Peggy J. Farnham - Publications

Affiliations: 
1987-2004 University of Wisconsin, Madison, Madison, WI 
 2004-2010 University of California, Davis, Davis, CA 
 2011- Biochemistry University of Southern California, Los Angeles, CA, United States 
Area:
Human Genomics, Transcriptional Regulation
Website:
http://pibbs.usc.edu/faculty/profile/?fid=205

162 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, Segal DJ. dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Research. 45: 9901-9916. PMID 28973434 DOI: 10.1093/nar/gkx578  0.56
2016 Cai M, Kim S, Wang K, Farnham PJ, Coetzee GA, Lu W. 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Scientific Reports. 6: 22462. PMID 26934861 DOI: 10.1038/srep22462  1
2016 Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O'Geen H, Segal DJ, Farnham PJ. Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Nucleic Acids Research. PMID 26743005 DOI: 10.1093/nar/gkv1530  1
2015 Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics & Chromatin. 8: 57. PMID 26719772 DOI: 10.1186/s13072-015-0050-4  1
2015 Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Critical Reviews in Biochemistry and Molecular Biology. 1-24. PMID 26446758 DOI: 10.3109/10409238.2015.1087961  1
2015 Gaddis M, Gerrard D, Frietze S, Farnham PJ. Altering cancer transcriptomes using epigenomic inhibitors. Epigenetics & Chromatin. 8: 9. PMID 26191083 DOI: 10.1186/1756-8935-8-9  1
2015 Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biology. 16: 105. PMID 25994056 DOI: 10.1186/s13059-015-0668-3  1
2015 Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Research. 25: 467-77. PMID 25747664 DOI: 10.1101/gr.183368.114  1
2015 Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, ... ... Farnham PJ, et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nature Communications. 6: 6363. PMID 25691127 DOI: 10.1038/ncomms7363  1
2015 Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, ... ... Farnham PJ, et al. Epigenetic and transcriptional determinants of the human breast. Nature Communications. 6: 6351. PMID 25690954 DOI: 10.1038/ncomms7351  1
2014 Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 6: 493-501. PMID 25431942 DOI: 10.2217/epi.14.30  1
2014 Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nature Communications. 5: 5442. PMID 25421844 DOI: 10.1038/ncomms6442  1
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/pnas.1410434111  1
2014 Yao L, Tak YG, Berman BP, Farnham PJ. Functional annotation of colon cancer risk SNPs. Nature Communications. 5: 5114. PMID 25268989 DOI: 10.1038/ncomms6114  1
2014 Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biology. 15: 469. PMID 25239471 DOI: 10.1186/s13059-014-0469-0  1
2014 Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Research. 42: 10856-68. PMID 25122745 DOI: 10.1093/nar/gku708  1
2014 Frietze S, O'Geen H, Littlepage LE, Simion C, Sweeney CA, Farnham PJ, Krig SR. Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. Bmc Genomics. 15: 520. PMID 24962896 DOI: 10.1186/1471-2164-15-520  1
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/pnas.1318948111  1
2014 Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, ... ... Farnham PJ, et al. Comprehensive functional annotation of 77 prostate cancer risk loci. Plos Genetics. 10: e1004102. PMID 24497837 DOI: 10.1371/journal.pgen.1004102  1
2013 Blattler A, Farnham PJ. Cross-talk between site-specific transcription factors and DNA methylation states. The Journal of Biological Chemistry. 288: 34287-94. PMID 24151070 DOI: 10.1074/jbc.R113.512517  1
2013 Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST. Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nature Immunology. 14: 1073-83. PMID 24013668 DOI: 10.1038/ni.2707  1
2013 Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone post-translational modifications. Nature Methods. 10: 992-5. PMID 23955773 DOI: 10.1038/nmeth.2605  1
2013 Wang R, Hsu HK, Blattler A, Wang Y, Lan X, Wang Y, Hsu PY, Leu YW, Huang TH, Farnham PJ, Jin VX. LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data. Plos One. 8: e67788. PMID 23825685 DOI: 10.1371/journal.pone.0067788  1
2013 Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, ... ... Farnham PJ, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Research. 23: 1522-40. PMID 23804400 DOI: 10.1101/gr.156539.113  1
2013 Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, ... ... Farnham PJ, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature Genetics. 45: 836-41. PMID 23708189 DOI: 10.1038/ng.2649  1
2013 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 & Chromatin. 6: 13. PMID 23693142 DOI: 10.1186/1756-8935-6-13  1
2012 Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Spark: a navigational paradigm for genomic data exploration. Genome Research. 22: 2262-9. PMID 22960372 DOI: 10.1101/gr.140665.112  1
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Farnham PJ, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/gr.136184.111  1
2012 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, ... ... Farnham PJ, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/nature11245  1
2012 . An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247  1
2012 Lan X, Farnham PJ, Jin VX. Uncovering transcription factor modules using one- and three-dimensional analyses. The Journal of Biological Chemistry. 287: 30914-21. PMID 22952238 DOI: 10.1074/jbc.R111.309229  1
2012 Frietze S, Wang R, Yao L, Tak YG, 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. PMID 22951069 DOI: 10.1186/gb-2012-13-9-r52  1
2012 Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX. Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Research. 40: 7690-704. PMID 22675074 DOI: 10.1093/nar/gks501  1
2012 Jung CJ, Iyengar S, Blahnik KR, Jiang JX, Tahimic C, Torok NJ, de vere White RW, Farnham PJ, Zern M. Human ESC self-renewal promoting microRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFβ tumor suppressor signaling pathways. Molecular Cancer Research : McR. 10: 979-91. PMID 22622027 DOI: 10.1158/1541-7786.MCR-11-0421  1
2012 Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, ... ... Farnham PJ, et al. The transcription factor encyclopedia. Genome Biology. 13: R24. PMID 22458515 DOI: 10.1186/gb-2012-13-3-r24  1
2012 Farnham PJ. Thematic minireview series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome. The Journal of Biological Chemistry. 287: 30885-7. PMID 22451669 DOI: 10.1074/jbc.R112.365940  1
2012 Kennedy BA, Lan X, Huang TH, Farnham PJ, Jin VX. Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. Methods in Molecular Biology (Clifton, N.J.). 802: 323-34. PMID 22130890 DOI: 10.1007/978-1-61779-400-1_21  1
2012 Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Molecular and Cellular Biology. 32: 226-39. PMID 22025678 DOI: 10.1128/MCB.06166-11  1
2011 Jung CJ, Iyengar S, Blahnik KR, Ajuha TP, Jiang JX, Farnham PJ, Zern M. Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation. Plos One. 6: e27740. PMID 22140464 DOI: 10.1371/journal.pone.0027740  1
2011 Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, et al. The Human Epigenome Browser at Washington University. Nature Methods. 8: 989-90. PMID 22127213 DOI: 10.1038/nmeth.1772  1
2011 O'Geen H, Echipare L, Farnham PJ. Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods in Molecular Biology (Clifton, N.J.). 791: 265-86. PMID 21913086 DOI: 10.1007/978-1-61779-316-5_20  1
2011 Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proceedings of the National Academy of Sciences of the United States of America. 108: 13641-6. PMID 21808000 DOI: 10.1073/pnas.1108440108  1
2011 Iyengar S, Farnham PJ. KAP1 protein: an enigmatic master regulator of the genome. The Journal of Biological Chemistry. 286: 26267-76. PMID 21652716 DOI: 10.1074/jbc.R111.252569  1
2011 Trojer P, Cao AR, Gao Z, Li Y, Zhang J, Xu X, Li G, Losson R, Erdjument-Bromage H, Tempst P, Farnham PJ, Reinberg D. L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Molecular Cell. 42: 438-50. PMID 21596310 DOI: 10.1016/j.molcel.2011.04.004  1
2011 Frietze S, Farnham PJ. Transcription factor effector domains. Sub-Cellular Biochemistry. 52: 261-77. PMID 21557087 DOI: 10.1007/978-90-481-9069-0_12  1
2011 Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. Plos One. 6: e17121. PMID 21347206 DOI: 10.1371/journal.pone.0017121  1
2011 Iyengar S, Ivanov AV, Jin VX, Rauscher FJ, Farnham PJ. Functional analysis of KAP1 genomic recruitment. Molecular and Cellular Biology. 31: 1833-47. PMID 21343339 DOI: 10.1128/MCB.01331-10  1
2011 Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ. Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. The Journal of Biological Chemistry. 286: 11985-96. PMID 21310950 DOI: 10.1074/jbc.M110.217158  1
2010 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. PMID 21170338 DOI: 10.1371/journal.pone.0015082  1
2010 O'Geen H, Lin YH, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA, Engel JD, Farnham PJ. Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. Bmc Genomics. 11: 689. PMID 21126370 DOI: 10.1186/1471-2164-11-689  1
2010 Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/nbt1010-1045  1
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Farnham PJ, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/nbt.1682  1
2010 O'Geen H, Frietze S, Farnham PJ. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods in Molecular Biology (Clifton, N.J.). 649: 437-55. PMID 20680851 DOI: 10.1007/978-1-60761-753-2_27  1
2010 Krig SR, Miller JK, Frietze S, Beckett LA, Neve RM, Farnham PJ, Yaswen PI, Sweeney CA. ZNF217, a candidate breast cancer oncogene amplified at 20q13, regulates expression of the ErbB3 receptor tyrosine kinase in breast cancer cells. Oncogene. 29: 5500-10. PMID 20661224 DOI: 10.1038/onc.2010.289  1
2010 Komashko VM, Farnham PJ. 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics. 5: 229-40. PMID 20305384 DOI: 10.4161/epi.5.3.11409  1
2010 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. Nucleic Acids Research. 38: e13. PMID 19906703 DOI: 10.1093/nar/gkp1012  1
2010 Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. The Journal of Biological Chemistry. 285: 1393-403. PMID 19887448 DOI: 10.1074/jbc.M109.063032  1
2009 Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Molecular Cell. 36: 667-81. PMID 19941826 DOI: 10.1016/j.molcel.2009.11.001  1
2009 Jin VX, Apostolos J, Nagisetty NS, Farnham PJ. W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics (Oxford, England). 25: 3191-3. PMID 19797408 DOI: 10.1093/bioinformatics/btp570  1
2009 Farnham PJ. Insights from genomic profiling of transcription factors. Nature Reviews. Genetics. 10: 605-16. PMID 19668247 DOI: 10.1038/nrg2636  1
2008 Cotterman R, Jin VX, Krig SR, Lemen JM, Wey A, Farnham PJ, Knoepfler PS. N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Research. 68: 9654-62. PMID 19047142 DOI: 10.1158/0008-5472.CAN-08-1961  1
2008 Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Research. 18: 1763-77. PMID 18836037 DOI: 10.1101/gr.080622.108  1
2008 Acevedo LG, Bieda M, Green R, Farnham PJ. Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Research. 68: 2641-51. PMID 18413731 DOI: 10.1158/0008-5472.CAN-07-5590  1
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: 521-32. PMID 18347325 DOI: 10.1101/gr.074609.107  1
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/gr.7080508  1
2007 Acevedo LG, Iniguez AL, Holster HL, Zhang X, Green R, Farnham PJ. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques. 43: 791-7. PMID 18251256 DOI: 10.2144/000112625  1
2007 Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, Lasalle JM. Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proceedings of the National Academy of Sciences of the United States of America. 104: 19416-21. PMID 18042715 DOI: 10.1073/pnas.0707442104  1
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 Research. 17: 1550-61. PMID 17908821 DOI: 10.1101/gr.6783507  1
2007 Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 129: 1311-23. PMID 17604720 DOI: 10.1016/j.cell.2007.05.022  1
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 Research. 17: 807-17. PMID 17567999 DOI: 10.1101/gr.6006107  1
2007 O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. Plos Genetics. 3: e89. PMID 17542650 DOI: 10.1371/journal.pgen.0030089  1
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 chromatin immunoprecipitation (ChIP)-chip assays. The Journal of Biological Chemistry. 282: 9703-12. PMID 17259635 DOI: 10.1074/jbc.M611752200  1
2006 O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques. 41: 577-80. PMID 17140114 DOI: 10.2144/000112268  1
2006 Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Research. 16: 1455-64. PMID 17053094 DOI: 10.1101/gr.4140006  1
2006 Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Research. 16: 1585-95. PMID 17053090 DOI: 10.1101/gr.5520206  1
2006 Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Research. 16: 890-900. PMID 16751344 DOI: 10.1101/gr.5306606  1
2006 Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenetic and Genome Research. 114: 1-15. PMID 16717444 DOI: 10.1159/000091922  1
2006 Bieda M, Xu X, Singer MA, 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. PMID 16606705 DOI: 10.1101/gr.4887606  1
2005 Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang THM, 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 Research. 33: 2952-2961. PMID 15911630 DOI: 10.1093/nar/gki582  1
2005 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. Proceedings of the National Academy of Sciences of the United States of America. 102: 1859-64. PMID 15684044 DOI: 10.1073/pnas.0409875102  1
2004 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 Harbor Symposia On Quantitative Biology. 69: 171-82. PMID 16117647 DOI: 10.1101/sqb.2004.69.171  1
2004 Kirmizis A, Farnham PJ. Genomic approaches that aid in the identification of transcription factor target genes. Experimental Biology and Medicine (Maywood, N.J.). 229: 705-21. PMID 15337825  1
2004 Lavrrar JL, Farnham PJ. The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. The Journal of Biological Chemistry. 279: 46343-9. PMID 15328355 DOI: 10.1074/jbc.M402692200  1
2004 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 Lys 27. Genes & Development. 18: 1592-605. PMID 15231737 DOI: 10.1101/gad.1200204  1
2004 Townsend MJ, Weinmann AS, Matsuda JL, Salomon R, Farnham PJ, Biron CA, Gapin L, Glimcher LH. T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. Immunity. 20: 477-94. PMID 15084276 DOI: 10.1016/S1074-7613(04)00076-7  1
2004 Oberley MJ, Tsao J, Yau P, Farnham PJ. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods in Enzymology. 376: 315-34. PMID 14975315 DOI: 10.1016/S0076-6879(03)76021-2  1
2003 Oberley MJ, Farnham PJ. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods in Enzymology. 371: 577-96. PMID 14712730 DOI: 10.1016/S0076-6879(03)71043-X  1
2003 Oberley MJ, Inman DR, Farnham PJ. E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. The Journal of Biological Chemistry. 278: 42466-76. PMID 12909625 DOI: 10.1074/jbc.M307733200  1
2003 Mao DY, Watson JD, Yan PS, Barsyte-Lovejoy D, Khosravi F, Wong WW, Farnham PJ, Huang TH, Penn LZ. Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Current Biology : Cb. 13: 882-6. PMID 12747840 DOI: 10.1016/S0960-9822(03)00297-5  1
2003 Graveel CR, Harkins-Perry SR, Acevedo LG, Farnham PJ. Identification and characterization of CRG-L2, a new marker for liver tumor development. Oncogene. 22: 1730-6. PMID 12642876 DOI: 10.1038/sj.onc.1206309  1
2003 Wells J, Yan PS, Cechvala M, Huang T, 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: 1445-60. PMID 12629508 DOI: 10.1038/sj.onc.1206264  1
2003 Kirmizis A, Bartley SM, Farnham PJ. Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Molecular Cancer Therapeutics. 2: 113-21. PMID 12533679  1
2002 Eberhardy SR, Farnham PJ. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. The Journal of Biological Chemistry. 277: 40156-62. PMID 12177005 DOI: 10.1074/jbc.M207441200  1
2002 Wells J, Farnham PJ. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods (San Diego, Calif.). 26: 48-56. PMID 12054904 DOI: 10.1016/S1046-2023(02)00007-5  1
2002 Weinmann AS, Farnham PJ. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods (San Diego, Calif.). 26: 37-47. PMID 12054903 DOI: 10.1016/S1046-2023(02)00006-3  1
2002 Farnham PJ. In vivo assays to examine transcription factor localization and target gene specificity. Methods (San Diego, Calif.). 26: 1-2. PMID 12054898 DOI: 10.1016/S1046-2023(02)00001-4  1
2002 Wells J, Graveel CR, Bartley SM, Madore SJ, Farnham PJ. The identification of E2F1-specific target genes. Proceedings of the National Academy of Sciences of the United States of America. 99: 3890-5. PMID 11904439 DOI: 10.1073/pnas.062047499  1
2002 Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes & Development. 16: 235-44. PMID 11799066 DOI: 10.1101/gad.943102  1
2001 Eberhardy SR, Farnham PJ. c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. The Journal of Biological Chemistry. 276: 48562-71. PMID 11673469 DOI: 10.1074/jbc.M109014200  1
2001 Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Molecular and Cellular Biology. 21: 6820-32. PMID 11564866 DOI: 10.1128/MCB.21.20.6820-6832.2001  1
2001 Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ. Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology. 309: 99-120. PMID 11491305 DOI: 10.1006/jmbi.2001.4650  1
2001 Maser RS, Mirzoeva OK, Wells J, Olivares H, Williams BR, Zinkel RA, Farnham PJ, Petrini JH. Mre11 complex and DNA replication: linkage to E2F and sites of DNA synthesis. Molecular and Cellular Biology. 21: 6006-16. PMID 11486038 DOI: 10.1128/MCB.21.17.6006-6016.2001  1
2001 Graveel CR, Jatkoe T, Madore SJ, Holt AL, Farnham PJ. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene. 20: 2704-12. PMID 11420682 DOI: 10.1038/sj.onc.1204391  1
2001 Albert T, Wells J, Funk JO, Pullner A, Raschke EE, Stelzer G, Meisterernst M, Farnham PJ, Eick D. The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements. The Journal of Biological Chemistry. 276: 20482-90. PMID 11279041 DOI: 10.1074/jbc.M100265200  1
2000 Mac SM, D'Cunha CA, Farnham PJ. Direct recruitment of N-myc to target gene promoters. Molecular Carcinogenesis. 29: 76-86. PMID 11074604 DOI: 10.1002/1098-2744(200010)29:2<76::AID-MC4>3.0.CO;2-Y  1
2000 Eberhardy SR, D'Cunha CA, Farnham PJ. Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation. The Journal of Biological Chemistry. 275: 33798-805. PMID 10931841 DOI: 10.1074/jbc.M005154200  1
2000 Wells J, Boyd KE, Fry CJ, Bartley SM, Farnham PJ. Target gene specificity of E2F and pocket protein family members in living cells. Molecular and Cellular Biology. 20: 5797-807. PMID 10913163 DOI: 10.1128/MCB.20.16.5797-5807.2000  1
2000 Lee TA, Farnham PJ. Exogenous E2F expression is growth inhibitory before, during, and after cellular transformation. Oncogene. 19: 2257-68. PMID 10822376 DOI: 10.1038/sj.onc.1203556  1
2000 Mac SM, Farnham PJ. CAD, a c-Myc target gene, is not deregulated in Burkitt's lymphoma cell lines. Molecular Carcinogenesis. 27: 84-96. PMID 10657901 DOI: 10.1002/(SICI)1098-2744(200002)27:2<84::AID-MC4>3.0.CO;2-3  1
1999 Boyd KE, Farnham PJ. Coexamination of site-specific transcription factor binding and promoter activity in living cells. Molecular and Cellular Biology. 19: 8393-9. PMID 10567564  1
1999 Fry CJ, Farnham PJ. Context-dependent transcriptional regulation. The Journal of Biological Chemistry. 274: 29583-6. PMID 10514422 DOI: 10.1074/jbc.274.42.29583  1
1999 Boyd KE, Farnham PJ. Identification of target genes of oncogenic transcription factors. Proceedings of the Society For Experimental Biology and Medicine. Society For Experimental Biology and Medicine (New York, N.Y.). 222: 9-28. PMID 10510243  1
1999 Lukas ER, Bartley SM, Graveel CR, Diaz ZM, Dyson N, Harlow E, Yamasaki L, Farnham PJ. No effect of loss of E2F1 on liver regeneration or hepatocarcinogenesis in C57BL/6J or C3H/HeJ mice. Molecular Carcinogenesis. 25: 295-303. PMID 10449036 DOI: 10.1002/(SICI)1098-2744(199908)25:4<295::AID-MC8>3.0.CO;2-9  1
1999 Fry CJ, Pearson A, Malinowski E, Bartley SM, Greenblatt J, Farnham PJ. Activation of the murine dihydrofolate reductase promoter by E2F1. A requirement for CBP recruitment. The Journal of Biological Chemistry. 274: 15883-91. PMID 10336493  0.56
1998 Bartley SM, Szakaly RJ, Farnham PJ. Characterization of the 3' untranslated region of mouse E2F1 mRNA. Gene. 223: 355-60. PMID 9858765 DOI: 10.1016/S0378-1119(98)00239-X  1
1998 Boyd KE, Wells J, Gutman J, Bartley SM, Farnham PJ. c-Myc target gene specificity is determined by a post-DNAbinding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 95: 13887-92. PMID 9811896 DOI: 10.1073/pnas.95.23.13887  1
1997 van Ginkel PR, Hsiao KM, Schjerven H, Farnham PJ. E2F-mediated growth regulation requires transcription factor cooperation. The Journal of Biological Chemistry. 272: 18367-74. PMID 9218478 DOI: 10.1074/jbc.272.29.18367  1
1997 Fry CJ, Slansky JE, Farnham PJ. Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain. Molecular and Cellular Biology. 17: 1966-76. PMID 9121444  1
1997 Boyd KE, Farnham PJ. Myc versus USF: discrimination at the cad gene is determined by core promoter elements. Molecular and Cellular Biology. 17: 2529-37. PMID 9111322  1
1996 Slansky JE, Farnham PJ. Transcriptional regulation of the dihydrofolate reductase gene. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 18: 55-62. PMID 8593164 DOI: 10.1002/bies.950180111  1
1996 Farnham PJ. Conclusions and future directions. Current Topics in Microbiology and Immunology. 208: 129-37. PMID 8575211  1
1996 Slansky JE, Farnham PJ. Introduction to the E2F family: protein structure and gene regulation. Current Topics in Microbiology and Immunology. 208: 1-30. PMID 8575210  1
1996 Slansky JE, Farnham PJ. Introduction to the E2F family:Protein structure and gene regulation Current Topics in Microbiology and Immunology. 208: X-30.  1
1996 Farnham PJ. Transcriptional control of cell growth: The E2F gene family [An issue of 6 reviews] Current Topics in Microbiology and Immunology. 208: 1-37.  1
1995 Buermeyer AB, Strasheim LA, McMahon SL, Farnham PJ. Identification of cis-acting elements that can obviate a requirement for the C-terminal domain of RNA polymerase II. The Journal of Biological Chemistry. 270: 6798-807. PMID 7896826 DOI: 10.1074/jbc.270.12.6798  1
1995 Miltenberger RJ, Sukow KA, Farnham PJ. An E-box-mediated increase in cad transcription at the G1/S-phase boundary is suppressed by inhibitory c-Myc mutants. Molecular and Cellular Biology. 15: 2527-35. PMID 7739536  1
1995 Miltenberger RJ, Farnham PJ, Smith DE, Stommel JM, Cornwell MM. v-Raf activates transcription of growth-responsive promoters via GC-rich sequences that bind the transcription factor Sp1. Cell Growth & Differentiation : the Molecular Biology Journal of the American Association For Cancer Research. 6: 549-56. PMID 7647038  1
1995 Schilling LJ, Farnham PJ. The bidirectionally transcribed dihydrofolate reductase and rep-3a promoters are growth regulated by distinct mechanisms. Cell Growth & Differentiation : the Molecular Biology Journal of the American Association For Cancer Research. 6: 541-8. PMID 7647037  1
1995 Bennett LM, Farnham PJ, Drinkwater NR. Strain-dependent differences in DNA synthesis and gene expression in the regenerating livers of CB57BL/6J and C3H/HeJ mice. Molecular Carcinogenesis. 14: 46-52. PMID 7546224 DOI: 10.1002/mc.2940140109  1
1994 Li Y, Slansky JE, Myers DJ, Drinkwater NR, Kaelin WG, Farnham PJ. Cloning, chromosomal location, and characterization of mouse E2F1. Molecular and Cellular Biology. 14: 1861-9. PMID 8114719  1
1994 Schilling LJ, Farnham PJ. Transcriptional regulation of the dihydrofolate reductase/rep-3 locus. Critical Reviews in Eukaryotic Gene Expression. 4: 19-53. PMID 7987046  1
1994 Hsiao KM, McMahon SL, Farnham PJ. Multiple DNA elements are required for the growth regulation of the mouse E2F1 promoter. Genes & Development. 8: 1526-37. PMID 7958837  1
1994 Kollmar R, Sukow KA, Sponagle SK, Farnham PJ. Start site selection at the TATA-less carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter. The Journal of Biological Chemistry. 269: 2252-7. PMID 7905000  1
1994 Schilling LJ, Farnham PJ. Inappropriate transcription from the 5' end of the murine dihydrofolate reductase gene masks transcriptional regulation. Nucleic Acids Research. 22: 3061-8. PMID 7520569  1
1993 Kollmar R, Farnham PJ. Site-specific initiation of transcription by RNA polymerase II. Proceedings of the Society For Experimental Biology and Medicine. Society For Experimental Biology and Medicine (New York, N.Y.). 203: 127-39. PMID 8502653  1
1993 Slansky JE, Li Y, Kaelin WG, Farnham PJ. A protein synthesis-dependent increase in E2F1 mRNA correlates with growth regulation of the dihydrofolate reductase promoter. Molecular and Cellular Biology. 13: 1610-8. PMID 8441401  1
1993 Farnham PJ, Slansky JE, Kollmar R. The role of E2F in the mammalian cell cycle. Biochimica Et Biophysica Acta. 1155: 125-31. PMID 8357823 DOI: 10.1016/0304-419X(93)90001-S  1
1993 Miltenberger RJ, Cortner J, Farnham PJ. An inhibitory Raf-1 mutant suppresses expression of a subset of v-raf-activated genes. The Journal of Biological Chemistry. 268: 15674-80. PMID 8340392  1
1992 Kaelin WG, Krek W, Sellers WR, DeCaprio JA, Ajchenbaum F, Fuchs CS, Chittenden T, Li Y, Farnham PJ, Blanar MA. Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties. Cell. 70: 351-64. PMID 1638635 DOI: 10.1016/0092-8674(92)90108-O  1
1992 Buermeyer AB, Thompson NE, Strasheim LA, Burgess RR, Farnham PJ. The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II. Molecular and Cellular Biology. 12: 2250-9. PMID 1569952  1
1992 Means AL, Slansky JE, McMahon SL, Knuth MW, Farnham PJ. The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter. Molecular and Cellular Biology. 12: 1054-63. PMID 1545788  1
1992 Kollmar R, Lindstrom MJ, Farnham PJ. Heat sensitivity and Sp1 activation of complex formation at the Syrian hamster carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter in vitro. The Journal of Biological Chemistry. 267: 385-91. PMID 1346130  1
1992 Mack KJ, Cortner J, Mack P, Farnham PJ. krox 20 messenger RNA and protein expression in the adult central nervous system. Brain Research. Molecular Brain Research. 14: 117-23. PMID 1323008 DOI: 10.1016/0169-328X(92)90018-7  1
1991 Farnham PJ, Cornwell MM. Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component Gene Expression. 1: 137-148. PMID 1820211  1
1991 Cortner J, Farnham PJ. Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH3T3 fibroblasts Cell Growth & Differentiation : the Molecular Biology Journal of the American Association For Cancer Research. 2: 465-473. PMID 1721529  1
1990 Farnham PJ, Means AL. Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter Molecular and Cellular Biology. 10: 1390-1398. PMID 2320003  1
1990 Means AL, Farnham PJ. Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site Molecular and Cellular Biology. 10: 653-661. PMID 2300058  1
1990 Cortner J, Farnham PJ. Identification of the Serum-Responsive Transcription Initiation Site of the Zinc Finger Gene Krox-20 Molecular and Cellular Biology. 10: 3788-3791. PMID 2113176  1
1990 Farnham PJ, Kollmar R. Characterization of the 5' end of the growth-regulated Syrian hamster CAD gene Cell Growth & Differentiation : the Molecular Biology Journal of the American Association For Cancer Research. 1: 179-189. PMID 1982061  1
1989 Schilling LJ, Farnham PJ. Identification of a new promoter upstream of the murine dihydrofolate reductase gene Molecular and Cellular Biology. 9: 4568-4570. PMID 2479829  1
1986 Farnham PJ, Schimke RT. In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene. Molecular and Cellular Biology. 6: 2392-401. PMID 3785199  1
1986 Farnham PJ, Schimke RT. Murine dihydrofolate reductase transcripts through the cell cycle. Molecular and Cellular Biology. 6: 365-71. PMID 3785152  1
1985 Hamkalo BA, Farnham PJ, Johnston R, Schimke RT. Ultrastructural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line. Proceedings of the National Academy of Sciences of the United States of America. 82: 1126-30. PMID 3856243  1
1985 Farnham PJ, Schimke RT. Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle. The Journal of Biological Chemistry. 260: 7675-80. PMID 2987264  1
1985 McGrogan M, Simonsen CC, Smouse DT, Farnham PJ, Schimke RT. Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. Evidence for multiple promoter regions. The Journal of Biological Chemistry. 260: 2307-14. PMID 2982814  1
1985 Farnham PJ, Abrams JM, Schimke RT. Opposite-strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene. Proceedings of the National Academy of Sciences of the United States of America. 82: 3978-82. PMID 2408272  1
1982 Farnham PJ, Platt T. Effects of DNA base analogs on transcription termination at the tryptophan operon attenuator of EScherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 79: 998-1002. PMID 7041118  1
1982 Farnham PJ, Greenblatt J, Platt T. Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli. Cell. 29: 945-51. PMID 6758952 DOI: 10.1016/0092-8674(82)90457-3  1
1981 Christie GE, Farnham PJ, Platt T. Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro. Proceedings of the National Academy of Sciences of the United States of America. 78: 4180-4. PMID 7027254  1
1981 Farnham PJ, Platt T. Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucleic Acids Research. 9: 563-77. PMID 7012794 DOI: 10.1093/nar/9.3.563  1
1980 Farnham PJ, Platt T. A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs. Cell. 20: 739-48. PMID 6998564  1
1978 Asch HL, Farnham PJ. Effects of gentamicin on trypsin, chymotrypsin, and collagenase Journal of Infectious Diseases. 138: 257-259. PMID 210240  1
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