Searching journal content for Peggy J. Farnham in author.

Displaying results 1-10 of 14
For checked items
  1. Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
    • Suhn Kyong Rhie,
    • Lijun Yao,
    • Zhifei Luo,
    • Heather Witt,
    • Shannon Schreiner,
    • Yu Guo,
    • Andrew A. Perez,
    • and Peggy J. Farnham
    Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
    OPEN ACCESS ARTICLE
  2. Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
    • Fides D. Lay,
    • Yaping Liu,
    • Theresa K. Kelly,
    • Heather Witt,
    • Peggy J. Farnham,
    • Peter A. Jones,
    • and Benjamin P. Berman
    Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
    OPEN ACCESS ARTICLE
  3. Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Bo Zhang,
    • Yan Zhou,
    • Nan Lin,
    • Rebecca F. Lowdon,
    • Chibo Hong,
    • Raman P. Nagarajan,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Michael Stevens,
    • Hyung Joo Lee,
    • Xiaoyun Xing,
    • Jia Zhou,
    • Vasavi Sundaram,
    • GiNell Elliott,
    • Junchen Gu,
    • Taoping Shi,
    • Philippe Gascard,
    • Mahvash Sigaroudinia,
    • Thea D. Tlsty,
    • Theresa Kadlecek,
    • Arthur Weiss,
    • Henriette O’Geen,
    • Peggy J. Farnham,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Pamela A.F. Madden,
    • Angela Tam,
    • Richard Moore,
    • Martin Hirst,
    • Marco A. Marra,
    • Baoxue Zhang,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
    OPEN ACCESS ARTICLE
  4. Method: Spark: A navigational paradigm for genomic data exploration
    • Cydney B. Nielsen,
    • Hamid Younesy,
    • Henriette O'Geen,
    • Xiaoqin Xu,
    • Andrew R. Jackson,
    • Aleksandar Milosavljevic,
    • Ting Wang,
    • Joseph F. Costello,
    • Martin Hirst,
    • Peggy J. Farnham,
    • and Steven J.M. Jones
    Genome Res. November 2012 22: 2262-2269; Published in Advance September 7, 2012, doi:10.1101/gr.140665.112
  5. 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
  6. LETTER: E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
    • Alina Rabinovich,
    • Victor X. Jin,
    • Roman Rabinovich,
    • Xiaoqin Xu,
    • and Peggy J. Farnham
    Genome Res. November 2008 18: 1763-1777; Published in Advance October 3, 2008, doi:10.1101/gr.080622.108
  7. LETTER: Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
    • Vitalina M. Komashko,
    • Luis G. Acevedo,
    • Sharon L. Squazzo,
    • Sushma S. Iyengar,
    • Alina Rabinovich,
    • Henriette O’Geen,
    • Roland Green,
    • and Peggy J. Farnham
    Genome Res. April 2008 18: 521-532; Published in Advance March 17, 2008, doi:10.1101/gr.074609.107
  8. 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
  9. ARTICLE: A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
    • Xiaoqin Xu,
    • Mark Bieda,
    • Victor X. Jin,
    • Alina Rabinovich,
    • Mathew J. Oberley,
    • Roland Green,
    • and Peggy J. Farnham
    Genome Res. November 2007 17: 1550-1561; Published in Advance October 1, 2007, doi:10.1101/gr.6783507
  10. LETTER: Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
    • Victor X. Jin,
    • Henriette O’Geen,
    • Sushma Iyengar,
    • Roland Green,
    • and Peggy J. Farnham
    Genome Res. June 2007 17: 807-817; doi:10.1101/gr.6006107
    OPEN ACCESS ARTICLE
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