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ST. Differential regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nature Immunology 14:1073-1083, 2013. PMID:24013668 153 Hattori 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 152 The ENCODE Project. McGraw-Hill Yearbook of Science & Technology, In Press, 2014 151 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, 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. Jun 26 Epub ahead of print, 2013. PMID:23804400 150 Wang 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 149 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 and Chromatin, 6:13, 2013. PMID:23693142 148 Xie 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 147 KAP1: Friend or Foe? McGraw-Hill Yearbook of Science & Technology, 223-225, 2013 146 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 Research 22:2262-2269, 2012. PMID:22960372 145 Wasserman et al. The Transcription Factor Encyclopedia. Genome Biology, 13:R24, 2012. Designated as Highly Accessed. PMID:22458515 144 Landt, 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, Peggy Farnham*, Jason Lieb*, Barbara Wold*, and Michael Snyder* ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia. Genome Research, 22:1813-31, 2012. PMID:22955991 143 Gerstein, 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 142 THE ENCODE CONSORTIUM. An integrated encyclopedia of DNA Elements in the human genome. Nature, 489:57-74, 2012. PMID:22955616 141 Jung 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 TGF_ tumor suppressor signaling pathways. Mol. Cancer Research 10:979-91, 2012. PMID:22622027

140 Lan X, Farnham PJ, Jin VX. Uncovering transcription factor modules using one- and threedimensional analyses. J. Biol.Chem. 287:30914-21, 2012. PMID:22952238 139 Farnham 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 138 Frietze S, Wang R, Tak YG, Yao L, Ye Z, Gaddis M, Witt H, Farnham PJ*, Jin VX*. Cell typespecific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biology, 13:R52. 2012. Designated as Highly Accessed. PMID:22951069 137 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, 40:7690-7704, 2012. PMID:22675074 136 Kennedy 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. 135 Kang 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 134 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 6:e27740, 2011. PMID:22140464 133 Zhou 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. PMID:22127213 132 O'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. 131 Iyengar S, Farnham PJ. KAP1 Protein: An enigmatic master regulator of the genome. J Biol Chem. 286:26267-26276, 2011. PMID: 21652716. 130 Linnemann A, O'Geen H, Keles S, Farnham PJ, and Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci 108:13641-136466.2011. PMID:21808000. 129 Trojer 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. 42:438450, 2011. PMID: 21596310. This article was given a Recommended ranking at Faculty of 1000: 128 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. 286:1198596, 2011. PMID: 21310950. PMC3069401. 127 Iyengar 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 126 The ENCODE Project Consortium. A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLOS Biology 9: e1001046, 2011. PMID:21526222 125 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 6:e17121, 2011. PMID: 21347206. PMC3039671 124 Frietze S, Farnham PJ. Transcription factor effector domains. In A handbook of transcription factors. Subcell Biochem;52:261-77, 2011. PMID: 21557087 123 O'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





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its general role in fundamental biological processes. BMC Genomics 11:689, 2010. PMID: 21126370. PMC3019231 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, 5:e15082, 2010. PMID: 21170338. PMC2999557. Bernstein, 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 Harris et al. Comparisons of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotech. 28: 1097-1105, 2010. PMID:20852635 Krig 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 Komashko VM and Farnham PJ. 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics 5: 229-240, 2010. PMID: 20305384 O'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 Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludscher B, Korf I, Farnham PJ. Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nuc. Acids Res. 38:e13, 2010. PMID:19906703. PMC2817454 Jin 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. PMC2778340 Fujiwara 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; PMC2784893 Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domaincontaining zinc finger protein ZNF263. J. Biol. Chem. 285:1393-1403, 2010. PMID:19887448. PMC2801265 Farnham, PJ. Insights from genomic profiling of transcription factors. Nature Reviews Genetics 10:605-616, 2009. PMID: 19668247. PMC2846386 Cotterman R, Jin V, Krig S, Lemen, J, Wey A, Farnham P, 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. PMC2637654 Rabinovich 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. PMC2577861 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 Research 18:521-532, 2008. PMID: 18347325. PMC2279240 Johnson DS, et al. Systematic evaluation of variability in simulated ChIP-chip experiments. Genome Research 18:393-403, 2008. PMID: 18258921. PMC2259103. This article was given a Recommended ranking at Faculty of 1000:

107 Acevedo LG, Bieda M, Green R, and 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. PMC2567918 106 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 regulation of active genes. PNAS, 104:19416-21, 2007. PMID: 18042715. PMC2148304 105 Acevedo 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. PMC2268896 104 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. 17:1550-61, 2007. PMID: 17908821. PMC2045138 103 O'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; PMC1885280. This article was given a Recommended ranking at Faculty of 1000: /1087864/. 102 Rinn 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; PMC2084369. This article was given an Exceptional ranking at Faculty of 1000: 101 The 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. PMC2212820. 100 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 ChIP-chip assays. J. Biol. Chem. 282:97039712, 2007. PMID: 17259635. PMC2269729 99 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. 17:807-817, 2007. PMID: 17567999; PMC1891340 98 O'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. PMC2268903 97 Elnitski L, Jin VX, Farnham PJ, Jones SJM. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Research, 16: 14551464, 2006. PMID: 17053094 96 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 Research, 16:1585-1595, 2006. PMID:17053090; PMC1665642 95 Squazzo 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; PMC1484456 94 Bieda 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, 16:595605, 2006. PMID:16606705; PMC1457046. This article was given a must read ranking at Faculty of 1000: /1029798/. 93 Lieb 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 92 Oberley 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.


Oberley MJ, Farnham PJ. Identification of mammalian E2F regulatory networks using DNA microarray hybridization analyses. In: Shannon MF, Rao S, eds. Microarrays and Transcription Networks. Landes Bioscience/ 2005 90 Farnham, PJ. New insights into transcriptional regulation by RB: One size no longer fits all. In: Fanciulli, M. ed. Rb Regulation of Oncogenesis, Landes Bioscience/, 2005. 89 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. USA 102:1859-64, 2005. PMID:15684044 88 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. 33:2952-2961, 2005. PMID:15911630; PMC1137027 87 Feingold et al. (see for a complete list of authors). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306:636-640, 2004. 86 Reinberg 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. 85 Lavrrar 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 84 Kirmizis A, Farnham, PJ. Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med 229:705-721, 2004. PMID:15337825 83. Townsend 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; PMID:15084276. This article was given a recommended ranking at Faculty of 1000: 82. 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 lysine 27. Genes & Devel. 18:1592-1605, 2004. PMID:15231737; PMC443521 81. Oberley 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 80. Oberley 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 79. Mao 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 78. Oberley MJ, Farnham PJ. Probing chromatin immunoprecipitates with CpG island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods in Enzymology 371:577596,2003. PMID:14712730 77. Graveel 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 76. Wells 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

75. 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 Therapeutics 2:113-121,2003. PMID:12533679 74. Eberhardy 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. 73. Wells J, Farnham PJ. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26:48-56,2002. PMID:12054904 72. Weinmann AS, Farnham PJ. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26:37-47,2002. PMID:12054903 71. Wells 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; PMC122619 70. Weinmann 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; PMC155318. This article was given a must read ranking at Faculty of 1000: 69. Eberhardy 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 68. Weinmann 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; PMC99859 67. Maser 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; PMC87318 66. Albert 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 65. Kel AE, Kel-Margoulis OV, Bartley SM, Farnham PJ, Wingender E, Zhang MQ. Computerassisted identification of cell cycle-related genes-new targets for E2F transcription factors. J. Mol. Biol. 309:99-120,2001. PMID:11491305 64. Graveel 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 63. Eberhardy 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 62. Mac SM, D'Cunha C, Farnham PJ. Direct recruitment of N-Myc to target gene promoters. Molecular Carcinogenesis 29:76-86,2000. PMID:11074604 61. 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. 20: 5987-5807,2000. PMID:10913163; PMC86057 60. Lee TA, Farnham PJ. Exogenous E2F1 is growth inhibitory before, during, and after cellular transformation, Oncogene. 19:2257-2268,2000. PMID:10822376 59. Mac SM, Farnham PJ. Cad, a c-Myc target gene, is not deregulated in Burkitt's lymphomas, Molecular Carcinogenesis 27:84-96, 2000. PMID:10657901 58. Boyd 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; PMC84934 57. 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 56. Fry CJ, Bartley SM, Malinowski E, Pearson A, Greenblatt J, Farnham P. Activation of the murine dihydrofolate reductase promoter by E2F1: A requirement for CBP recruitment. J. Biol. Chem 274:15883-15891,1999. PMID:10336493

55. Fry CJ, Farnham PJ. Context-dependent activation of transcription, J. Biol. Chem. 274: 2958329586,1999. PMID:10514422 54. Boyd KE, Farnham PJ. Identification of Target Genes of Oncogenic Transcription Factors, Proc. Soc. Exp. Biol. Med. 222:9-28,1999. PMID:10510243 53. Farnham PJ. Review of the 1998 Keystone Symposium on Transcriptional Mechanisms, Taos, NM, February 21-26, 1998. BBA 1378: R33-R42, 1998. 52. Boyd 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; PMC24949 51. Bartley SM, Szakaly RJ, Farnham PJ. Characterization of the 3' untranslated region of mouse E2F1 mRNA. Gene,223:355-360,1998. PMID:9858765 50. van 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 49. Dagnino 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. 48. Dagnino 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. 47. Boyd 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; PMC232102 46. Fry CJ, Slansky JE, Farnham PJ. Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain. Mol. Cell. Biol., 17: 19661976, 1997. PMID:9121444; PMC232043 45. Boyd KE, Farnham PJ. Understanding the link between cad gene expression and cell growth. in Paths to Pyrimidines,Vol. 5, 1997. 44. Slansky 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 43. Slansky JE, Farnham PJ. Transcriptional Regulation of the Dihydrofolate Reductase Gene. in BioEssays, Vol. 18:55-62,1996. PMID:8593164 42. Bennett 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 41. 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. 15:25272535,1995. PMID:7739536; PMC230483 40. 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 and Diff. 6:549-556,1995. PMID:7647038 39. Schilling 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 38. Buermeyer 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 37. Slansky 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. 36. Schilling 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; PMC310276

35. Hsiao 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 34. Li 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; PMC358544 33. 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. 269: 2252-2257, 1994. PMID:7905000 32. Schilling LJ, Farnham PJ. Transcriptional Regulation of the DHFR/REP-2 Locus. Critical Reviews in Eukaryotic Gene Expression 4: 19-53,1994. PMID:7987046 31. Farnham PJ, Slansky JE, Kollmar R. The role of E2F in the mammalian cell cycle. Biochem. Biophys. Acta, 1155:125-131,1993. PMID:8357823 30. Kollmar R, Farnham PJ. Site-specific initiation of transcription by RNA polymerase II. Proc. Soc. Exp. Biol. Med. 203:127-139,1993. PMID:8502653 29. Miltenberger 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 28. 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. 13: 1610-1618,1993. PMID:8441401; PMC359473 27. Kaelin 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 26. 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 DHFR promoter for the Cterminal domain of RNA polymerase II. Mol. Cell. Biol. 12: 2250-2259,1992. PMID:1569952; PMC364397 25. Mack 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 24. Means 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; PMC369537 23. Kollmar 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 22. Cortner 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 21. Farnham 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 20. Cortner 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; PMC360834 19. Farnham 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 18. Farnham 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; PMC362241 17. Means 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; PMC360863 16. Schilling LJ, Farnham PJ. Identification of a new promoter upstream of the murine dihydrofolate reductase gene. Mol. Cell. Biol. 9:4568-4570,1989. PMID:2479829; PMC362546

15. Farnham 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; PMC367792 14. Farnham PJ, Schimke RT. Murine dihydrofolate reductase transcripts through the cell cycle. Mol. Cell. Biol. 6: 365-371,1986. PMID:3785152; PMC367525 13. Farnham 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; PMC397917 12. Farnham PJ, Schimke RT. Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle. J. Biol. Chem. 260: 7675-7680,1985. PMID:2987264 11. McGrogan 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 10. Hamkalo 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; PMC397207 9. Price 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. 8. Platt T, Horowitz H, Farnham PJ. A kinetic view of transcription termination. Microbiology 83:2125,1983. 7. Farnham 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 6. Farnham 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; PMC345886 5. 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; PMC319752 4. Farnham 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. PMC327222 3. Farnham 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 2. Asch HL, Farnham PJ. Effects of gentamicin on trypsin, chymotrypsin, and collagenase. J. Infect. Dis. 138:257-259,1978. PMID:210240 1. Farnham 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