Nir Yosef

American Committee for the Weizmann Institute of Science

Also affiliated with Weizmann Institute of Science

Biochemistry, Genetics and Molecular BiologyImmunology and Microbiology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

11.5Author DataRank

Indexed papers

11in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 11 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

Papers

Driven by 84 papers — median percentile 47. Top paper: “A Python library for probabilistic analysis of single-cell omics data”.

A Python library for probabilistic analysis of single-cell omics data

Nature Biotechnology(2022)10.1038/s41587-021-01206-w

N/A

9.4DataRank · unranked

825 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong +24 more

Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

Cell(2021)10.1016/j.cell.2021.05.045

N/A

8.1DataRank · unranked

514 citations

Chao Wang, Johannes Fessler, David DeTomaso, Julián Ávila-Pacheco, James J. Kaminski +21 more

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Science(2022)10.1126/science.abl4896

Top 4%

5.3DataRank

Top 4%1018 citations

Robert C. Jones, Jim Karkanias, Naftali Kaminski, Angela Oliveira Pisco, Stephen R. Quake +181 more

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

Cell(2021)10.1016/j.cell.2021.05.039

N/A

4.1DataRank · unranked

285 citations

Michele Donato, Alex Kuo, Tal Ashuach, Shakti Gupta, Chunfeng Li +18 more

Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis

Journal of Clinical Investigation(2020)10.1172/jci138519

N/A

3.5DataRank · unranked

107 citations

Allon Wagner, Alexandra Kitz, Jacob Laperche, Nir Yosef, Margarita Dominguez‐Villar +2 more

Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma

Cell(2024)10.1016/j.cell.2023.11.032

N/A

3.4DataRank · unranked

195 citations

Ken Xie, Florian Ingelfinger, Yonatan Katzenelenbogen, Kathleen Abadie, Thomas Look +24 more

Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity

Journal of Experimental Medicine(2016)10.1084/jem.20151118

N/A

2.5DataRank · unranked

62 citations

Takaaki Kondo, Sheng Xiao, Nir Yosef, Jellert T. Gaublomme, Chuan Wu +6 more

An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets

Cell Reports(2020)10.1016/j.celrep.2020.108433

N/A

2.5DataRank · unranked

90 citations

Asaf Madi, Nir Yosef, Norio Chihara, Amit Awasthi, Caroline Pot +20 more

Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages

Genome Research(2022)10.1101/gr.275509.121

N/A

2.5DataRank · unranked

55 citations

Farnaz Shamsi, Nicolas Altemose, Gabriel F. Dorlhiac, Aaron M. Cypess, Andrew P. White +5 more

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Nature Methods(2023)10.1038/s41592-023-01994-w

N/A

2.3DataRank · unranked

123 citations

Herbert B. Schiller, Mohammad Lotfollahi, Dominik Klein, Michal Klein, Aaron Streets +3 more

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.28.441833

N/A

2.3DataRank · unranked

72 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Katherine Wu, Michael Jayasuriya +20 more

Pluripotency Transcription Factor Oct4 Mediates Stepwise Nucleosome Demethylation and Depletion

Molecular and Cellular Biology(2015)10.1128/mcb.01105-14

N/A

2.1DataRank · unranked

55 citations

Catherine Callister, Alon Goren, Nir Yosef, Neha Garg, Vahid Khoddami +4 more

Predicting gene expression in massively parallel reporter assays: A comparative study

Human Mutation(2017)10.1002/humu.23197

N/A

1.7DataRank · unranked

52 citations

Haoyang Zeng, Matthew D. Edwards, Gamze Gürsoy, Kevin Tian, R. Alan Harris +20 more

Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

eLife(2021)10.7554/elife.61276

N/A

1.5DataRank · unranked

77 citations

Melanie I. Worley, Riku Yasutomi, Nir Yosef, Iswar K. Hariharan, Nicholas J. Everetts

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.12.503709

N/A

1.4DataRank · unranked

33 citations

Herbert B. Schiller, Mohammad Lotfollahi, Dominik Klein, Michal Klein, Aaron Streets +3 more

Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling

Immunity(2022)10.1016/j.immuni.2022.08.007

N/A

1.2DataRank · unranked

49 citations

David DeTomaso, Alexandra Schnell, Youjin Lee, Jackson Nyman, Danielle Dionne +15 more

Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation

Frontiers in Immunology(2022)10.3389/fimmu.2022.917232

N/A

1.1DataRank · unranked

50 citations

Wataru Fujii, Theodore S. Kapellos, Erika Dudkin, Nico Reusch, Ari Horne +44 more

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Nature(2013)10.1038/nature12172

N/A

1.1DataRank · unranked

1301 citations

Rahul Satija, Xian Adiconis, Rona S. Gertner, Jellert T. Gaublomme, Raktima Raychowdhury +14 more

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Science(2022)10.1126/science.abl5197

N/A

1.1DataRank · unranked

1186 citations

Chuan Xu, Lorna B. Jarvis, Daniel B. Rainbow, Steven B. Wells, Tomás Gomes +36 more

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling

Cell Reports(2017)10.1016/j.celrep.2017.06.016

N/A

1.1DataRank · unranked

31 citations

Dariusz Przybylski, Nir Yosef, Jana W Qiao, Raktima Raychowdhury, Tanja Maritzen +10 more

Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation

Nature Communications(2022)10.1038/s41467-022-28659-0

N/A

1.1DataRank · unranked

48 citations

Tal Ashuach, Fumitaka Inoue, Alex Khodaverdian, Chengyu Deng, Nir Yosef +2 more

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

Cell(2011)10.1016/j.cell.2011.01.004

N/A

1.0DataRank · unranked

984 citations

Aravind Subramanian, Lee N. Lawton, Raymond H. Mak, W. Nicholas Haining, Naomi Habib +23 more

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

Molecular Systems Biology(2021)10.15252/msb.20209620

N/A

0.988DataRank · unranked

725 citations

Romain Lopez, Edouard Melhman, Jeffrey Regier, Michael I. Jordan, Nir Yosef +1 more

Revealing the vectors of cellular identity with single-cell genomics

Nature Biotechnology(2016)10.1038/nbt.3711

N/A

0.983DataRank · unranked

701 citations

Prisca Liberali, Nir Yosef, Allon Wagner

Mapping single-cell data to reference atlases by transfer learning

Nature Biotechnology(2021)10.1038/s41587-021-01001-7

N/A

0.962DataRank · unranked

610 citations

Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter +9 more

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

Cell(2015)10.1016/j.cell.2015.11.009

N/A

0.960DataRank · unranked

601 citations

Nir Yosef, Youjin Lee, Rona S. Gertner, Li V. Yang, Chuan Wu +9 more

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity

Cell(2015)10.1016/j.cell.2015.10.068

N/A

0.898DataRank · unranked

398 citations

Nir Yosef, Chuan Wu, Youjin Lee, Clary B. Clish, Jim Kaminski +17 more

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

Cell(2022)10.1016/j.cell.2022.04.015

N/A

0.879DataRank · unranked

350 citations

Matthew G. Jones, Santiago Naranjo, William M. Rideout, Kyung Hoi Min, Raymond Ho +18 more

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

Cell(2011)10.1016/j.cell.2011.09.057

N/A

0.872DataRank · unranked

334 citations

Alon Goren, Ido Amit, Noam Shoresh, Nir Yosef, Jason Ernst +12 more

MultiVI: deep generative model for the integration of multimodal data

Nature Methods(2023)10.1038/s41592-023-01909-9

N/A

0.871DataRank · unranked

331 citations

Mariano I. Gabitto, Rohan V. Koodli, Giuseppe-Antonio Saldi, Michael I. Jordan, Nir Yosef +1 more

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

Science(2021)10.1126/science.abc1944

N/A

0.867DataRank · unranked

323 citations

Matthew G. Jones, Ross A. Okimoto, Shigeki Nanjo, Michelle M. Chan, Nir Yosef +3 more

T cell self-reactivity during thymic development dictates the timing of positive selection

eLife(2021)10.7554/elife.65435

N/A

0.862DataRank · unranked

26 citations

Zoë Steier, Laura L. McIntyre, Shraddha Pandey, James J. Kaminski, Ashley R. Hoover +5 more

Impulse Control: Temporal Dynamics in Gene Transcription

Cell(2011)10.1016/j.cell.2011.02.015

N/A

0.852DataRank · unranked

291 citations

Prisca Liberali, Nir Yosef

Small-Molecule RORγt Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms

Immunity(2014)10.1016/j.immuni.2014.04.004

N/A

0.844DataRank · unranked

276 citations

Nir Yosef, Jianfei Yang, Yonghui Wang, Ling Zhou, Chen Zhu +23 more

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

Cell(2011)10.1016/j.cell.2011.10.022

N/A

0.781DataRank · unranked

182 citations

Philipp Mertins, Maxim N. Artyomov, Alex K. Shalek, Matteo Iannacone, Mark F. Ciaccio +21 more

Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia

Nano Letters(2012)10.1021/nl3042917

N/A

0.776DataRank · unranked

175 citations

Jellert T. Gaublomme, Lili Wang, Nir Yosef, Nicolas Chevrier, Mette S. Andersen +12 more

In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.23.912717

N/A

0.737DataRank · unranked

12 citations

Chao Wang, David DeTomaso, Julian Avila-Pacheco, Sarah Zaghouani, Johannes Fessler +17 more

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

Nature Immunology(2017)10.1038/ni.3683

N/A

0.729DataRank · unranked

128 citations

Emily R. Miraldi, Maria Pokrovskii, Asaf Madi, Nir Yosef, Ivo Wortman +10 more

Author response: The Human Cell Atlas

(2017)10.7554/elife.27041.011

Top 29%

0.700DataRank

Top 29%14 citations

Sarah A. Teichmann, Matthew E. Hurles, Ido Amit, Kerstin Lindblad‐Toh, Bernd Bodenmiller +60 more

Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs

Cell Metabolism(2023)10.1016/j.cmet.2023.01.009

N/A

0.652DataRank · unranked

76 citations

Ibrahim Hamad, Rebeca Arroyo Hornero, Sabrina Geisberger, Joris Roels, Lauren Van Zeebroeck +23 more

Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment

Nature Immunology(2023)10.1038/s41590-023-01584-0

N/A

0.609DataRank · unranked

57 citations

Dominik A. Aylard, Laura L. McIntyre, Isabel Baldwin, Esther Jeong Yoon Kim, Lydia K. Lutes +6 more

Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs

Current Biology(2022)10.1016/j.cub.2022.06.040

N/A

0.596DataRank · unranked

52 citations

Nicholas J. Everetts, Riku Yasutomi, Rebecca J. Chang, Shrey Saretha, Nir Yosef +2 more

Writ large: Genomic dissection of the effect of cellular environment on immune response

Science(2016)10.1126/science.aaf5453

N/A

0.590DataRank · unranked

50 citations

Prisca Liberali, Nir Yosef

Consensus prediction of cell type labels in single-cell data with popV

Nature Genetics(2024)10.1038/s41588-024-01993-3

N/A

0.581DataRank · unranked

47 citations

Galen Xing, Chenling Xu, Martin Kim, Michael Jayasuriya, Erin McGeever +4 more

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.16.045245

N/A

0.553DataRank · unranked

39 citations

Matthew G. Jones, Ross A. Okimoto, Shigeki Nanjo, Michelle M. Chan, Nir Yosef +3 more

Impulse model-based differential expression analysis of time course sequencing data

Nucleic Acids Research(2018)10.1093/nar/gky675

N/A

0.553DataRank · unranked

39 citations

Fabian Joachim Theis, Nir Yosef, David S. Fischer

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumour growth and metastasis

10.1101/2024.10.21.619529

N/A

0.489DataRank · unranked

25 citations

Dawei Sun, Kyung Hoi Min, William N. Colgan, Haoyu Wang, Tivadar Török +26 more

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.03.573877

N/A

0.449DataRank · unranked

19 citations

Daniel B. Rainbow, Michal Mark, Peter A. Szabo, Can Ergen, Ana Raquel Maceiras +26 more

Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.12.464111

N/A

0.439DataRank · unranked

10 citations

Matthew G. Jones, Santiago Naranjo, William M. Rideout, Kyung Hoi Min, Raymond Ho +18 more

Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.08.083337

N/A

0.396DataRank · unranked

13 citations

Zoë Steier, Romain Lopez, Jeffrey Regier, Kristopher L. Nazor, Aaron Streets +2 more

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.28.121541

N/A

0.385DataRank · unranked

12 citations

Wataru Fujii, Theodore S. Kapellos, Arik Horne, Benedikt Reiz, Erika Dudkin +41 more

Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.23.911966

N/A

0.361DataRank · unranked

7 citations

Allon Wagner, Johannes Fessler, Julian Avila-Pacheco, Jim Karminski, Sarah Zaghouani +22 more

ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.03.569785

N/A

0.360DataRank · unranked

10 citations

Akshay Ravoor, Nir Yosef, Yun S. Song, Sebastian Prillo

A heterogeneous pharmaco-transcriptomic landscape induced by targeting a single oncogenic kinase

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.08.587960

N/A

0.292DataRank · unranked

6 citations

Nicholas Hou, Lingting Shi, Adeya Wyatt, Justin Hong, Mathini Vaikunthan +9 more

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.02.502100

N/A

0.282DataRank · unranked

3 citations

Peiyi Chen, Galen Xing, Mir M. Khalid, Nathan L. Meyers, Jennifer M. Hayashi +18 more

The glycolytic reaction PGAM restrains Th17 pathogenicity and Th17-dependent autoimmunity

Cell Reports(2025)10.1016/j.celrep.2025.115799

N/A

0.208DataRank · unranked

3 citations

Allon Wagner, Johannes Fessler, David DeTomaso, Sarah Zaghouani, Yulin Zhou +6 more

Impulse model-based differential expression analysis of time course sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/113548

N/A

0.208DataRank · unranked

3 citations

Fabian Joachim Theis, Nir Yosef, David S. Fischer

High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.15.659774

N/A

0.208DataRank · unranked

3 citations

Kathryn E. Yost, Pu Zheng, William N. Colgan, Matthew G. Jones, Dian Yang +11 more

Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans

medRxiv(2021)10.1101/2021.05.24.21253087

N/A

0.165DataRank · unranked

2 citations

Michele Donato, Alex Kuo, Tal Ashuach, Shakti Gupta, Chunfeng Li +18 more

The Transcription Factor BATF Controls CD8+ T Cell Effector Differentiation

Blood(2013)10.1182/blood.v122.21.189.189

N/A

0.142DataRank · unranked

1 citations

Makoto Kurachi, Madeleine E. Lemieux, Nir Yosef, Michael A. DiIorio, Kathleen B. Yates +8 more

Cross-Species Analysis of Protein-protein Interaction Networks

Computational Biology(2008)10.1007/978-1-84800-125-1_9

N/A

0.133DataRank · unranked

1 citations

Eytan Ruppin, Roded Sharan, Nir Yosef

Hepatitis C Virus Infects and Perturbs Liver Stem Cells

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.26.465357

N/A

0.120DataRank · unranked

1 citations

Tal Ashuach, Danielle E. Lyons, Camille R. Simoneau, Ann L. Erickson, Mehdi Bouhaddou +15 more

Molecular cues dictating positive and negative selection in the thymus

The Journal of Immunology(2020)10.4049/jimmunol.204.supp.61.13

N/A

0.109DataRank · unranked

1 citations

Zoe Steier, Lydia Lutes, Aaron Streets, Nir Yosef, Ellen A Robey +1 more

Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.27.222976

Top 78%

0.104DataRank

Top 78%1 citations

Melanie I. Worley, Riku Yasutomi, Nir Yosef, Iswar K. Hariharan, Nicholas J. Everetts

Additional file 5 of MPRAnalyze: statistical framework for massively parallel reporter assays

Figshare(2019)10.6084/m9.figshare.9760595

Top 100%

0DataRank

Top 100%0 citations

David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian Joachim Theis, Nir Yosef +1 more

Directed Shortest Walk on Temporal Graphs

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.08.499368

N/A

0DataRank · unranked

2 citations

Nir Yosef, Alex Khodaverdian

The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5‘ and 3‘ gene regions

Journal of Biological Chemistry(2020)10.1074/jbc.ra120.013426

N/A

0DataRank · unranked

45 citations

Yun S. Song, Nir Yosef, Julia di Iulio, L. Stirling Churchman, Mordechai Choder +1 more

Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.04.425241

N/A

0DataRank · unranked

3 citations

James J. Kaminski, Makoto Kurachi, R. Anthony Barnitz, Michael DiIorio, Martin W. LaFleur +6 more

Critical genetic program for Drosophila imaginal disc regeneration revealed by single-cell analysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.08.451678

N/A

0DataRank · unranked

2 citations

Nicholas J. Everetts, Riku Yasutomi, Nir Yosef, Iswar K. Hariharan, Melanie I. Worley

PhyloVision : Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and Phylogenetic Data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.13.460142

N/A

0DataRank · unranked

1 citations

Yanay Rosen, Nir Yosef, Matthew G. Jones

CD4+ and CD8+ cytotoxic T lymphocytes may induce mesenchymal cell apoptosis in IgG4-related disease

Journal of Allergy and Clinical Immunology(2020)10.1016/j.jaci.2020.05.022

N/A

0DataRank · unranked

99 citations

Naoki Kaneko, Takashi Maehara, Hamid Mattoo, Jesper Kers, Hugues Allard‐Chamard +23 more

Interpretable factor models of single-cell RNA-seq via variational autoencoders

Bioinformatics(2020)10.1093/bioinformatics/btaa169

N/A

0DataRank · unranked

221 citations

Adam Gayoso, Nir Yosef, Lior Pachter, Valentine Svensson

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia

Genome biology(2020)10.1186/s13059-020-02000-8

N/A

0DataRank · unranked

145 citations

Alex Khodaverdian, Jeffrey J. Quinn, Michelle M. Chan, Jeffrey A. Hussmann, Robert Wang +4 more

Systems-based approaches to study immunometabolism

Cellular and Molecular Immunology(2022)10.1038/s41423-021-00783-9

N/A

0DataRank · unranked

59 citations

Allon Wagner, Nir Yosef, Vijay K. Kuchroo, Vinee Purohit

CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels

Cell Reports(2022)10.1016/j.celrep.2021.110266

N/A

0DataRank · unranked

41 citations

Alexandra Tsitsiklis, Zoë Steier, Shiao Wei Chan, James J. Kaminski, Aaron Streets +3 more

Additional file 6 of MPRAnalyze: statistical framework for massively parallel reporter assays

Figshare(2019)10.6084/m9.figshare.9760601

N/A

0DataRank · unranked

0 citations

David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian Joachim Theis, Nir Yosef +1 more

Mucosal vaccination with cyclic-di-nucleotide adjuvants induces effective T cell homing and IL-17 dependent protection against M. tuberculosis infection

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.25.398651

N/A

0DataRank · unranked

0 citations

Erik Van Dis, Xammy Nguyenla, Alexander Baltodano, Gabrielle Pastenkos, Chenling Xu +4 more

Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors

Research Square(2022)10.21203/rs.3.rs-1641376/v1

N/A

0DataRank · unranked

0 citations

Sanju Sinha, Rahulsimham Vegesna, Ashwin V. Kammula, Saugato Rahman Dhruba, Wei Wu +14 more

Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Science Immunology(2024)10.1126/sciimmunol.adn3954

N/A

0DataRank · unranked

84 citations

Daniel P. Caron, Steven B. Wells, Rebecca Guyer, Peter A. Szabo, Daniel B. Rainbow +16 more

NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids

Scientific Reports(2024)10.1038/s41598-024-66003-2

N/A

0DataRank · unranked

14 citations

Peiyi Chen, Galen Xing, Jennifer M. Hayashi, Irene P. Chen, Mir M. Khalid +21 more

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

Nature Immunology(2025)10.1038/s41590-025-02241-4

N/A

0DataRank · unranked

30 citations

Daniel B. Rainbow, Michal Mark, Peter A. Szabo, Can Ergen, Daniel P. Caron +26 more

ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing

Systematic Biology(2025)10.1093/sysbio/syaf054

N/A

0DataRank · unranked

6 citations

Akshay Ravoor, Nir Yosef, Yun S. Song, Sebastian Prillo

Additional file 4 of MPRAnalyze: statistical framework for massively parallel reporter assays

Figshare(2019)10.6084/m9.figshare.9760592

Top 100%

0DataRank

Top 100%0 citations

David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian Joachim Theis, Nir Yosef +1 more

Nir Yosef

Indexed papers

Top data-sharing exemplar

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