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Peggy Farnham, PhD

TitleChair and Professor of Biochemistry & Molecular Medicine
InstitutionUniversity of Southern California
DepartmentBiochemistry and Molecular Biology
AddressNRT 511 B 1450 Biggy Street
Health Sciences Campus
Los Angeles CA 90089
Phone+1 323 442 8015
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    Other Positions
    TitleW.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
    THE ROLE OF FAF KINASE IN CELL PROLIFERATION
    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
    TRANSCRIPTIONAL REGULATION OF GROWTH-RELATED GENES
    NIH/NCI R29CA045240Apr 1, 1987 - Mar 31, 1992
    Role: Principal Investigator
    CELL CYCLE REGULATION OF THE DIHYDROFOLATE REDUCTASE GEN
    NIH/NIGMS F32GM008853Jun 30, 1985
    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. 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 Oct 08; 19(1):160. PMID: 30296942.
      View in: PubMed
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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.
    8. 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.
    9. 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.
    10. The PsychENCODE project. Nat Neurosci. 2015 Dec; 18(12):1707-12. PMID: 26605881.
      View in: PubMed
    11. 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.
    12. 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.
    13. 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.
    14. Gaddis M, Gerrard D, Frietze S, Farnham PJ. Altering cancer transcriptomes using epigenomic inhibitors. Epigenetics Chromatin. 2015; 8:9. PMID: 26191083; PMCID: PMC4506402.
    15. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
    16. 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.
    17. 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.
    18. 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.
    19. 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.
    20. 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
    21. 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.
    22. 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.
    23. 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.
    24. Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 2014 Jan; 10(1):e1004102. PMID: 24497837; PMCID: PMC3907334.
    25. Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 2014; 6(5):493-501. PMID: 25431942; PMCID: PMC4259145.
    26. 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.
    27. 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.
    28. 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.
    29. 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.
    30. 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.
    31. 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.
    32. 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.
    33. 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.
    34. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      View in: PubMed
    35. 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.
    36. 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.
    37. 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.
    38. 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.
    39. 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.
    40. 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.
    41. 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.
    42. 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.
    43. 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.
    44. 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.
    45. 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.
    46. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
      View in: PubMed
    47. 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.
    48. 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.
      View in: PubMed
    49. 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.
    50. 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.
    51. Frietze S, Farnham PJ. Transcription factor effector domains. Subcell Biochem. 2011; 52:261-77. PMID: 21557087; PMCID: PMC4151296.
    52. 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
    53. 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.
    54. 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.
    55. 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. 2010 Oct 07; 29(40):5500-10. PMID: 20661224; PMCID: PMC4256946.
    56. Komashko VM, Farnham PJ. 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics. 2010 Apr; 5(3):229-40. PMID: 20305384.
      View in: PubMed
    57. O'Geen H, Frietze S, Farnham PJ. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol. 2010; 649:437-55. PMID: 20680851; PMCID: PMC4151297.
    58. 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. Mol Cell. 2009 Nov 25; 36(4):667-81. PMID: 19941826; PMCID: PMC2784893.
    59. 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 Res. 2010 Jan; 38(3):e13. PMID: 19906703; PMCID: PMC2817454.
    60. Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010 Jan 08; 285(2):1393-403. PMID: 19887448; PMCID: PMC2801265.
    61. 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. 2009 Dec 01; 25(23):3191-3. PMID: 19797408; PMCID: PMC2778340.
    62. Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009 Sep; 10(9):605-16. PMID: 19668247; PMCID: PMC2846386.
    63. 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 Res. 2008 Dec 01; 68(23):9654-62. PMID: 19047142; PMCID: PMC2637654.
    64. Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res. 2008 Nov; 18(11):1763-77. PMID: 18836037; PMCID: PMC2577861.
    65. Acevedo LG, Bieda M, Green R, Farnham PJ. Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res. 2008 Apr 15; 68(8):2641-51. PMID: 18413731; PMCID: PMC2567918.
    66. 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 Res. 2008 Apr; 18(4):521-32. PMID: 18347325; PMCID: PMC2279240.
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    69. 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. Proc Natl Acad Sci U S A. 2007 Dec 04; 104(49):19416-21. PMID: 18042715; PMCID: PMC2148304.
    70. 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 Res. 2007 Nov; 17(11):1550-61. PMID: 17908821; PMCID: PMC2045138.
    71. 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. 2007 Jun 29; 129(7):1311-23. PMID: 17604720; PMCID: PMC2084369.
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    73. 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 Res. 2007 Jun; 17(6):807-17. PMID: 17567999; PMCID: PMC1891340.
    74. 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 Genet. 2007 Jun; 3(6):e89. PMID: 17542650; PMCID: PMC1885280.
    75. 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. J Biol Chem. 2007 Mar 30; 282(13):9703-12. PMID: 17259635; PMCID: PMC2269729.
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    77. 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 Res. 2006 Dec; 16(12):1585-95. PMID: 17053090; PMCID: PMC1665642.
    78. Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 2006 Dec; 16(12):1455-64. PMID: 17053094.
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    79. 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 Res. 2006 Jul; 16(7):890-900. PMID: 16751344; PMCID: PMC1484456.
    80. 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 Res. 2006 May; 16(5):595-605. PMID: 16606705; PMCID: PMC1457046.
    81. Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res. 2005; 33(9):2952-61. PMID: 15911630; PMCID: PMC1137027.
    82. Kuzmichev A, Margueron R, Vaquero A, Preissner TS, Scher M, Kirmizis A, Ouyang X, Brockdorff N, Abate-Shen C, Farnham P, Reinberg D. Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation. Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):1859-64. PMID: 15684044; PMCID: PMC548563.
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    84. Lavrrar JL, Farnham PJ. The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. J Biol Chem. 2004 Oct 29; 279(44):46343-9. PMID: 15328355.
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    85. 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 Dev. 2004 Jul 01; 18(13):1592-605. PMID: 15231737; PMCID: PMC443521.
    86. 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. 2004 Apr; 20(4):477-94. PMID: 15084276.
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    88. Oberley MJ, Inman DR, Farnham PJ. E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. J Biol Chem. 2003 Oct 24; 278(43):42466-76. PMID: 12909625.
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    89. 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. Curr Biol. 2003 May 13; 13(10):882-6. PMID: 12747840.
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    90. Graveel CR, Harkins-Perry SR, Acevedo LG, Farnham PJ. Identification and characterization of CRG-L2, a new marker for liver tumor development. Oncogene. 2003 Mar 20; 22(11):1730-6. PMID: 12642876.
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    91. 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. 2003 Mar 13; 22(10):1445-60. PMID: 12629508.
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    92. Kirmizis A, Bartley SM, Farnham PJ. Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther. 2003 Jan; 2(1):113-21. PMID: 12533679.
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    93. Oberley MJ, Farnham PJ. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol. 2003; 371:577-96. PMID: 14712730.
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    94. Eberhardy SR, Farnham PJ. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem. 2002 Oct 18; 277(42):40156-62. PMID: 12177005.
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    95. Wells J, Graveel CR, Bartley SM, Madore SJ, Farnham PJ. The identification of E2F1-specific target genes. Proc Natl Acad Sci U S A. 2002 Mar 19; 99(6):3890-5. PMID: 11904439; PMCID: PMC122619.
    96. 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 Dev. 2002 Jan 15; 16(2):235-44. PMID: 11799066; PMCID: PMC155318.
    97. Farnham PJ. In vivo assays to examine transcription factor localization and target gene specificity. Methods. 2002 Jan; 26(1):1-2. PMID: 12054898.
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    100. Eberhardy SR, Farnham PJ. c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. J Biol Chem. 2001 Dec 21; 276(51):48562-71. PMID: 11673469.
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    101. Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol Cell Biol. 2001 Oct; 21(20):6820-32. PMID: 11564866; PMCID: PMC99859.
    102. 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. Mol Cell Biol. 2001 Sep; 21(17):6006-16. PMID: 11486038; PMCID: PMC87318.
    103. 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. J Mol Biol. 2001 May 25; 309(1):99-120. PMID: 11491305.
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    104. Graveel CR, Jatkoe T, Madore SJ, Holt AL, Farnham PJ. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene. 2001 May 10; 20(21):2704-12. PMID: 11420682.
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    105. 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. J Biol Chem. 2001 Jun 08; 276(23):20482-90. PMID: 11279041.
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    106. Eberhardy SR, D'Cunha CA, Farnham PJ. Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation. J Biol Chem. 2000 Oct 27; 275(43):33798-805. PMID: 10931841.
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    107. Mac SM, D'Cunha CA, Farnham PJ. Direct recruitment of N-myc to target gene promoters. Mol Carcinog. 2000 Oct; 29(2):76-86. PMID: 11074604.
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    108. Wells J, Boyd KE, Fry CJ, Bartley SM, Farnham PJ. Target gene specificity of E2F and pocket protein family members in living cells. Mol Cell Biol. 2000 Aug; 20(16):5797-807. PMID: 10913163; PMCID: PMC86057.
    109. Lee TA, Farnham PJ. Exogenous E2F expression is growth inhibitory before, during, and after cellular transformation. Oncogene. 2000 Apr 27; 19(18):2257-68. PMID: 10822376.
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    110. Mac SM, Farnham PJ. CAD, a c-Myc target gene, is not deregulated in Burkitt's lymphoma cell lines. Mol Carcinog. 2000 Feb; 27(2):84-96. PMID: 10657901.
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    111. Boyd KE, Farnham PJ. Coexamination of site-specific transcription factor binding and promoter activity in living cells. Mol Cell Biol. 1999 Dec; 19(12):8393-9. PMID: 10567564; PMCID: PMC84934.
    112. Fry CJ, Farnham PJ. Context-dependent transcriptional regulation. J Biol Chem. 1999 Oct 15; 274(42):29583-6. PMID: 10514422.
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    113. Boyd KE, Farnham PJ. Identification of target genes of oncogenic transcription factors. Proc Soc Exp Biol Med. 1999 Oct; 222(1):9-28. PMID: 10510243.
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    114. 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. Mol Carcinog. 1999 Aug; 25(4):295-303. PMID: 10449036.
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    115. 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. J Biol Chem. 1999 May 28; 274(22):15883-91. PMID: 10336493.
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    116. Bartley SM, Szakaly RJ, Farnham PJ. Characterization of the 3' untranslated region of mouse E2F1 mRNA. Gene. 1998 Nov 26; 223(1-2):355-60. PMID: 9858765.
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    117. Boyd KE, Wells J, Gutman J, Bartley SM, Farnham PJ. c-Myc target gene specificity is determined by a post-DNAbinding mechanism. Proc Natl Acad Sci U S A. 1998 Nov 10; 95(23):13887-92. PMID: 9811896; PMCID: PMC24949.
    118. van Ginkel PR, Hsiao KM, Schjerven H, Farnham PJ. E2F-mediated growth regulation requires transcription factor cooperation. J Biol Chem. 1997 Jul 18; 272(29):18367-74. PMID: 9218478.
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    120. Fry CJ, Slansky JE, Farnham PJ. Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain. Mol Cell Biol. 1997 Apr; 17(4):1966-76. PMID: 9121444; PMCID: PMC232043.
    121. Slansky JE, Farnham PJ. Transcriptional regulation of the dihydrofolate reductase gene. Bioessays. 1996 Jan; 18(1):55-62. PMID: 8593164.
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    122. Slansky JE, Farnham PJ. Introduction to the E2F family: protein structure and gene regulation. Curr Top Microbiol Immunol. 1996; 208:1-30. PMID: 8575210.
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    124. 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. Mol Carcinog. 1995 Sep; 14(1):46-52. PMID: 7546224.
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    125. 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. Mol Cell Biol. 1995 May; 15(5):2527-35. PMID: 7739536; PMCID: PMC230483.
    126. 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 Differ. 1995 May; 6(5):549-56. PMID: 7647038.
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    127. Schilling LJ, Farnham PJ. The bidirectionally transcribed dihydrofolate reductase and rep-3a promoters are growth regulated by distinct mechanisms. Cell Growth Differ. 1995 May; 6(5):541-8. PMID: 7647037.
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    128. 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. J Biol Chem. 1995 Mar 24; 270(12):6798-807. PMID: 7896826.
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    129. Schilling LJ, Farnham PJ. Inappropriate transcription from the 5' end of the murine dihydrofolate reductase gene masks transcriptional regulation. Nucleic Acids Res. 1994 Aug 11; 22(15):3061-8. PMID: 7520569; PMCID: PMC310276.
    130. Hsiao KM, McMahon SL, Farnham PJ. Multiple DNA elements are required for the growth regulation of the mouse E2F1 promoter. Genes Dev. 1994 Jul 01; 8(13):1526-37. PMID: 7958837.
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    131. Li Y, Slansky JE, Myers DJ, Drinkwater NR, Kaelin WG, Farnham PJ. Cloning, chromosomal location, and characterization of mouse E2F1. Mol Cell Biol. 1994 Mar; 14(3):1861-9. PMID: 8114719; PMCID: PMC358544.
    132. Kollmar R, Sukow KA, Sponagle SK, Farnham PJ. Start site selection at the TATA-less carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter. J Biol Chem. 1994 Jan 21; 269(3):2252-7. PMID: 7905000.
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    133. Schilling LJ, Farnham PJ. Transcriptional regulation of the dihydrofolate reductase/rep-3 locus. Crit Rev Eukaryot Gene Expr. 1994; 4(1):19-53. PMID: 7987046.
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    134. Farnham PJ, Slansky JE, Kollmar R. The role of E2F in the mammalian cell cycle. Biochim Biophys Acta. 1993 Aug 23; 1155(2):125-31. PMID: 8357823.
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    135. Miltenberger RJ, Cortner J, Farnham PJ. An inhibitory Raf-1 mutant suppresses expression of a subset of v-raf-activated genes. J Biol Chem. 1993 Jul 25; 268(21):15674-80. PMID: 8340392.
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    136. 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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    137. 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.
    138. 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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    139. 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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    140. 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.
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    142. 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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    143. 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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    144. 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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    145. 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.
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    147. 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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    148. 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.
    149. 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.
    150. 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.
    151. 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.
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    153. 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.
    154. 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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    155. 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.
    156. 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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    157. 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.
    158. 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.
    159. 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.
    160. 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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    161. 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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    162. 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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