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Peggy J. Farnham
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Displaying results 1-10 of
14
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
Full Text
Full Text (PDF)
Supplementary Research Data
OPEN ACCESS ARTICLE
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