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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters. Nucleic Acids Res. 2024 Jul 08; 52(12):6850-6865.
Hsu E, Hutchison K, Liu Y, Nicolet CM, Schreiner S, Zemke NR, Farnham PJ. PMID: 38726870; PMCID: PMC11229363.
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PubMed Mentions: Fields:
Translation:
HumansAnimalsCells
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Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am J Hum Genet. 2024 03 07; 111(3):487-508.
Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, Amor DJ, Banka S, Basel DG, Buch LD, Carere DA, Carroll R, Clayton-Smith J, Crawford A, Dunø M, Faivre L, Gilfillan CP, Gold NB, Gripp KW, Hobson E, Holtz AM, Innes AM, Isidor B, Jackson A, Katsonis P, Amel Riazat Kesh L, Genomics England Research Consortium, Küry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, Németh AH, Østergaard E, Patel R, Pope K, Posey JE, Schnur RE, Shaw M, Stolerman E, Taylor JP, Wadman E, Wakeling E, White SM, Wong LC, Lupski JR, Lichtarge O, Corbett MA, Gecz J, Nicolet CM, Farnham PJ, Kim CH, Shinawi M. PMID: 38325380; PMCID: PMC10940019.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimals
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m6A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer. NAR Cancer. 2023 Dec; 5(4):zcad054.
Hodara E, Mades A, Swartz L, Iqbal M, Xu T, Bsteh D, Farnham PJ, Rhie SK, Goldkorn A. PMID: 38023731; PMCID: PMC10653028.
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PubMed Mentions:
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Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol. 2022 07 26; 23(1):163.
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. PMID: 35883107; PMCID: PMC9316731.
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PubMed Mentions:
19 Fields:
Translation:
HumansCells
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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 35474001; PMCID: PMC9095460.
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PubMed Mentions:
6 Fields:
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FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer. Cancers (Basel). 2022 Mar 28; 14(7).
Lu YT, Xu T, Iqbal M, Hsieh TC, Luo Z, Liang G, Farnham PJ, Rhie SK, Goldkorn A. PMID: 35406487; PMCID: PMC8996937.
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PubMed Mentions:
5
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TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet. 2020 09; 16(9):e1009023.
Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK. PMID: 32925947; PMCID: PMC7515200.
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PubMed Mentions:
15 Fields:
Translation:
HumansCells
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Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 32728249; PMCID: PMC7410828.
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PubMed Mentions:
724 Fields:
Translation:
HumansAnimalsCells
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Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters. Nucleic Acids Res. 2020 06 19; 48(11):5986-6000.
Ni W, Perez AA, Schreiner S, Nicolet CM, Farnham PJ. PMID: 32406922; PMCID: PMC7293018.
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PubMed Mentions:
15 Fields:
Translation:
HumansCells
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Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells. PLoS One. 2020; 15(2):e0228590.
Luo Z, Farnham PJ. PMID: 32012197; PMCID: PMC6996832.
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PubMed Mentions:
6 Fields:
Translation:
HumansCells
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A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun. 2019 09 12; 10(1):4154.
Rhie SK, Perez AA, Lay FD, Schreiner S, Shi J, Polin J, Farnham PJ. PMID: 31515496; PMCID: PMC6742760.
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PubMed Mentions:
53 Fields:
Translation:
HumansCells
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The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression. Sci Adv. 2019 07; 5(7):eaaw6710.
Qian Y, Zhang L, Cai M, Li H, Xu H, Yang H, Zhao Z, Rhie SK, Farnham PJ, Shi J, Lu W. PMID: 31328168; PMCID: PMC6636982.
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PubMed Mentions:
22 Fields:
Translation:
HumansCells
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Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin. 2019 May 03; 12(1):26.
O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ. PMID: 31053162; PMCID: PMC6498470.
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PubMed Mentions:
60 Fields:
Translation:
HumansAnimalsCells
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The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel). 2019 Mar 07; 11(3).
Luo Z, Rhie SK, Farnham PJ. PMID: 30866492; PMCID: PMC6468460.
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PubMed Mentions:
26
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Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv. 2018 12; 4(12):eaav8550.
Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. PMID: 30555922; PMCID: PMC6292713.
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PubMed Mentions:
28 Fields:
Translation:
HumansCells
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Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. J Cell Biochem. 2019 03; 120(3):3056-3070.
Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE. PMID: 30548288; PMCID: PMC6476548.
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PubMed Mentions:
6 Fields:
Translation:
HumansCells
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CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops. Genome Biol. 2018 10 08; 19(1):160.
Guo Y, Perez AA, Hazelett DJ, Coetzee GA, Rhie SK, Farnham PJ. PMID: 30296942; PMCID: PMC6176514.
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PubMed Mentions:
37 Fields:
Translation:
HumansCells
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ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters. Genome Res. 2018 Mar 01; 28(3):310-320.
Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. PMID: 29429977; PMCID: PMC5848610.
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PubMed Mentions:
33 Fields:
Translation:
HumansCells
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Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq). Methods Mol Biol. 2018; 1766:209-229.
Rhie SK, Schreiner S, Farnham PJ. PMID: 29605855; PMCID: PMC6019634.
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PubMed Mentions:
8 Fields:
Translation:
HumansCells
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A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13. Cell Rep. 2017 Nov 07; 21(6):1411-1417.
Luo Z, Rhie SK, Lay FD, Farnham PJ. PMID: 29117547; PMCID: PMC5726543.
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PubMed Mentions:
30 Fields:
Translation:
HumansCells
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dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Res. 2017 Sep 29; 45(17):9901-9916.
O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, Segal DJ. PMID: 28973434; PMCID: PMC5622328.
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PubMed Mentions:
89 Fields:
Translation:
HumansCells
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Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin. 2016; 9:50.
Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ. PMID: 27833659; PMCID: PMC5103450.
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PubMed Mentions:
33 Fields:
Translation:
HumansCells
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4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Sci Rep. 2016 Mar 03; 6:22462.
Cai M, Kim S, Wang K, Farnham PJ, Coetzee GA, Lu W. PMID: 26934861; PMCID: PMC4776156.
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PubMed Mentions:
22 Fields:
Translation:
HumansCells
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Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Nucleic Acids Res. 2016 05 19; 44(9):4123-33.
Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O'Geen H, Segal DJ, Farnham PJ. PMID: 26743005; PMCID: PMC4872074.
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PubMed Mentions:
24 Fields:
Translation:
HumansCells
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Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin. 2015; 8:57.
Tak YG, Farnham PJ. PMID: 26719772; PMCID: PMC4696349.
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PubMed Mentions:
153 Fields:
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The PsychENCODE project. Nat Neurosci. 2015 Dec; 18(12):1707-12.
PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. PMID: 26605881; PMCID: PMC4675669.
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PubMed Mentions:
218 Fields:
Translation:
HumansAnimalsCells
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Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol. 2015; 50(6):550-73.
Yao L, Berman BP, Farnham PJ. PMID: 26446758; PMCID: PMC4666684.
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PubMed Mentions:
41 Fields:
Translation:
HumansAnimalsCells
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Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015 May 21; 16:105.
Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. PMID: 25994056; PMCID: PMC4460959.
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PubMed Mentions:
103 Fields:
Translation:
HumansCells
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The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 2015 Apr; 25(4):467-77.
Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. PMID: 25747664; PMCID: PMC4381519.
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PubMed Mentions:
56 Fields:
Translation:
HumansCells
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Altering cancer transcriptomes using epigenomic inhibitors. Epigenetics Chromatin. 2015; 8:9.
Gaddis M, Gerrard D, Frietze S, Farnham PJ. PMID: 26191083; PMCID: PMC4506402.
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PubMed Mentions:
21 Fields:
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Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30.
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. PMID: 25693563; PMCID: PMC4530010.
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PubMed Mentions:
3104 Fields:
Translation:
HumansCells
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Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18; 6:6351.
Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. PMID: 25690954; PMCID: PMC4346612.
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PubMed Mentions:
38 Fields:
Translation:
HumansCells
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Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363.
Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF. PMID: 25691127; PMCID: PMC4333717.
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PubMed Mentions:
54 Fields:
Translation:
HumansAnimalsCells
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Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nat Commun. 2014 Nov 25; 5:5442.
Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB. PMID: 25421844; PMCID: PMC4385735.
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PubMed Mentions:
17 Fields:
Translation:
HumansCells
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Functional annotation of colon cancer risk SNPs. Nat Commun. 2014 Sep 30; 5:5114.
Yao L, Tak YG, Berman BP, Farnham PJ. PMID: 25268989; PMCID: PMC4200523.
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PubMed Mentions:
68 Fields:
Translation:
HumansCells
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Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol. 2014 Sep 20; 15(9):469.
Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ. PMID: 25239471; PMCID: PMC4203885.
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PubMed Mentions:
92 Fields:
Translation:
HumansCells
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Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):E3366.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC. PMID: 25275169; PMCID: PMC4143047.
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PubMed Mentions:
2 Fields:
Translation:
Humans
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Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res. 2014; 42(16):10856-68.
Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ. PMID: 25122745; PMCID: PMC4176344.
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PubMed Mentions:
40 Fields:
Translation:
HumansCells
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Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. BMC Genomics. 2014 Jun 24; 15:520.
Frietze S, O'Geen H, Littlepage LE, Simion C, Sweeney CA, Farnham PJ, Krig SR. PMID: 24962896; PMCID: PMC4082627.
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PubMed Mentions:
20 Fields:
Translation:
HumansCells
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Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. PMID: 24753594; PMCID: PMC4035993.
View in:
PubMed Mentions:
325 Fields:
Translation:
HumansCells
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Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 2014 Jan; 10(1):e1004102.
Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Ellipse/GAME-ON consortium, Practical consortium, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. PMID: 24497837; PMCID: PMC3907334.
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PubMed Mentions:
113 Fields:
Translation:
HumansCells
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Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 2014; 6(5):493-501.
Grimmer MR, Farnham PJ. PMID: 25431942; PMCID: PMC4259145.
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PubMed Mentions:
7 Fields:
Translation:
HumansAnimalsCells
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Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem. 2013 Nov 29; 288(48):34287-94.
Blattler A, Farnham PJ. PMID: 24151070; PMCID: PMC3843044.
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PubMed Mentions:
118 Fields:
Translation:
HumansAnimalsCells
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Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol. 2013 Oct; 14(10):1073-83.
Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST. PMID: 24013668; PMCID: PMC3800053.
View in:
PubMed Mentions:
68 Fields:
Translation:
AnimalsCells
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Recombinant antibodies to histone post-translational modifications. Nat Methods. 2013 Oct; 10(10):992-5.
Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. PMID: 23955773; PMCID: PMC3828030.
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PubMed Mentions:
32 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC3759728.
View in:
PubMed Mentions:
97 Fields:
Translation:
HumansCells
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LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data. PLoS One. 2013; 8(6):e67788.
Wang R, Hsu HK, Blattler A, Wang Y, Lan X, Wang Y, Hsu PY, Leu YW, Huang TH, Farnham PJ, Jin VX. PMID: 23825685; PMCID: PMC3692479.
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PubMed Mentions:
10 Fields:
Translation:
HumansCells
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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; PMCID: PMC3695047.
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PubMed Mentions:
132 Fields:
Translation:
HumansCells
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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; PMCID: PMC3663758.
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PubMed Mentions:
38 Fields:
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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; PMCID: PMC3491396.
View in:
PubMed Mentions:
76 Fields:
Translation:
HumansCells
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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; PMCID: PMC3483555.
View in:
PubMed Mentions:
17 Fields:
Translation:
HumansCells
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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; PMCID: PMC4154057.
View in:
PubMed Mentions:
792 Fields:
Translation:
HumansCells
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An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74.
ENCODE Project Consortium. PMID: 22955616; PMCID: PMC3439153.
View in:
PubMed Mentions:
8680 Fields:
Translation:
HumansAnimalsCells
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Uncovering transcription factor modules using one- and three-dimensional analyses. J Biol Chem. 2012 Sep 07; 287(37):30914-21.
Lan X, Farnham PJ, Jin VX. PMID: 22952238; PMCID: PMC3438924.
View in:
PubMed Mentions:
5 Fields:
Translation:
Humans
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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; PMCID: PMC3438920.
View in:
PubMed Mentions:
10 Fields:
Translation:
Humans
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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; PMCID: PMC3431496.
View in:
PubMed Mentions:
1025 Fields:
Translation:
HumansAnimals
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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; PMCID: PMC3439894.
View in:
PubMed Mentions:
64 Fields:
Translation:
HumansCells
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Human ESC self-renewal promoting microRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFβ 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; PMCID: PMC4166560.
View in:
PubMed Mentions:
12 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC3439975.
View in:
PubMed Mentions:
69 Fields:
Translation:
HumansAnimalsCells
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Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. Methods Mol Biol. 2012; 802:323-34.
Kennedy BA, Lan X, Huang TH, Farnham PJ, Jin VX. PMID: 22130890; PMCID: PMC4160035.
View in:
PubMed Mentions:
2 Fields:
Translation:
HumansAnimalsCells
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The Human Epigenome Browser at Washington University. Nat Methods. 2011 Nov 29; 8(12):989-90.
Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PA, Costello JF, Wang T. PMID: 22127213; PMCID: PMC3552640.
View in:
PubMed Mentions:
193 Fields:
Translation:
Humans
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Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation. PLoS One. 2011; 6(11):e27740.
Jung CJ, Iyengar S, Blahnik KR, Ajuha TP, Jiang JX, Farnham PJ, Zern M. PMID: 22140464; PMCID: PMC3225380.
View in:
PubMed Mentions:
40 Fields:
Translation:
HumansAnimalsCells
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Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012 Jan; 32(1):226-39.
Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. PMID: 22025678; PMCID: PMC3255705.
View in:
PubMed Mentions:
77 Fields:
Translation:
HumansAnimalsCells
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Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13641-6.
Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. PMID: 21808000; PMCID: PMC3158141.
View in:
PubMed Mentions:
65 Fields:
Translation:
HumansCells
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KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem. 2011 Jul 29; 286(30):26267-76.
Iyengar S, Farnham PJ. PMID: 21652716; PMCID: PMC3143589.
View in:
PubMed Mentions:
203 Fields:
Translation:
HumansAnimalsCells
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L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol Cell. 2011 May 20; 42(4):438-50.
Trojer P, Cao AR, Gao Z, Li Y, Zhang J, Xu X, Li G, Losson R, Erdjument-Bromage H, Tempst P, Farnham PJ, Reinberg D. PMID: 21596310; PMCID: PMC3142354.
View in:
PubMed Mentions:
86 Fields:
Translation:
HumansCells
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A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046.
ENCODE Project Consortium. PMID: 21526222; PMCID: PMC3079585.
View in:
PubMed Mentions:
891 Fields:
Translation:
HumansCells
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Functional analysis of KAP1 genomic recruitment. Mol Cell Biol. 2011 May; 31(9):1833-47.
Iyengar S, Ivanov AV, Jin VX, Rauscher FJ, Farnham PJ. PMID: 21343339; PMCID: PMC3133220.
View in:
PubMed Mentions:
77 Fields:
Translation:
HumansCells
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Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15; 6(2):e17121.
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. PMID: 21347206; PMCID: PMC3039671.
View in:
PubMed Mentions:
53 Fields:
Translation:
HumansCells
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Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. J Biol Chem. 2011 Apr 08; 286(14):11985-96.
Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ. PMID: 21310950; PMCID: PMC3069401.
View in:
PubMed Mentions:
33 Fields:
Translation:
HumansCells
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Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol. 2011; 791:265-86.
O'Geen H, Echipare L, Farnham PJ. PMID: 21913086; PMCID: PMC4151291.
View in:
PubMed Mentions:
72 Fields:
Translation:
HumansCells
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Transcription factor effector domains. Subcell Biochem. 2011; 52:261-77.
Frietze S, Farnham PJ. PMID: 21557087; PMCID: PMC4151296.
View in:
PubMed Mentions:
27 Fields:
Translation:
Cells
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ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One. 2010 Dec 08; 5(12):e15082.
Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ. PMID: 21170338; PMCID: PMC2999557.
View in:
PubMed Mentions:
100 Fields:
Translation:
HumansCells
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Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics. 2010 Dec 02; 11:689.
O'Geen H, Lin YH, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA, Engel JD, Farnham PJ. PMID: 21126370; PMCID: PMC3019231.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansCells
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The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8.
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. PMID: 20944595; PMCID: PMC3607281.
View in:
PubMed Mentions:
999 Fields:
Translation:
HumansCells
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105.
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. PMID: 20852635; PMCID: PMC2955169.
View in:
PubMed Mentions:
346 Fields:
Translation:
HumansCells
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ZNF217, a candidate breast cancer oncogene amplified at 20q13, regulates expression of the ErbB3 receptor tyrosine kinase in breast cancer cells. Oncogene. 2010 Oct 07; 29(40):5500-10.
Krig SR, Miller JK, Frietze S, Beckett LA, Neve RM, Farnham PJ, Yaswen PI, Sweeney CA. PMID: 20661224; PMCID: PMC4256946.
View in:
PubMed Mentions:
35 Fields:
Translation:
HumansAnimalsCells
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5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics. 2010 Apr; 5(3):229-40.
Komashko VM, Farnham PJ. PMID: 20305384.
View in:
PubMed Mentions:
62 Fields:
Translation:
HumansCells
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Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol. 2010; 649:437-55.
O'Geen H, Frietze S, Farnham PJ. PMID: 20680851; PMCID: PMC4151297.
View in:
PubMed Mentions:
40 Fields:
Translation:
HumansCells
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Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009 Nov 25; 36(4):667-81.
Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. PMID: 19941826; PMCID: PMC2784893.
View in:
PubMed Mentions:
226 Fields:
Translation:
HumansAnimalsCells
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Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010 Jan; 38(3):e13.
Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ. PMID: 19906703; PMCID: PMC2817454.
View in:
PubMed Mentions:
84 Fields:
Translation:
HumansCells
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Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010 Jan 08; 285(2):1393-403.
Frietze S, Lan X, Jin VX, Farnham PJ. PMID: 19887448; PMCID: PMC2801265.
View in:
PubMed Mentions:
63 Fields:
Translation:
HumansCells
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W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics. 2009 Dec 01; 25(23):3191-3.
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ. PMID: 19797408; PMCID: PMC2778340.
View in:
PubMed Mentions:
26 Fields:
Translation:
Cells
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Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009 Sep; 10(9):605-16.
Farnham PJ. PMID: 19668247; PMCID: PMC2846386.
View in:
PubMed Mentions:
279 Fields:
Translation:
HumansAnimalsCells
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N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res. 2008 Dec 01; 68(23):9654-62.
Cotterman R, Jin VX, Krig SR, Lemen JM, Wey A, Farnham PJ, Knoepfler PS. PMID: 19047142; PMCID: PMC2637654.
View in:
PubMed Mentions:
68 Fields:
Translation:
HumansCells
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E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res. 2008 Nov; 18(11):1763-77.
Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ. PMID: 18836037; PMCID: PMC2577861.
View in:
PubMed Mentions:
85 Fields:
Translation:
HumansAnimalsCells
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Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res. 2008 Apr 15; 68(8):2641-51.
Acevedo LG, Bieda M, Green R, Farnham PJ. PMID: 18413731; PMCID: PMC2567918.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansCells
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Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res. 2008 Apr; 18(4):521-32.
Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ. PMID: 18347325; PMCID: PMC2279240.
View in:
PubMed Mentions:
32 Fields:
Translation:
HumansAnimalsCells
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Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. PMID: 18258921; PMCID: PMC2259103.
View in:
PubMed Mentions:
77 Fields:
Translation:
HumansCells
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Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques. 2007 Dec; 43(6):791-7.
Acevedo LG, Iniguez AL, Holster HL, Zhang X, Green R, Farnham PJ. PMID: 18251256; PMCID: PMC2268896.
View in:
PubMed Mentions:
35 Fields:
Translation:
HumansCells
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Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A. 2007 Dec 04; 104(49):19416-21.
Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, Lasalle JM. PMID: 18042715; PMCID: PMC2148304.
View in:
PubMed Mentions:
189 Fields:
Translation:
HumansCells
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A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res. 2007 Nov; 17(11):1550-61.
Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. PMID: 17908821; PMCID: PMC2045138.
View in:
PubMed Mentions:
135 Fields:
Translation:
HumansCells
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Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007 Jun 29; 129(7):1311-23.
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. PMID: 17604720; PMCID: PMC2084369.
View in:
PubMed Mentions:
2245 Fields:
Translation:
HumansAnimalsCells
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816.
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. PMID: 17571346; PMCID: PMC2212820.
View in:
PubMed Mentions:
2627 Fields:
Translation:
HumansCells
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Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 2007 Jun; 17(6):807-17.
Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ. PMID: 17567999; PMCID: PMC1891340.
View in:
PubMed Mentions:
35 Fields:
Translation:
HumansCells
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Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 2007 Jun; 3(6):e89.
O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. PMID: 17542650; PMCID: PMC1885280.
View in:
PubMed Mentions:
120 Fields:
Translation:
HumansCells
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Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem. 2007 Mar 30; 282(13):9703-9712.
Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ. PMID: 17259635; PMCID: PMC2269729.
View in:
PubMed Mentions:
51 Fields:
Translation:
HumansCells
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Comparison of sample preparation methods for ChIP-chip assays. Biotechniques. 2006 Nov; 41(5):577-80.
O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ. PMID: 17140114; PMCID: PMC2268903.
View in:
PubMed Mentions:
85 Fields:
Translation:
HumansAnimalsCells
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A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res. 2006 Dec; 16(12):1585-95.
Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ. PMID: 17053090; PMCID: PMC1665642.
View in:
PubMed Mentions:
38 Fields:
Translation:
HumansCells
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Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 2006 Dec; 16(12):1455-64.
Elnitski L, Jin VX, Farnham PJ, Jones SJ. PMID: 17053094.
View in:
PubMed Mentions:
91 Fields:
Translation:
HumansAnimalsCells
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Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 2006 Jul; 16(7):890-900.
Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ. PMID: 16751344; PMCID: PMC1484456.
View in:
PubMed Mentions:
161 Fields:
Translation:
HumansAnimalsCells
-
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 2006 May; 16(5):595-605.
Bieda M, Xu X, Singer MA, Green R, Farnham PJ. PMID: 16606705; PMCID: PMC1457046.
View in:
PubMed Mentions:
193 Fields:
Translation:
HumansCells
-
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res. 2005; 33(9):2952-61.
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. PMID: 15911630; PMCID: PMC1137027.
View in:
PubMed Mentions:
39 Fields:
Translation:
HumansCells
-
Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation. Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):1859-64.
Kuzmichev A, Margueron R, Vaquero A, Preissner TS, Scher M, Kirmizis A, Ouyang X, Brockdorff N, Abate-Shen C, Farnham P, Reinberg D. PMID: 15684044; PMCID: PMC548563.
View in:
PubMed Mentions:
175 Fields:
Translation:
HumansAnimalsCells
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Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med (Maywood). 2004 Sep; 229(8):705-21.
Kirmizis A, Farnham PJ. PMID: 15337825.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansAnimalsCells
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The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. J Biol Chem. 2004 Oct 29; 279(44):46343-9.
Lavrrar JL, Farnham PJ. PMID: 15328355.
View in:
PubMed Mentions:
22 Fields:
Translation:
AnimalsCells
-
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 2004 Jul 01; 18(13):1592-605.
Kirmizis A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, Green R, Farnham PJ. PMID: 15231737; PMCID: PMC443521.
View in:
PubMed Mentions:
225 Fields:
Translation:
HumansCells
-
T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. Immunity. 2004 Apr; 20(4):477-94.
Townsend MJ, Weinmann AS, Matsuda JL, Salomon R, Farnham PJ, Biron CA, Gapin L, Glimcher LH. PMID: 15084276.
View in:
PubMed Mentions:
379 Fields:
Translation:
AnimalsCells
-
High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol. 2004; 376:315-34.
Oberley MJ, Tsao J, Yau P, Farnham PJ. PMID: 14975315.
View in:
PubMed Mentions:
52 Fields:
Translation:
HumansCells
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E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. J Biol Chem. 2003 Oct 24; 278(43):42466-76.
Oberley MJ, Inman DR, Farnham PJ. PMID: 12909625.
View in:
PubMed Mentions:
34 Fields:
Translation:
HumansCells
-
Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Curr Biol. 2003 May 13; 13(10):882-6.
Mao DY, Watson JD, Yan PS, Barsyte-Lovejoy D, Khosravi F, Wong WW, Farnham PJ, Huang TH, Penn LZ. PMID: 12747840.
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PubMed Mentions:
73 Fields:
Translation:
HumansCells
-
Identification and characterization of CRG-L2, a new marker for liver tumor development. Oncogene. 2003 Mar 20; 22(11):1730-6.
Graveel CR, Harkins-Perry SR, Acevedo LG, Farnham PJ. PMID: 12642876.
View in:
PubMed Mentions:
6 Fields:
Translation:
HumansCells
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Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene. 2003 Mar 13; 22(10):1445-60.
Wells J, Yan PS, Cechvala M, Huang T, Farnham PJ. PMID: 12629508.
View in:
PubMed Mentions:
45 Fields:
Translation:
HumansCells
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Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther. 2003 Jan; 2(1):113-21.
Kirmizis A, Bartley SM, Farnham PJ. PMID: 12533679.
View in:
PubMed Mentions:
60 Fields:
Translation:
HumansAnimalsCells
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Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol. 2003; 371:577-96.
Oberley MJ, Farnham PJ. PMID: 14712730.
View in:
PubMed Mentions:
43 Fields:
Translation:
HumansCells
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Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem. 2002 Oct 18; 277(42):40156-62.
Eberhardy SR, Farnham PJ. PMID: 12177005.
View in:
PubMed Mentions:
128 Fields:
Translation:
HumansAnimalsCells
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The identification of E2F1-specific target genes. Proc Natl Acad Sci U S A. 2002 Mar 19; 99(6):3890-5.
Wells J, Graveel CR, Bartley SM, Madore SJ, Farnham PJ. PMID: 11904439; PMCID: PMC122619.
View in:
PubMed Mentions:
58 Fields:
Translation:
AnimalsCells
-
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 2002 Jan 15; 16(2):235-44.
Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ. PMID: 11799066; PMCID: PMC155318.
View in:
PubMed Mentions:
156 Fields:
Translation:
HumansCells
-
In vivo assays to examine transcription factor localization and target gene specificity. Methods. 2002 Jan; 26(1):1-2.
Farnham PJ. PMID: 12054898.
View in:
PubMed Mentions:
2 Fields:
Translation:
AnimalsCells
-
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.
View in:
PubMed Mentions:
135 Fields:
Translation:
AnimalsCells
-
Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods. 2002 Jan; 26(1):48-56.
Wells J, Farnham PJ. PMID: 12054904.
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PubMed Mentions:
96 Fields:
Translation:
HumansAnimalsCells
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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.
View in:
PubMed Mentions:
101 Fields:
Translation:
AnimalsCells
-
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; PMCID: PMC99859.
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PubMed Mentions:
139 Fields:
Translation:
HumansCells
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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; PMCID: PMC87318.
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PubMed Mentions:
92 Fields:
Translation:
HumansAnimalsCells
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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.
View in:
PubMed Mentions:
59 Fields:
Translation:
HumansAnimalsCells
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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.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansAnimalsCells
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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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PubMed Mentions:
28 Fields:
Translation:
HumansCells
-
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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PubMed Mentions:
19 Fields:
Translation:
HumansAnimalsCells
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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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PubMed Mentions:
21 Fields:
Translation:
HumansCells
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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; PMCID: PMC86057.
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PubMed Mentions:
80 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
7 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
4 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC84934.
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PubMed Mentions:
64 Fields:
Translation:
AnimalsCells
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Context-dependent transcriptional regulation. J Biol Chem. 1999 Oct 15; 274(42):29583-6.
Fry CJ, Farnham PJ. PMID: 10514422.
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PubMed Mentions:
48 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
10 Fields:
Translation:
Humans
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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
-
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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PubMed Mentions:
23 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions: Fields:
Translation:
AnimalsCells
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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; PMCID: PMC24949.
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PubMed Mentions:
99 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
24 Fields:
Translation:
AnimalsCells
-
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; PMCID: PMC232102.
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PubMed Mentions:
59 Fields:
Translation:
AnimalsCells
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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; PMCID: PMC232043.
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PubMed Mentions:
20 Fields:
Translation:
HumansAnimalsCells
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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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PubMed Mentions:
72 Fields:
Translation:
HumansAnimalsCells
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Conclusions and future directions. Curr Top Microbiol Immunol. 1996; 208:129-37.
Farnham PJ. PMID: 8575211.
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PubMed Mentions: Fields:
Translation:
Animals
-
Transcriptional regulation of the dihydrofolate reductase gene. Bioessays. 1996 Jan; 18(1):55-62.
Slansky JE, Farnham PJ. PMID: 8593164.
View in:
PubMed Mentions:
28 Fields:
Translation:
HumansAnimalsCells
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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
-
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; PMCID: PMC230483.
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PubMed Mentions:
62 Fields:
Translation:
AnimalsCells
-
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
-
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
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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.
View in:
PubMed Mentions:
4 Fields:
Translation:
Cells
-
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; PMCID: PMC310276.
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PubMed Mentions:
8 Fields:
Translation:
AnimalsCells
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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.
View in:
PubMed Mentions:
81 Fields:
Translation:
AnimalsCells
-
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; PMCID: PMC358544.
View in:
PubMed Mentions:
20 Fields:
Translation:
AnimalsCells
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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.
View in:
PubMed Mentions:
24 Fields:
Translation:
AnimalsCells
-
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.
View in:
PubMed Mentions:
8 Fields:
Translation:
HumansAnimalsCells
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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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PubMed Mentions:
35 Fields:
Translation:
AnimalsCells
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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.
View in:
PubMed Mentions:
10 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
31 Fields:
Translation:
Cells
-
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; PMCID: PMC359473.
View in:
PubMed Mentions:
96 Fields:
Translation:
AnimalsCells
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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, et al. PMID: 1638635.
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PubMed Mentions:
303 Fields:
Translation:
Cells
-
krox 20 messenger RNA and protein expression in the adult central nervous system. Brain Res Mol Brain Res. 1992 Jun; 14(1-2):117-23.
Mack KJ, Cortner J, Mack P, Farnham PJ. PMID: 1323008.
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PubMed Mentions:
6 Fields:
Translation:
AnimalsCells
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The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II. Mol Cell Biol. 1992 May; 12(5):2250-9.
Buermeyer AB, Thompson NE, Strasheim LA, Burgess RR, Farnham PJ. PMID: 1569952; PMCID: PMC364397.
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PubMed Mentions:
19 Fields:
Translation:
HumansAnimalsCells
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The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter. Mol Cell Biol. 1992 Mar; 12(3):1054-63.
Means AL, Slansky JE, McMahon SL, Knuth MW, Farnham PJ. PMID: 1545788; PMCID: PMC369537.
View in:
PubMed Mentions:
69 Fields:
Translation:
AnimalsCells
-
Heat sensitivity and Sp1 activation of complex formation at the Syrian hamster carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter in vitro. J Biol Chem. 1992 Jan 05; 267(1):385-91.
Kollmar R, Lindstrom MJ, Farnham PJ. PMID: 1346130.
View in:
PubMed Mentions:
3 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
2 Fields:
Translation:
AnimalsCells
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Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component. Gene Expr. 1991 May; 1(2):137-48.
Farnham PJ, Cornwell MM. PMID: 1820211; PMCID: PMC5952208.
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PubMed Mentions:
3 Fields:
Translation:
HumansCells
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Identification of the serum-responsive transcription initiation site of the zinc finger gene Krox-20. Mol Cell Biol. 1990 Jul; 10(7):3788-91.
Cortner J, Farnham PJ. PMID: 2113176; PMCID: PMC360834.
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PubMed Mentions:
5 Fields:
Translation:
AnimalsCells
-
Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter. Mol Cell Biol. 1990 Apr; 10(4):1390-8.
Farnham PJ, Means AL. PMID: 2320003; PMCID: PMC362241.
View in:
PubMed Mentions:
37 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
9 Fields:
Translation:
AnimalsCells
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Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site. Mol Cell Biol. 1990 Feb; 10(2):653-61.
Means AL, Farnham PJ. PMID: 2300058; PMCID: PMC360863.
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PubMed Mentions:
85 Fields:
Translation:
HumansCells
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Identification of a new promoter upstream of the murine dihydrofolate reductase gene. Mol Cell Biol. 1989 Oct; 9(10):4568-70.
Schilling LJ, Farnham PJ. PMID: 2479829; PMCID: PMC362546.
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PubMed Mentions:
7 Fields:
Translation:
AnimalsCells
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In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene. Mol Cell Biol. 1986 Jul; 6(7):2392-401.
Farnham PJ, Schimke RT. PMID: 3785199; PMCID: PMC367792.
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PubMed Mentions:
28 Fields:
Translation:
HumansAnimalsCells
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Murine dihydrofolate reductase transcripts through the cell cycle. Mol Cell Biol. 1986 Feb; 6(2):365-71.
Farnham PJ, Schimke RT. PMID: 3785152; PMCID: PMC367525.
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PubMed Mentions:
22 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
49 Fields:
Translation:
AnimalsCells
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Opposite-strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene. Proc Natl Acad Sci U S A. 1985 Jun; 82(12):3978-82.
Farnham PJ, Abrams JM, Schimke RT. PMID: 2408272; PMCID: PMC397917.
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PubMed Mentions:
48 Fields:
Translation:
AnimalsCells
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Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. Evidence for multiple promoter regions. J Biol Chem. 1985 Feb 25; 260(4):2307-14.
McGrogan M, Simonsen CC, Smouse DT, Farnham PJ, Schimke RT. PMID: 2982814.
View in:
PubMed Mentions:
52 Fields:
Translation:
AnimalsCells
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Ultrastructural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line. Proc Natl Acad Sci U S A. 1985 Feb; 82(4):1126-30.
Hamkalo BA, Farnham PJ, Johnston R, Schimke RT. PMID: 3856243; PMCID: PMC397207.
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PubMed Mentions:
36 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
60 Fields:
Translation:
Cells
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Effects of DNA base analogs on transcription termination at the tryptophan operon attenuator of EScherichia coli. Proc Natl Acad Sci U S A. 1982 Feb; 79(4):998-1002.
Farnham PJ, Platt T. PMID: 7041118; PMCID: PMC345886.
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PubMed Mentions:
5 Fields:
Translation:
Cells
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Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro. Proc Natl Acad Sci U S A. 1981 Jul; 78(7):4180-4.
Christie GE, Farnham PJ, Platt T. PMID: 7027254; PMCID: PMC319752.
View in:
PubMed Mentions:
54 Fields:
Translation:
Cells
-
Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucleic Acids Res. 1981 Feb 11; 9(3):563-77.
Farnham PJ, Platt T. PMID: 7012794; PMCID: PMC327222.
View in:
PubMed Mentions:
62 Fields:
Translation:
Cells
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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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PubMed Mentions:
43 Fields:
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Cells
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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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PubMed Mentions:
5 Fields:
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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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1 Fields:
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Animals