Peggy J Farnham
Professor and Associate Director of Genomics
pjfarnham@ucdavis.edu

Pharmacology - Medicine

Office
4512 GBSF
530-754-4988

Lab
530-754-9653


Picture of Peggy J Farnham
 
Degrees:
1982 PhD Yale University Molecular Biophysics and Biochemistry
1978 BA Rice University Biochemistry
Research Interests:

The Farnham laboratory has been a leader in developing the technique of chromatin immunoprecipitation (ChIP) to study mammalian transcription factors. Recently, they have extended these studies to allow a high throughput, global analysis of transcription factor target genes by combining chromatin immunoprecipitation with genomic microarray hybridization (ChIP-chip assays) and with high throughput sequencing (ChIP-seq). Current projects include the analysis of chromatin structure in embryonic stem cells and other normal and tumor cell types and the genome-wide identification of target genes of a variety of human transcription factors. In addition to bench work, the Farnham lab is also developing programs to assist in the analysis of genome-scale ChIP-chip and ChIP-seq data and to derive consensus motifs from experimentally identified binding sites. Dr. Farnham is a member of the ENCODE Consortium, whose goal is to map all the functional elements in the human genome. She is also a member of the recently funded NIH Roadmap UC Reference Epigenome Mapping Center; her lab is determining the histone modifications for a variety of different human cell types.
Awards:
NIH Predoctoral Trainee, 1978-1982.
Damon Runyon-Walter Winchell Postdoctoral Fellow, 1982-1983.
NIH Postdoctoral Fellow, 1983-1986.
Outstanding Mentor in the U.W. Medical School, 1997, 1998
Vilas Associates Award, 1999-2000.
Department and Center Affiliations:
Pharmacology
Genome Center
Cancer Center
Professional Societies:
Associate Editor for the Journal of Biological Chemistry (2001-2006)
Editorial Board Member for Molecular and Cellular Biology (1998-2006)
Secretary for the American Society of Biochemistry and Molecular Biology (ASBMB)
Member, American Association for Cancer Research
CBS Graduate Group Affiliations:
Biochemistry, Molecular, Cellular and Developmental Biology  
Genetics  
Publications: Last updated 11/20/2009
  • Farnham, PJ. Insights from genomic profiling of transcription factors. Nature Reviews Genetics 10:605-616, 2009
  • Frietze S, Lan X, Jin VX, Farnham PJ. Genome-wide targets of the KRAB and SCAN domain-containing zinc finger protein ZNF263. J. Biol. Chem. In Press.
  • Fujiwara T, O'Geen H, Keles S, Blahnik K, Kang Y-A, Choi K, Farnham PJ, Bresnick EH. Discovering Hematopoietic Mechanisms Through Genome-Wide Analysis of GATA Factor Chromatin Occupancy. Molecular Cell. In Press.
  • Blahnik KR, Dou L, O’Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ. Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nuc. Acids Res. In Press.
  • Jin V, Apostolos, J., Nagisetty, NS, Farnham, PJ W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data. Bioinformatics. In Press.
  • Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ E2F in vivo binding specificity: comparison of consensus vs. non-consensus binding sites. Genome Research 18:1763-1777, 2008
  • Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ. Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Research 18:521-532, 2008
  • Acevedo LG, Bieda M, Green R, and Farnham PJ. Analysis of the mechanisms mediating tumor specific changes in gene expression in human liver tumors. Cancer Research 68:2641-2651, 2008.
  • O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide Analysis of KAP1 Binding Suggests an Auto-regulation of KRAB-ZNFs. PLOS Genetics 3, e89 doi:10.1371/journal.pgen.0030089, 2007.
  • Jin VX, O'Geen H., Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 17:807-817, 2007.
  • The ENCODE Project Consortium. The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome. Nature 447, 799-816, 2007.
  • Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays. J. Biol. Chem. 282:9703-9712, 2007
  • Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res. 17:1550-1561, 2007.
  • Squazzo SL, Komashko VM, OGeen H, Krig S, Jin VX, Jang S-W, Green R, Margueron R, Reinberg D, and Farnham PJ. Suz12 silences large regions of the genome in a cell type-specific manner. Genome Research, 16:890-900, 2006
  • Bieda M, Xu S, Singer M, Green R, and Farnham PJ. Unbiased Location Analysis of E2F1 Binding Sites Suggests a Widespread Role for E2F1 in the Human Genome. Genome Research, 16:595-605, 2006
  • Jin VX, Rabinovich A, Squazzo SL, Green R, and Farnham PJ. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data: a case study using E2F1. Genome Research, 16:1585-1595, 2006
  • Kirmizis, A., Bartley, S. M., Kuzmichev, A., Margueron R., Reinberg. R., Green, R., and Farnham, P. J. Silencing of human polycomb target genes is associated with methylation of histone H3 lysine 27. Genes & Devel. 18:1592-1605, 2004.
  • Feingold et al. (see http://www.sciencemag.org/cgi/content/full/306/5696/636/DC1 for a complete list of authors). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306:636-640, 2004.
  • Wells, J., Yan, P.S., Cechvala, M., Huang, H.-M.T, and Farnham, P.J. Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene 22:1445-1460, 2003
  • Wells, J., Graveel, C.R., Bartley, S.M., and Farnham, P.J. The identification of E2F1-specific target genes. Proc. Natl. Acad. Sci. USA, 99:3890-3895,2002.
  • Weinmann, A.S., Yan, P.S., Oberley, M.J., Huang, H.-M.T., and Farnham, P.J. Isolating human transcription factor targets by combining chromatin immunoprecipitation and CpG microarray analysis. Genes & Devel. 16:235-244, 2002
Laboratory Personnel:
Farnham Laboratory/4617 GBSF
http://genomics.ucdavis.edu/farnham/
Henny O'Geen (project scientist) Seth Frietze (postdoc) Cheryl Serchen (postdoc) Alina Rabinovich (grad student) Vitalina Komashko (grad student) Sushma Iyengar (grad student) Kim Blahnik (grad student) Adam Blattler (grad student) Shally Xu (research associate) Lorigail Echipare (research associate)

Courses:
Genomics Pharm250 Functional Genomics Spring Quarter 2010