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Peggy Farnham, PhD

Title(s)Chair and Professor of Biochemistry & Molecular Medicine
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/NIGMS R01GM133450Apr 1, 2020 - Mar 31, 2024
    Role: Principal Investigator
    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 - May 31, 2015
    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
    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. 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. Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters. Nucleic Acids Res. 2020 May 14. Ni W, Perez AA, Schreiner S, Nicolet CM, Farnham PJ. PMID: 32406922.
      View in: PubMed   Mentions:    Fields:    
    2. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    4. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    5. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin. 2019 05 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    6. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel). 2019 Mar 07; 11(3). Luo Z, Rhie SK, Farnham PJ. PMID: 30866492.
      View in: PubMed   Mentions:
    7. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    8. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    10. 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. Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. PMID: 29429977.
      View in: PubMed   Mentions: 3     Fields:    
    11. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    12. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    13. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    14. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    15. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    16. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    17. 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.
      View in: PubMed   Mentions: 58     Fields:    
    18. The PsychENCODE project. Nat Neurosci. 2015 Dec; 18(12):1707-12. 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.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansAnimalsCells
    19. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    20. 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.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    21. 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.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    22. Altering cancer transcriptomes using epigenomic inhibitors. Epigenetics Chromatin. 2015; 8:9. Gaddis M, Gerrard D, Frietze S, Farnham PJ. PMID: 26191083.
      View in: PubMed   Mentions: 13     Fields:    
    23. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. 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.
      View in: PubMed   Mentions: 1291     Fields:    Translation:HumansCells
    24. 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.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    25. 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.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    26. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    27. Functional annotation of colon cancer risk SNPs. Nat Commun. 2014 Sep 30; 5:5114. Yao L, Tak YG, Berman BP, Farnham PJ. PMID: 25268989.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    28. 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.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    29. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    30. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    31. 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.
      View in: PubMed   Mentions: 190     Fields:    Translation:HumansCells
    32. 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, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. PMID: 24497837.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansCells
    33. Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 2014; 6(5):493-501. Grimmer MR, Farnham PJ. PMID: 25431942.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    34. 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.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimalsCells
    35. 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.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    36. 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. 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. PMID: 23804400.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    37. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 2013 Jul; 45(7):836-41. 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. PMID: 23708189.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansCells
    38. ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. Epigenetics Chromatin. 2013 May 21; 6(1):13. Blattler A, Yao L, Wang Y, Ye Z, Jin VX, Farnham PJ. PMID: 23693142.
      View in: PubMed   Mentions: 25     Fields:    
    39. 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. Frietze S, Wang R, Yao L, Tak YG, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX. PMID: 22951069.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    40. Spark: a navigational paradigm for genomic data exploration. Genome Res. 2012 Nov; 22(11):2262-9. Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. PMID: 22960372.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    41. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      View in: PubMed   Mentions: 4590     Fields:    Translation:HumansAnimalsCells
    42. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489(7414):91-100. 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. PMID: 22955619.
      View in: PubMed   Mentions: 552     Fields:    Translation:HumansCells
    43. 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. Farnham PJ. PMID: 22451669.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    44. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. 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. PMID: 22955991.
      View in: PubMed   Mentions: 500     Fields:    Translation:HumansAnimals
    45. Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Res. 2012 Sep; 40(16):7690-704. Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX. PMID: 22675074.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    46. 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. Jung CJ, Iyengar S, Blahnik KR, Jiang JX, Tahimic C, Torok NJ, de vere White RW, Farnham PJ, Zern M. PMID: 22622027.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    47. The transcription factor encyclopedia. Genome Biol. 2012; 13(3):R24. 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. PMID: 22458515.
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    106. In vivo assays to examine transcription factor localization and target gene specificity. Methods. 2002 Jan; 26(1):1-2. Farnham PJ. PMID: 12054898.
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    107. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods. 2002 Jan; 26(1):37-47. Weinmann AS, Farnham PJ. PMID: 12054903.
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    108. 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. Eberhardy SR, Farnham PJ. PMID: 11673469.
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    109. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol Cell Biol. 2001 Oct; 21(20):6820-32. Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ. PMID: 11564866.
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    110. Mre11 complex and DNA replication: linkage to E2F and sites of DNA synthesis. Mol Cell Biol. 2001 Sep; 21(17):6006-16. Maser RS, Mirzoeva OK, Wells J, Olivares H, Williams BR, Zinkel RA, Farnham PJ, Petrini JH. PMID: 11486038.
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    111. Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. J Mol Biol. 2001 May 25; 309(1):99-120. Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ. PMID: 11491305.
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    112. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene. 2001 May 10; 20(21):2704-12. Graveel CR, Jatkoe T, Madore SJ, Holt AL, Farnham PJ. PMID: 11420682.
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    113. 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. Albert T, Wells J, Funk JO, Pullner A, Raschke EE, Stelzer G, Meisterernst M, Farnham PJ, Eick D. PMID: 11279041.
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    114. Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation. J Biol Chem. 2000 Oct 27; 275(43):33798-805. Eberhardy SR, D'Cunha CA, Farnham PJ. PMID: 10931841.
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    115. Direct recruitment of N-myc to target gene promoters. Mol Carcinog. 2000 Oct; 29(2):76-86. Mac SM, D'Cunha CA, Farnham PJ. PMID: 11074604.
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    116. Target gene specificity of E2F and pocket protein family members in living cells. Mol Cell Biol. 2000 Aug; 20(16):5797-807. Wells J, Boyd KE, Fry CJ, Bartley SM, Farnham PJ. PMID: 10913163.
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    117. Exogenous E2F expression is growth inhibitory before, during, and after cellular transformation. Oncogene. 2000 Apr 27; 19(18):2257-68. Lee TA, Farnham PJ. PMID: 10822376.
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    118. CAD, a c-Myc target gene, is not deregulated in Burkitt's lymphoma cell lines. Mol Carcinog. 2000 Feb; 27(2):84-96. Mac SM, Farnham PJ. PMID: 10657901.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    119. Coexamination of site-specific transcription factor binding and promoter activity in living cells. Mol Cell Biol. 1999 Dec; 19(12):8393-9. Boyd KE, Farnham PJ. PMID: 10567564.
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    120. Context-dependent transcriptional regulation. J Biol Chem. 1999 Oct 15; 274(42):29583-6. Fry CJ, Farnham PJ. PMID: 10514422.
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    121. Identification of target genes of oncogenic transcription factors. Proc Soc Exp Biol Med. 1999 Oct; 222(1):9-28. Boyd KE, Farnham PJ. PMID: 10510243.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    122. 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. Lukas ER, Bartley SM, Graveel CR, Diaz ZM, Dyson N, Harlow E, Yamasaki L, Farnham PJ. PMID: 10449036.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    123. Activation of the murine dihydrofolate reductase promoter by E2F1. A requirement for CBP recruitment. J Biol Chem. 1999 May 28; 274(22):15883-91. Fry CJ, Pearson A, Malinowski E, Bartley SM, Greenblatt J, Farnham PJ. PMID: 10336493.
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    124. Characterization of the 3' untranslated region of mouse E2F1 mRNA. Gene. 1998 Nov 26; 223(1-2):355-60. Bartley SM, Szakaly RJ, Farnham PJ. PMID: 9858765.
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    125. 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. Boyd KE, Wells J, Gutman J, Bartley SM, Farnham PJ. PMID: 9811896.
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    126. E2F-mediated growth regulation requires transcription factor cooperation. J Biol Chem. 1997 Jul 18; 272(29):18367-74. van Ginkel PR, Hsiao KM, Schjerven H, Farnham PJ. PMID: 9218478.
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    127. Myc versus USF: discrimination at the cad gene is determined by core promoter elements. Mol Cell Biol. 1997 May; 17(5):2529-37. Boyd KE, Farnham PJ. PMID: 9111322.
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    128. Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain. Mol Cell Biol. 1997 Apr; 17(4):1966-76. Fry CJ, Slansky JE, Farnham PJ. PMID: 9121444.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    129. Conclusions and future directions. Curr Top Microbiol Immunol. 1996; 208:129-37. Farnham PJ. PMID: 8575211.
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    130. Introduction to the E2F family: protein structure and gene regulation. Curr Top Microbiol Immunol. 1996; 208:1-30. Slansky JE, Farnham PJ. PMID: 8575210.
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    131. Transcriptional regulation of the dihydrofolate reductase gene. Bioessays. 1996 Jan; 18(1):55-62. Slansky JE, Farnham PJ. PMID: 8593164.
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    132. 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. Bennett LM, Farnham PJ, Drinkwater NR. PMID: 7546224.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    133. 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. Miltenberger RJ, Sukow KA, Farnham PJ. PMID: 7739536.
      View in: PubMed   Mentions: 55     Fields:    Translation:AnimalsCells
    134. The bidirectionally transcribed dihydrofolate reductase and rep-3a promoters are growth regulated by distinct mechanisms. Cell Growth Differ. 1995 May; 6(5):541-8. Schilling LJ, Farnham PJ. PMID: 7647037.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    135. 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. Miltenberger RJ, Farnham PJ, Smith DE, Stommel JM, Cornwell MM. PMID: 7647038.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    136. 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. Buermeyer AB, Strasheim LA, McMahon SL, Farnham PJ. PMID: 7896826.
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    137. 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. Schilling LJ, Farnham PJ. PMID: 7520569.
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    138. Multiple DNA elements are required for the growth regulation of the mouse E2F1 promoter. Genes Dev. 1994 Jul 01; 8(13):1526-37. Hsiao KM, McMahon SL, Farnham PJ. PMID: 7958837.
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    139. Cloning, chromosomal location, and characterization of mouse E2F1. Mol Cell Biol. 1994 Mar; 14(3):1861-9. Li Y, Slansky JE, Myers DJ, Drinkwater NR, Kaelin WG, Farnham PJ. PMID: 8114719.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    140. 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. Kollmar R, Sukow KA, Sponagle SK, Farnham PJ. PMID: 7905000.
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    141. Transcriptional regulation of the dihydrofolate reductase/rep-3 locus. Crit Rev Eukaryot Gene Expr. 1994; 4(1):19-53. Schilling LJ, Farnham PJ. PMID: 7987046.
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    142. The role of E2F in the mammalian cell cycle. Biochim Biophys Acta. 1993 Aug 23; 1155(2):125-31. Farnham PJ, Slansky JE, Kollmar R. PMID: 8357823.
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    143. 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. Miltenberger RJ, Cortner J, Farnham PJ. PMID: 8340392.
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    144. Site-specific initiation of transcription by RNA polymerase II. Proc Soc Exp Biol Med. 1993 Jun; 203(2):127-39. Kollmar R, Farnham PJ. PMID: 8502653.
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    145. 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. Slansky JE, Li Y, Kaelin WG, Farnham PJ. PMID: 8441401.
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    146. Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties. Cell. 1992 Jul 24; 70(2):351-64. Kaelin WG, Krek W, Sellers WR, DeCaprio JA, Ajchenbaum F, Fuchs CS, Chittenden T, Li Y, Farnham PJ, Blanar MA. PMID: 1638635.
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    147. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    148. 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.
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    149. 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.
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    150. 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.
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    151. 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.
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    152. 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.
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    153. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    154. 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
    155. 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.
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    156. 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.
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    157. 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.
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    158. 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.
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    159. Murine dihydrofolate reductase transcripts through the cell cycle. Mol Cell Biol. 1986 Feb; 6(2):365-71. Farnham PJ, Schimke RT. PMID: 3785152.
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    160. 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.
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    161. 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.
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    162. 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.
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    163. 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.
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    164. 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.
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    165. 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.
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    166. 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.
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    167. 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.
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    168. 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.
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    169. Effects of gentamicin on trypsin, chymotrypsin, and collagenase. J Infect Dis. 1978 Aug; 138(2):257-9. Asch HL, Farnham PJ. PMID: 210240.
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    170. 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.
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