Nir Yosef (N Yosef)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 38

Top Topics

Gene Expression

Top Venues

Nucleic acids research

Nature biotechnology

Nature communications

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

Publications

Joshua I Gray, Daniel P Caron, Steven B Wells, Rebecca Guyer, Peter A Szabo, Daniel B Rainbow, Can Ergen, Ksenia Rybkina, Marissa C Bradley, Rei Matsumoto, Kalpana Pethe, Masaru Kubota, Sarah A Teichmann, Joanne Louise Jones, Nir Yosef, Mark A Atkinson, Maigan A Brusko, Todd M Brusko, Thomas J Connors, Peter A Sims, Donna L Farber
Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span. Science immunology 9 (96) (2024)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic acids research 52 (4) (2024)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic acids research (2024)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic acids research (2024)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic acids research 52 (4) (2024)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic acids research 52 (4) (2024)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic acids research 52 (4) (2024)
Tal Ashuach, Mariano I Gabitto, Rohan V Koodli, Giuseppe-Antonio Saldi, Michael I Jordan, Nir Yosef
MultiVI: deep generative model for the integration of multimodal data. Nature methods (2023)
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer
Best practices for perturbation MPRA-a computational evaluation framework of sequence design strategies. bioRxiv : the preprint server for biology (2023)
Zoë Steier, Dominik A Aylard, Laura L McIntyre, Isabel Baldwin, Esther Jeong Yoon Kim, Lydia K Lutes, Can Ergen, Tse-Shun Huang, Ellen A Robey, Nir Yosef, Aaron Streets
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4 + T cell and CD8 + T cell lineage commitment. Nature immunology (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)
Nathan L Meyers, Tal Ashuach, Danielle E Lyons, Mir Mubashir Khalid, Camille R Simoneau, Ann L Erickson, Mehdi Bouhaddou, Thong T Nguyen, G Renuka Kumar, Taha Y Taha, Vaishaali Natarajan, Jody L Baron, Norma Neff, Fabio Zanini, Tokameh Mahmoudi, Stephen R Quake, Nevan J Krogan, Stewart Cooper, Todd C McDevitt, Nir Yosef, Melanie M Ott
Hepatitis C virus infects and perturbs liver stem cells. mBio (2023)
Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, null null, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A Teichmann, Francesca Finotello, F Alexander Wolf, Nir Yosef, Oliver Stegle, Fabian Joachim Theis
The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature biotechnology (2023)
Hsiao-Wei Tsao, James Kaminski, Makoto Kurachi, R Anthony Barnitz, Michael A DiIorio, Martin W LaFleur, Wataru Ise, Tomohiro Kurosaki, E John Wherry, W Nicholas Haining, Nir Yosef
Batf-mediated epigenetic control of effector CD8 + T cell differentiation. Science immunology 7 (68) (2022)
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)
Cecilia Domínguez Conde, Chuan Xu, Lorna B Jarvis, Daniel B Rainbow, Steven B Wells, Tomas Gomes, S K Howlett, O Suchanek, Krzysztof Polański, Hamish W King, Lira Mamanova, Ni Huang, Peter A Szabo, Laura Richardson, Liam Bolt, Eirini S Fasouli, Krishnaa T A Mahbubani, Martin Prete, Elizabeth Tuck, N Richoz, Zewen Kelvin Tuong, L Campos, Hani S Mousa, Edward J Needham, S Pritchard, Tong Li, Rasa Elmentaite, Jong-Eun Park, E Rahmani, David Chen, David K Menon, O A Bayraktar, Louisa Katherine James, Kerstin B Meyer, Nir Yosef, Menna R Clatworthy, Peter A Sims, Donna L Farber, Kourosh Saeb Parsy, Joanne Louise Jones, Sarah A Teichmann
Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science (New York, N.Y.) 376 (6594) (2022)
Anat Kreimer, Tal Ashuach, Fumitaka Inoue, Alex Khodaverdian, Chengyu Deng, Nir Yosef, Nadav Ahituv
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Nature communications 13 (1) (2022)
Romain Lopez, Baoguo Li, Hadas Keren-Shaul, Pierre Boyeau, Merav Kedmi, David Pilzer, Adam Jelinski, Ido Yofe, Eyal David, Allon Wagner, Can Ergen, Yoseph Addadi, Ofra Golani, Franca Ronchese, Michael I Jordan, Bjørt K Kragesteen, Nir Yosef
DestVI identifies continuums of cell types in spatial transcriptomics data. Nature biotechnology 40 (9) (2022)
Jeffrey J Quinn, Matthew G Jones, Ross A Okimoto, Shigeki Nanjo, Michelle M Chan, Nir Yosef, Trever G Bivona, Jonathan S Weissman
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science (New York, N.Y.) 371 (6532) (2021)
Alyssa Kramer Morrow, John Weston Hughes, Jahnavi Singh, Anthony Douglas Joseph, Nir Yosef
Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning. Nucleic acids research 49 (19) (2021)
Lydia Kay Lutes, Zoë Steier, Laura L McIntyre, Shraddha Pandey, James Kaminski, Ashley R Hoover, Silvia Ariotti, Aaron Streets, Nir Yosef, Ellen A Robey
T cell self-reactivity during thymic development dictates the timing of positive selection. eLife 10 (2021)
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)
Moritz M Gaidt, Alyssa Kramer Morrow, Marian R Fairgrieve, Jonathan P Karr, Nir Yosef, Russell E Vance
Self-guarding of MORC3 enables virulence factor-triggered immunity. Nature 600 (7887) (2021)
Romain Lopez, Adam Gayoso, Nir Yosef
Enhancing scientific discoveries in molecular biology with deep generative models. Molecular systems biology 16 (9) (2021)
Adam Gayoso, Zoë Steier, Romain Lopez, Jeffrey Regier, Kristopher L Nazor, Aaron Streets, Nir Yosef
Joint probabilistic modeling of single-cell multi-omic data with totalVI. Nature methods 18 (3) (2021)
Chenling A Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef
Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. Molecular systems biology 17 (1) (2021)
Nicholas J Everetts, Melanie I Worley, Riku Yasutomi, Nir Yosef, Iswar K Hariharan
Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions. eLife 10 (2021)
David Schafflick, Chenling A Xu, Maike Hartlehnert, Michael Cole, Andreas Schulte-Mecklenbeck, Tobias Lautwein, Jolien Wolbert, Michael Heming, Sven Guenther Meuth, Tanja Kuhlmann, Catharina C Gross, Heinz Wiendl, Nir Yosef, Gerd Meyer Zu Hörste
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. Nature communications 11 (1) (2020)
Carlos F Buen Abad Najar, Nir Yosef, Liana F Lareau
Coverage-dependent bias creates the appearance of binary splicing in single cells. eLife 9 (2020)
Xiuwei Zhang, Chenling A Xu, Nir Yosef
Simulating multiple faceted variability in single cell RNA sequencing. Nature communications 10 (1) (2019)
David DeTomaso, Matthew G Jones, Meena Subramaniam, Tal Ashuach, Chun Jimmie Ye, Nir Yosef
Functional interpretation of single cell similarity maps. Nature communications 10 (1) (2019)
Shaked Afik, Gabriel Raulet, Nir Yosef
Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS. Life science alliance 2 (4) (2019)
Anat Kreimer, Zhongxia Yan, Nadav Ahituv, Nir Yosef
Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types. Human mutation 40 (9) (2019)
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef
Deep generative modeling for single-cell transcriptomics. Nature methods 15 (12) (2018)
Ann H Ryu, Walter L Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Scientific reports 7 (1) (2017)
Xiuwei Zhang, Nir Yosef
A new way to build cell lineages. eLife 6 (2017)
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carnici, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah A Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed S Lein, Sten Linnarsson, Emma Lundberg, Joakim Lundeberg, Partha Majumder, John C Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe'er, Anthony Phillipakis, Chris Paul Ponting, Stephen Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua R Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael J T Stubbington, Fabian J Theis, Matthias Uhlen, Alexander van Oudenaarden, Allon Wagner, Fiona M Watt, Jonathan S Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, null null
The Human Cell Atlas. eLife 6 (2017)
Yasuhiro Kishi, Takaaki Kondo, Sheng Xiao, Nir Yosef, Jellert T Gaublomme, Chuan Wu, Chao Wang, Norio Chihara, Aviv Regev, Nicole Joller, Vijay K Kuchroo
Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity. The Journal of experimental medicine 213 (11) (2016)