Publications

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

2019

  • 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 pii: S1934-5909(19)30421-7. doi: 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; 20:183 10.1186/s13059-019-1787-z
    • Download MPRAnalyze [here]
  • Functional Interpretation of Single-Cell Similarity Maps. D. Detomaso*, M. Jones*. M. Subramanian, J. Ye, N. Yosef.  Nature Communications 2019; 10(1):4376. doi: 10.1038/s41467-019-12235-0
    • Example report (PBMC with CITE-seq from Stoeckius et al., Nature Biotech 2017)
    • Download VISION here and UI tutorial here
  • 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; 2(4). pii: e201900371. doi: 10.26508/lsa.201900371
    • Download BRAPeS [here]
  • Simulating multi-faceted variability in single cell RNA sequencing/ X. Zhang*, C. Xu*, N. Yosef. Nature Communications 2019 13;10(1):2611. doi: 10.1038/s41467-019-10500-w
  • Meta-analysis of massively parallel reporter assays enables the prediction of regulatory elements. A. Kreimer *, Z. Yan *, N. Ahituv, N. Yosef. Human Mutation 2019. doi: 10.1002/humu.23820
  • Connectivity Problems on Heterogeneous GraphsJ. Wu, A. Khodaverdian, B.Weitz, N. Yosef. Algorithms for Molecular Biology 2019. 14:5; doi:10.1186/s13015-019-0141-z
    • Download Directed Condition Steiner Network (DCSN) solver and simulator [here]
  • 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. 8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010
    • Download SCONE (R Bioconductor) [here]
  • 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. 570, pages77–8
  • Conferences and workshops
    • 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 (oral presentation; best student’s poster) [arXiv]
    • Deep Generative Models for Detecting Differential Expression in Single Cells. P. Boyeau, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N. Yosef. MLCB 2019 [bioRxiv]
    • Detecting Zero-Inflated Genes in Single-Cell Transcriptomics Data O. Clivio, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N Yosef. MLCB 2019 [bioRxiv]
    • 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 MLCB 2019 [bioRxiv]

New tools and preprints

  • 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[bioRxiv]
    • Access Cassiopeia [here]
  • 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 [bioRxiv]
  • LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data in pseudo time/  DS Fischer,  FJ Theis, N. Yosef†
    • Download LineagePulse (R Bioconductor) [here]
  • Mango: Distributed Visualization for Genomic Analysis. AK Morrow, GZ He, FA Nothaft, ET Tu, J Paschall, N Yosef, AD. Joseph. [bioRxiv]
    • Download MANGO [here]
  • Single cell transcriptomics identifies T follicular helper cells driving local inflammation in multiple sclerosis. David Schafflick *, Michael Cole *, Maike Hartlehnert, Tobias Lautwein, Konrad Buscher, Jolien Wolbert, Sven G. Meuth1, Tanja Kuhlmann, Catharina Gross, Heinz Wiendl, Nir Yosef, Gerd Meyer zu Horste  [bioRxiv]

2018

  • Deep Generative Modeling for Single-cell Transcriptomics/ R. Lopez, J. Regier, MB. Cole, M. Jordan, N. Yosef. Nature Methods 15, 1053–1058 2018. DOI: 10.1038/s41592-018-0229-2
    ==> Download scVI here
    ==> Associated N&V
  • 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;  doi: 10.1186/s13059-017-1385
  • Impulse model-based differential expression analysis of time course sequencing data/  DS Fischer,  FJ Theis, N. Yosef†. Nucleic Acids Research 2018; doi: 10.1093/nar/gky675
    • Download ImpulseDE2 (R Bioconductor)  [here]
      ==> [Summary of ImpulseDE2 performance in a recent comparative analysis]
  • Conferences and workshops
    • Information Constraints on Auto-Encoding Variational Bayes/ R. Lopez, J. Regier, M. Jordan, N. Yosef.  NIPS [arXiv]
    • A Deep Generative Model for Semi-Supervised Classification with Noisy Labels. M/ Langevin, E. Mehlman, J. Regier, R. Lopez, M. Jordan, N. Yosef. BayLearn Symposium (oral presentation) [arXiv]

2017

  • 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
    [download TRAPeS here]
  • A deep generative model for gene expression profiles from single-cell RNA sequencing/ R. Lopez, J. Regier, M. Jordan, N. Yosef. BayLearn Symposium and NIPS Workshop on Machine Learning in Computational Biology arXiv
  • A new way to build cell lineages (Insight article)/ X. Zhang and N. Yosef. eLife 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
  • 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 Jun 27;19(13):2853-2866. doi: 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. doi.org/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. doi.org/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 (in press)
  • 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 18, 412–421 (2017) doi:10.1038/ni.3683

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
  • 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.
    ==> Featured on journal’s cover
    ==> Associated N&V: [Cell]
  • 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.
      ==>  [Nature news], [Science], [Scientific American]
    • 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
      ==> Associated N&V: [Nature]
    • 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.