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Nir Hacohen

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Irit Gat-Viks; Nir Hacohen; Raktima Raychowdhury; Ido Amit; Nicolas Chevrier; Thomas Eisenhaure; Alex K Shalek; Yael Steuerman; Roni Wilentzik; Aviv Regev
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.
Dan A Landau; Eric S Lander; Michael S Lawrence; Aaron McKenna; Matthew Meyerson; Donna Neuberg; Gordon Saksena; Sachet A Shukla; Andrey Sivachenko; Carrie Sougnez; Kristen Stevenson; Chip Stewart; Petar Stojanov; Bethany Tesar; Alexander Vartanov; Youzhong Wan; Lili Wang; Jennifer R Brown; Scott L Carter; Kristian Cibulskis; Stacey M Fernandes; Stacey Gabriel; Gad Getz; Nir Hacohen; Wandi Zhang; Catherine J Wu
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.
Mark N Lee; Weibo Li; Judy Lieberman; Philipp Mertins; Shao-En Ong; Megan H Orzalli; Matthew Roy; Jayita Sen; Alexandra-Chloé Villani; Steven A Carr; John G Doench; Farokh Dotiwala; David M Knipe; Igor Kramnik; Nir Hacohen
Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.

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All Publications

2013: Irit Gat-Viks; Nir Hacohen; Raktima Raychowdhury; Ido Amit; Nicolas Chevrier; Thomas Eisenhaure; Alex K Shalek; Yael Steuerman; Roni Wilentzik; Aviv Regev
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.
Nature biotechnology 2013;31(4):342-9.
2013: Dan A Landau; Eric S Lander; Michael S Lawrence; Aaron McKenna; Matthew Meyerson; Donna Neuberg; Gordon Saksena; Sachet A Shukla; Andrey Sivachenko; Carrie Sougnez; Kristen Stevenson; Chip Stewart; Petar Stojanov; Bethany Tesar; Alexander Vartanov; Youzhong Wan; Lili Wang; Jennifer R Brown; Scott L Carter; Kristian Cibulskis; Stacey M Fernandes; Stacey Gabriel; Gad Getz; Nir Hacohen; Wandi Zhang; Catherine J Wu
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.
Cell 2013;152(4):714-26.
2013: Mark N Lee; Weibo Li; Judy Lieberman; Philipp Mertins; Shao-En Ong; Megan H Orzalli; Matthew Roy; Jayita Sen; Alexandra-Chloé Villani; Steven A Carr; John G Doench; Farokh Dotiwala; David M Knipe; Igor Kramnik; Nir Hacohen
Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.
Nature immunology 2013;14(2):179-85.
2012: Alex K Shalek; Lili Wang; Catherine J Wu; Nir Yosef; Nathalie Pochet; Aviv Regev; Jacob T Robinson; Ido Amit; Mette S Andersen; Jennifer R Brown; Nicolas Chevrier; Jellert T Gaublomme; Rona S Gertner; Nir Hacohen; Donna Neuberg; Hongkun Park
Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.
Nano letters 2012;12(12):6498-504.
2012: Manuel Garber; Andreas Gnirke; Alon Goren; Mitchell Guttman; Nir Hacohen; Zohar Itzhaki; James Meldrim; Brian Minie; Chad Nusbaum; Oren Ram; Raktima Raychowdhury; Aviv Regev; James Robinson; Anne Thielke; Assaf Weiner; Bang Wong; Nir Yosef; Bradley E Bernstein; Ronnie Blecher-Gonen; Chamutal Bornstein; Christine Cheng; Nicolas Chevrier; Sheila Fisher; Nir Friedman; Dennis Friedrich; Daniela Amann-Zalcenstein; Ido Amit
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.
Molecular cell 2012;47(5):810-22.
2012: Catarina F Moita; Nir Hacohen; Angelo Chora; Luis F Moita
RNAi screen for kinases and phosphatases that play a role in antigen presentation by dendritic cells.
European journal of immunology 2012;42(7):1843-9.
2012: Namrata D Udeshi; Karl R Clauser; Thomas Eisenhaure; Nir Hacohen; Jacob D Jaffe; D R Mani; Philipp Mertins; Steven A Carr
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
Molecular & cellular proteomics : MCP 2012;11(5):148-59.
2012: E Ashley Moseman; Elena Tonti; Alexei Tumanov; Lidia Bosurgi; Nicolas Chevrier; Yang-Xin Fu; Nir Hacohen; Matteo Iannacone; Ulrich H von Andrian
B cell maintenance of subcapsular sinus macrophages protects against a fatal viral infection independent of adaptive immunity.
Immunity 2012;36(3):415-26.
2011: Ido Amit; Aviv Regev; Nir Hacohen
Strategies to discover regulatory circuits of the mammalian immune system.
Nature reviews. Immunology 2011;11(12):873-80.
2011: Nicolas Chevrier; Mark F Ciaccio; Karl R Clauser; Marciela M DeGrace; Thomas M Eisenhaure; Manuel Garber; Irit Gat-Viks; Matteo Iannacone; Richard B Jones; Philipp Mertins; Hongkun Park; Aviv Regev; Jacob Robinson; David E Root; Alex K Shalek; Amy Sutton; Elena Tonti; Ulrich von Andrian; Nir Yosef; Ido Amit; Mette S Andersen; Maxim N Artyomov; Steven A Carr; Nir Hacohen
Systematic discovery of TLR signaling components delineates viral-sensing circuits.
Cell 2011;147(4):853-67.
2011: Salil Garg; Nir Hacohen; David L Hava; Mahak Sharma; Amit Tuli; Cindy Ung; Natacha Veerapen; Duarte C Barral; Gurdyal S Besra; Michael B Brenner
Lysosomal trafficking, antigen presentation, and microbial killing are controlled by the Arf-like GTPase Arl8b.
Immunity 2011;35(2):182-93.
2011: Sen Wang; Ramnik J Xavier; Cathryn Nagler; Deanna D Nguyen; Hans-Christian Reinecker; Bartira Rossi-Bergmann; Scott B Snapper; Eduardo J Villablanca; Rune Blomhoff; Yi-Bin Chen; Jaime De Calisto; Daniel C O Gomes; Nir Hacohen; Jonathan C Kagan; Emiko Mizoguchi; J Rodrigo Mora
MyD88-dependent TLR1/2 signals educate dendritic cells with gut-specific imprinting properties.
Journal of immunology (Baltimore, Md. : 1950) 2011;187(1):141-50.
2011: Manfred G Grabherr; Brian J Haas; Nir Hacohen; Joshua Z Levin; Kerstin Lindblad-Toh; Evan Mauceli; Chad Nusbaum; Raktima Raychowdhury; Xian Adiconis; Ido Amit; Bruce W Birren; Zehua Chen; Federica di Palma; Lin Fan; Nir Friedman; Andreas Gnirke; Nicholas Rhind; Dawn A Thompson; Moran Yassour; Qiandong Zeng; Aviv Regev
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Nature biotechnology 2011;29(7):644-52.
2011: Christophe Benoist; Nir Hacohen
Immunology. Flow cytometry, amped up.
Science (New York, N.Y.) 2011;332(6030):677-8.
2011: Michal Rabani; Joshua Z Levin; Lin Fan; Xian Adiconis; Raktima Raychowdhury; Manuel Garber; Andreas Gnirke; Chad Nusbaum; Nir Hacohen; Nir Friedman; Ido Amit; Aviv Regev
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.
Nature biotechnology 2011;29(5):436-42.
2011: Yun Lin; Li Zhang; Ann X Cai; Mark Lee; Wandi Zhang; Donna Neuberg; Christine M Canning; Robert J Soiffer; Edwin P Alyea; Jerome Ritz; Nir Hacohen; Terry K Means; Catherine J Wu
Effective posttransplant antitumor immunity is associated with TLR-stimulating nucleic acid-immunoglobulin complexes in humans.
The Journal of clinical investigation 2011;121(4):1574-84.
2011: Dana Pe'er; Nir Hacohen
Principles and strategies for developing network models in cancer.
Cell 2011;144(6):864-73.
2011: Sagi D Shapira; Nir Hacohen
Systems biology approaches to dissect mammalian innate immunity.
Current opinion in immunology 2011;23(1):71-7.
2011: Bryan Vander Lugt; Zachary T Beck; Robert C Fuhlbrigge; Nir Hacohen; James J Campbell; Marianne Boes
TGF-β suppresses β-catenin-dependent tolerogenic activation program in dendritic cells.
PloS one 2011;6(5):e20099.
2011: Pedro Moura-Alves; Ana Neves-Costa; Helena Raquel; Teresa Raquel Pacheco; Bruno D'Almeida; Raquel Rodrigues; Iris Cadima-Couto; Mariana Oliveira; Margarida Gama-Carvalho; Nir Hacohen; Angelo Chora; Luis F Moita
An shRNA-based screen of splicing regulators identifies SFRS3 as a negative regulator of IL-1β secretion.
PloS one 2011;6(5):e19829.
2010: Michael Dougan; Stephanie Dougan; Joanna Slisz; Brant Firestone; Matthew Vanneman; Dobrin Draganov; Girija Goyal; Weibo Li; Donna Neuberg; Richard Blumberg; Nir Hacohen; Dale Porter; Leigh Zawel; Glenn Dranoff
IAP inhibitors enhance co-stimulation to promote tumor immunity.
The Journal of experimental medicine 2010;207(10):2195-206.
2010: Bibhuti B Mishra; Pedro Moura-Alves; Avinash Sonawane; Nir Hacohen; Gareth Griffiths; Luis F Moita; Elsa Anes
Mycobacterium tuberculosis protein ESAT-6 is a potent activator of the NLRP3/ASC inflammasome.
Cellular microbiology 2010;12(8):1046-63.
2010: Richard A Colvin; Terry K Means; Thomas J Diefenbach; Luis F Moita; Robert P Friday; Sanja Sever; Gabriele S V Campanella; Tabitha Abrazinski; Lindsay A Manice; Catarina Moita; Norma W Andrews; Dianqing Wu; Nir Hacohen; Andrew D Luster
Synaptotagmin-mediated vesicle fusion regulates cell migration.
Nature immunology 2010;11(6):495-502.
2010: Evelyn Dixit; Steeve Boulant; Yijing Zhang; Amy S Y Lee; Charlotte Odendall; Bennett Shum; Nir Hacohen; Zhijian J Chen; Sean Whelan; Marc Fransen; Max L Nibert; Giulio Superti-Furga; Jonathan C Kagan
Peroxisomes are signaling platforms for antiviral innate immunity.
Cell 2010;141(4):668-81.
2010: Anne L Astier; Gaëlle Beriou; Thomas M Eisenhaure; Stephen M Anderton; David A Hafler; Nir Hacohen
RNA interference screen in primary human T cells reveals FLT3 as a modulator of IL-10 levels.
Journal of immunology (Baltimore, Md. : 1950) 2010;184(2):685-93.
2010: Sylvie Rato; Sara Maia; Paula M Brito; Leonor Resende; Carina F Pereira; Catarina Moita; Rui P Freitas; José Moniz-Pereira; Nir Hacohen; Luis Ferreira Moita; Joao Goncalves
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.
2010: Matias Ostrowski; Nuno B Carmo; Sophie Krumeich; Isabelle Fanget; Graça Raposo; Ariel Savina; Catarina F Moita; Kristine Schauer; Alistair N Hume; Rui P Freitas; Bruno Goud; Philippe Benaroch; Nir Hacohen; Mitsunori Fukuda; Claire Desnos; Miguel C Seabra; François Darchen; Sebastian Amigorena; Luis F Moita; Clotilde Thery
Rab27a and Rab27b control different steps of the exosome secretion pathway.
Nature cell biology 2010;12(1):19-30; sup pp 1-13.
2009: Sagi D Shapira; Irit Gat-Viks; Bennett O V Shum; Amelie Dricot; Marciela M de Grace; Liguo Wu; Piyush B Gupta; Tong Hao; Serena J Silver; David E Root; David E Hill; Aviv Regev; Nir Hacohen
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.
Cell 2009;139(7):1255-67.
2009: Ido Amit; manuel garber; Nicolas Chevrier; Ana Paula Leite; Yoni Donner; Thomas Eisenhaure; Mitchell Guttman; Jennifer K Grenier; Weibo Li; Or Zuk; Lisa A Schubert; Brian Birditt; Tal Shay; Alon Goren; Xiaolan Zhang; Zachary Smith; Raquel Deering; Rebecca C McDonald; Moran Cabili; Bradley E Bernstein; John L Rinn; Alex Meissner; David E Root; Nir Hacohen; Aviv Regev
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.
Science (New York, N.Y.) 2009;326(5950):257-63.
2009: Ariel Savina; Audrey Peres; Ignacio Cebrian; Nuno Carmo; Catarina Moita; Nir Hacohen; Luis F Moita; Sebastian Amigorena
The small GTPase Rac2 controls phagosomal alkalinization and antigen crosspresentation selectively in CD8(+) dendritic cells.
Immunity 2009;30(4):544-55.
2009: Nicole Ali; Christine Karlsson; Marie Aspling; Guang Hu; Nir Hacohen; David T Scadden; Jonas Larsson
Forward RNAi screens in primary human hematopoietic stem/progenitor cells.
Blood 2009;113(16):3690-5.
2009: Terry K Means; Eleftherios Mylonakis; Emmanouil Tampakakis; Richard A Colvin; Edward Seung; Lindsay Puckett; Melissa F Tai; Cameron R Stewart; Read Pukkila-Worley; Suzanne E Hickman; Kathryn J Moore; Stephen B Calderwood; Nir Hacohen; Andrew D Luster; Joseph B El-Khoury
Evolutionarily conserved recognition and innate immunity to fungal pathogens by the scavenger receptors SCARF1 and CD36.
The Journal of experimental medicine 2009;206(3):637-53.
2009: Mitchell Guttman; Ido Amit; manuel garber; Courtney French; Michael F Lin; David M. Feldser; Maite Huarte; Or Zuk; Bryce W Carey; John P Cassady; Moran N Cabili; Rudolf Jaenisch; Tarjei S Mikkelsen; Tyler Jacks; Nir Hacohen; Bradley E Bernstein; Manolis Kellis; Aviv Regev; John L Rinn; Eric S Lander
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
Nature 2009;458(7235):223-7.
2008: Shalini Oberdoerffer; Luis Ferreira Moita; Daniel Neems; Rui P Freitas; Nir Hacohen; Anjana Rao
Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL.
Science (New York, N.Y.) 2008;321(5889):686-91.
2008: Eddie W Adams; Daniel M Ratner; Peter H Seeberger; Nir Hacohen
Carbohydrate-mediated targeting of antigen to dendritic cells leads to enhanced presentation of antigen to T cells.
Chembiochem : a European journal of chemical biology 2008;9(2):294-303.
2006: Christophe Echeverri; Philip A Beachy; Buzz Baum; Michael Boutros; Frank Buchholz; Sumit K Chanda; Julian Downward; Jan Ellenberg; Andrew G Fraser; Nir Hacohen; William C Hahn; Aimee L Jackson; Amy Kiger; Peter Linsley; Lawrence Lum; Yong Ma; Bernard Mathey-Prévôt; David E Root; David M Sabatini; Jussi Taipale; Norbert Perrimon; René Bernards
Minimizing the risk of reporting false positives in large-scale RNAi screens.
Nature methods 2006;3(10):777-9.
2006: Teresa R Pacheco; Luis F Moita; Anita Q Gomes; Nir Hacohen; Maria Carmo-Fonseca
RNA interference knockdown of hU2AF35 impairs cell cycle progression and modulates alternative splicing of Cdc25 transcripts.
Molecular biology of the cell 2006;17(10):4187-99.
2006: David E Root; Nir Hacohen; William C Hahn; Eric S Lander; David M Sabatini
Genome-scale loss-of-function screening with a lentiviral RNAi library.
Nature methods 2006;3(9):715-9.
2006: Jason Moffat; Dorre A Grueneberg; Xiaoping Yang; So Young Kim; Angela M Kloepfer; Gregory Hinkle; Bruno Piqani; Thomas M Eisenhaure; Biao Luo; Jennifer K Grenier; Anne E Carpenter; Shi Yin Foo; Sheila A Stewart; Brent R Stockwell; Nir Hacohen; William C Hahn; Eric S Lander; David M Sabatini; David E Root
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.
Cell 2006;124(6):1283-98.
2004: Deborah Palliser; Qian Huang; Nir Hacohen; Steven P Lamontagne; Eduardo Guillen; Richard A Young; Herman N Eisen
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.
Journal of immunology (Baltimore, Md. : 1950) 2004;172(5):2885-93.
2002: Hong Ruan; Nir Hacohen; Todd R Golub; Luk Van Parijs; Harvey Lodish
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;51(5):1319-36.
2002: Elizabeth Alcamo; Nir Hacohen; Leah C Schulte; Paul D Rennert; Richard O Hynes; David Baltimore
Requirement for the NF-kappaB family member RelA in the development of secondary lymphoid organs.
The Journal of experimental medicine 2002;195(2):233-44.
2001: Q Huang; D Liu; P Majewski; L C Schulte; J M Korn; Richard A Young; Eric S Lander; Nir Hacohen
The plasticity of dendritic cell responses to pathogens and their components.
Science (New York, N.Y.) 2001;294(5543):870-5.