Mohammad Lotfollahi

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 19

Top Topics

Respiratory Syndrome Coronavirus

Gene Expression

Top Venues

Nature cell biology

Nature communications

Nature biotechnology

This page only lists publications with an associated author ORCID identifier.

Publications

Felix Drost, Yang An, Irene Bonafonte-Pardàs, Lisa M Dratva, Rik G H Lindeboom, Muzlifah A Haniffa, Sarah A Teichmann, Fabian Joachim Theis, Mohammad Lotfollahi, Benjamin Schubert
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nature communications 15 (1) (2024)
Felix Drost, Yang An, Irene Bonafonte-Pardàs, Lisa M Dratva, Rik G H Lindeboom, Muzlifah A Haniffa, Sarah A Teichmann, Fabian Joachim Theis, Mohammad Lotfollahi, Benjamin Schubert
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nature communications 15 (1) (2024)
Felix Drost, Yang An, Irene Bonafonte-Pardàs, Lisa M Dratva, Rik G H Lindeboom, Muzlifah A Haniffa, Sarah A Teichmann, Fabian Joachim Theis, Mohammad Lotfollahi, Benjamin Schubert
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nature communications 15 (1) (2024)
Mohammad Lotfollahi
Toward learning a foundational representation of cells and genes. Nature methods 21 (8) (2024)
Mohammad Lotfollahi
Toward learning a foundational representation of cells and genes. Nature methods 21 (8) (2024)
Magda Marečková, Luz Garcia-Alonso, Marie Moullet, Valentina Lorenzi, Robert Petryszak, Carmen Sancho-Serra, Agnes Oszlanczi, Cecilia Icoresi Mazzeo, Frederick C K Wong, Iva Kelava, Sophie Hoffman, Michal Krassowski, Kurtis Garbutt, Kezia Gaitskell, Slaveya Yancheva, Ee Von Woon, Victoria Male, Ingrid Granne, Karin Hellner, Krishnaa T A Mahbubani, Kourosh Saeb Parsy, Mohammad Lotfollahi, Elena Prigmore, Jennifer Southcombe, Rebecca A Dragovic, Christian M Becker, Krina T Zondervan, Roser Vento-Tormo
An integrated single-cell reference atlas of the human endometrium. Nature genetics (2024)
Carlo de Donno, Soroor Hediyeh-Zadeh, Amir Ali Moinfar, Marco Wagenstetter, Luke Zappia, Mohammad Lotfollahi, Fabian Joachim Theis
Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nature methods (2023)
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian Joachim Theis
Biologically informed deep learning to query gene programs in single-cell atlases. Nature cell biology 25 (2) (2023)
Adam Gayoso, Philipp Weiler, Mohammad Lotfollahi, Dominik Klein, Justin Hong, Aaron Streets, Fabian Joachim Theis, Nir Yosef
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells. Nature methods (2023)
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian Joachim Theis
Biologically informed deep learning to query gene programs in single-cell atlases. Nature cell biology (2023)
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian Joachim Theis
Biologically informed deep learning to query gene programs in single-cell atlases. Nature cell biology 25 (2) (2023)
Lisa Sikkema, Ciro Ramírez-Suástegui, Daniel C Strobl, Tessa E Gillett, Luke Zappia, Elo Madissoon, Nikolay S Markov, Laure-Emmanuelle Zaragosi, Yuge Ji, Meshal Ansari, Marie-Jeanne Arguel, Leonie Apperloo, Martin Banchero, Christophe Bécavin, Marijn Berg, Evgeny Chichelnitskiy, Mei-I Chung, Antoine Collin, Aurore C A Gay, Janine Gote-Schniering, Baharak Hooshiar Kashani, Kemal Inecik, Manu Jain, Theodore S Kapellos, Tessa M Kole, Sylvie Leroy, Christoph H Mayr, Amanda J Oliver, Michael von Papen, Lance Peter, Chase J Taylor, Thomas Walzthoeni, Chuan Xu, Linh T Bui, Carlo De Donno, Leander Dony, Alen Faiz, Minzhe Guo, Austin J Gutierrez, Lukas Heumos, Ni Huang, Ignacio L Ibarra, Nathan D Jackson, Preetish Kadur Lakshminarasimha Murthy, Mohammad Lotfollahi, Tracy Tabib, Carlos Talavera-López, Kyle J Travaglini, Anna Wilbrey-Clark, Kaylee B Worlock, Masahiro Yoshida, null null, Maarten van den Berge, Yohan Bosse, Tushar J Desai, Oliver Eickelberg, Naftali Kaminski, Mark A Krasnow, Robert A Lafyatis, Marko Z Nikolić, Joseph E Powell, Jayaraj Rajagopal, Mauricio Rojas, Orit Rozenblatt-Rosen, Max A Seibold, Dean Sheppard, Douglas P Shepherd, Don D Sin, Hidde J Haisma, Alexander M Tsankov, Jeffrey A Whitsett, Yan Xu, Nicholas E Banovich, Pascal Barbry, Elizabeth Thu Duong, Christine S Falk, Kerstin B Meyer, Jonathan A Kropski, Dana Pe'er, Herbert B Schiller, Purushothama Rao Tata, Joachim L Schultze, Sarah A Teichmann, Alexander V Misharin, Martijn C Nawijn, Malte Daniel Luecken, Fabian Joachim Theis
An integrated cell atlas of the lung in health and disease. Nature medicine (2023)
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian Joachim Theis
Biologically informed deep learning to query gene programs in single-cell atlases. Nature cell biology 25 (2) (2023)
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian Joachim Theis
Biologically informed deep learning to query gene programs in single-cell atlases. Nature cell biology 25 (2) (2023)
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian Joachim Theis
Biologically informed deep learning to query gene programs in single-cell atlases. Nature cell biology 25 (2) (2023)
Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling A Xu, Tal Ashuach, Mariano Gabitto, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-López, Lior Pachter, Fabian Joachim Theis, Aaron Streets, Michael I Jordan, Jeffrey Regier, Nir Yosef
A Python library for probabilistic analysis of single-cell omics data. Nature biotechnology 40 (2) (2022)
Giovanni Palla, Hannah Spitzer, Michal Klein, David S Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, Fabian Joachim Theis
Squidpy: a scalable framework for spatial omics analysis. Nature methods 19 (2) (2022)
Mohammad Lotfollahi, Mohsen Naghipourfar, Malte Daniel Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander V Misharin, Fabian Joachim Theis
Mapping single-cell data to reference atlases by transfer learning. Nature biotechnology (2021)
Mohammad Lotfollahi, F Alexander Wolf, Fabian Joachim Theis
scGen predicts single-cell perturbation responses. Nature methods 16 (8) (2019)