Theis, Fabian J.

Biologically informed deep learning to infer gene program activity in single cells

Lotfollahi, M., Rybakov, S., Hrovatin, K., Hediyeh-zadeh, S., Talavera-López, C., Misharin, A. V., & Theis, F. J. (2022) · Nature Cell Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 100

Nicheformer: a foundation model for single-cell and spatial omics

Tejada-Lapuerta, A., Schaar, A. C., Gutgesell, R., Palla, G., Halle, L., Minaeva, M., Vornholz, L., Dony, L., Drummer, F., Richter, T., et al. (2025) · Nature Methods

Single-cell and spatial transcriptomicsCell Image Analysis Techniques

Cited by 100

A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection

Bosch, M., Kallin, N., Donakonda, S., Zhang, J. D., Wintersteller, H., Hegenbarth, S., Heim, K., Ramirez, C., Fürst, A., Lattouf, E. I., et al. (2024) · Nature

Hepatitis B Virus StudiesT-cell and B-cell Immunology

Cited by 97

Multimodal single cell data integration challenge: results and lessons learned

Lance, C., Luecken, M. D., Burkhardt, D. B., Cannoodt, R., Rautenstrauch, P., Laddach, A., Ubingazhibov, A., Cao, Z.-J., Deng, K., Khan, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 81

MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

Siebenmorgen, T., Menezes, F., Benassou, S., Merdivan, E., Didi, K., Mourão, A. S. D., Kitel, R., Liò, P., Kesselheim, S., Piraud, M., et al. (2024) · Nature Computational Science

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 75

A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes

Winkler, C., Krumsiek, J., Lempainen, J., Achenbach, P., Grallert, H., Giannopoulou, E., Bunk, M., Theis, F. J., Bonifacio, E., & Ziegler, A.-G. (2012) · Genes & Immunity

Diabetes and associated disordersGenetic Associations and Epidemiology

Cited by 68

Graph representation learning for single-cell biology

Hetzel, L., Fischer, D. S., Günnemann, S., & Theis, F. J. (2021) · Current Opinion in Systems Biology

Single-cell and spatial transcriptomicsAdvanced Graph Neural Networks

Cited by 55

Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis

Bast, L., Calzolari, F., Strasser, M. K., Hasenauer, J., Theis, F. J., Ninkovic, J., & Marr, C. (2018) · Cell Reports

Neurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Cited by 50

Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex

Koupourtidou, C., Schwarz, V., Aliee, H., Frerich, S., Fischer-Sternjak, J., Bocchi, R., Simon-Ebert, T., Bai, X., Sirko, S., Kirchhoff, F., et al. (2024) · Nature Communications

Traumatic Brain Injury and Neurovascular DisturbancesNeuroinflammation and Neurodegeneration Mechanisms

Cited by 48

Sfaira accelerates data and model reuse in single cell genomics

Fischer, D. S., Dony, L., König, M., Moeed, A., Zappia, L., Heumos, L., Tritschler, S., Holmberg, O., Aliee, H., & Theis, F. J. (2021) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 33

Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib

Sobotta, S., Raue, A., Huang, X., Vanlier, J., Jünger, A., Bohl, S., Albrecht, U., Hahnel, M. J., Wolf, S., Mueller, N. S., et al. (2017) · Frontiers in Physiology

Cytokine Signaling Pathways and InteractionsGene Regulatory Network Analysis

Cited by 28

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm

Strasser, M. K., Hoppe, P. S., Loeffler, D., Kokkaliaris, K. D., Schroeder, T., Theis, F. J., & Marr, C. (2018) · Nature Communications

Gene Regulatory Network AnalysisHematopoietic Stem Cell Transplantation

Cited by 26

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis

Uzbas, F., Opperer, F., Sönmezer, C., Shaposhnikov, D., Sass, S., Krendl, C., Angerer, P., Theis, F. J., Mueller, N. S., & Drukker, M. (2019) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 23

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data

Buettner, F., Moignard, V., Göttgens, B., & Theis, F. J. (2014) · Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 21

Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species

Lotfollahi, M., Wolf, F. A., & Theis, F. J. (2018) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 21

cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics

Blasi, T., Buettner, F., Strasser, M. K., Marr, C., & Theis, F. J. (2017) · Physical Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 18

MultiCPA: Multimodal Compositional Perturbation Autoencoder

Inecik, K., Uhlmann, A., Lotfollahi, M., & Theis, F. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 16

iVUN: interactive Visualization of Uncertain biochemical reaction Networks

Vehlow, C., Hasenauer, J., Kramer, A., Raue, A., Hug, S., Timmer, J., Radde, N., Theis, F. J., & Weiskopf, D. (2013) · BMC Bioinformatics

Data Visualization and AnalyticsGene Regulatory Network Analysis

Cited by 11

Inferring catalysis in biological systems

Kondofersky, I., Theis, F. J., & Fuchs, C. (2016) · IET Systems Biology

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 1