publications

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis
MG. Jones, D. Sun, KH. Min, WN. Colgan, L. Tian, JA. Weir, VZ. Chen, W. Koblan, KE. Yost, N. Mathey-Andrews, A.J.C. Russell, RR. Stickels, KS. Balderrama, WM. Rideout III, HY. Chang, T. Jacks, F. Chen†, JS. Weissman†, N. Yosef† , Dian Yang†
bioRxiv , 2024
10.1101/2024.10.21.619529
bioRxiv preprint

The glycolytic reaction PGAM unexpectedly restrains Th17 pathogenicity and Th17-dependent autoimmunity
C. Wang*, A. Wagner*, J. Fessler*, D. DeTomaso, S. Zaghouani, Y. Zhou, K. Pierce, RA. Sobel, C. Clish, Nir Yosef†, VK. Kuchroo†
bioRxiv , 2024
10.1101/2024.08.18.607992v1
bioRxiv preprint

Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics
P. Boyeau*, J. Hong*, A. Gayoso, M. Kim, JL. McFaline-Figueroa, M. Jordan, E. Azizi, C. Ergen†, N. Yosef†
bioRxiv , 2024
10.1101/2022.10.04.510898
bioRxiv preprint

Scvi-hub: an actionable repository for model-driven single cell analysis
C. Ergen, VV. Pour Amiri, M. Kim, A. Streets, A. Gayoso, N. Yosef
bioRxiv , 2024
10.1101/2024.03.01.582887
bioRxiv preprint

ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data
S. Prillo, A. Ravoor, N. Yosef†, YS. Song†
bioRxiv , 2024
10.1101/2023.12.03.569785
bioRxiv preprint

Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining
S. Prillo, K. An, W. Wu, I. Kristanto, MG. Jones, YS. Song† , N. Yosef†
bioRxiv , 2024

AutoEval Done Right: Using Synthetic Data for Model Evaluation
P. Boyeau, AN. Angelopoulos, N. Yosef, J. Malik, MI. Jordan
arXiv , 2024
10.48550/arXiv.2403.07008

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age
SB. Wells*, DB. Rainbow*, M. Mark*, PA. Szabo*, C. Ergen*, A. Maceiras*, DP. Caron, E. Rahmani, E. Benuck, V. Pour Amiri, D. Chen, A. Wagner, SK. Howlett, LB. Jarvis, KL. Ellis, M. Kubota, R. Matsumoto, K. Mahbubani, K. Saeb-Parsy, C. Dominguez-Conde, L. Richardson, C. Xu, S. Li, L. Mamanova, L. Bolt, A. Wilk, SA. Teichmann†, DL. Farber†, PA. Sims†, JL. Jones†, N. Yosef†
bioRxiv , 2024
10.1101/2022.07.08.499368
GitHub
bioRxiv preprint

Calibrated Identification of Feature Dependencies in Single-cell Multiomics
P. Boyeau, S. Bates, C. Ergen, MI. Jordan, N. Yosef
Genome Biology (in press) , 2024
10.1101/2023.11.03.565520
bioRxiv preprint

Consensus prediction of cell type labels with popV
C. Ergen, G. Xing, C. Xu, M. Jayasuriya, E. McGeever, A.O. Pisco, A. Streets, N. Yosef
Nature Genetics (in press) , 2024
10.1101/2023.08.18.553912
GitHub
bioRxiv preprint

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
A. Gayoso*, P. Weiler*, M. Lotfollahi, D. Klein, J. Hong, A. Streets, FJ. Theis†, N. Yosef†
Nature Methods , 2024
10.1038/s41592-023-01994-w

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids
CR. Simoneau*, P. Chen*, GK. Xing*, MM. Khalid, NL. Meyers, JM. Hayashi, TY. Taha, KE. Leon, T. Ashuach, KA. Fontaine, L. Rodriguez, B. Joehnk, K. Walcott, S. Vasudevan, X. Fang, M. Maishan, S. Schultz, J. Roose, MA. Matthay, A. Sil, M. Arjomandi, N. Yosef†, M. Ott†
Scientific Reports , 2024
10.1038/s41598-024-66003-2

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
The Critical Assessment of Genome Interpretation Consortium
Genome Biology , 2024
10.1186/s13059-023-03113-6

Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span
Gray, J. I., Caron, D. P., Wells, S. B., Guyer, R., Szabo, P., Rainbow, D., Ergen, C., Rybkina, K., Bradley, M. C., Matsumoto, R., Pethe, K., Kubota, M., Teichmann, S., Jones, J., Yosef, N., Atkinson, M., Brusko, M., Brusko, T. M., Connors, T. J., Sims, P. A., Farber, D. L.
Genome Biology , 2024
10.1126/sciimmunol.adn3954

PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors
Sinha, S., Vegesna, R., Mukherjee, S., Kammula, A. V., Dhruba, S. R., Wu, W., Kerr, D. L., Nair, N. U., Jones, M. G., Yosef, N., Stroganov, O. V., Grishagin, I., Aldape, K. D., Blakely, C. M., Jiang, P., Thomas, C. J., Benes, C. H., Bivona, T. G., Schäffer, A. A., & Ruppin, E.
Nature cancer , 2024
10.1038/s43018-024-00756-7

Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma
D. Kirschenbaum, K. Xie, F. Ingelfinger, Y. Katzenelenbogen, K. Abadie, T. Look, F. Sheban, T. San Phan, B. Li, P. Zwicky, I. Yofe, E. David, K. Mazuz, J. Hou, Y. Chen, H. Shaim, M. Shanley, S. Becker, J. Qian, M. Colonna, F. Ginhoux, K. Rezvani, FJ. Theis, N. Yosef, T. Weiss, A. Weiner, I. Amit
Cell , 2024
10.1016/j.cell.2023.11.032

Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework
J. Liu, T. Ashuach, F. Inoue, N. Ahituv, N. Yosef, A. Kreimer
Nucleic Acids Research , 2024
10.1093/nar/gkae012

Single-cell multi-omic analysis of thymocyte development reveals NFAT as a driver of CD4/CD8 lineage commitment
Z. Steier, LL. McIntyre, LK. Lutes, T Huang, EA. Robey†, N. Yosef†, A. Streets†
Nature Immunology , 2023
10.1038/s41590-023-01584-0

An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models
P. Boyeau, J. Regier, A. Gayoso, M.I. Jordan, R. Lopez†, N. Yosef†
Proc Natl Acad Sci , 2023
10.1073/pnas.2209124120

MultiVI: deep generative model for the integration of multi-modal data.
T. Ashuach*, M. Gabitto*, M. Jordan, N. Yosef
Nature Methods , 2023
10.1038/s41592-023-01909-9
GitHub

Theoretical Guarantees for Phylogeny Inference from Single-Cell Lineage Tracing
R. Wang*, RY. Zhang*, A. Khodaverdian*, Nir Yosef
Proc Natl Acad Sci , 2023
10.1073/pnas.2203352120

The scverse project provides a computational ecosystem for single-cell omics data analysis
Virshup I*, Bredikhin D*, Heumos L*, Palla G*, Sturm G*, Gayoso A*, Kats I, Koutrouli M; Scverse Community; Berger B, Pe’er D, Regev A, Teichmann SA, Finotello F†, Wolf FA†, Yosef N†, Stegle O†, Theis FJ†
Nature Biotechnology , 2023
10.1038/s41587-023-01733-8

Hepatitis C Virus Infects and Perturbs Liver Stem Cells
Meyers NL, Ashuach T, Lyons DE, Simoneau CR, Erickson AL, Bouhaddou M, Nguyen TT, Khalid MM, Taha TY, Natajaran V, Baron JL, Neff N, Zanini F, Mahmoud T, Quake SR, Krogan NJ, Cooper S, McDevitt TC, N. Yosef†, M. Ott†
mBio , 2023
10.1128/mbio.01318-23

Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs
B.F. Côrte-Real, I. Hamad, R. Arroyo Hornero, S. Geisberger, J. Roels, L. Van Zeebroeck, A. Dyczko, M.W. van Gisbergen, H. Kurniawan, A. Wagner, N. Yosef, S.N.Y. Weiss, K.G. Schmetterer, A. Schröder, L. Krampert, S. Haase, H. Bartolomaeus, N. Hellings, Y. Saeys, L.J. Dubois, D. Brenner, S. Kempa, D.A. Hafler, J. Stegbauer, R.A. Linker, J. Jantsch, D.N. Müller, M. Kleinewietfeld
Cell Metabolism , 2023
10.1016/j.cmet.2023.01.009

Directed Shortest Walk on Temporal Graphs
A. Khodaverdian and N. Yosef
bioRxiv , 2023
10.1101/2022.07.08.499368
GitHub
bioRxiv preprint

Induction of a colitogenic phenotype in Th1 cells depends on interleukin 23 receptor signaling
M. Pawlak*, D. DeTomaso*, GM. zu Horste, Y. Lee, J. Nyman, D. Dionne, C. Wang, A. Wallrapp, PR. Burkett, SJ. Riesenfeld, AC. Anderson, A. Regev, RJ. Xavier, N. Yosef†, VK. Kuchroo†
Immunity (in press) , 2022
10.1016/j.immuni.2022.08.007

A Python library for probabilistic analysis of single-cell omics data.
A. Gayoso*, R. Lopez*, G. Xing*, P. Boyeau, V. Valiollah Pour Amiri, J. Hong, K. Wu, M. Jayasuriya, E. Melhman, M. Langevin, Y. Liu, J. Samaran, G. Misrachi, A. Nazaret, O. Clivio, C. Xu, T. Ashuach, M. Lotfollahi, V.Svensson, E. da Veiga Beltrame, V. Kleshchevnikov, C. Talavera-Lopez, L. Pachter, F.J. Theis, A. Streets, M.I. Jordan, J. Regier, N. Yosef
Nature Biotechnology , 2022
10.1038/s41587-021-01206-w
GitHub
bioRxiv preprint

DestVI identifies continuums of cell types in spatial transcriptomics data
R. Lopez*, B. Li*, H. Keren-Shaul*, P. Boyeau, M. Kedmi, D. Pilzer, A.Jelinski, E. David, A. Wagner, Y. Addadi, M.I. Jordan, I. Amit†, N. Yosef†
Nature Biotechnology , 2022
10.1038/s41587-022-01272-8
GitHub

Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation.
H.W. Tsao*, J. Kaminski*, M. Kurachi, R.A. Barnitz, M.A. DiIorio, M.W. LaFleur, W. Ise, T. Kurosaki, E.J. Wherry, W.N. Haining†, N. Yosef†
Science Immunology , 2022
10.1126/sciimmunol.abi4919

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution
D. Yang*, MG. Jones*, S. Naranjo, WM. Rideout III, KH. Min, R. Ho, W. Wu, RM. Replogle, JL. Page, JJ. Quinn, F. Horns, X. Qiu, MZ. Chen, WA. Freed-Pastor, CS. McGinnis, DM. Patterson, ZJ. Gartner, ED. Chow, TG. Bivona, MM. Chan, N. Yosef†, T. Jacks†, JS. Weissman†
Cell , 2022
10.1016/j.cell.2022.04.015
GitHub

The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors
The Tabula Sapiens Consortium
Science , 2022
10.1126/science.abq2116

Identifying systematic variation at the single-cell level by leveraging low-resolution population-level data.
E. Rahmani, MI. Jordan, N. Yosef
RECOMB , 2022
GitHub
bioRxiv preprint

Identifying cell-state associated alternative splicing events and their co-regulation
CF. Buen Abad Najar, P. Burra, N. Yosef†, LF. Lareau†
Genome Research , 2022
bioRxiv preprint

Systems-based approaches to study immunometabolism.
V. Purohit, A. Wagner, N. Yosef, V.K. Kuchroo
Cellular & Molecular Immunology , 2022
https://doi.org/10.1038/s41423-021-00783-9

PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis.
T. Ashuach, DA. Reidenbach, A. Gayoso, N. Yosef
Cell Reports Methods , 2022
10.1016/j.crmeth.2022.100182
GitHub

Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision
MG. Jones*, Y. Rosen*, N. Yosef
Cell Reports Methods , 2022
Content Sharing link
10.1016/j.crmeth.2022.100200
GitHub

Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation
A. Kreimer*, T. Ashuach*, F. Inoue*, A. Khodaverdian, N. Yosef†, N. Ahituv†
Nature Communications , 2022
0.1038/s41467-022-28659-0

Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs.
MI .Worley*, N. Everetts*, R. Yasutomi, RJ. Chang, S. Saretha, N. Yosef†, IK. Hariharan†
Current Biology , 2022
10.1016/j.cub.2022.06.040

Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
A. Gupta, F. Shamsi, N. Altemose, GF. Dorlhiac, AM. Cypess, AP. White, N. Yosef, ME. Patti, Y. Tseng, A. Streets
Genome Research , 2022
10.1101/gr.275509.121

CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels
DJ. Bangs, A. Tsitsiklis, Z. Steier, SW. Chan, J. Kaminski, A. Streets, N. Yosef, EA. Robey
Cell Reports , 2022
10.1016/j.celrep.2021.110266

Mucosal Vaccination with Cyclic Dinucleotide Adjuvants Induces Effective T Cell Homing and IL-17–Dependent Protection against Mycobacterium tuberculosis Infection
RM. Jong, E. Van Dis, SB. Berry, X. Nguyenla, A. Baltodano, G. Pastenkos, C. Xu, D. Fox, N. Yosef, SM. McWhirter, SA. Stanley
J Immunol , 2022
10.4049/jimmunol.2100029

Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
K. Baßler, W. Fujii, T. S. Kapellos, E. Dudkin, N. Reusch, A. Horne, B. Reiz, M. D. Luecken, C. Osei-Sarpong, S. Warnat-Herresthal, L. Bonaguro, J. Schulte-Schrepping, A. Wagner, P. Günther, C. Pizarro, T. Schreiber, R. Knoll, L. Holsten, C. Kröger, E. De Domenico, M. Becker, K. Händler, C. T. Wohnhaas, F. Baumgartner, M. Köhler, H. Theis, M. Kraut, M. H. Wadsworth II, T. K. Hughes, H. J. Ferreira, E. Hinkley, I. H. Kaltheuner, M. Geyer, C. Thiele, A. K. Shalek, A. Feißt, D. Thomas, H. Dickten, M. Beyer, P. Baum, N. Yosef, A. C. Aschenbrenner, T. Ulas, J. Hasenauer, F. J. Theis, D. Skowasch, J. L. Schultze
Frontiers in Immunology , 2022
10.3389/fimmu.2022.917232

Metabolic modeling of single Th17 cells reveals regulators of autoimmunity.
A. Wagner*, C. Wang*, D. DeTomaso, J. Avila-Pacheco, S. Zaghouani, J. Fessler, E. Akama-Garren, K. Pierce, N. Ron-Harel, V. Paraskevi Douglas, M. Haigis, R.A. Sobel, C. Clish, A. Regev, V.K. Kuchroo†, N. Yosef†
Cell , 2021
10.1016/j.cell.2021.05.045
GitHub
Previewed in Cell; Commentary in Immunometabolism.

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts.
JJ. Quinn*, MG. Jones*, RA. Okimoto, S. Nanjo, MM. Chan, N. Yosef†, TG. Bivona†, JS. Weissman†
Science , 2021
10.1126/science.abc1944
GitHub
bioRxiv preprint

Joint probabilistic modeling of single-cell multi-omic data with totalVI.
A. Gayoso*, Z. Steier*, R. Lopez, J. Regier, KL. Nazor, A. Streets†, N Yosef†
Nature Methods , 2021
10.1038/s41592-020-01050-x
GitHub
bioRxiv preprint
Reproducibility code

Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning.
A.K. Morrow, J.W. Hughes, J. Singh, A.D. Joseph, N. Yosef
Nucleic Acids Research , 2021
https://doi.org/10.1093/nar/gkab676
GitHub

Identifying Informative Gene Modules Across Modalities of Single Cell Genomics.
D. DeTomaso and N. Yosef
Cell Systems , 2021
10.1016/j.cels.2021.04.005
GitHub

Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions.
N. Everetts*, MI .Worley*, R. Yasutomi, N. Yosef†, IK. Hariharan†
eLife , 2021
10.7554/eLife.61276

Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees.
W. Gong*, AA Granados*, J Hu*, MG. Jones*, O. Raz*, I. Salvador-Martinez*, H. Zhang*,…, N. Yosef, J. Shendure, M. Telford, E. Shapiro, MB. Elowitz, P. Meyer
Cell Systems , 2021
10.1016/j.cels.2021.05.008
GitHub

Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data.
K. Ouardini, R. Lopez, MG. Jones, S. Prillo, R. Zhang, MI. Jordan, N. Yosef
ICML 2021 Workshop on Computational Biology , 2021
10.1101/2021.05.28.446021
GitHub
bioRxiv preprint

Mapping single-cell data to reference atlases by transfer learning
M. Lotfollahi, M. Naghipourfar, M. D. Luecken, M. Khajavi, M. Büttner, M. Wagenstetter, Z. Avsec, A. Gayoso, N. Yosef, M. Interlandi,S. Rybakov, A.V. Misharin, F.J. Theis.
Nature Biotechnology , 2021
10.1038/s41587-021-01001-7

T cell self-reactivity during thymic development dictates the timing of positive selection.
LK. Lutes, Z. Steier, LL. McIntyre, S. Pandey, J. Kaminski, AR. Hoover, S. Ariotti, A. Streets, N. Yosef, EA. Robey
eLife , 2021
10.7554/eLife.65435

Polyamine metabolism is a central determinant of helper T cell lineage fidelity
D.J. Puleston, F. Baixauli, D.E. Sanin, J. Edwards-Hicks, M. Villa, A. Kabat, M.M. Kaminski, M. Stanckzak, H.J. Weiss, K.M. Grzes, K. Piletic, C.S. Field, M. Corrado, F. Haessler, C. Wang, Y. Musa, L. Schimmelpfennig, L. Flachsmann, G. Mittler, N. Yosef, V.K Kuchroo, J.M. Buescher, S. Balabanov, E.J. Pearce, D.R. Green, E.L. Pearce
Cell , 2021
10.1016/j.cell.2021.06.007
bioRxiv preprint
Previewed in Cell

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination
F. Wimmers, M. Donato, A. Kuo, T. Ashuach, S. Gupta, C. Li, M. Dvorak, MH. Foecke, SE. Chang, T. Hagan, SE. De Jong, HT. Maecker, R. van der Most, P. Cheung, M. Cortese, SE. Bosinger, M. Davis, N. Rouphael, S. Subramaniam, N. Yosef, PJ. Utz, P. Khatri, B. Pulendran
Cell , 2021
10.1016/j.cell.2021.05.039

Self-guarding of MORC3 enables virulence factor-triggered immunity
Gaidt, M.M., Morrow, A., Fairgrieve, M.R, Karr, J.P, Yosef, N. Vance, R.E
Nature , 2021
10.1038/s41586-021-04054-5

Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis.
SL. Pompura*, A. Wagner*, A. Kitz, J. LaPerche, N. Yosef†, M. Dominguez-Villar†, DA, Hafler†
The Journal of Clinical Investigation , 2020
10.1172/JCI138519
Highlighted in The New England Journal of Medicine, clinical implications of basic research

Decision-making with auto-encoding variational Bayes.
R. Lopez, P. Boyeau, N. Yosef, M. Jordan & J. Regier.
Advances in Neural Information Processing Systems , 2020
GitHub
arXiv preprint

Enhancing scientific discoveries in molecular biology with deep generative models.
R. Lopez, A. Gayoso & N. Yosef.
Molecular Systems Biology , 2020
10.15252/msb.20199198

Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
C. Xu*, R. Lopez*, E. Mehlman*, J. Regier, M.I. Jordan, N. Yosef
Molecular Systems Biology , 2020
10.15252/msb.20209620
GitHub
Reproducibility code

Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis.
D. Schafflick*, C. Xu*, M. Hartlehnert*, M. Cole*, T. Lautwein, K. Buscher, J.Wolbert, SG. Meuth, T. Kuhlmann, C. Gross, H. Wiendl, N. Yosef† , G.M zu Horste†
Nature Communications , 2020
10.1038/s41467-019-14118-w

Inference of Single-Cell Phylogenies from Lineage Tracing Data.
MG. Jones*, A. Khodaverdian*, JJ. Quinn*, MM. Chan, JA. Hussmann, R. Wang, C. Xu, JS. Weissman†, N. Yosef†
Genome Biology , 2020
10.1186/s13059-020-02000-8
GitHub

Interpretable factor models of single-cell RNA-seq via variational autoencoders.
V. Svensson, A. Gayoso, N. Yosef, L. Pachter.
Bioinformatics , 2020
10.1093/bioinformatics/btaa169

Coverage-dependent bias creates the appearance of binary splicing in single cells.
CF. Buen Abad Najar, N. Yosef†, LF. Lareau†.
eLife , 2020
10.7554/eLife.54603

LentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
Gordon, M. G., Inoue, F., Martin, B., Schubach, M., Agarwal, V., Whalen, S., Feng, S., Zhao, J., Ashuach, T., Ziffra, R., Kreimer, A., Georgakopoulous-Soares, I., Yosef, N., Ye, C. J., Pollard, K. S., Shendure, J., Kircher, M., & Ahituv, N.
Nature Protocols , 2020
10.1038/s41596-020-0333-5

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
F. Inoue*, A. Kreimer*, T. Ashuach, N. Ahituv†, N. Yosef†
Cell Stem Cell , 2019
10.1016/j.stem.2019.09.010

MPRAnalyze—A statistical framework for Massively Parallel Reporter Assays.
T. Ashuach*, DS Fischer*, FJ Theis, N. Yosef.
Genome Biology , 2019
10.1186/s13059-019-1787-z

Functional Interpretation of Single-Cell Similarity Maps.
D. Detomaso*, M. Jones*, M. Subramanian, J. Ye, N. Yosef.
Nature Communications , 2019
10.1038/s41467-019-12235-0
GitHub

Simulating multi-faceted variability in single cell RNA sequencing.
X. Zhang*, C. Xu*, N. Yosef.
Nature Communications , 2019
10.1038/s41467-019-10500-w
GitHub

Reconstructing B cell receptor sequences from short-read single cell RNA-sequencing with BRAPeS.
S. Afik*, G. Raulet* and N. Yosef.
Life Science Alliance , 2019
10.26508/lsa.201900371

Meta-analysis of massively parallel reporter assays enables the prediction of regulatory elements.
A. Kreimer*, Z. Yan*, N. Ahituv, N. Yosef
Human Mutation , 2019
10.1002/humu.23820

Connectivity Problems on Heterogeneous Graphs
J. Wu, A. Khodaverdian, B.Weitz, N. Yosef
Algorithms for Molecular Biology , 2019
10.1186/s13015-019-0141-z

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.
MB. Cole, D. Risso, A. Wagner, D. DeTomaso, J. Ngai, E. Purdom, S. Dudoit†, N. Yosef†
Cell Systems , 2019
10.1016/j.cels.2019.03.010
GitHub

Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets.
AK Morrow, GZ He, FA Nothaft, ET Tu, J Paschall, N Yosef, AD. Joseph
Cell Systems , 2019
10.1016/j.cels.2019.11.002

Molecular recording of mammalian embryogenesis.
MM. Chan, ZD. Smith, S. Grosswendt, H. Kretzmer, TM. Norman, B. Adamson, M. Jost, JJ. Quinn, D. Yang, MG. Jones, A. Khodaverdian, N. Yosef, A. Meissner, JS. Weissman
Nature , 2019
10.1038/s41586-019-1184-5

A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements.
R. Lopez*, A. Nazaret*, M. Langevin*, J. Samaran*, J. Regier*, M.I. Jordan, N. Yosef
ICML 2019 Workshop on Computational Biology (spotlight presentation; best student’s poster) , 2019
arXiv preprint
Reproducibility code

Deep generative models for detecting differential expression in single cells.
P. Boyeau, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N. Yosef
Machine Learning in Computational Biology meeting , 2019
bioRxiv preprint

Detecting zero-inflated genes in single-cell transcriptomics data.
O. Clivio, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N Yosef
Machine Learning in Computational Biology meeting (spotlight presentation) , 2019
bioRxiv preprint
Reproducibility code

A joint model of RNA expression and surface protein abundance in single cells
A. Gayoso, R. Lopez, ZR. Steier, J. Regier, AM Streets, N. Yosef
Machine Learning in Computational Biology meeting , 2019
bioRxiv preprint

Deep generative modeling for single-cell transcriptomics.
R. Lopez, J. Regier, MB. Cole, M. Jordan, N. Yosef.
Nature Methods , 2018
10.1038/s41592-018-0229-2
GitHub
News and Views

A Reproducibility-Based Computational Framework Identifies An Inducible Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers.
EM Gayo, MB. Cole, KE Kolb*, Z. Ouyang, J. Cronin, SW. Kazer, J. Ordovas-Montanes, M. Lichterfeld, BD. Walker, N Yosef†, AK. Shalek†, XG. Yu†
Genome Biology , 2018
10.1186/s13059-017-1385-x
GitHub

Impulse model-based differential expression analysis of time course sequencing data.
DS Fischer, FJ Theis, N. Yosef.
Nucleic Acids Research , 2018
10.1093/nar/gky675
GitHub

Information constraints on auto-encoding variational Bayes.
R. Lopez, J. Regier, M. Jordan, N. Yosef.
Advances in Neural Information Processing Systems , 2018
arXiv preprint

A deep generative model for semi-supervised classification with noisy labels.
M. Langevin, E. Mehlman, J. Regier, R. Lopez, M. Jordan, N. Yosef.
Bay Area Machine Learning Symposium (oral presentation) , 2018
arXiv preprint

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.
S. Afik, K. Yates, K Bi, S. Darko, J. Godec, U. Gerdemann, L. Swadling, DC. Douek, P. Klenerman, EJ. Barnes, AH. Sharpe, N. Haining†, N. Yosef.
Nucleic Acids Research , 2017
doi.org/10.1093/nar/gkx615
GitHub

A deep generative model for gene expression profiles from single-cell RNA sequencing.
R. Lopez, J. Regier, M. Jordan, N. Yosef.
BayLearn Symposium (oral presentation) and NIPS Workshop on Machine Learning in Computational Biology (spotlight talk) , 2017
arXiv preprint

A new way to build cell lineages.
X. Zhang and N. Yosef.
eLife , 2017
10.7554/eLife.25654

Predicting gene expression in massively parallel reporter assays: a comparative study.
A. Kreimer, H. Zeng, MD. Edwards, Y. Guo, K. Tian, S. Shin, R. Welch, M. Wainberg, R. Mohan, NA. Sinnott-Armstrong, Y. Li, G. Eraslan, T.l Bin AMIN, J. Goke, NS. Mueller, M. Kellis, A. Kundaje, MA Beer, S. Keles, DK. Gifford and N. Yosef†.
Human Mutation , 2017
10.1002/humu.23197

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.
P. Mertins, D. Przybylski, N. Yosef, J. Qiao, K. Clauser, R. Raychowdhury, TM. Eisenhaure, T. Maritzen, V. Haucke, T. Satoh, S. Akira, SA. Carr, A. Regev, N. Hacohen, N. Chevrier.
Cell Reports , 2017
10.1016/j.celrep.2017.06.016

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.
RB. Fletcher, D. Das, L. Gadye, KN. Street, A. Baudhuin, A. Wagner, MB. Cole, Q. Flores, YG. Choi, N. Yosef, E. Purdom, S. Dudoit, D. Risso, J. Ngai.
Cell Stem Cell , 2017
10.1016/j.stem.2017.04.003

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.
L. Gadye, D. Das, MA. Sanchez, K. Street, A. Bauduin, A. Wagner, MB. Cole, YG Choi, N. Yosef ,E. Purdom, S. Dudoit, D. Risso, J. Ngai, RB. Fletcher.
Cell Stem Cell , 2017
10.1016/j.stem.2017.10.014

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.
AH. Ryu, WL. Eckalbar, A. Kreimer, N. Yosef, Nadav Ahituv.
Scientific Reports , 2017
10.1038/s41598-017-07757-w

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.
K. Karwacz, ER. Miraldi, M. Pokrovskii, A. Madi, N. Yosef, I. Wortman, X. Chen, A. Watters, N. Carriero, A. Awasthi, A. Regev, R. Bonneau, D. Littman, VK. Kuchroo.
Nature Immunology , 2017
10.1038/ni.3683

The Epigenetic Landscape of T Cell Exhaustion
D.R. Sen*, J. Kaminski*, R.A Barnitz, M. Kurachi, U. Gerdemann, K.B. Yates, H Tsao, J. Godec, M.W. LaFleur, F.D. Brown, P. Tonnerre, R.T. Chung, D.C. Tully, T.M. Allen, N. Frahm, G.M. Lauer, E. J. Wherry, N. Yosef†, and W.N. Haining†.
Science , 2016
10.1126/science.aae0491
Featured on journal’s cover, Perspectives: [Science], [Nature]

Writ large: Genomic Dissection of the Effect of Cellular Environment on Immune Response.
N. Yosef† and A. Regev†
Science , 2016
10.1126/science.aaf5453

Revealing the vectors of cellular identity with single cell genomics
A. Wagner, A. Regev*, N. Yosef*
Nature Biotechnology , 2016
10.1038/nbt.3711

FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data
D. DeTomaso, N. Yosef.
BMC Bioinformatics , 2016
10.1186/s12859-016-1176-5
GitHub

ImpulseDE: detection of differentially expressed genes in time series data using impulse models/
J. Sander, J. Schultze, N. Yosef.
Bioinformatics , 2016
GitHub
Available on Bioconductor

Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction
A. Morrow*, V. Shankar*, A. Joseph, B. Recht, and N. Yosef.
NeurIps Workshop on Machine Learning in Computational Biology , 2016

Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity
Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK
ACS Chem Biol , 2016

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
JT. Gaublomme*, N. Yosef*, Y. Lee, RS. Gertner, LV. Yang, PP. Pandolfi, T. Mak, R. Satija, AK. Shalek, VK. Kuchroo, A. Regev, H. Park.
Cell , 2015
10.1016/j.cell.2015.11.009
News and Views
Featured on journal’s cover

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity
C. Wang, N. Yosef, JT. Gaublomme, C. Wu, Y. Lee, CB. Clish, J. Kaminski, S. Xiao, G. Meyer Zu Horste, M. Pawlak, Y. Kishi, N. Joller, K. Karwacz, C. Zhu, M. Ordovas-Montanes, A. Madi, I. Wortman, T. Miyazaki, RA. Sobel, H. Park, A. Regev, VK. Kuchroo.
Cell , 2015
10.1016/j.cell.2015.10.068

Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor
R. Tian, H. Wang, GD. Gish, E. Petsalaki, A. Pasculescu, Y. Shi, M. Mollenauer, RD. Bagshaw, N. Yosef, T. Hunter, AC. Gingras, A. Weiss, and T. Pawson.
PNAS , 2015
10.1073/pnas.1503286112-2

Oct1 and OCA-B are selectively required for CD4 memory T cell function
Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D.
J Exp Med. , 2015
10.1084/jem.20150363

Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion
A. Shakya, C. Callister C, A. Goren, N. Yosef, N. Garg, V. Khoddami V, D. Nix, A. Regev, D. Tantin D.
Molecular and cellular biology , 2015

MicroRNA-21 promotes Th17 differentiation and mediates experimental autoimmune encephalomyelitis
G. Murugaiyan G, AP. da Cunha, AK. Ajay, N. Joller, LP. Garo, S. Kumaradevan, N. Yosef, VS Vaidya, HL. Weiner.
The Journal of Clinical Investigation (JCI) , 2015

Small-Molecule RORγt Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms
S. Xiao*, N. Yosef*, J. Yang, Y. Wang, L. Zhou, C. Zhu, E Baloglu, D. Schmidt, R. Ramesh, M. Lobera, M.S. Sundrud, P. Tsai, Z. Xiang, J. Wang, Y. Xu, X. Lin, K. Kretschmer, P.B. Rahl, R.A. Young, Z. Zhong, D.A. Hafler, A. Regev, S. Ghosh, A. Marson, V.K. Kuchroo.
Immunity , 2014
10.1016/j.immuni.2014.04.004

Understanding Th17 cells through systematic genomic analyses
A. Peters, N. Yosef
Current Opinion in Immunology , 2014
10.1016/j.coi.2014.01.017

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells
M. Kurachi, R.A. Barnitz, N. Yosef, P.M. Odorizzi, M.A. Dilorio, M.E. Lemieux, K. Yates, J. Godec, M.G. Klatt, A. Regev, E.J Wherry, W.N. Haining
Nature Immunology , 2014
10.1038/ni.2834

Single cell RNA Seq reveals dynamic paracrine control of cellular variation
A. Shalek, R. Satija, J. Shuga, J. Trombetta, D. Gennert, D. Lu, P. Chen, R. Gertner, J. Gaublomme, N. Yosef, S. Schwartz, B. Fowler, S. Weaver, J. Wang, X. Wang, R. Ding, R. Raychowdhury, N. Friedman, N. Hacohen, H. Park, A. May, A. Regev.
Nature , 2014
10.1038/nature13437

Dynamic regulatory network controlling TH17 cell differentiation
N. Yosef*, A.K. Shalek*, J. Gaublomme*, Y. Lee, A. Awasthi, H. Jin, C. Wu, K. Karwacz, S. Xiao, M. Jorgolli, D. Gennert, R. Satija, A. Shakya, D.Y. Lu, J.J. Trombetta, M. Pillai, P.J. Ratcliffe, M.L. Coleman, M. Bix, D. Tantin, H. Park, V.K Kuchroo, A. Regev.
Nature , 2013
10.1038/nature11981

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1
C. Wu*, N.Yosef*, T. Thalhamer*, C. Zhu, S. Xiao, Y. Kishi, A. Regev, V.K. Kuchroo.
Nature , 2013
10.1038/nature11984

Sodium Chloride Drives Autoimmune Disease by the Induction of Pathogenic Th17 Cells
M. Kleinewietfeld, A. Manzel, J. Titze, H. Kvakan, N. Yosef, R.A. Linker, D.N. Muller, D.A. Hafler.
Nature , 2013
10.1038/nature11868

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
AK. Shalek, R. Satija, X. Adiconis, RS. Gertner, JT. Gaublomme, R. Raychowdhury, S. Schwartz, N. Yosef, C. Malboeuf, D. Lu, JT. Trombetta, D. Gennert, A. Gnirke, A. Goren, N. Hacohen, JZ. Levin, H. Park, Aviv Regev.
Nature , 2013
10.1038/nature1217

Metallothioneins negatively regulate IL-27-induced type 1 regulatory T-cell differentiation
C. Wu, C. Pot, L. Apetoh, T. Thalhamer, B. Zhu, G. Murugaiyan, S. Xiao, Y. Lee, M. Rangachari, N. Yosef, VK. Kuchroo.
Proc Natl Acad Sci USA , 2013
10.1073/pnas.1211776110

A high throughput in vivo protein-DNA mapping approach reveals principles of dynamic gene regulation in mammals
M. Garber*, N. Yosef*, A. Goren, R. Raychowdhury, A. Thielke, M. Guttman, J. Robinson, B. Minie, N. Chevrier, Z. Itzhaki, A. Weiner, D. Friedrich, J. Meldrim, O. Ram, C. Chang, A. Gnirke, S. Fisher, N. Friedman, B. Wong, B. Bernstein, C. Nusbaum, N. Hacohen, A. Regev, I. Amit.
Molecular Cell , 2012
0.1016/j.molcel.2012.07.030

Systematic identification of gene annotation errors in the widely used yeast mutation collections
T. Ben-Shitrit*, N. Yosef*, K. Shemesh, R. Sharan, E. Ruppin and M. Kupiec
Nature Methods , 2012
10.1038/nmeth.1890

Induction and molecular signature of pathogenic TH17 cells
Y. Lee, A. Awasthi, N. Yosef, F.J. Quintana, S. Xiao, S. Kunder, R.A. Sobel, A. Regev, V.K. Kuchroo.
Nature Immunology , 2012
10.1038/ni.2416

Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
A.K. Shalek, J. Gaublomme, L. Wang, N. Yosef, N. Chevrier, M.S. Andersen, J.T. Robinson, N. Pochet, D. Neuberg, R.S. Gertner, I. Amit, J.R. Brown, N. Hacohen, A. Regev, C.V. Wu, H. Park.
Nano Letters , 2012
10.1021/nl3042917

Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival
G.Y. Stein, N. Yosef, H. Reichman, J. Horev, A. Laser-Azogui, A. Berens, J. Resau, E. Ruppin, R. Sharan and I. Tsarfaty.
PLoS One , 2012
10.1371/journal.pone.0045969

Impulse control: Temporal dynamics in gene transcription
N. Yosef, A. Regev.
Cell , 2011
Included in Cell’s top reviews for 2011. Featured on journal’s cover.

ANAT – A Software Tool for Reconstructing and Analyzing Functional Networks of Proteins
N. Yosef, E. Zalckvar, N. Atias, AD. Rubinstein, M. Homilius, L. Vardi, H. Zur, A. Kimchi, E. Ruppin, and R. Sharan.
Science Signaling , 2011

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
N.Novershtern, A. Subramanian, L. Lawton, RH. Mak, W. Haining, ME. McConkey, N. Habib, N. Yosef, CY. Chang, T. Shay, GM. Frampton, ACB. Drake, I. Leskov, B. Nilsson, F. Preffer, D. Dombkowski, JW. Evans, T. Liefeld, JS. Smutko, J. Chen, N. Friedman, R. Young, T. Golub, A. Regev, BL. Ebert.
Cell , 2011

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
O. Ram, A. Goren, I. Amit, N. Shoresh, N. Yosef, J. Ernst, M. Kellis, M. Gymrek, R. Issner, M. Coyne, T. Durham, X. Zhang, J. Donaghey, CB. Epstein, A. Regev, and BE. Bernstein.
Cell , 2011

Systematic Discovery of Signaling Components Identifies New Branches in Viral-Sensing Pathways
N. Chevrier P. Mertins, MN Artyomov, AK Shalek, M Iannacone, MF Ciaccio, I Gat-Viks, E Tonti, MM DeGrace, KR Clauser, M Garber, TM Eisenhaure, N Yosef, JT Robinson, A Sutton, MS Andersen, DE Root U von Andrian, RB Jones, H Park, SA Carr, A Regev, I Amit, N Hacohen.
Cell , 2011

Network-free inference of knockout effects in yeast
T. Peleg, N. Yosef, E. Ruppin, and R. Sharan.
PLoS Computational Biology , 2010

Prediction of Phenotype Information from Genotype Data
N.Yosef, J. Gramm, Q. Wang, W.S. Noble, R. Karp, and R. Sharan.
Communications in Information and Systems , 2010

A Systems Level Strategy for Analyzing the Cell Death Network: implications in exploring the apoptosis/ autophagy connection
E. Zalckvar, N. Yosef, S. Reef, R. Sharan, E. Ruppin, and A. Kimchi.
Cell Death and Differentiation , 2010
10.1038/cdd.2010.7

Transcription Regulation by CHIP/LDB Complexes
R. Bronstein, L. Levkovitz, N. Yosef, E. Ruppin, R. Sharan, He. Westphal, B. Oliver, D. Segal.
PLoS Genetics , 2010

A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology
L. Levkovitz, N. Yosef, MC. Gershengorn, E. Ruppin, R. Sharan and Y. Oron.
PLoS ONE , 2010

Toward Accurate Reconstruction of Functional Protein Networks
N.Yosef*, L. ungar*, E. Zalckvar, A.Kimchi, M.Kupeic, E. Ruppin and R. Sharan.
Molecular Systems Biology , 2009

A Complex-Centric View of Protein Network Evolution
N.Yosef, M.Kupeic, E. Ruppin and R. Sharan.
Nucleic Acids Research , 2009
10.1093/nar/gkp414

A genome-wide screen for essential yeast genes that affect telomere length maintenance
L. Ungar*, N.Yosef*, Y. Sela, R. Sharan, E. Ruppin, M. Kupiec.
Nucleic Acids Research , 2009
10.1093/nar/gkp259

Metabolic environmental modeling predicts ecological strategies for bacterial growth
S. Freilich, A. Kreimer, E. Borenstein, N.Yosef, R. Sharan, U. Gophna, E. Ruppin.
Genome Biology , 2009
10.1186/gb-2009-10-6-r61

Cross-species Analysis of Protein-protein Interaction Networks
N.Yosef, E. Ruppin and R. Sharan.
In Protein-protein interactions and networks: identification analysis and prediction, Panchenko& Przytycka (ed) pp 163-186. Springer , 2008

Improved Network-based Identification of Protein Orthologs
N.Yosef, R. Sharan and W. S. Noble.
Bioinformatics 24 (ECCB 2008) , 2008

From sequence to structure to networks
N. Yosef, L. Käll.
Genome Biology , 2008

A Supervised Approach for Identifying Discriminating Genotype Patterns and its Application to Breast Cancer Data
N.Yosef, Z.Yakhini, A.Tsalenko, E.Ruppin and R.Sharan
Bioinformatics 23 (ECCB 2006) , 2007

Medical sequencing at the extremes of human body mass
N. Ahituv, N. Kavaslar, W. Schackwitz, A. Ustaszewska, J. Martin, S. Hébert, H. Doelle, B. Ersoy, G. Kryukov, S. Schmidt, N. Yosef, E. Ruppin, R. Sharan, C. Vaisse, S. Sunyaev, R. Dent, J. Cohen, R. McPherson, and L.A. Pennacchio.
American Journal of Human Genetics , 2007

Inferring Functional Pathways from Multi-Perturbation Data
N. Yosef, A. Kaufman and E. Ruppin
Bioinformatics (ISMB 2006) , 2006