Generalizing RNA velocity to transient cell states through dynamical modeling
Bergen, Volker, Lange, Marius, Peidli, Stefan, Wolf, F. Alexander, Theis, Fabian J.
Published in Nature biotechnology (01.12.2020)
Published in Nature biotechnology (01.12.2020)
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Journal Article
Single-cell RNA-seq denoising using a deep count autoencoder
Eraslan, Gökcen, Simon, Lukas M., Mircea, Maria, Mueller, Nikola S., Theis, Fabian J.
Published in Nature communications (23.01.2019)
Published in Nature communications (23.01.2019)
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Journal Article
Spatial components of molecular tissue biology
Palla, Giovanni, Fischer, David S., Regev, Aviv, Theis, Fabian J.
Published in Nature biotechnology (01.03.2022)
Published in Nature biotechnology (01.03.2022)
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Journal Article
A test metric for assessing single-cell RNA-seq batch correction
Büttner, Maren, Miao, Zhichao, Wolf, F. Alexander, Teichmann, Sarah A., Theis, Fabian J.
Published in Nature methods (01.01.2019)
Published in Nature methods (01.01.2019)
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Journal Article
destiny: diffusion maps for large-scale single-cell data in R
Angerer, Philipp, Haghverdi, Laleh, Büttner, Maren, Theis, Fabian J, Marr, Carsten, Buettner, Florian
Published in Bioinformatics (15.04.2016)
Published in Bioinformatics (15.04.2016)
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Journal Article
CellRank for directed single-cell fate mapping
Lange, Marius, Bergen, Volker, Klein, Michal, Setty, Manu, Reuter, Bernhard, Bakhti, Mostafa, Lickert, Heiko, Ansari, Meshal, Schniering, Janine, Schiller, Herbert B., Pe’er, Dana, Theis, Fabian J.
Published in Nature methods (01.02.2022)
Published in Nature methods (01.02.2022)
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Journal Article
Squidpy: a scalable framework for spatial omics analysis
Palla, Giovanni, Spitzer, Hannah, Klein, Michal, Fischer, David, Schaar, Anna Christina, Kuemmerle, Louis Benedikt, Rybakov, Sergei, Ibarra, Ignacio L., Holmberg, Olle, Virshup, Isaac, Lotfollahi, Mohammad, Richter, Sabrina, Theis, Fabian J.
Published in Nature methods (01.02.2022)
Published in Nature methods (01.02.2022)
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Journal Article
Benchmarking atlas-level data integration in single-cell genomics
Luecken, Malte D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., Theis, Fabian J.
Published in Nature methods (01.01.2022)
Published in Nature methods (01.01.2022)
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Journal Article
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Fröhlich, Fabian, Kaltenbacher, Barbara, Theis, Fabian J, Hasenauer, Jan
Published in PLoS computational biology (01.01.2017)
Published in PLoS computational biology (01.01.2017)
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Journal Article
RNA velocity—current challenges and future perspectives
Bergen, Volker, Soldatov, Ruslan A, Kharchenko, Peter V, Theis, Fabian J
Published in Molecular systems biology (01.08.2021)
Published in Molecular systems biology (01.08.2021)
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Journal Article
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Wolf, F Alexander, Hamey, Fiona K, Plass, Mireya, Solana, Jordi, Dahlin, Joakim S, Göttgens, Berthold, Rajewsky, Nikolaus, Simon, Lukas, Theis, Fabian J
Published in Genome Biology (19.03.2019)
Published in Genome Biology (19.03.2019)
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Journal Article
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Buettner, Florian, Natarajan, Kedar N, Casale, F Paolo, Proserpio, Valentina, Scialdone, Antonio, Theis, Fabian J, Teichmann, Sarah A, Marioni, John C, Stegle, Oliver
Published in Nature biotechnology (01.02.2015)
Published in Nature biotechnology (01.02.2015)
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Journal Article
A BaSiC tool for background and shading correction of optical microscopy images
Peng, Tingying, Thorn, Kurt, Schroeder, Timm, Wang, Lichao, Theis, Fabian J., Marr, Carsten, Navab, Nassir
Published in Nature communications (08.06.2017)
Published in Nature communications (08.06.2017)
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Journal Article
Predicting antigen specificity of single T cells based on TCR CDR3 regions
Fischer, David S, Wu, Yihan, Schubert, Benjamin, Theis, Fabian J
Published in Molecular systems biology (01.08.2020)
Published in Molecular systems biology (01.08.2020)
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Journal Article
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
Brunner, Andreas‐David, Thielert, Marvin, Vasilopoulou, Catherine, Ammar, Constantin, Coscia, Fabian, Mund, Andreas, Hoerning, Ole B, Bache, Nicolai, Apalategui, Amalia, Lubeck, Markus, Richter, Sabrina, Fischer, David S, Raether, Oliver, Park, Melvin A, Meier, Florian, Theis, Fabian J, Mann, Matthias
Published in Molecular systems biology (01.03.2022)
Published in Molecular systems biology (01.03.2022)
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Journal Article
Mapping single-cell data to reference atlases by transfer learning
Lotfollahi, Mohammad, Naghipourfar, Mohsen, Luecken, Malte D., Khajavi, Matin, Büttner, Maren, Wagenstetter, Marco, Avsec, Žiga, Gayoso, Adam, Yosef, Nir, Interlandi, Marta, Rybakov, Sergei, Misharin, Alexander V., Theis, Fabian J.
Published in Nature biotechnology (01.01.2022)
Published in Nature biotechnology (01.01.2022)
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Journal Article