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Fabian J Theis · SciRah

Researcher profile · Semantic Scholar

Fabian J Theis

Helmholtz Munich

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Fabian J Theis — researcher profile on SciRah

ORCID iD 0000-0002-2419-1943Homepage

h-index: 108
Works: 612
Citations: 62K

Most-cited papers

SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways
W. Sungnak, N. Huang, C. Bécavin, M. Berg +76 more
2020Nature Medicine2,366 citations Open access
Semantic Scholar
Eleven grand challenges in single-cell data science
David Lähnemann, J. Köster, Ewa Szczurek, Davis J. McCarthy +47 more
2020Genome Biology1,272 citations Open access
Semantic Scholar
Squidpy: a scalable framework for spatial omics analysis
G. Palla, Hannah Spitzer, Michal Klein, David S. Fischer +9 more
2022Nature Methods1,065 citations Open access
Semantic Scholar
Best practices for single-cell analysis across modalities
L. Heumos, A. Schaar, Christopher Lance, Anastasia Litinetskaya +38 more
2023Nature reviews genetics943 citations Open access
Semantic Scholar
A Python library for probabilistic analysis of single-cell omics data
Adam Gayoso, Romain Lopez, Galen K. Xing, Pierre Boyeau +25 more
2022Nature Biotechnology737 citations Open access
Semantic Scholar
CellRank for directed single-cell fate mapping
Marius Lange, Volker Bergen, Michal Klein, Manu Setty +8 more
2020Nature Methods723 citations Open access
Semantic Scholar
Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis
M. Strunz, L. Simon, M. Ansari, J. Kathiriya +23 more
2020Nature Communications651 citations Open access
Semantic Scholar
Mapping single-cell data to reference atlases by transfer learning
M. Lotfollahi, Mohsen Naghipourfar, M. Luecken, Matin Khajavi +9 more
2021Nature Biotechnology561 citations Open access
Semantic Scholar
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
Andreas-David Brunner, M. Thielert, Catherine G. Vasilopoulou, C. Ammar +13 more
2020bioRxiv531 citations Open access
Semantic Scholar
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
D. Wendisch, Oliver Dietrich, T. Mari, Saskia von Stillfried +58 more
2021Cell448 citations Open access
Semantic Scholar
Predicting cellular responses to complex perturbations in high‐throughput screens
M. Lotfollahi, Anna Klimovskaia Susmelj, C. de Donno, L. Hetzel +15 more
2023Molecular Systems Biology420 citations Open access
Semantic Scholar
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Dénes Türei, Alberto Valdeolivas, L. Gul, Nicolàs Palacio-Escat +8 more
2020bioRxiv356 citations Open access
Semantic Scholar
Spatial components of molecular tissue biology
G. Palla, David S. Fischer, A. Regev, Fabian J Theis
2022Nature Biotechnology315 citations Open access
Semantic Scholar
RNA velocity—current challenges and future perspectives
Volker Bergen, Ruslan A. Soldatov, P. Kharchenko, Fabian J Theis
2021Molecular Systems Biology250 citations Open access
Semantic Scholar
anndata: Annotated data
I. Virshup, Sergei Rybakov, Fabian J Theis, P. Angerer +1 more
2021bioRxiv234 citations Open access
Semantic Scholar
Modeling intercellular communication in tissues using spatial graphs of cells
David S. Fischer, A. Schaar, Fabian J Theis
2022Nature Biotechnology194 citations Open access
Semantic Scholar
The single-cell eQTLGen consortium
M. van der Wijst, Dylan H. de Vries, H. Groot, G. Trynka +12 more
2020eLife182 citations Open access
Semantic Scholar
The proteome landscape of the kingdoms of life
Johannes B. Müller, P. Geyer, Ana R. Colaço, Peter V. Treit +9 more
2020Nature177 citations
Semantic Scholar
Inhibition of LTβR-signalling activates Wnt-induced regeneration in lung
T. Conlon, G. John-Schuster, Danijela Heide, D. Pfister +45 more
2020Nature152 citations Open access
Semantic Scholar
Machine learning for perturbational single-cell omics.
Yuge Ji, M. Lotfollahi, F. Wolf, Fabian J Theis
2021Cell Systems146 citations Open access
Semantic Scholar
Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape
L. Zappia, Fabian J Theis
2021Genome Biology143 citations Open access
Semantic Scholar
LifeTime and improving European healthcare through cell-based interceptive medicine
N. Rajewsky, G. Almouzni, Stanislaw A. Gorski, S. Aerts +47 more
2020Nature142 citations Open access
Semantic Scholar
Conditional out-of-distribution generation for unpaired data using transfer VAE
M. Lotfollahi, Mohsen Naghipourfar, Fabian J Theis, F. Wolf
2020Bioinform.142 citations Open access
Semantic Scholar
Targeted pharmacological therapy restores β-cell function for diabetes remission
S. Sachs, Aimée Bastidas-Ponce, Sophie Tritschler, Mostafa Bakhti +23 more
2020Nature Metabolism135 citations Open access
Semantic Scholar
OME-Zarr: a cloud-optimized bioimaging file format with international community support
Josh Moore, Daniela Basurto-Lozada, S. Besson, J. Bogovic +65 more
2023Histochemistry and Cell Biology134 citations Open access
Semantic Scholar
Interpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study
Hannah Spitzer, M. Ripart, K. Whitaker, F. D'Arco +73 more
2022Brain : a journal of neurology130 citations Open access
Semantic Scholar
Predicting antigen specificity of single T cells based on TCR CDR3 regions
David S. Fischer, YiHan Wu, B. Schubert, Fabian J Theis
2019bioRxiv123 citations Open access
Semantic Scholar
Deep learning the collisional cross sections of the peptide universe from a million experimental values
F. Meier, Niklas D. Köhler, Andreas-David Brunner, Jean-Marc H. Wanka +4 more
2021Nature Communications120 citations Open access
Semantic Scholar
Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
A. Aliluev, Sophie Tritschler, Michael Sterr, Lena Oppenländer +14 more
2021Nature Metabolism109 citations Open access
Semantic Scholar
scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
Katharina T. Schmid, Barbara Höllbacher, C. Cruceanu, Anika Böttcher +4 more
2021Nature Communications90 citations Open access
Semantic Scholar
Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
C. Mayr, L. Simon, G. Leuschner, M. Ansari +19 more
2021EMBO Molecular Medicine87 citations Open access
Semantic Scholar
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution
Hananeh Aliee, Fabian J Theis
2020bioRxiv84 citations Open access
Semantic Scholar
Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation
J. Lopez, E. Brivio, A. Santambrogio, C. de Donno +26 more
2021Science Advances83 citations Open access
Semantic Scholar
Epithelial cell plasticity drives endoderm formation during gastrulation
Katharina Scheibner, S. Schirge, I. Burtscher, M. Büttner +10 more
2021Nature Cell Biology80 citations Open access
Semantic Scholar
Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates
Anika Böttcher, M. Büttner, Sophie Tritschler, Michael Sterr +13 more
2021Nature Cell Biology79 citations
Semantic Scholar
Post-surgical adhesions are triggered by calcium-dependent membrane bridges between mesothelial surfaces
A. Fischer, T. Koopmans, P. Ramesh, Simon Christ +12 more
2020Nature Communications73 citations Open access
Semantic Scholar
Squidpy: a scalable framework for spatial single cell analysis
G. Palla, Hannah Spitzer, Michal Klein, David S. Fischer +9 more
2021bioRxiv67 citations Open access
Semantic Scholar
scvi-tools: a library for deep probabilistic analysis of single-cell omics data
Adam Gayoso, Romain Lopez, Galen K. Xing, Pierre Boyeau +21 more
2021bioRxiv66 citations Open access
Semantic Scholar
Toward modeling metabolic state from single-cell transcriptomics
Karin Hrovatin, David S. Fischer, Fabian J Theis
2021Molecular Metabolism58 citations Open access
Semantic Scholar
Graph representation learning for single-cell biology
L. Hetzel, David S. Fischer, Stephan Günnemann, Fabian J Theis
202157 citations Open access
Semantic Scholar
MISATO - Machine learning dataset of protein-ligand complexes for structure-based drug discovery
Till Siebenmorgen, Filipe Menezes, Sabrina Benassou, Erinc Merdivan +5 more
2023bioRxiv54 citations Open access
Semantic Scholar
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
J. Arloth, G. Eraslan, T. Andlauer, Jade Martins +24 more
2020PLoS Comput. Biol.53 citations Open access
Semantic Scholar
A sandbox for prediction and integration of DNA, RNA, and protein data in single cells
M. Luecken, Daniel B. Burkhardt, Robrecht Cannoodt, Christopher Lance +33 more
202151 citations
Semantic Scholar
Learning interpretable cellular responses to complex perturbations in high-throughput screens
M. Lotfollahi, A. Susmelj, C. de Donno, Yuge Ji +5 more
2021bioRxiv49 citations Open access
Semantic Scholar
CD81 marks immature and dedifferentiated pancreatic β-cells
Ciro Salinno, M. Büttner, Perla Cota, Sophie Tritschler +8 more
2021Molecular Metabolism48 citations Open access
Semantic Scholar
A transcriptional cross species map of pancreatic islet cells
Sophie Tritschler, M. Thomas, Anika Böttcher, B. Ludwig +6 more
2022Molecular Metabolism45 citations Open access
Semantic Scholar
Query to reference single-cell integration with transfer learning
M. Lotfollahi, Mohsen Naghipourfar, M. Luecken, Matin Khajavi +4 more
2020bioRxiv40 citations Open access
Semantic Scholar
Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development
Margaret E. Magaletta, Macrina Lobo, Eric M Kernfeld, Hananeh Aliee +4 more
2022Nature Communications36 citations Open access
Semantic Scholar
Sfaira accelerates data and model reuse in single cell genomics
David S. Fischer, L. Dony, Martin König, Abdul Moeed +6 more
2020Genome Biology31 citations Open access
Semantic Scholar
Learning interpretable latent autoencoder representations with annotations of feature sets
Sergei Rybakov, M. Lotfollahi, Fabian J Theis, F. Wolf
2020bioRxiv31 citations Open access
Semantic Scholar

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