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Last Name
Institution

Nir Hacohen, Ph.D.

TitleAssociate Professor of Medicine
InstitutionMassachusetts General Hospital
DepartmentMedicine
AddressMassachusetts General Hospital
149-8410
149 13th Street
Charlestown MA 02129
Phone617/724-3768
Fax617/726-5651

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. 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-ß signaling in HSCs. J Exp Med. 2014 Jan 13; 211(1):71-87.
    View in: PubMed
  2. Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I. Semiconductor-based DNA sequencing of histone modification states. Nat Commun. 2013 Oct 25; 4:2672.
    View in: PubMed
  3. Ramirez-Ortiz ZG, Pendergraft WF, Prasad A, Byrne MH, Iram T, Blanchette CJ, Luster AD, Hacohen N, Khoury JE, Means TK. The scavenger receptor SCARF1 mediates the clearance of apoptotic cells and prevents autoimmunity. Nat Immunol. 2013 Sep; 14(9):917-26.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. 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.
    View in: PubMed
  6. 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.
    View in: PubMed
  7. Arazi A, Pendergraft WF, Ribeiro RM, Perelson AS, Hacohen N. Human systems immunology: Hypothesis-based modeling and unbiased data-driven approaches. Semin Immunol. 2013 Oct 31; 25(3):193-200.
    View in: PubMed
  8. 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. 2012 Dec 23; 14(2):179-85.
    View in: PubMed
  9. 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.
    View in: PubMed
  10. 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.
    View in: PubMed
  11. 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.
    View in: PubMed
  12. Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics. 2012 May; 11(5):148-59.
    View in: PubMed
  13. Moseman EA, Iannacone M, Bosurgi L, Tonti E, Chevrier N, Tumanov A, Fu YX, Hacohen N, von Andrian UH. B cell maintenance of subcapsular sinus macrophages protects against a fatal viral infection independent of adaptive immunity. Immunity. 2012 Mar 23; 36(3):415-26.
    View in: PubMed
  14. Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, Stevenson K, Werner L, Sivachenko A, DeLuca DS, Zhang L, Zhang W, Vartanov AR, Fernandes SM, Goldstein NR, Folco EG, Cibulskis K, Tesar B, Sievers QL, Shefler E, Gabriel S, Hacohen N, Reed R, Meyerson M, Golub TR, Lander ES, Neuberg D, Brown JR, Getz G, Wu CJ. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med. 2011 Dec 29; 365(26):2497-506.
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  15. Amit I, Regev A, Hacohen N. Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol. 2011 Dec; 11(12):873-80.
    View in: PubMed
  16. Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A, Amit I, Hacohen N. Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell. 2011 Nov 11; 147(4):853-67.
    View in: PubMed
  17. Garg S, Sharma M, Ung C, Tuli A, Barral DC, Hava DL, Veerapen N, Besra GS, Hacohen N, Brenner MB. Lysosomal trafficking, antigen presentation, and microbial killing are controlled by the Arf-like GTPase Arl8b. Immunity. 2011 Aug 26; 35(2):182-93.
    View in: PubMed
  18. Wang S, Villablanca EJ, De Calisto J, Gomes DC, Nguyen DD, Mizoguchi E, Kagan JC, Reinecker HC, Hacohen N, Nagler C, Xavier RJ, Rossi-Bergmann B, Chen YB, Blomhoff R, Snapper SB, Mora JR. MyD88-dependent TLR1/2 signals educate dendritic cells with gut-specific imprinting properties. J Immunol. 2011 Jul 1; 187(1):141-50.
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  19. Vander Lugt B, Beck ZT, Fuhlbrigge RC, Hacohen N, Campbell JJ, Boes M. TGF-ß suppresses ß-catenin-dependent tolerogenic activation program in dendritic cells. PLoS One. 2011; 6(5):e20099.
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  20. Moura-Alves P, Neves-Costa A, Raquel H, Pacheco TR, D'Almeida B, Rodrigues R, Cadima-Couto I, Chora Â, Oliveira M, Gama-Carvalho M, Hacohen N, Moita LF. An shRNA-based screen of splicing regulators identifies SFRS3 as a negative regulator of IL-1ß secretion. PLoS One. 2011; 6(5):e19829.
    View in: PubMed
  21. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 Jul; 29(7):644-52.
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  22. Benoist C, Hacohen N. Immunology. Flow cytometry, amped up. Science. 2011 May 6; 332(6030):677-8.
    View in: PubMed
  23. Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, Amit I, Regev A. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol. 2011 May; 29(5):436-42.
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  24. Pe'er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell. 2011 Mar 18; 144(6):864-73.
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  25. 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 Apr; 121(4):1574-84.
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  26. Shapira SD, Hacohen N. Systems biology approaches to dissect mammalian innate immunity. Curr Opin Immunol. 2011 Feb; 23(1):71-7.
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  27. 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.
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  28. 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.
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  29. 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.
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  30. Rato S, Maia S, Brito PM, Resende L, Pereira CF, Moita C, Freitas RP, Moniz-Pereira J, Hacohen N, Moita LF, Goncalves J. Novel HIV-1 knockdown targets identified by an enriched kinases/phosphatases shRNA library using a long-term iterative screen in Jurkat T-cells. PLoS One. 2010; 5(2):e9276.
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  31. Mishra BB, Moura-Alves P, Sonawane A, Hacohen N, Griffiths G, Moita LF, Anes E. Mycobacterium tuberculosis protein ESAT-6 is a potent activator of the NLRP3/ASC inflammasome. Cell Microbiol. 2010 Aug; 12(8):1046-63.
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  32. 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.
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  33. 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.
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  34. 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.
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  35. Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009 Oct 9; 326(5950):257-63.
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  36. 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 17; 30(4):544-55.
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  37. 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.
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  38. 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.
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  39. 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.
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  40. 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.
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  41. 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.
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  42. 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.
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  43. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prévôt B, Root DE, Sabatini DM, Taipale J, Perrimon N, Bernards R. Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods. 2006 Oct; 3(10):777-9.
    View in: PubMed
  44. Root DE, Hacohen N, Hahn WC, Lander ES, Sabatini DM. Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat Methods. 2006 Sep; 3(9):715-9.
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  45. Pacheco TR, Moita LF, Gomes AQ, Hacohen N, Carmo-Fonseca M. RNA interference knockdown of hU2AF35 impairs cell cycle progression and modulates alternative splicing of Cdc25 transcripts. Mol Biol Cell. 2006 Oct; 17(10):4187-99.
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  46. 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.
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  47. Palliser D, Huang Q, Hacohen N, Lamontagne SP, Guillen E, Young RA, Eisen HN. A role for Toll-like receptor 4 in dendritic cell activation and cytolytic CD8+ T cell differentiation in response to a recombinant heat shock fusion protein. J Immunol. 2004 Mar 1; 172(5):2885-93.
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  48. Ruan H, Hacohen N, Golub TR, Van Parijs L, Lodish HF. Tumor necrosis factor-alpha suppresses adipocyte-specific genes and activates expression of preadipocyte genes in 3T3-L1 adipocytes: nuclear factor-kappaB activation by TNF-alpha is obligatory. Diabetes. 2002 May; 51(5):1319-36.
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  49. Alcamo E, Hacohen N, Schulte LC, Rennert PD, Hynes RO, Baltimore D. Requirement for the NF-kappaB family member RelA in the development of secondary lymphoid organs. J Exp Med. 2002 Jan 21; 195(2):233-44.
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  50. 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.
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  51. Minowada G, Jarvis LA, Chi CL, Neubüser A, Sun X, Hacohen N, Krasnow MA, Martin GR. Vertebrate Sprouty genes are induced by FGF signaling and can cause chondrodysplasia when overexpressed. Development. 1999 Oct; 126(20):4465-75.
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  52. Kramer S, Okabe M, Hacohen N, Krasnow MA, Hiromi Y. Sprouty: a common antagonist of FGF and EGF signaling pathways in Drosophila. Development. 1999 Jun; 126(11):2515-25.
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  53. Hacohen N, Kramer S, Sutherland D, Hiromi Y, Krasnow MA. sprouty encodes a novel antagonist of FGF signaling that patterns apical branching of the Drosophila airways. Cell. 1998 Jan 23; 92(2):253-63.
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  54. Lee T, Hacohen N, Krasnow M, Montell DJ. Regulated Breathless receptor tyrosine kinase activity required to pattern cell migration and branching in the Drosophila tracheal system. Genes Dev. 1996 Nov 15; 10(22):2912-21.
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  55. Samakovlis C, Manning G, Steneberg P, Hacohen N, Cantera R, Krasnow MA. Genetic control of epithelial tube fusion during Drosophila tracheal development. Development. 1996 Nov; 122(11):3531-6.
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  56. Samakovlis C, Hacohen N, Manning G, Sutherland DC, Guillemin K, Krasnow MA. Development of the Drosophila tracheal system occurs by a series of morphologically distinct but genetically coupled branching events. Development. 1996 May; 122(5):1395-407.
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  57. Hacohen N, Assad JA, Smith WJ, Corey DP. Regulation of tension on hair-cell transduction channels: displacement and calcium dependence. J Neurosci. 1989 Nov; 9(11):3988-97.
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  58. Assad JA, Hacohen N, Corey DP. Voltage dependence of adaptation and active bundle movement in bullfrog saccular hair cells. Proc Natl Acad Sci U S A. 1989 Apr; 86(8):2918-22.
    View in: PubMed
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