Selected Publications
  • Blattler A, Yao L, Wang Y, Ye Z, Jin VX, Farnham PJ. ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. Epigenetics and Chromatin 6:13, 2013.
  • THE ENCODE CONSORTIUM. An integrated encyclopedia of DNA Elements in the human genome. Nature 489:57-74, 2012.
  • Frietze S, Wang R, Tak YG, Yao L, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biology 13:R52. 2012.
  • Iyengar S, Ivanov AV, Jin VX, Rauscher FJ III, Farnham, PJ. Functional analysis of KAP1 genomic recruitment. Molecular and Cellular Biology 31:833-1847, 2011.
  • Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ. ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLOS One 5:e15082, 2010.
  • Komashko VM and Farnham PJ. 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics 5: 229-240, 2010.
  • Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludscher B, Korf I, Farnham PJ. Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nuc. Acids Res. 38:e13, 2010.
  • 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.
  • O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests auto-regulation of KRAB-ZNFs. PLOS Genetics 3:e89, 2007.
  • Squazzo SL, Komashko VM, O'Geen H, Krig S, Jin VX, Jang S-W, Green R, Margueron R, Reinberg D, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell type-specific manner. Genome Research 16:890-900, 2006.
  • Bieda M, Xu S, Singer M, Green R, 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.
  • Kirmizis, A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, Green R, Farnham PJ. Silencing of human polycomb target genes is associated with methylation of histone H3 lysine 27. Genes & Devel. 18:1592-1605, 2004.
  • Weinmann AS, Yan PS, Oberley MJ, Huang H-MT, Farnham PJ. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG microarray analysis. Genes & Devel. 16:235-244, 2002.
List of Publications