Peggy Farnham, PhD

Title(s)Chair and Professor of Biochemistry & Molecular Medicine
SchoolKeck School of Medicine of Usc
Address1975 Zonal Avenue
Health Sciences Campus
Los Angeles CA 90089
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
    Characterization of a novel family of human transcription factors that bind at +240 downstream of the transcription start site.
    NIH R01GM133450Apr 1, 2020 - Mar 31, 2024
    Role: Principal Investigator
    Development of a novel promoter tagging technology to identify enhancer targets
    NIH R21HG009742Sep 1, 2017 - Jun 30, 2019
    Role: Principal Investigator
    The USC PsychENCODE Project
    NIH U01MH103346Jun 15, 2014 - May 31, 2018
    Role: Co-Principal Investigator
    Development of a nuclease-mediated technology to validate chromatin hubs
    NIH R21HG006761Apr 24, 2012 - Mar 31, 2015
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Stem Cells
    NIH R56DK067889Sep 21, 2009 - Jul 31, 2010
    Role: Principal Investigator
    Prostate Cancer Risk Enhancers
    NIH R01CA136924Dec 1, 2008 - Jan 31, 2021
    Role: Principal Investigator
    Scaling the ChIP-chip assay to improve analysis of clinical biospecimens
    NIH R21CA128471Jul 1, 2007 - Jun 30, 2010
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Stem Cells
    NIH R01DK067889Jul 1, 2005 - May 31, 2010
    Role: Principal Investigator
    THE ROLE OF FAF KINASE IN CELL PROLIFERATION
    NIH R01CA059524Mar 15, 1994 - Jan 31, 1997
    Role: Principal Investigator
    Transcriptional Regulation of Growth Related Genes
    NIH R01CA045240Apr 1, 1987 - May 31, 2013
    Role: Principal Investigator
    TRANSCRIPTIONAL REGULATION OF GROWTH-RELATED GENES
    NIH R29CA045240Apr 1, 1987 - Mar 31, 1992
    Role: Principal Investigator
    CELL CYCLE REGULATION OF THE DIHYDROFOLATE REDUCTASE GEN
    NIH F32GM008853Jun 30, 1985
    Role: Principal Investigator
    USC Norris Comprehensive Cancer Center (Core) Grant
    NIH P30CA014089Apr 1, 1980 - Nov 30, 2021
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Faculty Mentoring

    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. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters. Nucleic Acids Res. 2024 Jul 08; 52(12):6850-6865. Hsu E, Hutchison K, Liu Y, Nicolet CM, Schreiner S, Zemke NR, Farnham PJ. PMID: 38726870; PMCID: PMC11229363.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    2. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am J Hum Genet. 2024 03 07; 111(3):487-508. Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, Amor DJ, Banka S, Basel DG, Buch LD, Carere DA, Carroll R, Clayton-Smith J, Crawford A, Dunø M, Faivre L, Gilfillan CP, Gold NB, Gripp KW, Hobson E, Holtz AM, Innes AM, Isidor B, Jackson A, Katsonis P, Amel Riazat Kesh L, Genomics England Research Consortium, Küry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, Németh AH, Østergaard E, Patel R, Pope K, Posey JE, Schnur RE, Shaw M, Stolerman E, Taylor JP, Wadman E, Wakeling E, White SM, Wong LC, Lupski JR, Lichtarge O, Corbett MA, Gecz J, Nicolet CM, Farnham PJ, Kim CH, Shinawi M. PMID: 38325380; PMCID: PMC10940019.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    3. m6A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer. NAR Cancer. 2023 Dec; 5(4):zcad054. Hodara E, Mades A, Swartz L, Iqbal M, Xu T, Bsteh D, Farnham PJ, Rhie SK, Goldkorn A. PMID: 38023731; PMCID: PMC10653028.
      View in: PubMed   Mentions:
    4. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol. 2022 07 26; 23(1):163. de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. PMID: 35883107; PMCID: PMC9316731.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    5. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3. ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 35474001; PMCID: PMC9095460.
      View in: PubMed   Mentions: 6     Fields:    
    6. FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer. Cancers (Basel). 2022 Mar 28; 14(7). Lu YT, Xu T, Iqbal M, Hsieh TC, Luo Z, Liang G, Farnham PJ, Rhie SK, Goldkorn A. PMID: 35406487; PMCID: PMC8996937.
      View in: PubMed   Mentions: 6  
    7. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet. 2020 09; 16(9):e1009023. Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK. PMID: 32925947; PMCID: PMC7515200.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    8. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 32728249; PMCID: PMC7410828.
      View in: PubMed   Mentions: 821     Fields:    Translation:HumansAnimalsCells
    9. Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters. Nucleic Acids Res. 2020 06 19; 48(11):5986-6000. Ni W, Perez AA, Schreiner S, Nicolet CM, Farnham PJ. PMID: 32406922; PMCID: PMC7293018.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    10. Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells. PLoS One. 2020; 15(2):e0228590. Luo Z, Farnham PJ. PMID: 32012197; PMCID: PMC6996832.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    11. A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun. 2019 09 12; 10(1):4154. Rhie SK, Perez AA, Lay FD, Schreiner S, Shi J, Polin J, Farnham PJ. PMID: 31515496; PMCID: PMC6742760.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    12. The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression. Sci Adv. 2019 07; 5(7):eaaw6710. Qian Y, Zhang L, Cai M, Li H, Xu H, Yang H, Zhao Z, Rhie SK, Farnham PJ, Shi J, Lu W. PMID: 31328168; PMCID: PMC6636982.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    13. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin. 2019 May 03; 12(1):26. O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ. PMID: 31053162; PMCID: PMC6498470.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    14. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel). 2019 Mar 07; 11(3). Luo Z, Rhie SK, Farnham PJ. PMID: 30866492; PMCID: PMC6468460.
      View in: PubMed   Mentions: 29  
    15. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv. 2018 12; 4(12):eaav8550. Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. PMID: 30555922; PMCID: PMC6292713.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    16. Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. J Cell Biochem. 2019 03; 120(3):3056-3070. Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE. PMID: 30548288; PMCID: PMC6476548.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    17. CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops. Genome Biol. 2018 10 08; 19(1):160. Guo Y, Perez AA, Hazelett DJ, Coetzee GA, Rhie SK, Farnham PJ. PMID: 30296942; PMCID: PMC6176514.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    18. ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters. Genome Res. 2018 Mar 01; 28(3):310-320. Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. PMID: 29429977; PMCID: PMC5848610.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    19. Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq). Methods Mol Biol. 2018; 1766:209-229. Rhie SK, Schreiner S, Farnham PJ. PMID: 29605855; PMCID: PMC6019634.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    20. A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13. Cell Rep. 2017 Nov 07; 21(6):1411-1417. Luo Z, Rhie SK, Lay FD, Farnham PJ. PMID: 29117547; PMCID: PMC5726543.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    21. 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. O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, Segal DJ. PMID: 28973434; PMCID: PMC5622328.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansCells
    22. 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. Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ. PMID: 27833659; PMCID: PMC5103450.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    23. 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Sci Rep. 2016 Mar 03; 6:22462. Cai M, Kim S, Wang K, Farnham PJ, Coetzee GA, Lu W. PMID: 26934861; PMCID: PMC4776156.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    24. 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. Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O'Geen H, Segal DJ, Farnham PJ. PMID: 26743005; PMCID: PMC4872074.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    25. 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. Tak YG, Farnham PJ. PMID: 26719772; PMCID: PMC4696349.
      View in: PubMed   Mentions: 156     Fields:    
    26. The PsychENCODE project. Nat Neurosci. 2015 Dec; 18(12):1707-12. PsychENCODE Consortium, 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. PMID: 26605881; PMCID: PMC4675669.
      View in: PubMed   Mentions: 229     Fields:    Translation:HumansAnimalsCells
    27. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol. 2015; 50(6):550-73. Yao L, Berman BP, Farnham PJ. PMID: 26446758; PMCID: PMC4666684.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    28. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015 May 21; 16:105. Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. PMID: 25994056; PMCID: PMC4460959.
      View in: PubMed   Mentions: 104     Fields:    Translation:HumansCells
    29. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 2015 Apr; 25(4):467-77. Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. PMID: 25747664; PMCID: PMC4381519.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansCells
    30. Altering cancer transcriptomes using epigenomic inhibitors. Epigenetics Chromatin. 2015; 8:9. Gaddis M, Gerrard D, Frietze S, Farnham PJ. PMID: 26191083; PMCID: PMC4506402.
      View in: PubMed   Mentions: 21     Fields:    
    31. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. Roadmap Epigenomics Consortium, 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. PMID: 25693563; PMCID: PMC4530010.
      View in: PubMed   Mentions: 3196     Fields:    Translation:HumansCells
    32. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363. 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. PMID: 25691127; PMCID: PMC4333717.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansAnimalsCells
    33. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18; 6:6351. 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. PMID: 25690954; PMCID: PMC4346612.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    34. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nat Commun. 2014 Nov 25; 5:5442. 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. PMID: 25421844; PMCID: PMC4385735.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    35. Functional annotation of colon cancer risk SNPs. Nat Commun. 2014 Sep 30; 5:5114. Yao L, Tak YG, Berman BP, Farnham PJ. PMID: 25268989; PMCID: PMC4200523.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansCells
    36. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol. 2014 Sep 20; 15(9):469. Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ. PMID: 25239471; PMCID: PMC4203885.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansCells
    37. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):E3366. 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 J, Weng Z, White KP, Hardison RC. PMID: 25275169; PMCID: PMC4143047.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    38. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res. 2014; 42(16):10856-68. Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ. PMID: 25122745; PMCID: PMC4176344.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    39. Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. BMC Genomics. 2014 Jun 24; 15:520. Frietze S, O'Geen H, Littlepage LE, Simion C, Sweeney CA, Farnham PJ, Krig SR. PMID: 24962896; PMCID: PMC4082627.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    40. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. 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. PMID: 24753594; PMCID: PMC4035993.
      View in: PubMed   Mentions: 331     Fields:    Translation:HumansCells
    41. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 2014 Jan; 10(1):e1004102. Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Ellipse/GAME-ON consortium, Practical consortium, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. PMID: 24497837; PMCID: PMC3907334.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansCells
    42. Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 2014; 6(5):493-501. Grimmer MR, Farnham PJ. PMID: 25431942; PMCID: PMC4259145.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    43. Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem. 2013 Nov 29; 288(48):34287-94. Blattler A, Farnham PJ. PMID: 24151070; PMCID: PMC3843044.
      View in: PubMed   Mentions: 120     Fields:    Translation:HumansAnimalsCells
    44. Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol. 2013 Oct; 14(10):1073-83. Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST. PMID: 24013668; PMCID: PMC3800053.
      View in: PubMed   Mentions: 70     Fields:    Translation:AnimalsCells
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    161. 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. Mack KJ, Cortner J, Mack P, Farnham PJ. PMID: 1323008.
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    162. 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. Buermeyer AB, Thompson NE, Strasheim LA, Burgess RR, Farnham PJ. PMID: 1569952; PMCID: PMC364397.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    163. The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter. Mol Cell Biol. 1992 Mar; 12(3):1054-63. Means AL, Slansky JE, McMahon SL, Knuth MW, Farnham PJ. PMID: 1545788; PMCID: PMC369537.
      View in: PubMed   Mentions: 70     Fields:    Translation:AnimalsCells
    164. 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. Kollmar R, Lindstrom MJ, Farnham PJ. PMID: 1346130.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    165. Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH3T3 fibroblasts. Cell Growth Differ. 1991 Sep; 2(9):465-73. Cortner J, Farnham PJ. PMID: 1721529.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    166. Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component. Gene Expr. 1991 May; 1(2):137-48. Farnham PJ, Cornwell MM. PMID: 1820211; PMCID: PMC5952208.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    167. Identification of the serum-responsive transcription initiation site of the zinc finger gene Krox-20. Mol Cell Biol. 1990 Jul; 10(7):3788-91. Cortner J, Farnham PJ. PMID: 2113176; PMCID: PMC360834.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    168. Characterization of the 5' end of the growth-regulated Syrian hamster CAD gene. Cell Growth Differ. 1990 Apr; 1(4):179-89. Farnham PJ, Kollmar R. PMID: 1982061.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    169. 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. Farnham PJ, Means AL. PMID: 2320003; PMCID: PMC362241.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    170. 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. Means AL, Farnham PJ. PMID: 2300058; PMCID: PMC360863.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansCells
    171. Identification of a new promoter upstream of the murine dihydrofolate reductase gene. Mol Cell Biol. 1989 Oct; 9(10):4568-70. Schilling LJ, Farnham PJ. PMID: 2479829; PMCID: PMC362546.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    172. In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene. Mol Cell Biol. 1986 Jul; 6(7):2392-401. Farnham PJ, Schimke RT. PMID: 3785199; PMCID: PMC367792.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    173. Murine dihydrofolate reductase transcripts through the cell cycle. Mol Cell Biol. 1986 Feb; 6(2):365-71. Farnham PJ, Schimke RT. PMID: 3785152; PMCID: PMC367525.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    174. Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle. J Biol Chem. 1985 Jun 25; 260(12):7675-80. Farnham PJ, Schimke RT. PMID: 2987264.
      View in: PubMed   Mentions: 49     Fields:    Translation:AnimalsCells
    175. 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. Farnham PJ, Abrams JM, Schimke RT. PMID: 2408272; PMCID: PMC397917.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    176. 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. McGrogan M, Simonsen CC, Smouse DT, Farnham PJ, Schimke RT. PMID: 2982814.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    177. 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. Hamkalo BA, Farnham PJ, Johnston R, Schimke RT. PMID: 3856243; PMCID: PMC397207.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    178. Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli. Cell. 1982 Jul; 29(3):945-51. Farnham PJ, Greenblatt J, Platt T. PMID: 6758952.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    179. 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. Farnham PJ, Platt T. PMID: 7041118; PMCID: PMC345886.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    180. 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. Christie GE, Farnham PJ, Platt T. PMID: 7027254; PMCID: PMC319752.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    181. 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. Farnham PJ, Platt T. PMID: 7012794; PMCID: PMC327222.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    182. A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs. Cell. 1980 Jul; 20(3):739-48. Farnham PJ, Platt T. PMID: 6998564.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    183. Effects of gentamicin on trypsin, chymotrypsin, and collagenase. J Infect Dis. 1978 Aug; 138(2):257-9. Asch HL, Farnham PJ. PMID: 210240.
      View in: PubMed   Mentions: 5     Fields:    
    184. A re-examination of the distributions of octopamine and phenylethanolamine in the aplysia nervous system. J Neurochem. 1978 May; 30(5):1173-6. Farnham PJ, Novak RA, McAdoo DJ. PMID: 351144.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
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