Searching journal content for Joel Rozowsky in author.

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  1. Research: Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    • Chao Cheng,
    • Roger Alexander,
    • Renqiang Min,
    • Jing Leng,
    • Kevin Y. Yip,
    • Joel Rozowsky,
    • Koon-Kiu Yan,
    • Xianjun Dong,
    • Sarah Djebali,
    • Yijun Ruan,
    • Carrie A. Davis,
    • Piero Carninci,
    • Timo Lassman,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Ewan Birney,
    • Zhiping Weng,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. September 2012 22: 1658-1667; doi:10.1101/gr.136838.111
    OPEN ACCESS ARTICLE
  2. Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • Stephen G. Landt,
    • Georgi K. Marinov,
    • Anshul Kundaje,
    • Pouya Kheradpour,
    • Florencia Pauli,
    • Serafim Batzoglou,
    • Bradley E. Bernstein,
    • Peter Bickel,
    • James B. Brown,
    • Philip Cayting,
    • Yiwen Chen,
    • Gilberto DeSalvo,
    • Charles Epstein,
    • Katherine I. Fisher-Aylor,
    • Ghia Euskirchen,
    • Mark Gerstein,
    • Jason Gertz,
    • Alexander J. Hartemink,
    • Michael M. Hoffman,
    • Vishwanath R. Iyer,
    • Youngsook L. Jung,
    • Subhradip Karmakar,
    • Manolis Kellis,
    • Peter V. Kharchenko,
    • Qunhua Li,
    • Tao Liu,
    • X. Shirley Liu,
    • Lijia Ma,
    • Aleksandar Milosavljevic,
    • Richard M. Myers,
    • Peter J. Park,
    • Michael J. Pazin,
    • Marc D. Perry,
    • Debasish Raha,
    • Timothy E. Reddy,
    • Joel Rozowsky,
    • Noam Shoresh,
    • Arend Sidow,
    • Matthew Slattery,
    • John A. Stamatoyannopoulos,
    • Michael Y. Tolstorukov,
    • Kevin P. White,
    • Simon Xi,
    • Peggy J. Farnham,
    • Jason D. Lieb,
    • Barbara J. Wold,
    • and Michael Snyder
    Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
    OPEN ACCESS ARTICLE
  3. Method: Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
    • Zhi John Lu,
    • Kevin Y. Yip,
    • Guilin Wang,
    • Chong Shou,
    • LaDeana W. Hillier,
    • Ekta Khurana,
    • Ashish Agarwal,
    • Raymond Auerbach,
    • Joel Rozowsky,
    • Chao Cheng,
    • Masaomi Kato,
    • David M. Miller,
    • Frank Slack,
    • Michael Snyder,
    • Robert H. Waterston,
    • Valerie Reinke,
    • and Mark B. Gerstein
    Genome Res. February 2011 21: 276-285; Published in Advance December 22, 2010, doi:10.1101/gr.110189.110
    OPEN ACCESS ARTICLE
  4. LETTER: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    • David S. Johnson,
    • Wei Li,
    • D. Benjamin Gordon,
    • Arindam Bhattacharjee,
    • Bo Curry,
    • Jayati Ghosh,
    • Leonardo Brizuela,
    • Jason S. Carroll,
    • Myles Brown,
    • Paul Flicek,
    • Christoph M. Koch,
    • Ian Dunham,
    • Mark Bieda,
    • Xiaoqin Xu,
    • Peggy J. Farnham,
    • Philipp Kapranov,
    • David A. Nix,
    • Thomas R. Gingeras,
    • Xinmin Zhang,
    • Heather Holster,
    • Nan Jiang,
    • Roland D. Green,
    • Jun S. Song,
    • Scott A. McCuine,
    • Elizabeth Anton,
    • Loan Nguyen,
    • Nathan D. Trinklein,
    • Zhen Ye,
    • Keith Ching,
    • David Hawkins,
    • Bing Ren,
    • Peter C. Scacheri,
    • Joel Rozowsky,
    • Alexander Karpikov,
    • Ghia Euskirchen,
    • Sherman Weissman,
    • Mark Gerstein,
    • Michael Snyder,
    • Annie Yang,
    • Zarmik Moqtaderi,
    • Heather Hirsch,
    • Hennady P. Shulha,
    • Yutao Fu,
    • Zhiping Weng,
    • Kevin Struhl,
    • Richard M. Myers,
    • Jason D. Lieb,
    • and X. Shirley Liu
    Genome Res. March 2008 18: 393-403; Published in Advance February 7, 2008, doi:10.1101/gr.7080508
  5. Methods: Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
    • Ghia M. Euskirchen,
    • Joel S. Rozowsky,
    • Chia-Lin Wei,
    • Wah Heng Lee,
    • Zhengdong D. Zhang,
    • Stephen Hartman,
    • Olof Emanuelsson,
    • Viktor Stolc,
    • Sherman Weissman,
    • Mark B. Gerstein,
    • Yijun Ruan,
    • and Michael Snyder
    Genome Res. June 2007 17: 898-909; doi:10.1101/gr.5583007
    OPEN ACCESS ARTICLE
  6. ARTICLE: The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
    • Joel S. Rozowsky,
    • Daniel Newburger,
    • Fred Sayward,
    • Jiaqian Wu,
    • Greg Jordan,
    • Jan O. Korbel,
    • Ugrappa Nagalakshmi,
    • Jin Yang,
    • Deyou Zheng,
    • Roderic Guigó,
    • Thomas R. Gingeras,
    • Sherman Weissman,
    • Perry Miller,
    • Michael Snyder,
    • and Mark B. Gerstein
    Genome Res. June 2007 17: 732-745; doi:10.1101/gr.5696007
    OPEN ACCESS ARTICLE
  7. Methods: Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    • Olof Emanuelsson,
    • Ugrappa Nagalakshmi,
    • Deyou Zheng,
    • Joel S. Rozowsky,
    • Alexander E. Urban,
    • Jiang Du,
    • Zheng Lian,
    • Viktor Stolc,
    • Sherman Weissman,
    • Michael Snyder,
    • and Mark B. Gerstein
    Genome Res. June 2007 17: 886-897; Published in Advance November 21, 2006, doi:10.1101/gr.5014606
    OPEN ACCESS ARTICLE
  8. PERSPECTIVE: What is a gene, post-ENCODE? History and updated definition
    • Mark B. Gerstein,
    • Can Bruce,
    • Joel S. Rozowsky,
    • Deyou Zheng,
    • Jiang Du,
    • Jan O. Korbel,
    • Olof Emanuelsson,
    • Zhengdong D. Zhang,
    • Sherman Weissman,
    • and Michael Snyder
    Genome Res. June 2007 17: 669-681; doi:10.1101/gr.6339607
    OPEN ACCESS ARTICLE
  9. Methods: Design optimization methods for genomic DNA tiling arrays
    • Paul Bertone,
    • Valery Trifonov,
    • Joel S. Rozowsky,
    • Falk Schubert,
    • Olof Emanuelsson,
    • John Karro,
    • Ming-Yang Kao,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. February 2006 16: 271-281; Published in Advance December 19, 2005, doi:10.1101/gr.4452906
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