| Year |
Citation |
Score |
| 2024 |
Wang C, Wagner A, Fessler J, DeTomaso D, Zaghouani S, Zhou Y, Pierce K, Sobel RA, Clish C, Yosef N, Kuchroo VK. The glycolytic reaction PGAM unexpectedly restrains Th17 pathogenicity and Th17-dependent autoimmunity. Biorxiv : the Preprint Server For Biology. PMID 39229227 DOI: 10.1101/2024.08.18.607992 |
0.332 |
|
| 2023 |
Prillo S, Ravoor A, Yosef N, Song YS. ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data. Biorxiv : the Preprint Server For Biology. PMID 38076815 DOI: 10.1101/2023.12.03.569785 |
0.374 |
|
| 2023 |
Gayoso A, Weiler P, Lotfollahi M, Klein D, Hong J, Streets A, Theis FJ, Yosef N. Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells. Nature Methods. PMID 37735568 DOI: 10.1038/s41592-023-01994-w |
0.323 |
|
| 2023 |
Steier Z, Aylard DA, McIntyre LL, Baldwin I, Kim EJY, Lutes LK, Ergen C, Huang TS, Robey EA, Yosef N, Streets A. Single-cell multiomic analysis of thymocyte development reveals drivers of CD4 T cell and CD8 T cell lineage commitment. Nature Immunology. PMID 37580604 DOI: 10.1038/s41590-023-01584-0 |
0.307 |
|
| 2023 |
Ashuach T, Gabitto MI, Koodli RV, Saldi GA, Jordan MI, Yosef N. MultiVI: deep generative model for the integration of multimodal data. Nature Methods. PMID 37386189 DOI: 10.1038/s41592-023-01909-9 |
0.314 |
|
| 2023 |
Boyeau P, Regier J, Gayoso A, Jordan MI, Lopez R, Yosef N. An empirical Bayes method for differential expression analysis of single cells with deep generative models. Proceedings of the National Academy of Sciences of the United States of America. 120: e2209124120. PMID 37192164 DOI: 10.1073/pnas.2209124120 |
0.389 |
|
| 2023 |
Wang R, Zhang R, Khodaverdian A, Yosef N. Theoretical guarantees for phylogeny inference from single-cell lineage tracing. Proceedings of the National Academy of Sciences of the United States of America. 120: e2203352120. PMID 36927151 DOI: 10.1073/pnas.2203352120 |
0.304 |
|
| 2022 |
Pawlak M, DeTomaso D, Schnell A, Meyer Zu Horste G, Lee Y, Nyman J, Dionne D, Regan BML, Singh V, Delorey T, Schramm MA, Wang C, Wallrapp A, Burkett PR, Riesenfeld SJ, ... ... Yosef N, et al. Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling. Immunity. PMID 36070768 DOI: 10.1016/j.immuni.2022.08.007 |
0.31 |
|
| 2022 |
Buen Abad Najar CF, Burra P, Yosef N, Lareau LF. Identifying cell state-associated alternative splicing events and their coregulation. Genome Research. PMID 35858747 DOI: 10.1101/gr.276109.121 |
0.675 |
|
| 2022 |
Worley MI, Everetts NJ, Yasutomi R, Chang RJ, Saretha S, Yosef N, Hariharan IK. Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs. Current Biology : Cb. PMID 35820420 DOI: 10.1016/j.cub.2022.06.040 |
0.342 |
|
| 2022 |
Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, ... ... Yosef N, et al. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science (New York, N.Y.). 376: eabl4896. PMID 35549404 DOI: 10.1126/science.abl4896 |
0.398 |
|
| 2022 |
Jones MG, Rosen Y, Yosef N. Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision. Cell Reports Methods. 2: 100200. PMID 35497495 DOI: 10.1016/j.crmeth.2022.100200 |
0.343 |
|
| 2022 |
Ashuach T, Reidenbach DA, Gayoso A, Yosef N. PeakVI: A deep generative model for single-cell chromatin accessibility analysis. Cell Reports Methods. 2: 100182. PMID 35475224 DOI: 10.1016/j.crmeth.2022.100182 |
0.347 |
|
| 2022 |
Lopez R, Li B, Keren-Shaul H, Boyeau P, Kedmi M, Pilzer D, Jelinski A, Yofe I, David E, Wagner A, Ergen C, Addadi Y, Golani O, Ronchese F, Jordan MI, ... ... Yosef N, et al. DestVI identifies continuums of cell types in spatial transcriptomics data. Nature Biotechnology. PMID 35449415 DOI: 10.1038/s41587-022-01272-8 |
0.42 |
|
| 2022 |
Tsao HW, Kaminski J, Kurachi M, Barnitz RA, DiIorio MA, LaFleur MW, Ise W, Kurosaki T, Wherry EJ, Haining WN, Yosef N. Batf-mediated epigenetic control of effector CD8 T cell differentiation. Science Immunology. 7: eabi4919. PMID 35179948 DOI: 10.1126/sciimmunol.abi4919 |
0.373 |
|
| 2022 |
Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y, Samaran J, Misrachi G, Nazaret A, Clivio O, ... ... Yosef N, et al. A Python library for probabilistic analysis of single-cell omics data. Nature Biotechnology. PMID 35132262 DOI: 10.1038/s41587-021-01206-w |
0.378 |
|
| 2022 |
Bangs DJ, Tsitsiklis A, Steier Z, Chan SW, Kaminski J, Streets A, Yosef N, Robey EA. CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels. Cell Reports. 38: 110266. PMID 35045305 DOI: 10.1016/j.celrep.2021.110266 |
0.308 |
|
| 2022 |
Gupta A, Shamsi F, Altemose N, Dorlhiac GF, Cypess AM, White AP, Yosef N, Patti ME, Tseng YH, Streets A. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages. Genome Research. PMID 35042723 DOI: 10.1101/gr.275509.121 |
0.394 |
|
| 2021 |
Morrow AK, Hughes JW, Singh J, Joseph AD, Yosef N. Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning. Nucleic Acids Research. PMID 34379786 DOI: 10.1093/nar/gkab676 |
0.357 |
|
| 2021 |
Wagner A, Wang C, Fessler J, DeTomaso D, Avila-Pacheco J, Kaminski J, Zaghouani S, Christian E, Thakore P, Schellhaass B, Akama-Garren E, Pierce K, Singh V, Ron-Harel N, Douglas VP, ... ... Yosef N, et al. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity. Cell. PMID 34216539 DOI: 10.1016/j.cell.2021.05.045 |
0.306 |
|
| 2021 |
Everetts NJ, Worley MI, Yasutomi R, Yosef N, Hariharan IK. Single-cell transcriptomics of the wing disc reveals instructive epithelium-to-myoblast interactions. Elife. 10. PMID 33749594 DOI: 10.7554/eLife.61276 |
0.42 |
|
| 2021 |
Gayoso A, Steier Z, Lopez R, Regier J, Nazor KL, Streets A, Yosef N. Joint probabilistic modeling of single-cell multi-omic data with totalVI. Nature Methods. PMID 33589839 DOI: 10.1038/s41592-020-01050-x |
0.403 |
|
| 2021 |
Xu C, Lopez R, Mehlman E, Regier J, Jordan MI, Yosef N. Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. Molecular Systems Biology. 17: e9620. PMID 33491336 DOI: 10.15252/msb.20209620 |
0.418 |
|
| 2020 |
Sungnak W, Wagner A, Kowalczyk MS, Bod L, Kye YC, Sage PT, Sharpe AH, Sobel RA, Quintana FJ, Rozenblatt-Rosen O, Regev A, Wang C, Yosef N, Kuchroo VK. T Follicular Regulatory Cell-Derived Fibrinogen-like Protein 2 Regulates Production of Autoantibodies and Induction of Systemic Autoimmunity. Journal of Immunology (Baltimore, Md. : 1950). PMID 33168576 DOI: 10.4049/jimmunol.2000748 |
0.414 |
|
| 2020 |
Gordon MG, 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 CJ, Pollard KS, et al. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols. PMID 32641802 DOI: 10.1038/S41596-020-0333-5 |
0.416 |
|
| 2020 |
Buen Abad Najar CF, Yosef N, Lareau LF. Coverage-dependent bias creates the appearance of binary splicing in single cells. Elife. 9. PMID 32597758 DOI: 10.7554/Elife.54603 |
0.667 |
|
| 2020 |
Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. The Journal of Biological Chemistry. PMID 32518159 DOI: 10.1074/Jbc.Ra120.013426 |
0.421 |
|
| 2020 |
Jones MG, Khodaverdian A, Quinn JJ, Chan MM, Hussmann JA, Wang R, Xu C, Weissman JS, Yosef N. Inference of single-cell phylogenies from lineage tracing data using Cassiopeia. Genome Biology. 21: 92. PMID 32290857 DOI: 10.1186/S13059-020-02000-8 |
0.428 |
|
| 2020 |
Svensson V, Gayoso A, Yosef N, Pachter L. Interpretable factor models of single-cell RNA-seq via variational autoencoders. Bioinformatics (Oxford, England). PMID 32176273 DOI: 10.1093/Bioinformatics/Btaa169 |
0.572 |
|
| 2020 |
Schafflick D, Xu CA, Hartlehnert M, Cole M, Schulte-Mecklenbeck A, Lautwein T, Wolbert J, Heming M, Meuth SG, Kuhlmann T, Gross CC, Wiendl H, Yosef N, Meyer Zu Horste G. Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. Nature Communications. 11: 247. PMID 31937773 DOI: 10.1038/S41467-019-14118-W |
0.442 |
|
| 2019 |
Inoue F, Kreimer A, Ashuach T, Ahituv N, Yosef N. Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. Cell Stem Cell. PMID 31631012 DOI: 10.1016/J.Stem.2019.09.010 |
0.476 |
|
| 2019 |
DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N. Functional interpretation of single cell similarity maps. Nature Communications. 10: 4376. PMID 31558714 DOI: 10.1038/S41467-019-12235-0 |
0.514 |
|
| 2019 |
Ashuach T, Fischer DS, Kreimer A, Ahituv N, Theis FJ, Yosef N. MPRAnalyze: statistical framework for massively parallel reporter assays. Genome Biology. 20: 183. PMID 31477158 DOI: 10.1186/S13059-019-1787-Z |
0.339 |
|
| 2019 |
Afik S, Raulet G, Yosef N. Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS. Life Science Alliance. 2. PMID 31451449 DOI: 10.26508/lsa.201900371 |
0.35 |
|
| 2019 |
Zhang X, Xu C, Yosef N. Simulating multiple faceted variability in single cell RNA sequencing. Nature Communications. 10: 2611. PMID 31197158 DOI: 10.1038/S41467-019-10500-W |
0.54 |
|
| 2019 |
Kreimer A, Yan Z, Ahituv N, Yosef N. Meta-analysis of massively parallel reporter assays enables prediction of regulatory activity. Human Mutation. PMID 31131957 DOI: 10.1002/Humu.23820 |
0.37 |
|
| 2019 |
Shigaki D, Adato O, Adhikar AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DP, Schubach M, Xiong C, Yan Z, Boyle AP, ... ... Yosef N, et al. Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay. Human Mutation. PMID 31106481 DOI: 10.1002/Humu.23797 |
0.386 |
|
| 2019 |
Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS. Molecular recording of mammalian embryogenesis. Nature. PMID 31086336 DOI: 10.1038/S41586-019-1184-5 |
0.516 |
|
| 2019 |
Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N. Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Cell Systems. 8: 315-328.e8. PMID 31022373 DOI: 10.1016/J.Cels.2019.03.010 |
0.42 |
|
| 2018 |
Lopez R, Regier J, Cole MB, Jordan MI, Yosef N. Deep generative modeling for single-cell transcriptomics. Nature Methods. 15: 1053-1058. PMID 30504886 DOI: 10.1038/S41592-018-0229-2 |
0.504 |
|
| 2018 |
Fischer DS, Theis FJ, Yosef N. Impulse model-based differential expression analysis of time course sequencing data. Nucleic Acids Research. PMID 30102402 DOI: 10.1093/Nar/Gky675 |
0.371 |
|
| 2018 |
Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. Bmc Genomics. 19: 477. PMID 29914354 DOI: 10.1186/S12864-018-4772-0 |
0.527 |
|
| 2018 |
Donnard E, Vangala P, Afik S, McCauley S, Nowosielska A, Kucukural A, Tabak B, Zhu X, Diehl W, McDonel P, Yosef N, Luban J, Garber M. Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon. Cell Systems. PMID 29454939 DOI: 10.1016/J.Cels.2018.01.002 |
0.379 |
|
| 2018 |
Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. Genome Biology. 19: 10. PMID 29378643 DOI: 10.1186/S13059-017-1385-X |
0.404 |
|
| 2017 |
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, ... ... Yosef N, et al. Science Forum: The Human Cell Atlas. Elife. 6. PMID 29206104 DOI: 10.7554/Elife.27041 |
0.476 |
|
| 2017 |
Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB. Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities. Cell Stem Cell. 21: 775-790.e9. PMID 29174333 DOI: 10.1016/J.Stem.2017.10.014 |
0.424 |
|
| 2017 |
Afik S, Yates KB, Bi K, Darko S, Godec J, Gerdemann U, Swadling L, Douek DC, Klenerman P, Barnes EJ, Sharpe AH, Haining WN, Yosef N. Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. Nucleic Acids Research. 45: e148. PMID 28934479 DOI: 10.1093/Nar/Gkx615 |
0.512 |
|
| 2017 |
Ryu AH, Eckalbar WL, Kreimer A, Yosef N, Ahituv N. Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Scientific Reports. 7: 7533. PMID 28790348 DOI: 10.1038/S41598-017-07757-W |
0.478 |
|
| 2017 |
Mertins P, Przybylski D, Yosef N, Qiao J, Clauser K, Raychowdhury R, Eisenhaure TM, Maritzen T, Haucke V, Satoh T, Akira S, Carr SA, Regev A, Hacohen N, Chevrier N. An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling. Cell Reports. 19: 2853-2866. PMID 28658630 DOI: 10.1016/J.Celrep.2017.06.016 |
0.337 |
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| 2017 |
Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J. Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution. Cell Stem Cell. PMID 28506465 DOI: 10.1016/J.Stem.2017.04.003 |
0.484 |
|
| 2017 |
Zhang X, Yosef N. A new way to build cell lineages. Elife. 6. PMID 28332977 DOI: 10.7554/Elife.25654 |
0.483 |
|
| 2017 |
Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Goke J, Mueller NS, ... ... Yosef N, et al. Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation. PMID 28220625 DOI: 10.1002/Humu.23197 |
0.369 |
|
| 2017 |
Karwacz K, Miraldi ER, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK. Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation. Nature Immunology. PMID 28166218 DOI: 10.1038/Ni.3683 |
0.498 |
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| 2017 |
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, ... ... Yosef N, et al. Author response: The Human Cell Atlas Elife. DOI: 10.7554/Elife.27041.011 |
0.38 |
|
| 2016 |
Yosef N, Regev A. Writ large: Genomic dissection of the effect of cellular environment on immune response. Science (New York, N.Y.). 354: 64-68. PMID 27846493 DOI: 10.1126/Science.Aaf5453 |
0.427 |
|
| 2016 |
Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nature Biotechnology. 34: 1145-1160. PMID 27824854 DOI: 10.1038/Nbt.3711 |
0.562 |
|
| 2016 |
Sander J, Schultze JL, Yosef N. ImpulseDE: detection of differentially expressed genes in time series data using impulse models. Bioinformatics (Oxford, England). PMID 27797772 DOI: 10.1093/Bioinformatics/Btw665 |
0.409 |
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| 2016 |
Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, Tsao HW, Godec J, LaFleur MW, Brown FD, Tonnerre P, Chung RT, Tully DC, Allen TM, Frahm N, ... ... Yosef N, et al. The epigenetic landscape of T cell exhaustion. Science (New York, N.Y.). PMID 27789799 DOI: 10.1126/science.aae0491 |
0.312 |
|
| 2016 |
Ranasinghe S, Lamothe PA, Soghoian DZ, Kazer SW, Cole MB, Shalek AK, Yosef N, Jones RB, Donaghey F, Nwonu C, Jani P, Clayton GM, Crawford F, White J, Montoya A, et al. Antiviral CD8(+) T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion. Immunity. 45: 917-930. PMID 27760342 DOI: 10.1016/J.Immuni.2016.09.015 |
0.35 |
|
| 2016 |
Kishi Y, Kondo T, Xiao S, Yosef N, Gaublomme J, Wu C, Wang C, Chihara N, Regev A, Joller N, Kuchroo VK. Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity. The Journal of Experimental Medicine. PMID 27670590 DOI: 10.1084/Jem.20151118 |
0.467 |
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| 2016 |
DeTomaso D, Yosef N. FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. Bmc Bioinformatics. 17: 315. PMID 27553427 DOI: 10.1186/S12859-016-1176-5 |
0.502 |
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| 2016 |
Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK. Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity. Acs Chemical Biology. PMID 27380425 DOI: 10.1021/Acschembio.6B00433 |
0.307 |
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| 2015 |
Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, Pandolfi PP, Mak T, Satija R, Shalek AK, Kuchroo VK, Park H, Regev A. Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. Cell. PMID 26607794 DOI: 10.1016/J.Cell.2015.11.009 |
0.489 |
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| 2015 |
Wang C, Yosef N, Gaublomme J, Wu C, Lee Y, Clish CB, Kaminski J, Xiao S, Zu Horste GM, Pawlak M, Kishi Y, Joller N, Karwacz K, Zhu C, Ordovas-Montanes M, et al. CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity. Cell. PMID 26607793 DOI: 10.1016/J.Cell.2015.10.068 |
0.461 |
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| 2015 |
Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D. Oct1 and OCA-B are selectively required for CD4 memory T cell function. The Journal of Experimental Medicine. PMID 26481684 DOI: 10.1084/Jem.20150363 |
0.349 |
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| 2015 |
Tian R, Wang H, Gish GD, Petsalaki E, Pasculescu A, Shi Y, Mollenauer M, Bagshaw RD, Yosef N, Hunter T, Gingras AC, Weiss A, Pawson T. Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. Proceedings of the National Academy of Sciences of the United States of America. 112: E1594-603. PMID 25829543 DOI: 10.1073/Pnas.1503286112 |
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| 2015 |
Murugaiyan G, da Cunha AP, Ajay AK, Joller N, Garo LP, Kumaradevan S, Yosef N, Vaidya VS, Weiner HL. MicroRNA-21 promotes Th17 differentiation and mediates experimental autoimmune encephalomyelitis. The Journal of Clinical Investigation. 125: 1069-80. PMID 25642768 DOI: 10.1172/Jci74347 |
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| 2015 |
Shakya A, Callister C, Goren A, Yosef N, Garg N, Khoddami V, Nix D, Regev A, Tantin D. Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion. Molecular and Cellular Biology. 35: 1014-25. PMID 25582194 DOI: 10.1128/Mcb.01105-14 |
0.345 |
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| 2015 |
Uziel O, Yosef N, Sharan R, Ruppin E, Kupiec M, Kushnir M, Beery E, Cohen-Diker T, Nordenberg J, Lahav M. The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis. Genomics. 105: 5-16. PMID 25451739 DOI: 10.1016/J.Ygeno.2014.10.013 |
0.424 |
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| 2014 |
Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 510: 363-9. PMID 24919153 DOI: 10.1038/Nature13437 |
0.59 |
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| 2014 |
Xiao S, Yosef N, Yang J, Wang Y, Zhou L, Zhu C, Wu C, Baloglu E, Schmidt D, Ramesh R, Lobera M, Sundrud MS, Tsai PY, Xiang Z, Wang J, et al. Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms. Immunity. 40: 477-89. PMID 24745332 DOI: 10.1016/J.Immuni.2014.04.004 |
0.412 |
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| 2014 |
Peters A, Yosef N. Understanding Th17 cells through systematic genomic analyses. Current Opinion in Immunology. 28: 42-8. PMID 24594517 DOI: 10.1016/J.Coi.2014.01.017 |
0.494 |
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| 2014 |
Kurachi M, Barnitz RA, Yosef N, Odorizzi PM, DiIorio MA, Lemieux ME, Yates K, Godec J, Klatt MG, Regev A, Wherry EJ, Haining WN. The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells. Nature Immunology. 15: 373-83. PMID 24584090 DOI: 10.1038/Ni.2834 |
0.47 |
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| 2013 |
Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 498: 236-40. PMID 23685454 DOI: 10.1038/Nature12172 |
0.606 |
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| 2013 |
Wu C, Pot C, Apetoh L, Thalhamer T, Zhu B, Murugaiyan G, Xiao S, Lee Y, Rangachari M, Yosef N, Kuchroo VK. Metallothioneins negatively regulate IL-27-induced type 1 regulatory T-cell differentiation. Proceedings of the National Academy of Sciences of the United States of America. 110: 7802-7. PMID 23630250 DOI: 10.1073/Pnas.1211776110 |
0.33 |
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| 2013 |
Kleinewietfeld M, Manzel A, Titze J, Kvakan H, Yosef N, Linker RA, Muller DN, Hafler DA. Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells. Nature. 496: 518-22. PMID 23467095 DOI: 10.1038/Nature11868 |
0.414 |
|
| 2013 |
Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, et al. Dynamic regulatory network controlling TH17 cell differentiation. Nature. 496: 461-8. PMID 23467089 DOI: 10.1038/Nature11981 |
0.478 |
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| 2013 |
Wu C, Yosef N, Thalhamer T, Zhu C, Xiao S, Kishi Y, Regev A, Kuchroo VK. Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature. 496: 513-7. PMID 23467085 DOI: 10.1038/Nature11984 |
0.36 |
|
| 2013 |
Barnitz RA, Kurachi M, Lemieux ME, Yosef N, DiIorio MA, Yates KB, Godec J, Odorizzi P, Regev A, Wherry EJ, Haining WN. The Transcription Factor BATF Controls CD8+ T Cell Effector Differentiation Blood. 122: 189-189. DOI: 10.1182/Blood.V122.21.189.189 |
0.459 |
|
| 2012 |
Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner RS, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ, et al. Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Letters. 12: 6498-504. PMID 23190424 DOI: 10.1021/Nl3042917 |
0.424 |
|
| 2012 |
Stein GY, Yosef N, Reichman H, Horev J, Laser-Azogui A, Berens A, Resau J, Ruppin E, Sharan R, Tsarfaty I. Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival. Plos One. 7: e45969. PMID 23049908 DOI: 10.1371/Journal.Pone.0045969 |
0.301 |
|
| 2012 |
Lee Y, Awasthi A, Yosef N, Quintana FJ, Xiao S, Peters A, Wu C, Kleinewietfeld M, Kunder S, Hafler DA, Sobel RA, Regev A, Kuchroo VK. Induction and molecular signature of pathogenic TH17 cells. Nature Immunology. 13: 991-9. PMID 22961052 DOI: 10.1038/Ni.2416 |
0.346 |
|
| 2012 |
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular Cell. 47: 810-22. PMID 22940246 DOI: 10.1016/J.Molcel.2012.07.030 |
0.376 |
|
| 2011 |
Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 147: 1628-39. PMID 22196736 DOI: 10.1016/J.Cell.2011.09.057 |
0.345 |
|
| 2011 |
Yosef N, Zalckvar E, Rubinstein AD, Homilius M, Atias N, Vardi L, Berman I, Zur H, Kimchi A, Ruppin E, Sharan R. ANAT: a tool for constructing and analyzing functional protein networks. Science Signaling. 4: pl1. PMID 22028466 DOI: 10.1126/Scisignal.2001935 |
0.31 |
|
| 2011 |
Yosef N, Regev A. Impulse control: temporal dynamics in gene transcription. Cell. 144: 886-96. PMID 21414481 DOI: 10.1016/J.Cell.2011.02.015 |
0.348 |
|
| 2011 |
Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell. 144: 296-309. PMID 21241896 DOI: 10.1016/J.Cell.2011.01.004 |
0.445 |
|
| 2011 |
Wang L, Shalek AK, Gaublomme J, Yosef N, Brown JR, Neuberg D, Hacohen N, Park H, Wu CJ. Sensitivity to Wnt Pathway Inhibition in CLL Is Associated with Specific Gene Expression Signatures Blood. 118: 801-801. DOI: 10.1182/Blood.V118.21.801.801 |
0.47 |
|
| 2010 |
Levkovitz L, Yosef N, Gershengorn MC, Ruppin E, Sharan R, Oron Y. A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology. Plos One. 5: e14423. PMID 21203558 DOI: 10.1371/Journal.Pone.0014423 |
0.327 |
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| 2010 |
Bronstein R, Levkovitz L, Yosef N, Yanku M, Ruppin E, Sharan R, Westphal H, Oliver B, Segal D. Transcriptional regulation by CHIP/LDB complexes. Plos Genetics. 6: e1001063. PMID 20730086 DOI: 10.1371/Journal.Pgen.1001063 |
0.355 |
|
| 2010 |
Peleg T, Yosef N, Ruppin E, Sharan R. Network-free inference of knockout effects in yeast. Plos Computational Biology. 6: e1000635. PMID 20066032 DOI: 10.1371/Journal.Pcbi.1000635 |
0.365 |
|
| 2009 |
Ungar L, Yosef N, Sela Y, Sharan R, Ruppin E, Kupiec M. A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Research. 37: 3840-9. PMID 19386622 DOI: 10.1093/Nar/Gkp259 |
0.339 |
|
| 2009 |
Yosef N, Ungar L, Zalckvar E, Kimchi A, Kupiec M, Ruppin E, Sharan R. Toward accurate reconstruction of functional protein networks. Molecular Systems Biology. 5: 248. PMID 19293828 DOI: 10.1038/Msb.2009.3 |
0.344 |
|
| 2007 |
Yosef N, Yakhini Z, Tsalenko A, Kristensen V, Børresen-Dale AL, Ruppin E, Sharan R. A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. Bioinformatics (Oxford, England). 23: e91-8. PMID 17237111 DOI: 10.1093/Bioinformatics/Btl298 |
0.353 |
|
| 2006 |
Yosef N, Kaufman A, Ruppin E. Inferring functional pathways from multi-perturbation data. Bioinformatics (Oxford, England). 22: e539-46. PMID 16873518 DOI: 10.1093/Bioinformatics/Btl204 |
0.306 |
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