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Author Details

Peggy J Farnham
Keck School of Medicine of USC
1978
185
82
PMIDPaper TitleJournal TitlePublished Year
38023731m<sup>6</sup>A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer.NAR Cancer2023
38023731m<sup>6</sup>A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer.NAR Cancer2023
35883107Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.Genome Biol2022
35883107Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.Genome Biol2022
35474001Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.Nature2022
35406487FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer.Cancers (Basel)2022
35474001Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.Nature2022
35406487FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer.Cancers (Basel)2022
32406922Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters.Nucleic Acids Res2020
32012197Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells.PLoS One2020
32406922Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters.Nucleic Acids Res2020
32925947TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.PLoS Genet2020
32728249Expanded encyclopaedias of DNA elements in the human and mouse genomes.Nature2020
32012197Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells.PLoS One2020
32728249Expanded encyclopaedias of DNA elements in the human and mouse genomes.Nature2020
32925947TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.PLoS Genet2020
30548288Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature.J Cell Biochem2019
30548288Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature.J Cell Biochem2019
30866492The Enigmatic HOX Genes: Can We Crack Their Code?Cancers (Basel)2019
31053162Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.Epigenetics Chromatin2019
31328168The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression.Sci Adv2019
31515496A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome.Nat Commun2019
31328168The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression.Sci Adv2019
31515496A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome.Nat Commun2019
30866492The Enigmatic HOX Genes: Can We Crack Their Code?Cancers (Basel)2019
31053162Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.Epigenetics Chromatin2019
29429977ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters.Genome Res2018
30555922Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.Sci Adv2018
30296942CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops.Genome Biol2018
29605855Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq).Methods Mol Biol2018
29429977ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters.Genome Res2018
30296942CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops.Genome Biol2018
30555922Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.Sci Adv2018
29605855Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq).Methods Mol Biol2018
28973434dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.Nucleic Acids Res2017
28973434dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.Nucleic Acids Res2017
29117547A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13.Cell Rep2017
29117547A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13.Cell Rep2017
269348614C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus.Sci Rep2016
269348614C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus.Sci Rep2016
26743005Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.Nucleic Acids Res2016
27833659Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.Epigenetics Chromatin2016
27833659Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.Epigenetics Chromatin2016
26743005Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.Nucleic Acids Res2016
25747664The role of DNA methylation in directing the functional organization of the cancer epigenome.Genome Res2015
25747664The role of DNA methylation in directing the functional organization of the cancer epigenome.Genome Res2015
25693563Integrative analysis of 111 reference human epigenomes.Nature2015
25691127Intermediate DNA methylation is a conserved signature of genome regulation.Nat Commun2015
25690954Epigenetic and transcriptional determinants of the human breast.Nat Commun2015
26719772Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome.Epigenetics Chromatin2015
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Collaborators

Suhn K Rhie
Keck School of Medicine of USC
Co-authored papers 14
Roland D Green
NimbleGen Systems Inc.
Co-authored papers 14
Martin Hirst
University of British Columbia
Co-authored papers 11
Joseph F Costello
University of California san francisco
Co-authored papers 11
Xiaoqin Xu
Co-authored papers 10
Lijing Yao
Co-authored papers 10
Mark Gerstein
Yale University
Co-authored papers 9
Ting Wang
Washington University School of Medicine
Co-authored papers 9
Bing Ren
Center for Epigenomics, University of California San Diego
Co-authored papers 9
Heather Witt
Co-authored papers 9
Marco A Marra
University of British Columbia
Co-authored papers 9
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 8
Michael Snyder
Stanford University
Co-authored papers 8
Richard M Myers
HudsonAlpha Institute for Biotechnology
Co-authored papers 8
Bradley E Bernstein
Broad Institute of MIT and Harvard
Co-authored papers 8
John A Stamatoyannopoulos
Altius Institute for Biomedical Sciences
Co-authored papers 8
Zhiping Weng
University of Massachusetts Medical School
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Benjamin P Berman
Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem
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Mark C Bieda
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Anshul Kundaje
Stanford University.
Co-authored papers 7
Tim H-M Huang
University of Texas Health San Antonio (UTHSA)
Co-authored papers 6
Thomas R Gingeras
Stanley Institute for Cognitive Genomics
Co-authored papers 6
Aleksandar Milosavljevic
Baylor College of Medicine
Co-authored papers 6
Shannon Schreiner
Co-authored papers 6
Jason D Lieb
The University of Chicago
Co-authored papers 6
Joel Rozowsky
Co-authored papers 6
Sharon L Squazzo
Co-authored papers 6
Kevin P White
Co-authored papers 6
Matthew J Oberley
Co-authored papers 6
Danny Reinberg
HHMI/NYU Langone School of Medicine
Co-authored papers 5
Release 1.2