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Publications

1

Hodara, Mades, Swartz, Iqbal, Xu, Bsteh, Farnham, Rhie, Goldkorn. M6A Epitranscriptome Analysis Reveals Differentially Methylated Transcripts That Drive Early Chemo-Resistance in Bladder Cancer; In press, at Nucleic Acids Research- Cancer.link
2de Mendoza, Nguyen, Ford, Poppe, Buckberry, Pflueger, Grimmer, Stolzenburg, Bogdanovic, Oshlack, Farnham, Blancafort, Lister. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol. 23:163, 2022. PMID: 35883107.link
3Lu, Xu, Iqbal, Hsieh, Luo, Liang, Farnham, Rhie, Goldkorn.  FOXC1 binds enhancers and promotes cisplatin resistance in bladder cancer. Cancers. 14:1717, 2022. PMID: 35406487.link
4Hu, Won, Mah, Park, Kassim, Spiess, Kozlenkov, Crowley, Pochareddy, The PsychENCODE Consortium*, Li, Dracheva, Sestan, Akbarian, Geschwind. Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders.  Nat Commun. 12:3968, 2021. PMID: 34172755. Dr. Farnham was a PI in the PsychENCODE Consortium.link
5Mullen, Yan, Kang, Zhou, Borok, Marconett, Farnham, Offringa, Rhie. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet. 16:e1009023, 2020. PMID: 32925947. link
6ENCODE Project Consortium.  Perspectives on ENCODE. Nature. 583:693-698, 2020. PMID: 32728248.link
7ENCODE Project Consortium, Moore, … Farnham… Weng. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583:699-710, 2020. PMID: 32728249.link
8Ni, Perez, Schreiner, Nicolet, Farnham. Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters. Nucleic Acids Res. 48:5986-6000, 2020. PMID: 32406922.link
9Luo, Farnham. Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells. PLoS One 15:e0228590, 2020. PMID: 32012197. link
10Rhie, Perez, Lay, Schreiner, Shi, Polin, Farnham. A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun. 10:4154, 2019. PMID: 31515496. 
11Luo, Rhie, Farnham. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers. 11. 2019. pii: E323. PMID:30866492.
12Qian, Zhang, Cai, Li, Xu, Yang, Zhao, Rhie, Farnham, Shi, Lu.The prostate cancer risk variant rs55958994 regulates multiple genes expression through extreme long-range chromatin interaction to control tumor progression. Sci Adv. 5:eaaw6710. 2019. PMID:31328168.
13O’Geen, Bates, Carter, Nisson, Halmai, Fink, Rhie, Farnham, Segal. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin. 12:26, 2019. PMID:31053162.
14Gerrard, Wang, Gaddis, Zhou, Wang, Witt, Lin, Farnham, Jin, Frietze. Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. J Cell Biochem 120:3056-3070, 2019. PMID: 30548288. 
15Rhie SK, Schreiner S, Farnham. Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq). Methods Mol Biol. 1766:209-229, 2018. PMID:29605855. 
16Rhie, Schreiner, Witt, Armoskus, Lay, Camarena, Spitsyna, Guo, Berman, Evgrafov, Knowles, Farnham. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv.4:eaav8550. 2018. PMID: 30555922.
17Wang, Liu, Warrell, Won, Shi, Navarro, Clarke, Gu, Emani, Yang, Xu, Gandal, Lou, Zhang, Park, Yan, Rhie, Manakongtreecheep, Zhou, Nathan, Peters, Mattei, Fitzgerald, Brunetti, Moore, Jiang, Girdhar, Hoffman, Kalayci, Gümüş, Crawford, PsychENCODE Consortium, Roussos, Akbarian, Jaffe, White, Weng, Sestan, Geschwind, Knowles, Gerstein. Comprehensive functional genomic resource and integrative model for the human brain. Science 362. pii: eaat8464. 2018. PMID:30545857. 
18Amiri, Coppola, Scuderi, Wu, Roychowdhury, Liu, Pochareddy, Shin, Safi, Song, Zhu, Sousa; PsychENCODE Consortium, Gerstein, Crawford, Sestan, Abyzov, Vaccarino*. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science 362. pii: eaat6720. 2018. PMID: 30545853. 
19Li, Santpere, Imamura Kawasawa, Evgrafov, Gulden, Pochareddy,Sunkin, Li, Shin, Zhu, Sousa, Werling, Kitchen, Kang,Pletikos, Choi, Muchnik, Xu, Wang, Lorente-Galdos, Liu,Giusti-Rodríguez, Wo, de Leeuw, Pardiñas; BrainSpan Consortium; PsychENCODE Consortium; PsychENCODE Developmental Subgroup, Hu, Jin, Li, Owen, O’Donovan, Walters, Posthuma, Levitt, Weinberger, Hyde, Kleinman, Geschwind, Hawrylycz, State, Sanders, Sullivan, Gerstein, Lein, Knowles, Sestan. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362. 2018. pii: eaat7615. PMID: 30545854. 
20Gandal, Zhang, Hadjimichael , Walker, Chen, Liu, Won, van Bakel, Varghese, Wang, Shieh, Haney, Parhami, Belmont, Kim, Moran Losada, Khan, Mleczko, Xia, Dai, Wang, Yang, Xu, Fish, Hof, Warrell, Fitzgerald, White, Jaffe; PsychENCODE Consortium, Peters, Gerstein, Liu, Iakoucheva, Pinto, Geschwind. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science 362. pii: eaat8127. 2018. PMID:30545856. 
21Guo, Perez, Hazelett, Coetzee, Rhie, Farnham. CRISPR-mediated deletion of prostate cancer risk-associated CTCF sites identifies repressive chromatin loops. Genome Biology 19:160, 2018. PMID: 30296942. 
22Rhie, Yao, Witt, Schreiner, Luo, Farnham. 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 Research. 28: 310-320, 2018.  PMID:29429977.
23Luo, Rhie, Lay, Farnham. A prostate cancer risk element functions as a repressive loop that regulates HOXA13. Cell Reports. 21:1411-1417, 2017. PMID:29117547.
24O’Geen, Ren, Nicolet, Perez, Halmai, Le, Mackay, Farnham, Segal. dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression Nucleic Acids Res. 2017. doi.org/10.1093/nar/gkx578.
25Rhie, Guo, Yao, Shen, Coetzee, Laird, Farnham.  Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin. 9:50, 2016. PMID:27833659.
26Cai, Kim, Wang, Coetzee, Farnham, Lu. 4C revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Scientific Reports 6:22462, 2016. PMID:26934861.
27Tak, Farnham. 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 Dec 30;8:57. doi: 10.1186/s13072-015-0050-4. PMID: 26719772
28The PsychENCODE Project Consortium. Nat Neurosci. 2015 Nov 25;18(12):1707-12. doi: 10.1038/nn.4156. PMID:26605881
29Yao, Berman, Farnham. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol. 2015 Oct 8:1-24. PMID:26446758
30Tak, Hung, Yao, Grimmer, Do, Bhakta, O’Geen, Segal, Farnham. 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 Jan 6. pii: gkv1530. PMID:26743005
31Yao, Shen, Laird, Farnham, Berman. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 16:105, 2015. PMID: 25994056.
32Gaddis, Gerrard, Frietze, Farnham. Altering cancer transcriptomes using epigenomic inhibitors. Epigenomics and Chromatin 8:9, 2015. PMID: 26191083.
33Kundaje, Meuleman, Ernst, Bilenky, Yen, Wang, Ward, Sarkar, Quon, Kheradpour, Heravi-Moussavi, Coarfa, Harris, Ziller, Schultz, Eaton, Pfenning, Wang, Polak, Karlic, Amin, Wu, Sandstrom, Whitaker, Elliott, Lowdon, Onuchic, Shoresh, Epstein, Feizi, Gjoneska, Zhang, Bansal, Leung, Xie, Hawkins, Rajagopal, Ray, Wu, Kulkarni, Lister, Hong, Gascard, Carles, Mungall, Moore, Chau, Tam, Zhou, Li, Stevens, Zhang, Mercer, Neph, Siebenthall, Thurman, Canfield, Hansen, Kaul, Sabo, Beaudet, Boyer, De Jager, Farnham, Fisher, Haussler, Jones, Li, Marra, Sunyaev, Thomson, Tlsty, Tsai, Wang, Waterland, Zhang, Bernstein, Costello, Ecker, Hirst, Meissner, Milosavljevic, Ren, Stamatoyannopoulos, Wang, Kellis. Integrative analysis of 111 reference human epigenomes. Nature 518: 317-330, 2015. PMID: 25693563.
34Elliott, Hong, Zhou, Xie, Coarfa, Bell, Maire, Ligon, Gascard, Kadlecek, Weiss, Tlsty, Harris, Stormo, Schalkwyk, Mill, Farnham, Hirst, Kellis, Marra, Milosavljevic, Wang, Costello. Intermediate methylation is an evolutionarily conserved signature of genome regulation. Nat Commun. 6: 6363,  2015. PMID: 25691127.
35Gascard, Bilenky, Sigaroudinia, Zhao, Delaney, Tam, Kamoh, Cho, Griffith, Chu , Robertson, Cheung, Li, Li, Heravi-Moussavi, Carles, Nagarajan, Hong, Echipare , O’Geen, Hangauer, Cheng, Neel, McManus, Moore, Mungall, Ziv, Wang, Farnham, Jones, Marra, Tlsty, Costello, Hirst. Epigenetic and transcriptional determinants of mammary gland development. Nat Commun. 6: 6351, 2015. PMID: 25690954.
36Lay, Liu, Kelly, Witt, Farnham, Jones, Berman. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Research 25:467-477, 2015. PMID: 25747664.
37Lowdon, Zhang, Bilenky, Mauro, Li, Gascard, Sigaroudinia, Farnham, Bastian , Tlsty, Marra, Hirst, Costello, Wang, Cheng. Regulatory Network Decoded from Epigenomes of Surface Ectoderm-Derived Cell Types. Nat Commun. 2014 5:5442, 2014. PMID:25421844.
38Blattler, Yao, Witt, Guo, Nicolet, Berman, Farnham. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biology, 15:469, 2014. PMID:25239471.
39Grimmer, Farnham. Can Genome Engineering Be Used to Target Cancer-Associated Enhancers? Epigenomics 6:493-501, 2014. PMID:25431942.
40Yao L, Tak YG, Berman BP, Farnham PJ. Functional annotation of colon cancer risk SNPs. Nature Communications, 5:5114, 2014. PMID: 25268989.
41Frietze S, O’Geen H, Simion C, Littlepage LE, Sweeney CA, Farnham PJ, Krig SR. Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. BMC Genomics 15:520, 2014. PMID:24962896.
42Grimmer 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. 42:10856-10868. PMID:25122745. 
43Kellis 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. Science 111:6131-6138, 2014. PMID:24753594
44Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci. PLOS Genetics, 10:e1004102, 2014. PMID:24497837.
45Farnham PJ. The ENCODE Project. McGraw-Hill Yearbook of Science & Technology, 104-107, 2014.
46Blattler A, Farnham PJ. Crosstalk between site-specific transcription factors and DNA methylation.  J Biol Chem. 288:34287-34294, 2013. PMID:24151070.
47Schjerven H, McLaughlin J, Frietze S, Cheng D, Wadsworth S, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST. Differential regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nature Methods, 10:992-995., 2013. PMID:23955773
48Hattori T, Taft J, Swist K, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone posttranslational modifications. Nature Methods, 10:992-995., 2013. PMID:23955773
49Zhang 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, 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. 23:1522-1540, 2013. PMID:23804400 
50Wang R, Hsu H-K, Blattler A, Wang Y, Lan X, Wang Y, Hsu P-Y, Leu Y-W, Farnham PJ, Huang T H-M, Jin VX. LOcating Non-Unique matched Tags (LONUT) to improve the detection of the enriched regions for ChIP-seq. PLOS One 8:e67788, 2013. PMID:23825685
51Blattler A, Yao L, Wang Y, Ye Z, Jin VX, Farnham PJ.  ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. Epigenetics and Chromatin, 6:13, 2013. PMID:23693142
52Xie M, Hong C, Xing X, Lowdon R, Zhang B, 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 PAF, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T. DNA hypomethylation of specific transposable element families associates with tissue-specific enhancer landscapes. Nature Genetics, 45:836-41, 2013. PMID:23708189
53Farnham PJ. KAP1: Friend or Foe? McGraw-Hill Yearbook/Encyclopedia of Science & Technology, 223-225, 2013.
54Nielsen CB, O’Geen H, Xu X, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Spark: A navigational paradigm for genomic data exploration. Genome Research, 22:2262-2269, 2012. PMID:22960372.
55Wasserman et al. The Transcription Factor Encyclopedia. Genome Biology, 13:R24, 2012. PMID:22458515
56Landt, Marinov, Kheradpour, Kundaje, Pauli, Batzoglou, Bernstein, Bickel, Brown, Cayting, Chen, Epstein, Euskirchen, Fisher-Aylor, Gerstein, Gertz, Guigo, Hartemink, Hoffman, Iyer, Jung, Karmakar, Kellis, Kharchenko, Liu, Liu, Ma, Milosavljevic, Myers, Park, Pazin,  Pery, Raha, Reddy, Rozowsky, Shoresh, Sidow, Slattery, Stammatoyonnopoulous, Tolstorukov, White, Xi, Farnham, Lieb, Wold, Snyder. ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia. Genome Research, 22:1813-31, 2012. PMID:22955991
57Gerstein, Kundaje, Hariharan, Landt, Yan, Cheng, Mu, Khurana, Rozowsky, Alves, Abyzov, Addleman, Alexander, Bhardwaj, Boyle, Cayting, Charos, Cheng, Clarke, Eastman, Euskirchen, Frietze, Gertz, Grubert, Harmanci, Jain, Kasowski, Lacroute, Leng, Lian, Min, Monahan, O’Geen, Ouyang, Partridge, Patacsil, Pauli, Raha, Ramirez, Reddy, Reed, Shi, Slifer, Wang, Wu, Yang, Yip, Zilberman-Schapira, Batzoglou, Sidow, Farnham, Myers, Weissman, Snyder.  Architecture of the human regulatory network derived from ENCODE data. Nature, 489:91-100, 2012. PMID:22955619
58THE ENCODE CONSORTIUM. An integrated encyclopedia of DNA Elements in the human genome. Nature, 489:57-74, 2012. PMID:22955616
59Jung CJ, Iyengar S, Blahnik KR, Jiang JX, Tahimic, C, Torok, NJ, de vere White, RW, Farnham PJ, Zern MA. Human ESC self-renewal promoting miRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFβ tumor suppressor signaling pathways. Mol. Cancer Research 10:979-91, 2012. PMID:22622027
60Lan X, Farnham PJ, Jin VX. Uncovering transcription factor modules using one- and three-dimensional analyses. J. Biol.Chem. 287:30914-21, 2012. PMID:22952238
61Farnham PJ. Thematic miniseries on results from the ENCODE Project: Integrative analyses of regulatory regions in the human genome. J. Biol. Chem. 287:30885-30887, 2012. PMID:22451669
62Frietze S, Wang R, Tak YG, Yao L, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biology,13: R52, 2012. PMID:22951069
63Lan 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, 40:7690-7704, 2012. PMID:22675074
64Kennedy BA, Lan X, Huang TH-M, 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. 802:323-334, 2012. PMID:22130890
65Kang Y-A, Sanalkumar R, O’Geen H, Linnemann AK, Chang C-J, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH.  Autophagy driven by a master regulator of hematopoiesis. Mol. Cell. Biol. 32:226-239, 2012. PMID:22025678
66Jung CJ, Iyengar S, Blahnik KR, Ajuha TP, Jiang JX, Farnham PJ, Zern M. Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation. PLoS One 6:e27740, 2011. PMID:22140464
67Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn R, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PAF, Costello JF, Wang T. The Human Epigenome Browser at Washington University. Nature Methods 8:1056–1058, 2011.
68O’Geen H, Echipare L, Farnham PJ. Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods in Molecular Biology, Epigenetics Protocols II: 791:265-286, 2011. PMID:21913086
69Iyengar S, Farnham PJ. KAP1 Protein: An enigmatic master regulator of the genome. J Biol Chem. 286:26267-26276, 2011. PMID: 21652716.
70Linnemann A, O’Geen H, Keles S, Farnham PJ, and Bresnik EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci 108:13641-136466.2011. PMID:21808000.
71Trojer P, Rabinovich A, Li Y, Li G, Losson R, Chambon P, Erdjument-Bromage H, Tempst P, Farnham PJ, Reinberg D. L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitation of H2A to establish a repressive chromatin structure. Molecular Cell. 42:438-450, 2011. PMID: 21596310
72Cao 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. 286:11985-96, 2011. PMID: 21310950
73Iyengar S, Ivanov AV, Jin VX, Rauscher FJ III, Farnham, PJ. Functional analysis of KAP1 genomic recruitment. Molecular and Cellular Biology. 31:833-1847, 2011. PMID: 21343339
74The ENCODE Project Consortium. A user’s guide to the Encyclopedia of DNA Elements (ENCODE). PLOS Biology 9: e1001046, 2011. PMID:21526222.
75Blahnik KR, Dou L, Echipare, L, Iyengar S, O’Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3’ exons of zinc finger genes. PLOS One 6:e17121, 2011. PMID: 21347206.
76Frietze S, Farnham PJ. Transcription factor effector domains. In “A handbook of transcription factors”. Subcell Biochem. 52: 261-77, 2011. PMID: 21557087
77O’Geen H, Lin Y-H, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA, Engel JD, Farnham PJ. Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes.  BMC Genomics 11:689, 2010. PMID: 21126370
78Frietze S, O’Geen H, Blahnik KR, Jin VX, Farnham PJ. ZNF274 recruits the histone methyltransferase SETDB1 to the 3’ ends of ZNF genes. PLOS One, 5:e15082, 2010. PMID: 21170338. 
79Bernstein, Stamatoyannopoulos, Costello, Ren, Milosavlievic, Meissner, Kellis, Marra, Beaudet, Ecker, Farnham, Hirst, Lander, Mikkelsen, Thomson.  The NIH Roadmap Epigenome Mapping Consortium. Nature Biotech. 28:1045–1048, 2010. PMID:20944595
80Harris RA, ……,  Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparisons of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotech. 28: 1097–1105, 2010. PMID:20852635.
81Krig SR, Miller JK, Lua LL, Beckett LA, Neve RR, Farnham PJ, Yaswen PI, Sweeney CA.  ZNF217, a candidate breast cancer oncogene amplified at 20q13, regulates expression of the ErbB3 receptor tyrosine kinase in breast cancer cells. Oncogene, 29:5500-5510, 2010. PMID: 20661224
82Komashko VM and Farnham PJ. 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics 5: 229-240, 2010. PMID: 20305384
83O’Geen H, Frietze S, Farnham PJ. Using ChIP-seq technology to identify targets of zinc finger transcription factors. In “Methods in Molecular Biology: Zinc Finger Proteins: Methods and Protocols”. Methods Mol Biol 649:437-55, 2010. PMID: 20680851
84Blahnik 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. 38:e13, 2010. PMID:19906703
85Jin V, Apostolos, J, Nagisetty, NS, Farnham PJ. W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data. Bioinformatics. 25:3191-3193, 2009. PMID: 19797408
86Fujiwara T, O’Geen H, Keles S, Blahnik K, Kang Y-A, Choi K, Farnham PJ, Bresnick EH. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Molecular Cell. 36:667-681, 2009. PMID:19941826
87Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domain-containing zinc finger protein ZNF263. J. Biol. Chem. 285:1393-403, 2010. PMID:19887448
88Farnham PJ. Insights from genomic profiling of transcription factors. Nature Reviews Genetics 10:605-616, 2009. PMID: 19668247
89Cotterman R, Jin V, Krig S, Lemen, J, Wey A, Farnham PJ, Knoepfler P. N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Research 68: 9654-9662, 2008. PMID:19047142 
90Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ. E2F in vivo binding specificity: comparison of consensus vs. non-consensus binding sites. Genome Research 18:1763-1777, 2008. PMID: 18836037
91Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O’Geen H, Green R, Farnham PJ.  Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Research 18:521-532, 2008. PMID: 18347325
92Johnson DS, et al. Systematic evaluation of variability in simulated ChIP-chip experiments. Genome Research 18:393-403, 2008. 
93Acevedo LG, Bieda M, Green R, Farnham PJ. Analysis of the mechanisms mediating tumor specific changes in gene expression in human liver tumors. Cancer Research 68:2641-2651, 2008. PMID: 18413731
94Yasui 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 regulation of active genes. PNAS, 104:19416-21, 2007. PMID: 18042715
95Acevedo LG, Iniguez AL, Holster HL, Zhang X, Green R, Farnham PJ. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques. 43: 791-797, 2007. PMID: 18251256
96Xu 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. 17:1550-61, 2007. PMID: 17908821
97O’Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests auto-regulation of KRAB-ZNFs. PLOS Genetics Jun;3(6):e89, 2007. PMID: 17542650
98Rinn JL, Kertesz M, Wang J. Squazzo SL, Xu X, Brugmann S, Goodnough H, Helms JA, Farnham PJ, Segal E, Chang HY.  Functional demarcation of active and silent chromatin domains in human HOX loci by non-coding RNAs. Cell 129, 1311-1323, 2007. PMID: 17604720
99The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799—816, 2007. PMID: 17571346
100Krig SR, Jin VX, Bieda MC, O’Geen H, Yaswen P, Green R, Farnham PJ. Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays. J. Biol. Chem. 282:9703-9712, 2007. 
101Jin 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. 17:807-817, 2007. PMID: 17567999
102O’Geen H, Nicolet CM,  Blahnik K, Green R, Farnham PJ. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques, 41:577-580, 2006. PMID:17140114
103Elnitski L, Jin VX, Farnham PJ, Jones SJM. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Research, 16: 1455-1464, 2006. PMID: 17053094 
104Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ.  A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data – a case study using E2F1. Genome Research, 16:1585-1595, 2006. PMID:17053090
105Squazzo SL, Komashko VM, O’Geen H, Krig S, Jin VX, Jang S-W, Green R, Margueron R, Reinberg D, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell type-specific manner. Genome Research, 16:890-900, 2006. PMID:6751344
106Bieda M, Xu S, Singer M, Green R, Farnham PJ. Unbiased Location Analysis of E2F1 Binding Sites Suggests a Widespread Role for E2F1 in the Human Genome. Genome Research, 16:595-605, 2006. PMID:16606705
107Lieb JD, Beck S., Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenet. Genome Res. 114:1-15, 2006
108Oberley MO, Kirmizis A, Schelman WR, Farnham PJ. Using RNA interference to validate target genes identified by coupling chromatin immunoprecipitation with CpG-island microarrays. In Promoter and CpG Island Microarrays (Nuts & Bolts series) DNA Press, 2006.
109Oberley MJ, Farnham PJ. Identification of mammalian E2F regulatory networks using DNA microarray hybridization analyses.  In: Shannon MF, Rao S, eds. Microarrays and Transcription Networks. Georgetown: Landes Bioscience/Eurekah.com. 2005
110Farnham PJ. New insights into transcriptional regulation by RB: One size no longer fits all. In: Fanciulli, M. ed.  Rb Regulation of Oncogenesis, Georgetown: Landes Bioscience/Eurekah.com, 2005. 
111Kuzmichev 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. USA 102:1859-64, 2005. 
112Heisler 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. 33:2952-2961, 2005. PMID:15911630
113Feingold et al. (see http://www.sciencemag.org/cgi/content/full/306/5696/636/DC1 for a complete list of authors). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306:636-640, 2004.
114Reinberg D, Chuikov S, Farnham P, Karachentsev D, Kirmizis A, Kuzmichev A, Margueron R, Nishioka K, Preissner TS, Sarma K, Abate-Shen C, Steward R, Vaquero A. Steps toward understanding the inheritance of repressive methyl-lysine marks in histones. Cold Spring Harb Symp Quant Biol. 69:171-182, 2004.
115Lavrrar JL, Farnham PJ. The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation.  J Biol Chem. 279:46343-46349, 2004. PMID:15328355
116Kirmizis A, Farnham PJ. Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med 229:705-721, 2004. PMID:15337825
117Townsend MJ, Weinmann AS, Matsuda J, Saloman R, Farnham PJ, Biron CA, Gapin, L, Glimcher LH. T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. Immunity, 20: 477-494, 2004. PMID:15084276
118Kirmizis, 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 lysine 27.  Genes & Devel. 18:1592-1605, 2004. PMID:15231737
119Oberley MJ, Tsao J, Yau P, Farnham PJ. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods in Enzymology 376: 315-333, 2004. PMID:14975315
120Oberley MJ, Inman DR, Farnham PJ. E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. Journal of Biological Chem. 278:42466-42476, 2003. PMID:12909625
121Mao DY L, Watson JD, Yan PS, Barsyte-Lovejoy D, Khosravi F, Wong WW-L, Farnham PJ, Huang TH-M, Penn LZ. Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Current Biology 13:1-20, 2003. PMID:12747840
122Oberley MJ, Farnham PJ. Probing chromatin immunoprecipitates with CpG island microarrays to identify genomic sites occupied by DNA-binding proteins.  Methods in Enzymology 371:577-596, 2003. PMID:14712730
123Graveel CR, Harkins-Perry SR, Acevedo LG, Farnham PJ. Identification and characterization of CRG-L2, a new marker for liver tumor development.  Oncogene  22:1730-1736, 2003. PMID:12642876
124Wells J, Yan PS, Cechvala M, Huang H-MT, Farnham PJ.  Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene 22:1445-1460, 2003. PMID:12629508
125Kirmizis A, Bartley SM, Farnham PJ. Identification of the Polycomb Group protein SU(Z)12 as a potential molecular target for human cancer therapy. 2:113-121, 2003. PMID:12533679
126Eberhardy SR, Farnham PJ. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter.  J. Biol. Chem, 277: 40156-40162, 2002.
127Wells J, Farnham PJ. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation.  Methods 26:48-56, 2002. PMID:12054904
128Weinmann AS, Farnham PJ. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation.  Methods 26:37-47, 2002. PMID:12054903
129Wells J, Graveel CR, Bartley SM, Farnham PJ.  The identification of E2F1-specific target genes.  Proc. Natl. Acad. Sci. USA, 99:3890-3895,2002. PMID:11904439
130Weinmann AS, Yan PS, Oberley MJ, Huang H-MT, Farnham PJ. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG microarray analysis.  Genes & Devel. 16:235-244, 2002. PMID:11799066
131Eberhardy SR, Farnham PJ. c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. J. Biol. Chem. 276:48562-48571, 2001. PMID:11673469
132Weinmann AS, Bartley SM, Zhang MQ, Zhang T, Farnham PJ. Use of chromatin immunoprecipitation to clone novel E2F target promoters.  Mol. Cell. Biol. 21: 6820-6832, 2001. PMID:11564866
133Maser RS, Mirzoeva O, Wells J, Olivares H, Williams B, Zinkel R, Farnham PJ, Petrini JHJ. The MRE11 complex:  diverse roles in S phase progression. Mol. Cell. Biol. 21: 6006-6016, 2001. PMID:11486038
134Albert T, Wells J, Funk J-O, Pullner A, Raschke E-E, 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. 276: 20482-20490, 2001. PMID:11279041
135Kel AE, Kel-Margoulis OV, Bartley SM, Farnham PJ, Wingender E, Zhang MQ.  Computer-assisted identification of cell cycle-related genes – new targets for E2F transcription factors.   J. Mol. Biol. 309: 99-120, 2001. PMID:11491305
136Graveel CR, Jatkoe T, Madore S, Holt AL, Farnham PJ. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene 20: 2704-2712-2001. PMID:11420682
137Wells 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. 20: 5987-5807, 2000. PMID:10913163
138Mac SM, D’Cunha C, Farnham PJ. Direct recruitment of N-Myc to target gene promoters.  Molecular Carcinogenesis 29:76-86, 2000. PMID:11074604
139Mac SM, Farnham PJ. Cad, a c-Myc target gene, is not deregulated in Burkitt’s lymphomas, Molecular Carcinogenesis 27: 84-96, 2000. PMID:10657901
140Lee TA, Farnham PJ.  Exogenous E2F1 is growth inhibitory before, during, and after cellular transformation, Oncogene. 19:2257-2268, 2000. PMID:10822376
141Eberhardy SR, Farnham PJ. Direct examination of histone acetylation of c-Myc target genes using chromatin immunoprecipitation.  J. Biol. Chem. 275: 33798-33805, 2000. PMID:10931841
14258.     Lukas ER, Bartley SM, Graveel CR, Diaz ZM, Dyson N, Harlow E, Yamasaki L, Farnham PJ. No effect of loss of E2F1 on liver regeneration or hepatocarcinogenesis in C57BL/6J or C3H/HeJ mice.  Molecular Carcinogenesis: 25:295-303, 1999. PMID:10449036
143Fry CJ, Bartley SM, Malinowski E, Pearson A, Greenblatt J, Farnham PJ. Activation of the murine dihydrofolate reductase promoter by E2F1:  A requirement for CBP recruitment.  J. Biol. Chem 274:15883-15891, 1999. PMID:10336493
144Fry CJ, Farnham PJ.  Context-dependent activation of transcription, J. Biol. Chem. 274: 29583-29586, 1999. PMID:10514422
145Boyd KE, Farnham PJ. Co-examination of site-specific transcription factor binding and promoter activity in living cells. Mol. Cel. Biol. 19: 8393-8399, 1999. PMID:10567564
146Boyd KE, Farnham PJ. Identification of Target Genes of Oncogenic Transcription Factors, Proc. Soc. Exp. Biol. Med. 222:9-28, 1999. PMID:10510243
147Farnham PJ. Review of the 1998 Keystone Symposium on Transcriptional Mechanisms, Taos, NM, February 21-26, 1998.  BBA 1378: R33-R42, 1998.
148Boyd KE, Wells J, Gutman J, Bartley SM, Farnham PJ. c-Myc target gene specificity is determined by post-DNA binding specificity.  Proc. Natl. Acad. Sci. USA 95:13887-13892, 1998. PMID:9811896
149Bartley SM, Szakaly RJ, Farnham PJ.  Characterization of the 3′ untranslated region of mouse E2F1 mRNA.  Gene 223: 355-360, 1998. PMID:9858765
150van Ginkle PR, Hsiao K-M, Schjerven H, Farnham PJ.  E2F-mediated growth regulation requires transcription factor cooperation.  J. Biol. Chem., 272: 18367-18374, 1997. PMID:9218478
151Fry CJ, Slansky JE, Farnham PJ. Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain.  Mol. Cell. Biol., 17: 1966-1976, 1997. PMID:9121444
152Dagnino L, Fry CJ, Bartley SM, Farnham PJ, Gallie BL, Phillips RA. Expression patterns of the E2F family of transcription factors during murine nervous system development. Mech. of Devel. 66: 13-25, 1997.
153Dagnino L, Fry CJ, Bartley SM, Farnham PJ, Gallie BL, Phillips RA. Expression patterns of the E2F family of transcription factors during murine epithelial development.  Cell Growth and Diff.  8: 553-563, 1997.
154Boyd KE, Farnham PJ. Understanding the link between cad gene expression and cell growth. in Paths to Pyrimidines,Vol. 5, 1997.
155Boyd KE, Farnham PJ. Myc versus USF:  Discrimination at the cad gene is determined by core promoter elements.  Mol. Cell. Biol., 17:2529-2537, 1997. PMID:9111322
156Slansky JE, Farnham PJ.  Transcriptional Regulation of the Dihydrofolate Reductase Gene.  In BioEssays, Vol. 18: 55-62, 1996. PMID:8593164
157Slansky JE, Farnham PJ.  Introduction to the E2F family: Protein structure and gene regulation.  in “Transcriptional Control of Cell Growth: The E2F Gene Family” Springer-Verlag, Current Topics in Microbiology and Immunology, Vol. 208: pp 1-30, 1996. PMID:8575210
158Schilling LJ, Farnham PJ. The bidirectionally transcribed dihydrofolate reductase and rep-3a promoters are growth-regulated via distinct mechanisms.  Cell Growth and Diff. 6: 541-548, 1995. PMID:7647037
159Miltenberger 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. 15: 2527-2535, 1995. PMID:7739536
160Miltenberger 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 and Diff. 6: 549-556, 1995. PMID:7647038
161Buermeyer AB, McMahon SL, Strasheim L, Farnham PJ.  Identification of cis-acting elements that can obviate the requirement for the C-terminal domain of RNA polymerase II.  J. Biol. Chem. 270: 6798-6807, 1995. PMID:7896826
162Bennett LM, Farnham PJ, Drinkwater NR. Strain-specific differences in DNA synthesis and gene expression in the regenerating livers of C57BL/6J and C3H/HeJ mice.  Molecular Carcinogenesis 14: 46-52, 1995. PMID:7546224
163Slansky JE, Farnham PJ. The Role of the transcription factor E2F in the growth regulation of DHFR.  The Cell Cycle:  Regulators, targets and clinical applications.  XIIIth Washington International Spring Symposium, 1994.
164Schilling LJ, Farnham PJ. Transcriptional Regulation of the DHFR/REP-2 Locus.  Critical Reviews in Eukaryotic Gene Expression 4: 19-53, 1994. PMID:7987046
165Schilling LJ, Farnham PJ.  Inappropriate transcription from the 5′ end of the dhfr gene obscures growth regulation.  Nucleic Acids Res.15: 3061-3068, 1994. PMID:7520569
166Li Y, Slansky JE, Myers DJ, Drinkwater NR, Kaelin WG, Farnham PJ. Cloning, chromosomal location, and characterization of mouse E2F1, Mol. Cell. Biol.14: 1861-1869, 1994. PMID:8114719
167Kollmar 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. 269: 2252-2257, 1994. PMID:7905000
168Hsiao K-M, McMahon SL, Farnham PJ.  Multiple DNA elements are required for the growth regulation of the mouse E2F1 promoter.  Genes Dev. 8: 1526-1537, 1994. PMID:7958837
169Slansky 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. 13:  1610-1618, 1993. PMID:8441401
170Miltenberger RJ, Cortner J, Farnham PJ. An inhibitory Raf-1 mutant suppresses expression of a subset of v-raf activated promoters, J. Biol. Chem. 268: 15674-15680, 1993. PMID:8340392
171Kollmar R, Farnham PJ. Site-specific initiation of transcription by RNA polymerase II.  Proc. Soc. Exp. Biol. Med. 203:  127-139, 1993. PMID:8502653
172Farnham PJ, Slansky JE, Kollmar R. The role of E2F in the mammalian cell cycle.  Biochem. Biophys. Acta, 1155: 125-131, 1993. PMID:8357823
173Means AL, Slansky JE, McMahon SL, Knuth MW, Farnham PJ. The HIP1 binding site is required for growth regulation of the DHFR promoter.  Mol. Cell. Biol. 12: 1054-1063, 1992. PMID:1545788
174Mack KJ, Cortner J, Mack P, Farnham PJ. Krox 20 messenger RNA and protein expression in the adult central nervous system.  Molecular Brain Research, 14:117-123, 1992. PMID:1323008
175Kollmar R, Lindstrom M, Farnham PJ. Heat sensitivity and Sp1 activation of complex formation at the syrian hamster CAD promoter in vitro.  J. Biol. Chem. 267:385-391, 1992. PMID:1346130
176Kaelin WG, Krek W, Seller WR, DeCaprio JA, Ajchenbaum R, Fuchs CS, Chittenden,T,  Li Y, Farnham PJ, Blanar MA, Livingston DM, Flemington EK. Expressing cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties.  Cell 70: 351-364, 1992. PMID:1638635
177Buermeyer AB, Thompson NE, Strasheim LA, Burgess RR, Farnham PJ.  The HIP1 initiator element plays a role in determining the in vitro requirement of the DHFR promoter for the C-terminal domain of RNA polymerase II.  Mol. Cell. Biol. 12: 2250-2259, 1992. PMID:1569952
178Farnham PJ, Cornwell MM. Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component.  Gene Express. 1: 137-148, 1991. PMID:1820211
179Cortner J, Farnham PJ. Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH 3T3 fibroblasts.  Cell Growth and Diff. 2: 465-473, 1991. PMID:1721529
180Means AL, Farnham PJ.  Transcription Initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site.  Mol. Cell. Biol. 10:653-661, 1990. PMID:2300058;
181Farnham PJ, Means AL. Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter.  Mol. Cell. Biol. 10:1390-1398, 1990. PMID:2320003
182Farnham PJ, Kollmar R. Characterization of the 5′ end of the growth-regulated syrian hamster CAD gene.  Cell Growth and Diff. 1:179-189, 1990. PMID:1982061
183Cortner J, Farnham PJ. Identification of the serum-responsive transcription initiation site of the zinc finger gene, Krox-20.  Mol. Cell. Biol. 10:3788-3791, 1990. PMID:2113176
184Schilling LJ, Farnham PJ.  Identification of a new promoter upstream of the murine dihydrofolate reductase gene.  Mol. Cell. Biol. 9:4568-4570, 1989. PMID:2479829
185Farnham PJ, Schimke RT.  In vitro transcription and delimitation of promoter elements of the dihydrofolate reductase gene.  Mol. Cell. Biol. 6: 2392-2401, 1986. PMID:3785199
186Farnham PJ, Schimke RT.  Murine dihydrofolate reductase transcripts through the cell cycle. Mol. Cell. Biol. 6: 365-371, 1986. PMID:3785152
187McGrogan M, Simonsen CC, Smouse DT, Farnham PJ, Schimke RT.  Heterogeneity at the 5′ termini of mouse dihydrofolate reductase mRNAs. J. Biol. Chem. 260: 2307-2314, 1985. PMID:2982814
188Hamkalo BA, Farnham PJ, Johnston R, Schimke RT.  Ultra-structural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line.  Proc. Natl. Acad. Sci. USA 82: 1126-1130, 1985. PMID:3856243
189Farnham PJ, Abrams JA, Schimke RT. Opposite strand RNAs from the 5′ flanking region of the mouse dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA 82: 3978-3982, 1985. PMID:2408272
190Farnham PJ, Schimke RT. Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle.  J. Biol. Chem. 260: 7675-7680, 1985. PMID:2987264
191Price J, Farnham PJ, Korn LJ.  A protein factor regulates transcription of the Xenopus 5S ribosomal RNA genes in a positive fashion. In Gene Expression, UCLA Symposia on Molecular and Cellular Biology, New Series Volume III, 273-281, 1983.
192Platt T, Horowitz H, Farnham PJ.  A kinetic view of transcription termination. Microbiology 83: 21-25, 1983. 
193Farnham PJ, Greenblatt J, Platt T.  Effects of nusA protein on transcription termination in the tryptophan operon of E. coli.  Cell 29: 945-951, 1982. PMID:6758952
194Farnham PJ, Platt T. Effects of DNA analogs on transcription termination at the tryptophan operon attenuator of E. coli. Proc. Natl. Acad. Sci. USA 79: 998-1002,1982. PMID:7041118.
195Farnham PJ, Platt T.  Rho-independent termination: Dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro.  Nucl. Acids Res. 9: 563-577, 1981. PMID:7012794
196 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. USA 78: 4180-4184, 1981. PMID:7027254
197Farnham PJ, Platt, T.  A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs.  Cell 20: 739-748,1980. PMID:6998564
198Farnham PJ, Novak R A, McAdoo DJ.  A reexamination of the distributions of octopamine and phenylethanolamine in the Aplysia nervous system.  J. Neurochem. 30: 1173-1176, 1978. PMID:351144
199Asch HL, Farnham PJ.  Effects of gentamicin on trypsin, chymotrypsin, and  collagenase.  J. Infect. Dis.  138: 257-259, 1978. PMID:210240
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