Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res. 33:2952-2961, 2005. [pdf]
Kuzmichev A, Margueron R, Vaquero A, Preissner TS, Scher M, Kirmizis A, Ouyang X, Brockdorff N, Abate-Shen C, Farnham P, Reinberg D. Composition and Histone Substrates of Polycomb Repressive Group Complexes Change during Cellular Differentiation. Proc. Natl. Acad. Sci. USA 102:1859-64, 2005. [pdf]
Oberley MJ, Farnham PJ. Identification of mammalian E2F regulatory networks using DNA microarray hybridization analyses. In: Shannon MF, Rao S, eds. Microarrays and Transcription Networks. Georgetown: Landes Bioscience/Eurekah.com. in press, 2005[pdf]
Oberley MJ, Tsao J, Yau P, Farnham PJ. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods in Enzymology 376: 315-333, 2004. [pdf]
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. [pdf]
Townsend MJ, Weinmann AS, Matsuda J, Saloman R, Farnham PJ, Biron CA, Gapin, L, Glimcher LH. T-bet regulates the terminal maturation and homeostasis of NK and V_14i NKT cells. Immunity, 20: 477-494, 2004. This article was given a ârecommendedâ ranking at Faculty of 1000:
Kirmizis A, Farnham, PJ. Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med 229:705-721, 2004.[pdf]
Lavrrar JL, Farnham PJ. The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. J Biol Chem. 279:46343-46349, 2004. [pdf]
Reinberg D, Chuikov S, Farnham P, Karachentsev D, Kirmizis A, Kuzmichev A, Margueron R, Nishioka K, Preissner TS, Sarma K, Abate-Shen C, Steward R, Vaquero A. Steps toward understanding the inheritance of repressive methyl-lysine marks in histones. Cold Spring Harb Symp Quant Biol. 69:171-182, 2004.
Feingold et al. (complete list of authors). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306:636-640, 2004. [pdf]
Kirmizis A, Bartley SM, Farnham PJ. Identification of the Polycomb Group protein SU(Z)12 as a new _-catenin target gene which is upregulated in colon tumors. Mol. Cancer Therapeutics, 2:113-121, 2003.[pdf]
Wells J, Yan PS, Cechvala M, Huang H-MT, Farnham PJ. 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 [pdf]
Graveel CR, Harkins-Perry SR, Acevedo LG, Farnham PJ. Identification and characterization of CRG-L2, a new marker for liver tumor development. Oncogene 22:1730-1736, 2003.[pdf]
Oberley MJ, Farnham PJ. Probing chromatin immunoprecipitates with CpG island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods in Enzymology 371:577-596, 2003.[pdf]
Mao DY L, Watson JD, Yan PS, Barsyte-Lovejoy D, Khosravi F, Wong WW-L, Farnham PJ, Huang TH-M, Penn LZ. Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Current Biology 13;1-20, 2003.[pdf]
Oberley MJ, Inman DR, Farnham PJ. E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. Journal of Biological Chem. 278:42466-42476, 2003.[pdf]
Weinmann AS, Yan PS, Oberley MJ, Huang H-MT, Farnham PJ. Isolating human transcription factor targets by combining chromatin immunoprecipitation and CpG microarray analysis. Genes & Devel. 16:235-244, 2002. This article was given a âmust readâ ranking at Faculty of 1000:[pdf]
Wells J, Graveel CR, Bartley SM, Farnham PJ. The identification of E2F1-specific target genes. Proc. Natl. Acad. Sci. USA, 99:3890-3895,2002.[pdf]
Weinmann AS, Farnham PJ. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26:37-47, 2002.[pdf]
Wells J, Farnham PJ. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26:48-56, 2002. Eberhardy SR, Farnham PJ. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J. Biol. Chem, 277: 40156-40162, 2002. [pdf]
Graveel CR, Jatkoe T, Madore S, Holt AL, Farnham PJ. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene 20: 2704-2712-2001.[pdf]
Kel AE, Kel-Margoulis OV, Bartley SM, Farnham PJ, Wingender E, Zhang MQ. Computer-assisted identification of cell cycle-related genes - new targets for E2F transcription factors. J. Mol. Biol. 309: 99-120, 2001.[pdf]
Albert T, Wells J, Funk J-O, Pullner A, Raschke E-E, Stelzer G, Meisterernst M, Farnham PJ, Eick D. Chromatin remodeling and acetylation of the dual c-myc promoters P1/P2 is regulated by separate elements. J. Biol. Chem. 276: 20482-20490, 2001.[pdf]
Maser RS, Mirzoeva O, Wells J, Olivares H, Williams B, Zinkel R, Farnham PJ, Petrini JHJ. The MRE11 complex: diverse roles in S phase progression. Mol. Cell. Biol. 21: 6006-6016, 2001.[pdf]
Weinmann AS, Bartley SM, Zhang MQ, Zhang T, Farnham PJ. The use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21: 6820-6832, 2001.[pdf]
Eberhardy SR, Farnham PJ. c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. J. Biol. Chem. 276:48562-48571, 2001.[pdf]
Mac SM, Farnham PJ. Cad, a c-Myc target gene, is not deregulated in Burkitt's lymphomas, Molecular Carcinogenesis 27: 84-96, 2000.[pdf]
Lee TA, Farnham PJ. Exogenous E2F1 is growth inhibitory before, during, and after neoplastic transformation, Oncogene. 19:2257-2268, 2000. [pdf]
Wells J, Boyd KE, Fry CJ, Bartley SM, Farnham PJ. Target gene specificity of E2F and pocket protein family members in living cells. Mol. Cell Biol. 20: 5987-5807, 2000. [pdf]
Mac SM, D'Cunha C, Farnham PJ. Direct recruitment of N-Myc to target gene promoters. Molecular Carcinogenesis 29:76-86, 2000. [pdf]
Eberhardy SR, Farnham PJ. Direct examination of histone acetylation of c-Myc target genes using chromatin immunoprecipitation. J. Biol. Chem. 275: 33798-33805, 2000. [pdf]