Peggy J. Farnham
Peggy J. Farnham
WIlliam M Keck Professor of Biochemistry, University of Southern California
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An integrated encyclopedia of DNA elements in the human genome
BE Bernstein, E Birney, I Dunham, ED Green, C Gunter, M Snyder
Nature 489 (7414), 57-74, 2012
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium
nature 447 (7146), 799, 2007
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
JL Rinn, M Kertesz, JK Wang, SL Squazzo, X Xu, SA Brugmann, ...
cell 129 (7), 1311-1323, 2007
Integrative analysis of 111 reference human epigenomes
A Kundaje, W Meuleman, J Ernst, M Bilenky, A Yen, A Heravi-Moussavi, ...
Nature 518 (7539), 317-330, 2015
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ...
Genome research 22 (9), 1813-1831, 2012
Architecture of the human regulatory network derived from ENCODE data
MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, ...
Nature 489 (7414), 91-100, 2012
The NIH roadmap epigenomics mapping consortium
BE Bernstein, JA Stamatoyannopoulos, JF Costello, B Ren, ...
Nature biotechnology 28 (10), 1045-1048, 2010
Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties
WG Kaelin Jr, W Krek, WR Sellers, JA DeCaprio, F Ajchenbaum, ...
Cell 70 (2), 351-364, 1992
T-bet regulates the terminal maturation and homeostasis of NK and Vα14i NKT cells
MJ Townsend, AS Weinmann, JL Matsuda, R Salomon, PJ Farnham, ...
Immunity 20 (4), 477-494, 2004
Defining functional DNA elements in the human genome
M Kellis, B Wold, MP Snyder, BE Bernstein, A Kundaje, GK Marinov, ...
Proceedings of the National Academy of Sciences 111 (17), 6131-6138, 2014
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
RA Harris, T Wang, C Coarfa, RP Nagarajan, C Hong, SL Downey, ...
Nature biotechnology 28 (10), 1097-1105, 2010
Insights from genomic profiling of transcription factors
PJ Farnham
Nature Reviews Genetics 10 (9), 605-616, 2009
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
AS Weinmann, PS Yan, MJ Oberley, THM Huang, PJ Farnham
Genes & development 16 (2), 235-244, 2002
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27
A Kirmizis, SM Bartley, A Kuzmichev, R Margueron, D Reinberg, R Green, ...
Genes & development 18 (13), 1592-1605, 2004
Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation
A Kuzmichev, R Margueron, A Vaquero, TS Preissner, M Scher, A Kirmizis, ...
Proceedings of the National Academy of Sciences 102 (6), 1859-1864, 2005
Use of chromatin immunoprecipitation to clone novel E2F target promoters
AS Weinmann, SM Bartley, T Zhang, MQ Zhang, PJ Farnham
Molecular and cellular biology 21 (20), 6820-6832, 2001
Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation
AS Weinmann, PJ Farnham
Methods 26 (1), 37-47, 2002
Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
DH Yasui, S Peddada, MC Bieda, RO Vallero, A Hogart, RP Nagarajan, ...
Proceedings of the National Academy of Sciences 104 (49), 19416-19421, 2007
A protein synthesis-dependent increase in E2F1 mRNA correlates with growth regulation of the dihydrofolate reductase promoter
JE Slansky, Y Li, WG Kaelin, PJ Farnham
Molecular and cellular biology 13 (3), 1610-1618, 1993
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
M Bieda, X Xu, MA Singer, R Green, PJ Farnham
Genome research 16 (5), 595-605, 2006
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