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Nir Hacohen, PhD

Publications

  • Wang L, Shalek AK, Lawrence M, Ding R, Gaublomme JT, Pochet N, Stojanov P, Sougnez C, Shukla SA, Stevenson KE, Zhang W, Wong J, Sievers QL, MacDonald BT, Vartanov AR, Goldstein NR, Neuberg D, He X, Lander E, Hacohen N, Regev A, Getz G, Brown JR, Park H, Wu CJ.Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL.Blood. 2014 Aug 14(7):1089-98.
    24778153
  • Rajasagi M, Shukla SA, Fritsch EF, Keskin DB, DeLuca D, Carmona E, Zhang W, Sougnez C, Cibulskis K, Sidney J, Stevenson K, Ritz J, Neuberg D, Brusic V, Gabriel S, Lander ES, Getz G, Hacohen N, Wu CJ.Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.Blood. 2014 Jul 17(3):453-62.
    24891321
  • Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A.Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5' Sites.Cell Rep. 2014 Jun 25.
    24981863
  • 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, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A.Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.Nature. 2014 Jun 11.
    24919153
  • Fritsch EF, Rajasagi M, Ott PA, Brusic V, Hacohen N, Wu CJ.HLA-Binding Properties of Tumor Neoepitopes in Humans.Cancer Immunol Res. 2014 Jun;2(6):522-9.
    24894089
  • Hacohen N, Fritsch EF, Carter TA, Lander ES, Wu CJ.Getting personal with neoantigen-based therapeutic cancer vaccines.Cancer Immunol Res. 2013 Jul;1(1):11-5.
    24777245
  • Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, Moody SE, Shen RR, Schinzel AC, Thai TC, Reibel JB, Tamayo P, Godfrey JT, Qian ZR, Page AN, Maciag K, Chan EM, Silkworth W, Labowsky MT, Rozhansky L, Mesirov JP, Gillanders WE, Ogino S, Hacohen N, Gaudet S, Eck MJ, Engelman JA, Corcoran RB, Wong KK, Hahn WC, Barbie DA.Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit.Cancer Discovery. 2014 Apr;4(4):452-65.
    24444711
  • Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N.Common genetic variants modulate pathogen-sensing responses in human dendritic cells.Science. 2014 Mar 7;343(6175):1246980.
    24604203
  • Bachireddy P, Hainz U, Rooney M, Pozdnyakova O, Aldridge J, Zhang W, Liao X, Hodi FS, O'Connell K, Haining WN, Goldstein NR, Canning CM, Soiffer RJ, Ritz J, Hacohen N, Alyea EP, Kim HT, Wu CJ.Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion.Blood. 2014 Feb 27;123(9):1412-21.
    24357730
  • Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J.The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection.PLoS Pathog. 2014 Feb;10(2):e1003904.
    24516381
  • Zhou P, Shaffer DR, Alvarez Arias DA, Nakazaki Y, Pos W, Torres AJ, Cremasco V, Dougan SK, Cowley GS, Elpek K, Brogdon J, Lamb J, Turley SJ, Ploegh HL, Root DE, Love JC, Dranoff G, Hacohen N, Cantor H, Wucherpfennig KW.In vivo discovery of immunotherapy targets in the tumour microenvironment.Nature. 2014 Feb 6;506(7486):52-7.
    24476824
  • Giraud M, Jmari N, Du L, Carallis F, Nieland TJ, Perez-Campo FM, Bensaude O, Root DE, Hacohen N, Mathis D, Benoist C.An RNAi screen for Aire cofactors reveals a role for Hnrnpl in polymerase release and Aire-activated ectopic transcription.Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1491-6.
    24434558
  • Park SM, Deering RP, Lu Y, Tivnan P, Lianoglou S, Al-Shahrour F, Ebert BL, Hacohen N, Leslie C, Daley GQ, Lengner CJ, Kharas MG.Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs.J Exp Med. 2014 Jan 13;211(1):71-87.
    24395885
  • Bachireddy P, Hainz U, Rooney M, Pozdnyakova O, Aldridge J, Zhang W, Liao X, Hodi FS, O'Connell K, Haining WN, Goldstein NR, Canning CM, Soiffer RJ, Ritz J, Hacohen N, Alyea EP, Kim HT, Wu CJ.Reversal of in situ T cell exhaustion during effective human anti-leukemia responses to donor lymphocyte infusion.Blood..
  • Ramirez-Ortiz ZG, Pendergraft WF, Prasad A, Byrne MH, Iram T, Blanchette CJ, Luster AD, Hacohen N, El Khoury J, Means TK.The scavenger receptor SCARF1 mediates the clearance of apoptotic cells and prevents autoimmunity.Nat Immunol. 2013 Sep;14(9):917-26.
    23892722
  • 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, Levin JZ, Park H, Regev A.Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.Nature. 2013 Jun 13;498(7453):236-40.
    23685454
  • Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek AK, Hacohen N, Amit I, Regev A.Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.Nat Biotechnol. 2013 Apr;31(4):342-9.
    23503680
  • Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, Saksena G, Cibulskis K, Tesar B, Gabriel S, Hacohen N, Meyerson M, Lander ES, Neuberg D, Brown JR, Getz G, Wu CJ.Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.Cell. 2013 Feb 14;152(4):714-26.
    23415222
  • Lee MN, Roy M, Ong SE, Mertins P, Villani AC, Li W, Dotiwala F, Sen J, Doench JG, Orzalli MH, Kramnik I, Knipe DM, Lieberman J, Carr SA, Hacohen N.Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.Nat Immunol. 2013 Feb;14(2):179-85.
    23263557
  • 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, Park H.Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.Nano Lett. 2012 Dec 12;12(12):6498-504.
    23190424
  • 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, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.Mol Cell. 2012 Sep 14;47(5):810-22.
    22940246
  • Moita CF, Chora Â, Hacohen N, Moita LF.RNAi screen for kinases and phosphatases that play a role in antigen presentation by dendritic cells.Eur J Immunol. 2012 Jul;42(7):1843-9.
    22585713
  • Pe'er D, Hacohen N.Principles and strategies for developing network models in cancer.Cell. 2011 Mar 18;144(6):864-73.
    21414479
  • Lin Y, Zhang L, Cai AX, Lee M, Zhang W, Neuberg D, Canning CM, Soiffer RJ, Alyea EP, Ritz J, Hacohen N, Means TK, Wu CJ.Effective posttransplant antitumor immunity is associated with TLR-stimulating nucleic acid-immunoglobulin complexes in humans.J Clin Invest. 2011 Mar 14.
    21403403
  • Shapira SD, Hacohen N.Systems biology approaches to dissect mammalian innate immunity.Curr Opin Immunol. 2011 Feb;23(1):71-7. Review.
    21111589
  • Dougan M, Dougan S, Slisz J, Firestone B, Vanneman M, Draganov D, Goyal G, Li W, Neuberg D, Blumberg R, Hacohen N, Porter D, Zawel L, Dranoff G.IAP inhibitors enhance co-stimulation to promote tumor immunity.J Exp Med. 2010 Sep 27;207(10):2195-206.
    20837698
  • Colvin RA, Means TK, Diefenbach TJ, Moita LF, Friday RP, Sever S, Campanella GS, Abrazinski T, Manice LA, Moita C, Andrews NW, Wu D, Hacohen N, Luster AD.Synaptotagmin-mediated vesicle fusion regulates cell migration.Nat Immunol. 2010 Jun;11(6):495-502.
    20473299
  • Dixit E, Boulant S, Zhang Y, Lee AS, Odendall C, Shum B, Hacohen N, Chen ZJ, Whelan SP, Fransen M, Nibert ML, Superti-Furga G, Kagan JC.Peroxisomes are signaling platforms for antiviral innate immunity.Cell. 2010 May 14;141(4):668-81.
    20451243
  • Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N.A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.Cell. 2009 Dec 24;139(7):1255-67.
    20064372
  • Astier AL, Beriou G, Eisenhaure TM, Anderton SM, Hafler DA, Hacohen N.RNA interference screen in primary human T cells reveals FLT3 as a modulator of IL-10 levels.J Immunol. 2010 Jan 15;184(2):685-93.
    20018615
  • Ostrowski M, Carmo NB, Krumeich S, Fanget I, Raposo G, Savina A, Moita CF, Schauer K, Hume AN, Freitas RP, Goud B, Benaroch P, Hacohen N, Fukuda M, Desnos C, Seabra MC, Darchen F, Amigorena S, Moita LF, Thery C.Rab27a and Rab27b control different steps of the exosome secretion pathway.Nat Cell Biol. 2010 Jan;12(1):19-30; sup pp 1-13.
    19966785
  • Savina A,Peres A,Cebrian I,Carmo N,Moita C,Hacohen N,Moita LF,Amigorena S.The small GTPase Rac2 controls phagosomal alkalinization and antigen crosspresentation selectively in CD8(+) dendritic cells.Immunity. 2009 Apr;30(4):544-55.
    19328020
  • Means TK,Mylonakis E,Tampakakis E,Colvin RA,Seung E,Puckett L,Tai MF,Stewart CR,Pukkila-Worley R,Hickman SE,Moore KJ,Calderwood SB,Hacohen N,Luster AD,El Khoury J.Evolutionarily conserved recognition and innate immunity to fungal pathogens by the scavenger receptors SCARF1 and CD36.J Exp Med. 2009 Mar 16;206(3):637-53.
    19237602
  • Ali N,Karlsson C,Aspling M,Hu G,Hacohen N,Scadden DT,Larsson J.Forward RNAi screens in primary human hematopoietic stem/progenitor cells.Blood. 2009 Apr 16;113(16):3690-5.
    19188664
  • Guttman M,Amit I,Garber M,French C,Lin MF,Feldser D,Huarte M,Zuk O,Carey BW,Cassady JP,Cabili MN,Jaenisch R,Mikkelsen TS,Jacks T,Hacohen N,Bernstein BE,Kellis M,Regev A,Rinn JL,Lander ES.Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.Nature. 2009 Mar 12;458(7235):223-7.
    19182780
  • Luo B,Cheung HW,Subramanian A,Sharifnia T,Okamoto M,Yang X,Hinkle G,Boehm JS,Beroukhim R,Weir BA,Mermel C,Barbie DA,Awad T,Zhou X,Nguyen T,Piqani B,Li C,Golub TR,Meyerson M,Hacohen N,Hahn WC,Lander ES,Sabatini DM,Root DE.Highly parallel identification of essential genes in cancer cells.Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20380-5.
    19091943
  • Oberdoerffer S,Moita LF,Neems D,Freitas RP,Hacohen N,Rao A.Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL.Science. 2008 Aug 1;321(5889):686-91.
    18669861
  • Adams EW, Ratner DM, Seeberger PH, Hacohen N.Carbohydrate-mediated targeting of antigen to dendritic cells leads to enhanced presentation of antigen to T cells.Chembiochem. 2008 Jan 25;9(2):294-303.
    18186095
  • Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE.A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.Cell. 2006 Mar 24;124(6):1283-98.
    16564017
  • Huang Q, Liu D, Majewski P, Schulte LC, Korn JM, Young RA, Lander ES, Hacohen N.The plasticity of dendritic cell responses to pathogens and their components.Science. 2001 Oct 26;294(5543):870-5.
    11679675