Publications

Selected publications
[* Stands for equal contribution; † corresponding author]:

Complete list of publications

2017

  • 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. doi: 10.1002/humu.23197
  • A new way to build cell lineages (Insight article)/ X. Zhang and N. Yosef. eLife 2017
  • 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. doi.org/10.1016/j.stem.2017.04.003
  • Additional new Tools: 
    • SCONE: Correcting and Evaluating the Influence of Unwanted Variation on Single-Cell RNA-Seq Data/ M. Cole, D. Risso, A. Wagner, J. Ngai, E. Purdom, S. Dudoit, N. Yosef.
      • View the R Bioconductor package here
      • Presented at BioC2016. Stanford, CA. [Workshop materials here]
    • TRAPeS: TCR Reconstruction Algorithm for Paired-End Single-cell RNA-seq [bioRxiv; download here]
    • Impulse model-based differential expression analysis of time course sequencing data/  DS Fischer,  FJ Theis, N. Yosef  [bioRxiv; Bioconductor package here]

2016

  • 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. DOI: 10.1126/science.aae0491
  • Writ large: Genomic Dissection of the Effect of Cellular Environment on Immune Response/  N. Yosef† and A. Regev†. Science 2016.  354(6308): 64-68. DOI: 10.1126/science.aaf5453
  • Revealing the vectors of cellular identity with single cell genomics/ A. Wagner, A. Regev*, N. Yosef*. Nature Biotechnology 2016. 34(11):1145-1160. doi: 10.1038/nbt.3711
  • FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data/ D. DeTomaso, N. Yosef. BMC Bioinformatics 2016;17(1):315. doi: 10.1186/s12859-016-1176-5
    ==> [download FastProject Here]
  • ImpulseDE: detection of differentially expressed genes in time series data using impulse models/ J. Sander, J. Schultze, N. Yosef. Bioinformatics 2016 pii: btw665. [Epub ahead of print]
    ==> Also available on  Bioconductor 
  • Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction/ A. Morrow*, V. Shankar*, A. Joseph, B. Recht, and N. Yosef. NIPS Workshop on Machine Learning in Computational Biology
  • Offline Directed Steiner Network Problems on Dynamic Graphs/ B. Weitz, J. Wu, N. Yosef arXive
  • 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 Jul 5. [Epub ahead of print]

2015

  • 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;163(6):1400-12. doi: 10.1016/j.cell.2015.11.009.
  • 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;163(6):1413-27. doi: 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; doi: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 Nov 16;212(12):2115-31. doi: 10.1084/jem.20150363. 2015
  • 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; 35(6):1014-25.
  • 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. 2015; 125(3):1069-80.

2014

2013

    • 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 Apr 25;496(7446):461-8.
    • 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 Apr 25;496(7446):513-7
    • 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 Apr 25;496(7446):518-22
    • 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 May 19. doi: 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 U S A. 2013 May 7;110(19):7802-7

2012

    • 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. 47(5);810-22, 2012.
      ==> Featured on journal’s cove
    • 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 Apr;9(4):341, 343.
      ==> Associated N&V: [Nature Methods].
    • 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 Oct;13(10):991-9
    • 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. 12, 6498-6504, 2012.

2011

    • 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;7(9):e45969. doi: 10.1371/journal.pone.0045969. Epub 2012 Sep 25.
    • Impulse control: Temporal dynamics in gene transcription/ N. Yosef, A. Regev. Cell. 144(6):886-96, 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 4 (196), pl1 (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. 21;144(2):296-309, 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. (2011). Cell. 2011 Dec 23;147(7):1628-39.
    • 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 . (2011). Cell. 21;147(4):853-67, 2011

2010

    • Network-free inference of knockout effects in yeast/ T. Peleg*, N. Yosef*, E. Ruppin, and R. Sharan.  PLoS Computational Biology, 6(1): e1000635, 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 ; 10(2), pp. 99-114.
    • 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; doi: 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

2009 and earlier

  • 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;5;248.
  • A Complex-Centric View of Protein Network Evolution / N.Yosef, M.Kupeic, E. Ruppin and R. Sharan. Nucleic Acids Research, doi:10.1093/nar/gkp414 2009.
  • 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, doi:10.1093/nar/gkp259, 2009.
  • 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, doi:10.1186/gb-2009-10-6-r61, 2009
  • 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), pp i200-6, 2008
  • From sequence to structure to networks/ N. Yosef, L. Käll. Genome Biology, 9(11):3022-7, 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), pp. e91-e98, 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 80, pp. 779-791, 2007
  • Inferring Functional Pathways from Multi-Perturbation Data/ N. Yosef, A. Kaufman and E. Ruppin Bioinformatics (ISMB 2006), 22(14), e539-e546, 2006.