Author

Fabian J. Theis

Helmholtz Munich

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Cell Biology· 1 Genetics· 1 Neuroscience· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:scRNA-seq· 2 Approach:Bayesian inference· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Aarti Anand· 1 shared Adam Filipczyk· 1 shared Alena BoosiD· 1 shared Alison GoateiD· 1 shared Amelia Rossi· 1 shared Audrey V. ParentiD· 1 shared Barbara TreutleiniD· 1 shared Brigitte L. ArduiniiD· 1 shared

Activity by Year

2016-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperCell Biology

Aarti Anand

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Author profile →

5 papers

Recent·Most cited

MAFA drives pancreatic islet maturation through coordination of cell growth, metabolic maturation, and resilience to stress.

Veronica A. Cochrane, Michael Sterr, Marianne Aniag, Sara Jiménez, Madeline S. Wang, Ying Liu, Alena Boos, Juliane Merl‐Pham, Aarti Anand, Ryan E. Hoang, Rachita Gupta, Heiko Lickert, Tiago C. Alves, Jeeyeon Cha, Roland Stein, , Matthias Hebrok

This study shows that MAFA promotes pancreatic islet maturation by enhancing cell growth, metabolic function, and stress resilience in stem cell-derived islets.

bioRxiv · Sep 30, 2026 · PreprintCell Biology

Integrated Manufacturing Platform for Cortical Organoids Reveals Early Phosphatase and Prefoldin Dysregulation in MAPT V337M Neurons

Taylor B. Bertucci, Kathryn R. Bowles, Steven Lotz, Shiraz Bheda, Le Qi, Farhad Farjood, Katherine Whitton, Susan K. Goderie, Susan M. Borden, Amelia Rossi, Kate Tubbesing, Chiara Pedicone, Laura Maria Oja, Keith Lane, Ryan Lotz, , Sally Temple

The paper develops a scalable cortical organoid platform with quality control metrics and identifies early dysregulation of phosphatase and prefoldin genes in FTD-tau neurons.

bioRxiv · Jul 11, 2023 · PreprintNeuroscience

Diffusion pseudotime robustly reconstructs lineage branching

Laleh Haghverdi, Maren Buettner, F. Alexander Wolf, Florian Buettner, Fabian J. Theis

The paper introduces a method to estimate the temporal order of differentiating cells using diffusion pseudotime, identifying branching decisions and differentially regulated genes.

Nature Methods · Aug 29, 2016Peer-reviewedBioinformatics

Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells

Justin Feigelman, Stefan Ganscha, Simon Hastreiter, Michael Schwarzfischer, Adam Filipczyk, Timm Schroeder, Fabian J. Theis, Carsten Marr, Manfred Claassen

This paper uses STILT to infer Nanog's autoregulatory mechanism in mouse embryonic stem cells, finding weak negative feedback from the protein on DNA activation.

bioRxiv · May 13, 2016 · PreprintSystems Biology

Network-based metabolite ratios for an improved functional characterization of genome-wide association study results

Jan Krumsiek, Ferdinand Stückler, Karsten Suhre, Christian Gieger, Tim D. Spector, Nicole Soranzo, Gabi Kastenmüller, Fabian J. Theis

This paper introduces a network-based method to select biologically meaningful metabolite ratios for GWAS, improving prediction accuracy and reducing computational demands.

bioRxiv · Apr 13, 2016 · PreprintGenetics