Publications by authors named "Peggy Farnham"

100Publications

TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.

PLoS Genet 2020 09 14;16(9):e1009023. Epub 2020 Sep 14.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1009023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7515200PMC
September 2020

Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters.

Nucleic Acids Res 2020 06;48(11):5986-6000

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/nar/gkaa384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293018PMC
June 2020

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells.

PLoS One 2020 3;15(2):e0228590. Epub 2020 Feb 3.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228590PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6996832PMC
April 2020

A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome.

Nat Commun 2019 09 12;10(1):4154. Epub 2019 Sep 12.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.

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http://dx.doi.org/10.1038/s41467-019-12079-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742760PMC
September 2019

The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression.

Sci Adv 2019 07 17;5(7):eaaw6710. Epub 2019 Jul 17.

Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1126/sciadv.aaw6710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636982PMC
July 2019

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.

Epigenetics Chromatin 2019 05 3;12(1):26. Epub 2019 May 3.

Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1186/s13072-019-0275-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498470PMC
May 2019

The Enigmatic HOX Genes: Can We Crack Their Code?

Cancers (Basel) 2019 Mar 7;11(3). Epub 2019 Mar 7.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.3390/cancers11030323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468460PMC
March 2019

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.

Sci Adv 2018 12 13;4(12):eaav8550. Epub 2018 Dec 13.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1126/sciadv.aav8550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292713PMC
December 2018

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops.

Genome Biol 2018 10 8;19(1):160. Epub 2018 Oct 8.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 6503, Los Angeles, CA, 90089-9601, USA.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1531-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176514PMC
October 2018

Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq).

Methods Mol Biol 2018 ;1766:209-229

Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7768-0_12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019634PMC
May 2019

A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13.

Cell Rep 2017 Nov;21(6):1411-1417

Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.10.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726543PMC
November 2017

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.

Nucleic Acids Res 2017 Sep;45(17):9901-9916

Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/nar/gkx578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622328PMC
September 2017

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.

Epigenetics Chromatin 2016 9;9:50. Epub 2016 Nov 9.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA.

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http://dx.doi.org/10.1186/s13072-016-0102-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103450PMC
January 2018

4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus.

Sci Rep 2016 Mar 3;6:22462. Epub 2016 Mar 3.

Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1038/srep22462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776156PMC
March 2016

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.

Nucleic Acids Res 2016 05 6;44(9):4123-33. Epub 2016 Jan 6.

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA

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http://dx.doi.org/10.1093/nar/gkv1530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872074PMC
May 2016

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome.

Epigenetics Chromatin 2015 30;8:57. Epub 2015 Dec 30.

Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA.

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http://dx.doi.org/10.1186/s13072-015-0050-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696349PMC
December 2015

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.

Crit Rev Biochem Mol Biol 2015 8;50(6):550-73. Epub 2015 Oct 8.

a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and.

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http://dx.doi.org/10.3109/10409238.2015.1087961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666684PMC
September 2016

Altering cancer transcriptomes using epigenomic inhibitors.

Epigenetics Chromatin 2015 24;8. Epub 2015 Feb 24.

USC/Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, NRT 6503, Los Angeles, CA 90089-9601 USA.

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http://dx.doi.org/10.1186/1756-8935-8-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506402PMC
July 2015

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

Genome Biol 2015 May 21;16:105. Epub 2015 May 21.

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 6503, Los Angeles, CA, 90089-9601, USA.

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http://dx.doi.org/10.1186/s13059-015-0668-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460959PMC
May 2015

The role of DNA methylation in directing the functional organization of the cancer epigenome.

Genome Res 2015 Apr 6;25(4):467-77. Epub 2015 Mar 6.

USC Epigenome Center, University of Southern California, Los Angeles, California 90033, USA; Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033, USA

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http://dx.doi.org/10.1101/gr.183368.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381519PMC
April 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Can genome engineering be used to target cancer-associated enhancers?

Epigenomics 2014 ;6(5):493-501

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9601, USA.

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http://dx.doi.org/10.2217/epi.14.30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259145PMC
July 2015

Functional annotation of colon cancer risk SNPs.

Nat Commun 2014 Sep 30;5:5114. Epub 2014 Sep 30.

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1038/ncomms6114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4200523PMC
September 2014

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.

Nucleic Acids Res 2014 13;42(16):10856-68. Epub 2014 Aug 13.

Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA

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http://dx.doi.org/10.1093/nar/gku708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176344PMC
January 2015

Comprehensive functional annotation of 77 prostate cancer risk loci.

PLoS Genet 2014 Jan 30;10(1):e1004102. Epub 2014 Jan 30.

Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907334PMC
January 2014

Cross-talk between site-specific transcription factors and DNA methylation states.

J Biol Chem 2013 Nov 22;288(48):34287-94. Epub 2013 Oct 22.

From the Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 and.

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http://dx.doi.org/10.1074/jbc.R113.512517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843044PMC
November 2013

Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros.

Nat Immunol 2013 Oct 8;14(10):1073-83. Epub 2013 Sep 8.

1] Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA. [2] Molecular Biology Institute, University of California, Los Angeles, California, USA. [3].

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http://dx.doi.org/10.1038/ni.2707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800053PMC
October 2013

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes.

Epigenetics Chromatin 2013 May 21;6(1):13. Epub 2013 May 21.

Department of Biochemistry & Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.

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http://dx.doi.org/10.1186/1756-8935-6-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663758PMC
May 2013

Spark: a navigational paradigm for genomic data exploration.

Genome Res 2012 Nov 7;22(11):2262-9. Epub 2012 Sep 7.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.140665.112
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http://dx.doi.org/10.1101/gr.140665.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483555PMC
November 2012

Uncovering transcription factor modules using one- and three-dimensional analyses.

J Biol Chem 2012 Sep 5;287(37):30914-21. Epub 2012 Sep 5.

Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.

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http://dx.doi.org/10.1074/jbc.R111.309229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438924PMC
September 2012

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.

Genome Biol 2012 Sep 26;13(9):R52. Epub 2012 Sep 26.

Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2012-13-9-r52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491396PMC
September 2012

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Nucleic Acids Res 2012 Sep 6;40(16):7690-704. Epub 2012 Jun 6.

Department of Biomedical Informatics, 460 W 12th Avenue, 212 BRT, The Ohio State University, Columbus, OH 43210, USA.

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http://dx.doi.org/10.1093/nar/gks501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439894PMC
September 2012

The transcription factor encyclopedia.

Authors:
Dimas Yusuf Stefanie L Butland Magdalena I Swanson Eugene Bolotin Amy Ticoll Warren A Cheung Xiao Yu Cindy Zhang Christopher T D Dickman Debra L Fulton Jonathan S Lim Jake M Schnabl Oscar H P Ramos Mireille Vasseur-Cognet Charles N de Leeuw Elizabeth M Simpson Gerhart U Ryffel Eric W-F Lam Ralf Kist Miranda S C Wilson Raquel Marco-Ferreres Jan J Brosens Leonardo L Beccari Paola Bovolenta Bérénice A Benayoun Lara J Monteiro Helma D C Schwenen Lars Grontved Elizabeth Wederell Susanne Mandrup Reiner A Veitia Harini Chakravarthy Pamela A Hoodless M Michela Mancarelli Bruce E Torbett Alison H Banham Sekhar P Reddy Rebecca L Cullum Michaela Liedtke Mario P Tschan Michelle Vaz Angie Rizzino Mariastella Zannini Seth Frietze Peggy J Farnham Astrid Eijkelenboom Philip J Brown David Laperrière Dominique Leprince Tiziana de Cristofaro Kelly L Prince Marrit Putker Luis del Peso Gieri Camenisch Roland H Wenger Michal Mikula Marieke Rozendaal Sylvie Mader Jerzy Ostrowski Simon J Rhodes Capucine Van Rechem Gaylor Boulay Sam W Z Olechnowicz Mary B Breslin Michael S Lan Kyster K Nanan Michael Wegner Juan Hou Rachel D Mullen Stephanie C Colvin Peter John Noy Carol F Webb Matthew E Witek Scott Ferrell Juliet M Daniel Jason Park Scott A Waldman Daniel J Peet Michael Taggart Padma-Sheela Jayaraman Julien J Karrich Bianca Blom Farhad Vesuna Henriette O'Geen Yunfu Sun Richard M Gronostajski Mark W Woodcroft Margaret R Hough Edwin Chen G Nicholas Europe-Finner Magdalena Karolczak-Bayatti Jarrod Bailey Oliver Hankinson Venu Raman David P LeBrun Shyam Biswal Christopher J Harvey Jason P DeBruyne John B Hogenesch Robert F Hevner Christophe Héligon Xin M Luo Marissa Cathleen Blank Kathleen Joyce Millen David S Sharlin Douglas Forrest Karin Dahlman-Wright Chunyan Zhao Yuriko Mishima Satrajit Sinha Rumela Chakrabarti Elodie Portales-Casamar Frances M Sladek Philip H Bradley Wyeth W Wasserman

Genome Biol 2012 ;13(3):R24

Department of Medical Genetics, Faculty of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada.

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http://digital.csic.es/bitstream/10261/53044/2/gb-2012-13-3-
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http://genomebiology.com/2012/13/3/R24
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http://dx.doi.org/10.1186/gb-2012-13-3-r24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439975PMC
September 2012

Thematic minireview series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome.

Authors:
Peggy J Farnham

J Biol Chem 2012 Sep 5;287(37):30885-7. Epub 2012 Sep 5.

Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California 90089, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.R112.365940
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http://dx.doi.org/10.1074/jbc.R112.365940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438920PMC
September 2012

Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation.

PLoS One 2011 28;6(11):e27740. Epub 2011 Nov 28.

Transplant Research Program, University of California Davis Medical Center, Sacramento, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027740PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225380PMC
April 2012

Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments.

Methods Mol Biol 2012 ;802:323-34

Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.

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http://dx.doi.org/10.1007/978-1-61779-400-1_21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160035PMC
April 2012

Autophagy driven by a master regulator of hematopoiesis.

Mol Cell Biol 2012 Jan 24;32(1):226-39. Epub 2011 Oct 24.

Wisconsin Institutes for Medical Research, Paul Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1128/MCB.06166-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255705PMC
January 2012

Using ChIP-seq technology to generate high-resolution profiles of histone modifications.

Methods Mol Biol 2011 ;791:265-86

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, CA, USA.

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http://dx.doi.org/10.1007/978-1-61779-316-5_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151291PMC
December 2011

Genetic framework for GATA factor function in vascular biology.

Proc Natl Acad Sci U S A 2011 Aug 1;108(33):13641-6. Epub 2011 Aug 1.

Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.

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http://dx.doi.org/10.1073/pnas.1108440108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158141PMC
August 2011

KAP1 protein: an enigmatic master regulator of the genome.

J Biol Chem 2011 Jul 7;286(30):26267-76. Epub 2011 Jun 7.

From the Genetics Graduate Group, University of California, Davis, California 95616, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.R111.252569
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http://dx.doi.org/10.1074/jbc.R111.252569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143589PMC
July 2011

Transcription factor effector domains.

Subcell Biochem 2011 ;52:261-77

Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA,

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http://dx.doi.org/10.1007/978-90-481-9069-0_12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151296PMC
April 2016

Functional analysis of KAP1 genomic recruitment.

Mol Cell Biol 2011 May 22;31(9):1833-47. Epub 2011 Feb 22.

Department of Biochemistry & Molecular Biology, Norris Comprehensive Cancer Center, 1450 Biggy Street, NRT 6503, Mail Code 9601, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1128/MCB.01331-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133220PMC
May 2011

ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.

PLoS One 2010 Dec 8;5(12):e15082. Epub 2010 Dec 8.

Department of Pharmacology and the Genome Center, University of California Davis, Davis, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015082PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999557PMC
December 2010

Using ChIP-seq technology to identify targets of zinc finger transcription factors.

Methods Mol Biol 2010 ;649:437-55

Department of Pharmacology, Genome Center, University of California at Davis, Davis, CA, USA.

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http://dx.doi.org/10.1007/978-1-60761-753-2_27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151297PMC
December 2010

5-azacytidine treatment reorganizes genomic histone modification patterns.

Epigenetics 2010 Apr 1;5(3):229-40. Epub 2010 Apr 1.

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http://dx.doi.org/10.4161/epi.5.3.11409DOI Listing
April 2010

Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy.

Mol Cell 2009 Nov;36(4):667-81

University of Wisconsin School of Medicine and Public Health, Wisconsin Institutes for Medical Research, Madison, 53705, USA.

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http://dx.doi.org/10.1016/j.molcel.2009.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784893PMC
November 2009

Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263.

J Biol Chem 2010 Jan 2;285(2):1393-403. Epub 2009 Nov 2.

Department of Pharmacology and the Genome Center, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1074/jbc.M109.063032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801265PMC
January 2010

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.

Bioinformatics 2009 Dec 1;25(23):3191-3. Epub 2009 Oct 1.

Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778340PMC
December 2009

Insights from genomic profiling of transcription factors.

Authors:
Peggy J Farnham

Nat Rev Genet 2009 Sep 11;10(9):605-16. Epub 2009 Aug 11.

Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA.

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http://dx.doi.org/10.1038/nrg2636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846386PMC
September 2009

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites.

Genome Res 2008 Nov 3;18(11):1763-77. Epub 2008 Oct 3.

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

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http://dx.doi.org/10.1101/gr.080622.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577861PMC
November 2008

Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors.

Cancer Res 2008 Apr;68(8):2641-51

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-07-5590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567918PMC
April 2008

Genome-scale ChIP-chip analysis using 10,000 human cells.

Biotechniques 2007 Dec;43(6):791-7

Cell and Molecular Biology Program, University of Wisconsin-Madison, WI 95616, USA.

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https://www.future-science.com/doi/10.2144/000112625
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268896PMC
http://dx.doi.org/10.2144/000112625DOI Listing
December 2007

Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes.

Proc Natl Acad Sci U S A 2007 Dec 27;104(49):19416-21. Epub 2007 Nov 27.

Department of Medical Microbiology and Immunology, Rowe Program in Human Genetics, School of Medicine, University of California, 1 Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1073/pnas.0707442104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2148304PMC
December 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches.

Genome Res 2007 Jun;17(6):807-17

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6006107
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http://dx.doi.org/10.1101/gr.6006107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891340PMC
June 2007

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

PLoS Genet 2007 Jun 19;3(6):e89. Epub 2007 Apr 19.

Department of Pharmacology, University of California Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0030089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885280PMC
June 2007

Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays.

J Biol Chem 2007 Mar 26;282(13):9703-12. Epub 2007 Jan 26.

Department of Pharmacology and the Genome Center, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1074/jbc.M611752200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2269729PMC
March 2007

Comparison of sample preparation methods for ChIP-chip assays.

Biotechniques 2006 Nov;41(5):577-80

University of California-Davis, Davis, CA 95616, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268903PMC
http://dx.doi.org/10.2144/000112268DOI Listing
November 2006

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.

Genome Res 2006 Dec 19;16(12):1455-64. Epub 2006 Oct 19.

Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20878, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.4140006
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December 2006

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1.

Genome Res 2006 Dec 19;16(12):1585-95. Epub 2006 Oct 19.

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.5520206
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665642PMC
December 2006

Suz12 binds to silenced regions of the genome in a cell-type-specific manner.

Genome Res 2006 Jul 2;16(7):890-900. Epub 2006 Jun 2.

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

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http://dx.doi.org/10.1101/gr.5306606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484456PMC
July 2006

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.

Genome Res 2006 May 10;16(5):595-605. Epub 2006 Apr 10.

Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.4887606
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457046PMC
May 2006

Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation.

Proc Natl Acad Sci U S A 2005 Feb 31;102(6):1859-64. Epub 2005 Jan 31.

Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1073/pnas.0409875102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548563PMC
February 2005

Genomic approaches that aid in the identification of transcription factor target genes.

Exp Biol Med (Maywood) 2004 Sep;229(8):705-21

McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison 533706, USA.

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http://dx.doi.org/10.1177/153537020422900803DOI Listing
September 2004

The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation.

J Biol Chem 2004 Oct 24;279(44):46343-9. Epub 2004 Aug 24.

McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M402692200
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October 2004

Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27.

Genes Dev 2004 Jul;18(13):1592-605

McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1101/gad.1200204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC443521PMC
July 2004

T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells.

Immunity 2004 Apr;20(4):477-94

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/s1074-7613(04)00076-7DOI Listing
April 2004

High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays.

Methods Enzymol 2004 ;376:315-34

McArdle Laboratory for Cancer Research, University of Wisconsin, Madison 53706, USA.

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http://dx.doi.org/10.1016/S0076-6879(03)76021-2DOI Listing
July 2004