Peggy Farnham, PhD

Title(s)Chair and Professor of Biochemistry & Molecular Medicine
SchoolKeck School of Medicine of USC
Phone+1 323 442 8015
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    Other Positions
    Title(s)W.M. Keck Chair in Biochemistry

    Collapse Biography 
    Collapse Education and Training
    Rice University, Houston, TexasBA1978Biochemistry
    Yale University, New Haven, CTPhD1982Molecular Biochemistry
    Stanford University, Palo Alto, CAPostdoc1986Molecular Biology
    Collapse Awards and Honors
    2010AAAS Fellow
    2012ASBMB Herbert A. Sober Award

    Collapse Overview 
    Collapse Overview
    Dr. Farnham is the William M. Keck Professor of Biochemistry and the Chair of the Department of Biochemistry and Molecular Biology at the Keck School of Medicine at the University of Southern California in Los Angeles, California. Dr. Farnham received her bachelor’s degree from Rice University, her Ph.D. from Yale University, and performed her post-doctoral training at Stanford University. Dr. Farnham previously held Professorships at the McArdle Laboratory for Cancer Research at the University of Wisconsin-Madison and at the University of California-Davis where she was the Associate Director of the UC Davis Genome Center. Dr. Farnham is an international leader in the study of chromatin regulation and its control of transcription factor binding and function. She is a member of an international consortia of genomic scientists working on the ENCODE (Encyclopedia of DNA elements) Project and a member of an NIH Roadmap Reference Epigenome Mapping Center. Based on her contributions to biomedical research, she was elected as a fellow of AAAS in 2010 and in 2012 she received the ASBMB Herbert A Sober Award, which recognizes outstanding biochemical and molecular biological research with particular emphasis on the development of methods and techniques to aid in research.

    Research Interests: transcriptional genomics, genomic technologies
    Diseases Models: cancer cells and tissues, cultured neuroepithelial cells
    Consortia: ENCODE, Roadmap Epigenome Mapping Centers, PsychENCODE

    Collapse Research 
    Collapse Research Activities and Funding
    Development of a novel promoter tagging technology to identify enhancer targets
    NIH/NHGRI R21HG009742Sep 1, 2017 - Jun 30, 2019
    Role: Principal Investigator
    The USC PsychENCODE Project
    NIH/NIMH U01MH103346Jun 15, 2014 - May 31, 2018
    Role: Co-Principal Investigator
    Development of a nuclease-mediated technology to validate chromatin hubs
    NIH/NHGRI R21HG006761Apr 24, 2012 - Mar 31, 2014
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Stem Cells
    NIH/NIDDK R56DK067889Sep 21, 2009 - Jul 31, 2010
    Role: Principal Investigator
    Prostate Cancer Risk Enhancers
    NIH/NCI R01CA136924Dec 1, 2008 - Jan 31, 2020
    Role: Principal Investigator
    Scaling the ChIP-chip assay to improve analysis of clinical biospecimens
    NIH/NCI R21CA128471Jul 1, 2007 - Jun 30, 2010
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Stem Cells
    NIH/NIDDK R01DK067889Jul 1, 2005 - May 31, 2010
    Role: Principal Investigator
    NIH/NCI R01CA059524Mar 15, 1994 - Jan 31, 1997
    Role: Principal Investigator
    Transcriptional Regulation of Growth Related Genes
    NIH/NCI R01CA045240Apr 1, 1987 - May 31, 2013
    Role: Principal Investigator
    NIH/NCI R29CA045240Apr 1, 1987 - Mar 31, 1992
    Role: Principal Investigator
    NIH/NIGMS F32GM008853Jun 30, 1985
    Role: Principal Investigator
    USC Norris Comprehensive Cancer Center (Core) Grant
    NIH/NCI P30CA014089Apr 1, 1980 - Nov 30, 2020
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Luo Z, Rhie SK, Farnham PJ. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel). 2019 Mar 07; 11(3). PMID: 30866492.
      View in: PubMed
    2. Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv. 2018 Dec; 4(12):eaav8550. PMID: 30555922.
      View in: PubMed
    3. Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE. Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. J Cell Biochem. 2019 Mar; 120(3):3056-3070. PMID: 30548288.
      View in: PubMed
    4. Guo Y, Perez AA, Hazelett DJ, Coetzee GA, Rhie SK, Farnham PJ. CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops. Genome Biol. 2018 10 08; 19(1):160. PMID: 30296942.
      View in: PubMed
    5. Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters. Genome Res. 2018 Feb 02. PMID: 29429977.
      View in: PubMed
    6. Rhie SK, Schreiner S, Farnham PJ. Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq). Methods Mol Biol. 2018; 1766:209-229. PMID: 29605855.
      View in: PubMed
    7. Luo Z, Rhie SK, Lay FD, Farnham PJ. A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13. Cell Rep. 2017 Nov 07; 21(6):1411-1417. PMID: 29117547.
      View in: PubMed
    8. 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 Res. 2017 Sep 29; 45(17):9901-9916. PMID: 28973434.
      View in: PubMed
    9. Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin. 2016; 9:50. PMID: 27833659.
      View in: PubMed
    10. 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. Sci Rep. 2016 Mar 03; 6:22462. PMID: 26934861; PMCID: PMC4776156.
    11. 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 Res. 2016 05 19; 44(9):4123-33. PMID: 26743005; PMCID: PMC4872074.
    12. 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. 2015; 8:57. PMID: 26719772; PMCID: PMC4696349.
    13. Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nat Neurosci. 2015 Dec; 18(12):1707-12. PMID: 26605881.
      View in: PubMed
    14. Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol. 2015; 50(6):550-73. PMID: 26446758; PMCID: PMC4666684.
    15. Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015 May 21; 16:105. PMID: 25994056; PMCID: PMC4460959.
    16. 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 Res. 2015 Apr; 25(4):467-77. PMID: 25747664; PMCID: PMC4381519.
    17. Gaddis M, Gerrard D, Frietze S, Farnham PJ. Altering cancer transcriptomes using epigenomic inhibitors. Epigenetics Chromatin. 2015; 8:9. PMID: 26191083; PMCID: PMC4506402.
    18. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
    19. 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, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363. PMID: 25691127; PMCID: PMC4333717.
    20. 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, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18; 6:6351. PMID: 25690954; PMCID: PMC4346612.
    21. 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. Nat Commun. 2014 Nov 25; 5:5442. PMID: 25421844; PMCID: PMC4385735.
    22. Yao L, Tak YG, Berman BP, Farnham PJ. Functional annotation of colon cancer risk SNPs. Nat Commun. 2014 Sep 30; 5:5114. PMID: 25268989; PMCID: PMC4200523.
    23. 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 Biol. 2014 Sep 20; 15(9):469. PMID: 25239471.
      View in: PubMed
    24. 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 Res. 2014; 42(16):10856-68. PMID: 25122745; PMCID: PMC4176344.
    25. 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. 2014 Jun 24; 15:520. PMID: 24962896; PMCID: PMC4082627.
    26. 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, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. PMID: 24753594; PMCID: PMC4035993.
    27. 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, Lu W, Farnham PJ, Coetzee GA. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 2014 Jan; 10(1):e1004102. PMID: 24497837; PMCID: PMC3907334.
    28. Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 2014; 6(5):493-501. PMID: 25431942; PMCID: PMC4259145.
    29. Blattler A, Farnham PJ. Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem. 2013 Nov 29; 288(48):34287-94. PMID: 24151070; PMCID: PMC3843044.
    30. 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. Nat Immunol. 2013 Oct; 14(10):1073-83. PMID: 24013668; PMCID: PMC3800053.
    31. 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, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 2013 Sep; 23(9):1522-40. PMID: 23804400; PMCID: PMC3759728.
    32. 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, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 2013 Jul; 45(7):836-41. PMID: 23708189; PMCID: PMC3695047.
    33. 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. 2013 May 21; 6(1):13. PMID: 23693142; PMCID: PMC3663758.
    34. 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 Biol. 2012 Sep 26; 13(9):R52. PMID: 22951069; PMCID: PMC3491396.
    35. 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 Res. 2012 Nov; 22(11):2262-9. PMID: 22960372; PMCID: PMC3483555.
    36. 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, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489(7414):91-100. PMID: 22955619; PMCID: PMC4154057.
    37. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      View in: PubMed
    38. Farnham PJ. Thematic minireview series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome. J Biol Chem. 2012 Sep 07; 287(37):30885-7. PMID: 22451669; PMCID: PMC3438920.
    39. 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, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. PMID: 22955991; PMCID: PMC3431496.
    40. 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 Res. 2012 Sep; 40(16):7690-704. PMID: 22675074; PMCID: PMC3439894.
    41. 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 TGFß tumor suppressor signaling pathways. Mol Cancer Res. 2012 Jul; 10(7):979-91. PMID: 22622027; PMCID: PMC4166560.
    42. 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, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW. The transcription factor encyclopedia. Genome Biol. 2012; 13(3):R24. PMID: 22458515; PMCID: PMC3439975.
    43. 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 Mol Biol. 2012; 802:323-34. PMID: 22130890; PMCID: PMC4160035.
    44. 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. 2011; 6(11):e27740. PMID: 22140464; PMCID: PMC3225380.
    45. 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. Mol Cell Biol. 2012 Jan; 32(1):226-39. PMID: 22025678; PMCID: PMC3255705.
    46. Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13641-6. PMID: 21808000; PMCID: PMC3158141.
    47. Iyengar S, Farnham PJ. KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem. 2011 Jul 29; 286(30):26267-76. PMID: 21652716; PMCID: PMC3143589.
    48. 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. Mol Cell. 2011 May 20; 42(4):438-50. PMID: 21596310; PMCID: PMC3142354.
    49. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
      View in: PubMed
    50. Iyengar S, Ivanov AV, Jin VX, Rauscher FJ, Farnham PJ. Functional analysis of KAP1 genomic recruitment. Mol Cell Biol. 2011 May; 31(9):1833-47. PMID: 21343339; PMCID: PMC3133220.
    51. 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. 2011 Feb 15; 6(2):e17121. PMID: 21347206.
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    52. 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. J Biol Chem. 2011 Apr 08; 286(14):11985-96. PMID: 21310950; PMCID: PMC3069401.
    53. O'Geen H, Echipare L, Farnham PJ. Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol. 2011; 791:265-86. PMID: 21913086; PMCID: PMC4151291.
    54. Frietze S, Farnham PJ. Transcription factor effector domains. Subcell Biochem. 2011; 52:261-77. PMID: 21557087; PMCID: PMC4151296.
    55. 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. 2010 Dec 08; 5(12):e15082. PMID: 21170338.
      View in: PubMed
    56. 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. 2010 Dec 02; 11:689. PMID: 21126370; PMCID: PMC3019231.
    57. 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, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635; PMCID: PMC2955169.
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    139. Kollmar R, Farnham PJ. Site-specific initiation of transcription by RNA polymerase II. Proc Soc Exp Biol Med. 1993 Jun; 203(2):127-39. PMID: 8502653.
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    140. 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. Mol Cell Biol. 1993 Mar; 13(3):1610-8. PMID: 8441401; PMCID: PMC359473.
    141. 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. 1992 Jul 24; 70(2):351-64. PMID: 1638635.
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    142. Mack KJ, Cortner J, Mack P, Farnham PJ. krox 20 messenger RNA and protein expression in the adult central nervous system. Brain Res Mol Brain Res. 1992 Jun; 14(1-2):117-23. PMID: 1323008.
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    143. 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. Mol Cell Biol. 1992 May; 12(5):2250-9. PMID: 1569952; PMCID: PMC364397.
    144. 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. Mol Cell Biol. 1992 Mar; 12(3):1054-63. PMID: 1545788; PMCID: PMC369537.
    145. 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. J Biol Chem. 1992 Jan 05; 267(1):385-91. PMID: 1346130.
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    146. Cortner J, Farnham PJ. Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH3T3 fibroblasts. Cell Growth Differ. 1991 Sep; 2(9):465-73. PMID: 1721529.
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    147. Farnham PJ, Cornwell MM. Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component. Gene Expr. 1991 May; 1(2):137-48. PMID: 1820211.
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    148. Cortner J, Farnham PJ. Identification of the serum-responsive transcription initiation site of the zinc finger gene Krox-20. Mol Cell Biol. 1990 Jul; 10(7):3788-91. PMID: 2113176; PMCID: PMC360834.
    149. Farnham PJ, Means AL. Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter. Mol Cell Biol. 1990 Apr; 10(4):1390-8. PMID: 2320003; PMCID: PMC362241.
    150. Farnham PJ, Kollmar R. Characterization of the 5' end of the growth-regulated Syrian hamster CAD gene. Cell Growth Differ. 1990 Apr; 1(4):179-89. PMID: 1982061.
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    151. Means AL, Farnham PJ. Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site. Mol Cell Biol. 1990 Feb; 10(2):653-61. PMID: 2300058; PMCID: PMC360863.
    152. Schilling LJ, Farnham PJ. Identification of a new promoter upstream of the murine dihydrofolate reductase gene. Mol Cell Biol. 1989 Oct; 9(10):4568-70. PMID: 2479829; PMCID: PMC362546.
    153. Farnham PJ, Schimke RT. In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene. Mol Cell Biol. 1986 Jul; 6(7):2392-401. PMID: 3785199; PMCID: PMC367792.
    154. Farnham PJ, Schimke RT. Murine dihydrofolate reductase transcripts through the cell cycle. Mol Cell Biol. 1986 Feb; 6(2):365-71. PMID: 3785152; PMCID: PMC367525.
    155. Farnham PJ, Schimke RT. Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle. J Biol Chem. 1985 Jun 25; 260(12):7675-80. PMID: 2987264.
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    156. Farnham PJ, Abrams JM, Schimke RT. Opposite-strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene. Proc Natl Acad Sci U S A. 1985 Jun; 82(12):3978-82. PMID: 2408272; PMCID: PMC397917.
    157. 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. J Biol Chem. 1985 Feb 25; 260(4):2307-14. PMID: 2982814.
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    158. Hamkalo BA, Farnham PJ, Johnston R, Schimke RT. Ultrastructural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line. Proc Natl Acad Sci U S A. 1985 Feb; 82(4):1126-30. PMID: 3856243; PMCID: PMC397207.
    159. Farnham PJ, Greenblatt J, Platt T. Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli. Cell. 1982 Jul; 29(3):945-51. PMID: 6758952.
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    160. Farnham PJ, Platt T. Effects of DNA base analogs on transcription termination at the tryptophan operon attenuator of EScherichia coli. Proc Natl Acad Sci U S A. 1982 Feb; 79(4):998-1002. PMID: 7041118; PMCID: PMC345886.
    161. Christie GE, Farnham PJ, Platt T. Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro. Proc Natl Acad Sci U S A. 1981 Jul; 78(7):4180-4. PMID: 7027254; PMCID: PMC319752.
    162. Farnham PJ, Platt T. Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucleic Acids Res. 1981 Feb 11; 9(3):563-77. PMID: 7012794; PMCID: PMC327222.
    163. Farnham PJ, Platt T. A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs. Cell. 1980 Jul; 20(3):739-48. PMID: 6998564.
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    164. Asch HL, Farnham PJ. Effects of gentamicin on trypsin, chymotrypsin, and collagenase. J Infect Dis. 1978 Aug; 138(2):257-9. PMID: 210240.
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    165. Farnham PJ, Novak RA, McAdoo DJ. A re-examination of the distributions of octopamine and phenylethanolamine in the aplysia nervous system. J Neurochem. 1978 May; 30(5):1173-6. PMID: 351144.
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