Fabian J. Theis | Scholar Profiles and Rankings

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GraphCompass: spatial metrics for differential analyses of cell organization across conditions (journal article) Ali, Mayar \| Kuijs, Merel \| Hediyeh-zadeh, Soroor \| Treis, Tim \| Hrovatin, Karin \| Palla, Giovanni \| Schaar, Anna C \| Theis, Fabian J Bioinformatics, volume 40, issue Supplement_1, pages i548-i557 (2024). 10.1093/bioinformatics/btae242 Cite \| Source
CellRank 2: unified fate mapping in multiview single-cell data (journal article) Weiler, Philipp \| Lange, Marius \| Klein, Michal \| Pe’er, Dana \| Theis, Fabian Nature Methods (2024). 10.1038/s41592-024-02303-9 Cited by (1) \| Cite \| Source
Machine learning integrative approaches to advance computational immunology (journal article) Curion, Fabiola \| Theis, Fabian J. Genome Medicine, volume 16, issue 1 (2024). 10.1186/s13073-024-01350-3 Cite \| Source
Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin’s Protective Mechanisms in Experimental Bronchopulmonary Dysplasia (journal article) Palit, Subarna \| Shrestha, Amrit Kumar \| Thapa, Shyam \| L. Grimm, Sandra \| Coarfa, Cristian \| Theis, Fabian \| Simon, Lukas M. \| Shivanna, Binoy Genes, volume 15, issue 6, pages 806- (2024). 10.3390/genes15060806 Cite \| Source
The future of rapid and automated single-cell data analysis using reference mapping (journal article) Lotfollahi, Mohammad \| Theis, Fabian J. \| Satija, Rahul Cell, volume 187, issue 10, pages 2343-2358 (2024). 10.1016/j.cell.2024.03.009 Cite \| Source
MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery (journal article) Siebenmorgen, Till \| Menezes, Filipe \| Benassou, Sabrina \| Merdivan, Erinc \| Didi, Kieran \| Mourão, André Santos Dias \| Kitel, Radosław \| Liò, Pietro \| Kesselheim, Stefan \| Piraud, Marie \| ... \| Popowicz, Grzegorz M. Nature Computational Science, volume 4, issue 5, pages 367-378 (2024). 10.1038/s43588-024-00627-2 Cited by (2) \| Cite \| Source
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies (journal article) Curion, Fabiola \| Wu, Xichen \| Heumos, Lukas \| André, Mylene Mariana Gonzales \| Halle, Lennard \| Ozols, Matiss \| Grant-Peters, Melissa \| Rich-Griffin, Charlotte \| Yeung, Hing-Yuen \| Dendrou, Calliope A. \| ... \| Theis, Fabian J. Genome Biology, volume 25, issue 1 (2024). 10.1186/s13059-024-03249-z Cited by (1) \| Cite \| Source
Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex (journal article) Koupourtidou, Christina \| Schwarz, Veronika \| Aliee, Hananeh \| Frerich, Simon \| Fischer-Sternjak, Judith \| Bocchi, Riccardo \| Simon-Ebert, Tatiana \| Bai, Xianshu \| Sirko, Swetlana \| Kirchhoff, Frank \| ... \| Ninkovic, Jovica Nature Communications, volume 15, issue 1 (2024). 10.1038/s41467-024-46625-w Cited by (1) \| Cite \| Source
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types (journal article) Hagenberg, Jonas \| Budde, Monika \| Pandeva, Teodora \| Kondofersky, Ivan \| Schaupp, Sabrina K \| Theis, Fabian J \| Schulze, Thomas G \| Müller, Nikola S \| Heilbronner, Urs \| Batra, Richa \| Knauer-Arloth, Janine Bioinformatics, volume 40, issue 4 (2024). 10.1093/bioinformatics/btae137 Cite \| Source
Modeling fragment counts improves single-cell ATAC-seq analysis (journal article) Martens, Laura D. \| Fischer, David S. \| Yépez, Vicente A. \| Theis, Fabian J. \| Gagneur, Julien Nature Methods, volume 21, issue 1, pages 28-31 (2024). 10.1038/s41592-023-02112-6 Cited by (3) \| Cite \| Source
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells (journal article) Gayoso, Adam \| Weiler, Philipp \| Lotfollahi, Mohammad \| Klein, Dominik \| Hong, Justin \| Streets, Aaron \| Theis, Fabian J. \| Yosef, Nir Nature Methods, volume 21, issue 1, pages 50-59 (2024). 10.1038/s41592-023-01994-w Cited by (5) \| Cite \| Source
Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases (journal article) Eckardt, Franziska \| Mittas, Robin \| Horlava, Nastassya \| Schiefelbein, Johannes \| Asani, Ben \| Michalakis, Stylianos \| Gerhardt, Maximilian \| Priglinger, Claudia \| Keeser, Daniel \| Koutsouleris, Nikolaos \| ... \| Schworm, Benedikt Klinische Monatsblätter für Augenheilkunde (2023). 10.1055/a-2227-3742 Cite \| Source
Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus (journal article) Kos, Aron \| Lopez, Juan Pablo \| Bordes, Joeri \| de Donno, Carlo \| Dine, Julien \| Brivio, Elena \| Karamihalev, Stoyo \| Luecken, Malte D. \| Almeida-Correa, Suellen \| Gasperoni, Serena \| ... \| Chen, Alon Science Advances, volume 9, issue 48 (2023). 10.1126/sciadv.adj3793 Cited by (5) \| Cite \| Source
Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies (journal article) Shetab Boushehri, Sayedali \| Essig, Katharina \| Chlis, Nikolaos-Kosmas \| Herter, Sylvia \| Bacac, Marina \| Theis, Fabian J. \| Glasmacher, Elke \| Marr, Carsten \| Schmich, Fabian Nature Communications, volume 14, issue 1 (2023). 10.1038/s41467-023-43429-2 Cited by (2) \| Cite \| Source
Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors (journal article) Ori, Chaido \| Ansari, Meshal \| Angelidis, Ilias \| Olmer, Ruth \| Martin, Ulrich \| Theis, Fabian J. \| Schiller, Herbert B. \| Drukker, Micha iScience, volume 26, issue 11, pages 108205- (2023). 10.1016/j.isci.2023.108205 Cite \| Source
Reporting electricity consumption is essential for sustainable AI (journal article) Debus, Charlotte \| Piraud, Marie \| Streit, Achim \| Theis, Fabian \| Götz, Markus Nature Machine Intelligence, volume 5, issue 11, pages 1176-1178 (2023). 10.1038/s42256-023-00750-1 Cited by (5) \| Cite \| Source
Population-level integration of single-cell datasets enables multi-scale analysis across samples (journal article) De Donno, Carlo \| Hediyeh-Zadeh, Soroor \| Moinfar, Amir Ali \| Wagenstetter, Marco \| Zappia, Luke \| Lotfollahi, Mohammad \| Theis, Fabian J. Nature Methods, volume 20, issue 11, pages 1683-1692 (2023). 10.1038/s41592-023-02035-2 Cited by (7) \| Cite \| Source
Influence of cancer associated fibroblasts (CAFs) heterogeneity on shaping immunosuppressive tumour microenvironment in PDAC (journal article) Saka, Didem \| Ibarra, Ignacio \| Weltermann, Theresa \| Alnatsha, Ahmed \| Allawadhi, Prince \| Regel, Ivonne \| Beyer, Georg \| Ormanns, Steffen \| D’Haese, Jan \| Theis, Fabian \| ... \| Mahajan, Ujjwal Mukund Pancreatology, volume 23 (2023). 10.1016/j.pan.2023.06.762 Cite \| Source
Reconstructing disease dynamics for mechanistic insights and clinical benefit (journal article) Frishberg, Amit \| Milman, Neta \| Alpert, Ayelet \| Spitzer, Hannah \| Asani, Ben \| Schiefelbein, Johannes B. \| Bakin, Evgeny \| Regev-Berman, Karen \| Priglinger, Siegfried G. \| Schultze, Joachim L. \| ... \| Shen-Orr, Shai S. Nature Communications, volume 14, issue 1 (2023). 10.1038/s41467-023-42354-8 Cite \| Source
Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment (journal article) Rosowski, Simon \| Remmert, Caroline \| Marder, Maren \| Akishiba, Misao \| Bushe, Judith \| Feuchtinger, Annette \| Platen, Alina \| Ussar, Siegfried \| Theis, Fabian \| Wiedenmann, Sandra \| Meier, Matthias Stem Cell Reports, volume 18, issue 10, pages 1972-1986 (2023). 10.1016/j.stemcr.2023.08.008 Cited by (3) \| Cite \| Source