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Aviv Regev

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Nir Yosef; Rahul Satija; Arvind Shakya; Alex K Shalek; Dean Tantin; John J Trombetta; Chuan Wu; Sheng Xiao; Amit Awasthi; Mark Bix; Mathew L Coleman; Jellert T Gaublomme; David Gennert; Hulin Jin; Marsela Jorgolli; Katarzyna Karwacz; Vijay K Kuchroo; Youjin Lee; Diana Y Lu; Hongkun Park; Meenu R Pillai; Peter J Ratcliffe; Aviv Regev
Dynamic regulatory network controlling TH17 cell differentiation.
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.
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.

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All Publications

2013: Nir Yosef; Rahul Satija; Arvind Shakya; Alex K Shalek; Dean Tantin; John J Trombetta; Chuan Wu; Sheng Xiao; Amit Awasthi; Mark Bix; Mathew L Coleman; Jellert T Gaublomme; David Gennert; Hulin Jin; Marsela Jorgolli; Katarzyna Karwacz; Vijay K Kuchroo; Youjin Lee; Diana Y Lu; Hongkun Park; Meenu R Pillai; Peter J Ratcliffe; Aviv Regev
Dynamic regulatory network controlling TH17 cell differentiation.
Nature 2013;496(7446):461-8.
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.
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: Agnes Klochendler; Maya Moran; Omid Niazi; Nathalie Pochet; Aviv Regev; Virginia Savova; Avital Swisa; Yves Van de Peer; Jonas Vikeså; Noa Weinberg-Corem; Michael Brandeis; Yuval Dor; Amir Eden
A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation.
Developmental cell 2012;23(4):681-90.
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: Anne-Ruxandra Carvunis; Benoit Charloteaux; Michael E Cusick; César A Hidalgo; Aviv Regev; Thomas Rolland; Balaji Santhanam; Nicolas Simonis; Nicolas Thierry-Mieg; Justin Barbette; Gloria A Brar; Michael A Calderwood; Ilan Wapinski; Jonathan S Weissman; Muhammed A Yildirim; Marc Vidal
Proto-genes and de novo gene birth.
Nature 2012;487(7407):370-4.
2012: Jennifer R Brown; Mick Correll; Paola Dal Cin; Stacey M Fernandes; John M Asara; Megan Hanna; Laura Macconaill; Donna Neuberg; Nathalie Pochet; Aviv Regev; Bethany Tesar; Christina Thompson; Yves Van de Peer; Yaoyu E Wang; Lillian Werner; Catherine J Wu; Arnold S Freedman
Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia.
Clinical cancer research : an official journal of the American Association for Cancer Research 2012;18(14):3791-802.
2012: Zachary D Smith; Tarjei S Mikkelsen; Aviv Regev; Michelle M Chan; Andreas Gnirke; Hongcang Gu; Alexander Meissner
A unique regulatory phase of DNA methylation in the early mammalian embryo.
Nature 2012;484(7394):339-44.
2012: Andrea Pauli; Aviv Regev; John L Rinn; Albin Sandelin; Lin Fan; Manuel Garber; Joshua Z Levin; Michael F Lin; Eivind Valen; Nadine L Vastenhouw; Alexander F Schier
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Genome research 2012;22(3):577-91.
2012: Gloria A Brar; Nir Friedman; Nicholas T Ingolia; Aviv Regev; Moran Yassour; Jonathan S Weissman
High-resolution view of the yeast meiotic program revealed by ribosome profiling.
Science (New York, N.Y.) 2012;335(6068):552-7.
2012: Naomi Habib; Hanah Margalit; Aviv Regev; Ilan Wapinski; Nir Friedman
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks.
Molecular systems biology 2012;8():619.
2012: Assaf Weiner; Aviv Regev; Luis Soares; Stephen Buratowski; Hsiuyi V Chen; Nir Friedman; Mohanram Gudipati; Avital Klien; Chih Long Liu; Jenna Pfeffner; Jeffrey A Pleiss; Ayelet Rahat; Oliver J Rando
Systematic dissection of roles for chromatin regulators in a yeast stress response.
PLoS biology 2012;10(7):e1001369.
2012: Jia Xu; Yoshimi Yanagisawa; Carsten Russ; Kathleen E Steinmann; Alexander M Tsankov; Zhiping Weng; Keita Aoki; James Bochicchio; Christopher Hart; Naveen Kommajosyula; Patrice M Milos; Hironori Niki; Chad Nusbaum; Oliver J Rando; Aviv Regev; Nicholas Rhind
Genome-wide identification and characterization of replication origins by deep sequencing.
Genome biology 2012;13(4):R27.
2012: Abigail Manson McGuire; Sang Tae Park; Matthew Peterson; Sahadevan Raman; Aviv Regev; Robert Riley; Gary K Schoolnik; Peter Sisk; Christian Stolte; Ilan Wapinski; Brian Weiner; Jared White; Robert T Yamamoto; Jeremy Zucker; Milena Iacobelli-Martinez; Matthew J Kidd; Mike Koehrsen; Andreia M Maer; Thomas Abeel; Gregory Dolganov; James E Galagan
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.
BMC genomics 2012;13():120.
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: Alex Tsankov; Yoshimi Yanagisawa; Aviv Regev; Nicholas Rhind; Oliver J Rando
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.
Genome research 2011;21(11):1851-62.
2011: Moran N Cabili; Loyal Goff; Magdalena Koziol; Aviv Regev; Barbara Tazon-Vega; Cole Trapnell; John L Rinn
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.
Genes & development 2011;25(18):1915-27.
2011: Mitchell Guttman; Robert Ach; Ido Amit; Laurakay Bruhn; Bryce W Carey; Julie Donaghey; Manuel Garber; Jennifer K Grenier; Anne Bergstrom Lucas; Alexander Meissner; Glen Munson; Aviv Regev; John L Rinn; David E Root; Xiaoping Yang; Geneva Young; Eric S Lander
lincRNAs act in the circuitry controlling pluripotency and differentiation.
Nature 2011;477(7364):295-300.
2011: Noa Novershtern; Aviv Regev; Nir Friedman
Physical Module Networks: an integrative approach for reconstructing transcription regulation.
Bioinformatics (Oxford, England) 2011;27(13):i177-85.
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: 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: Nir Yosef; Aviv Regev
Impulse control: temporal dynamics in gene transcription.
Cell 2011;144(6):886-96.
2011: Noa Novershtern; Aravind Subramanian; Lee N Lawton; Raymond H Mak; W Nicholas Haining; Marie E McConkey; Naomi Habib; Nir Yosef; Cindy Y Chang; Tal Shay; Garrett M Frampton; Adam C B Drake; Ilya Leskov; Bjorn Nilsson; Fred Preffer; David Dombkowski; John W Evans; Ted Liefeld; John S Smutko; Jianzhu Chen; Nir Friedman; Richard A Young; Todd R Golub; Aviv Regev; Benjamin L Ebert
Densely interconnected transcriptional circuits control cell states in human hematopoiesis.
Cell 2011;144(2):296-309.
2010: Joshua Z Levin; Moran Yassour; Xian Adiconis; Chad Nusbaum; Dawn Anne Thompson; Nir Friedman; Andreas Gnirke; Aviv Regev
Comprehensive comparative analysis of strand-specific RNA sequencing methods.
Nature methods 2010;7(9):709-15.
2010: Maite Huarte; Mitchell Guttman; David M. Feldser; manuel garber; Magdalena J Koziol; Daniela Kenzelmann-Broz; Ahmad M Khalil; Or Zuk; Ido Amit; Michal Rabani; Laura D Attardi; Aviv Regev; Eric S Lander; Tyler Jacks; John L Rinn
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.
Cell 2010;142(3):409-19.
2010: Mitchell Guttman; manuel garber; Joshua Z Levin; Julie Donaghey; James Robinson; Xian Adiconis; Lin Fan; Magdalena J Koziol; Andreas Gnirke; Chad Nusbaum; John L Rinn; Eric S Lander; Aviv Regev
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.
Nature biotechnology 2010;28(5):503-10.
2010: Zachary D Smith; Iftach Nachman; Aviv Regev; Alexander Meissner
Dynamic single-cell imaging of direct reprogramming reveals an early specifying event.
Nature biotechnology 2010;28(5):521-6.
2010: Nadine L Vastenhouw; Yong Zhang; Ian G Woods; Farhad Imam; Aviv Regev; X Shirley Liu; John Rinn; Alexander F Schier
Chromatin signature of embryonic pluripotency is established during genome activation.
Nature 2010;464(7290):922-6.
2010: Moran Yassour; Jenna Pfiffner; Joshua Z Levin; Xian Adiconis; Andreas Gnirke; Chad Nusbaum; Dawn-Anne Thompson; Nir Friedman; Aviv Regev
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.
Genome biology 2010;11(8):R87.
2010: Alexander M Tsankov; Dawn Anne Thompson; Amanda Socha; Aviv Regev; Oliver J Rando
The role of nucleosome positioning in the evolution of gene regulation.
PLoS biology 2010;8(7):e1000414.
2009: Harold D Kim; Tal Shay; Erin K O'Shea; Aviv Regev
Transcriptional regulatory circuits: predicting numbers from alphabets.
Science (New York, N.Y.) 2009;325(5939):429-32.
2009: Moran Yassour; Tommy Kaplan; Hunter B Fraser; Joshua Z Levin; Jenna Pfiffner; Xian Adiconis; Gary Schroth; Shujun Luo; Irina Khrebtukova; Andreas Gnirke; Chad Nusbaum; Dawn-Anne Thompson; Nir Friedman; Aviv Regev
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(9):3264-9.
2009: Iftach Nachman; Aviv Regev
BRNI: Modular analysis of transcriptional regulatory programs.
BMC bioinformatics 2009;10():155.
2008: Gal Chechik; Eugene Oh; Oliver Rando; Jonathan Weissman; Aviv Regev; Daphne Koller
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network.
Nature biotechnology 2008;26(11):1251-9.
2008: Andrew P Capaldi; Tommy Kaplan; Ying Liu; Naomi Habib; Aviv Regev; Nir Friedman; Erin K O'Shea
Structure and function of a transcriptional network activated by the MAPK Hog1.
Nature genetics 2008;40(11):1300-6.
2008: David J Wong; Dimitry S A Nuyten; Aviv Regev; Meihong Lin; Adam S Adler; Eran Segal; Marc J van de Vijver; Howard Y Chang
Revealing targeted therapy for human cancer by gene module maps.
Cancer research 2008;68(2):369-78.
2007: Iftach Nachman; Aviv Regev; Sharad Ramanathan
Dissecting timing variability in yeast meiosis.
Cell 2007;131(3):544-56.
2005: Eran Segal; Nir Friedman; Naftali Kaminski; Aviv Regev; Daphne Koller
From signatures to models: understanding cancer using microarrays.
Nature genetics 2005;37 Suppl():S38-45.
2005: Amos Tanay; Aviv Regev; Ron Shamir
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(20):7203-8.
2004: Rosa M Marion; Aviv Regev; Eran Segal; Yoseph Barash; Daphne Koller; Nir Friedman; Erin K O'Shea
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(40):14315-22.
2004: Eran Segal; Nir Friedman; Daphne Koller; Aviv Regev
A module map showing conditional activity of expression modules in cancer.
Nature genetics 2004;36(10):1090-8.
2004: Iftach Nachman; Aviv Regev; Nir Friedman
Inferring quantitative models of regulatory networks from expression data.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i248-56.
2003: Eran Segal; Michael Shapira; Aviv Regev; Dana Pe'er; David Botstein; Daphne Koller; Nir Friedman
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.
Nature genetics 2003;34(2):166-76.
2002: Dana Pe'er; Aviv Regev; Amos Tanay
Minreg: inferring an active regulator set.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S258-67.
2001: Dana Pe'er; Aviv Regev; Gal Elidan; Nir Friedman
Inferring subnetworks from perturbed expression profiles.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S215-24.