; Christoph H. Mayr; Trine Berthing; Qiaoxia Zhou; Eva M. Guenther; Osama Huzain; Otmar Schmid; Ulla Vogel; Janine Gote-Schniering; Svenja Gaedcke; Fabian J. Theis; Herbert B. Schiller; Tobias Stoeger
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OmniPath: integrated knowledgebase for multi-omics analysis
err2025-11-01
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errOAAI
errTurei, Denes; Schaul, Jonathan; Palacio-Escat, Nicolas; Bohar, Balazs; Bai, Yunfan; Ceccarelli, Francesco; Cevrim, Elif; Daley, Macabe; Darcan, Melih; Dimitrov, Daniel; Dogan, Tunca; Domingo-Fernandez, Daniel; Dugourd, Aurelien; Gabor, Attila; Gul, Lejla; Hall, Benjamin A.; Hoyt, Charles Tapley; Ivanova, Olga; Klein, Michal; Lawrence, Toby; Mananes, Diego; Modos, Dezso; Muller-Dott, Sophia; Olbei, Marton; Schmidt, Christina; Sen, Bunyamin; Theis, Fabian J.; Unlu, Atabey; Ulusoy, Erva; Valdeolivas, Alberto; Korcsmaros, Tamas; Saez-Rodriguez, Julio
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Integrating single-cell RNA-seq datasets with substantial batch effects
err2025-10-31
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errOAAI
errKarin Hrovatin; Amir Ali Moinfar; Luke Zappia; Shrey Parikh; Alejandro Tejada Lapuerta; Ben Lengerich; Manolis Kellis; Fabian J. Theis
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Nicheformer: a foundation model for single-cell and spatial omics
err2025-10-30
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errOAAI
errAlejandro Tejada-Lapuerta; Anna C. Schaar; Robert Gutgesell; Giovanni Palla; Lennard Halle; Mariia Minaeva; Larsen Vornholz; Leander Dony; Francesca Drummer; Till Richter; Mojtaba Bahrami; Fabian J. Theis
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