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Items: 1 to 20 of 124

1.

A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease.

Wang T, Furey TS, Connelly JJ, Ji S, Nelson S, Heber S, Gregory SG, Hauser ER.

Hum Genomics. 2009 Apr;3(3):221-35.

2.

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.

Ameur A, Rada-Iglesias A, Komorowski J, Wadelius C.

Nucleic Acids Res. 2009 Jul;37(12):e85. doi: 10.1093/nar/gkp381. Epub 2009 May 18.

3.

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.

Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C.

Genome Res. 2008 Mar;18(3):380-92. doi: 10.1101/gr.6880908. Epub 2008 Jan 29.

4.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
5.

Genome-wide analyses in neuronal cells reveal that upstream transcription factors regulate lysosomal gene expression.

Yamanaka T, Tosaki A, Kurosawa M, Shimogori T, Hattori N, Nukina N.

FEBS J. 2016 Mar;283(6):1077-87. doi: 10.1111/febs.13650. Epub 2016 Feb 11.

6.

CTF: a CRF-based transcription factor binding sites finding system.

He Y, Zhang Y, Zheng G, Wei C.

BMC Genomics. 2012;13 Suppl 8:S18. doi: 10.1186/1471-2164-13-S8-S18. Epub 2012 Dec 17.

7.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data.

Levitsky VG, Kulakovskiy IV, Ershov NI, Oshchepkov DY, Makeev VJ, Hodgman TC, Merkulova TI.

BMC Genomics. 2014 Jan 29;15:80. doi: 10.1186/1471-2164-15-80.

8.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

9.

Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3.

Vallania F, Schiavone D, Dewilde S, Pupo E, Garbay S, Calogero R, Pontoglio M, Provero P, Poli V.

Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5117-22. doi: 10.1073/pnas.0900473106. Epub 2009 Mar 12.

10.

A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques.

Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M.

PLoS One. 2010 Dec 29;5(12):e15898. doi: 10.1371/journal.pone.0015898.

11.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

Whitington T, Perkins AC, Bailey TL.

Nucleic Acids Res. 2009 Jan;37(1):14-25. doi: 10.1093/nar/gkn866. Epub 2008 Nov 6.

12.

Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice.

Shimomura K, Kumar V, Koike N, Kim TK, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR, Richards M, Yoo SH, Hong HK, Vitaterna MH, Bass J, Pletcher MT, Wiltshire T, Hogenesch J, Lowrey PL, Takahashi JS.

Elife. 2013 Apr 9;2:e00426. doi: 10.7554/eLife.00426.

13.

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

Guo Y, Mahony S, Gifford DK.

PLoS Comput Biol. 2012;8(8):e1002638. doi: 10.1371/journal.pcbi.1002638. Epub 2012 Aug 9.

14.

Transcription factor binding sites prediction based on modified nucleosomes.

Talebzadeh M, Zare-Mirakabad F.

PLoS One. 2014 Feb 21;9(2):e89226. doi: 10.1371/journal.pone.0089226. eCollection 2014.

15.

Tree-based position weight matrix approach to model transcription factor binding site profiles.

Bi Y, Kim H, Gupta R, Davuluri RV.

PLoS One. 2011;6(9):e24210. doi: 10.1371/journal.pone.0024210. Epub 2011 Sep 2.

16.

A systems biology approach to transcription factor binding site prediction.

Zhou X, Sumazin P, Rajbhandari P, Califano A.

PLoS One. 2010 Mar 26;5(3):e9878. doi: 10.1371/journal.pone.0009878.

17.

Upstream stimulatory factor 1 activates GATA5 expression through an E-box motif.

Chen B, Hsu R, Li Z, Kogut PC, Du Q, Rouser K, Camoretti-Mercado B, Solway J.

Biochem J. 2012 Aug 15;446(1):89-98. doi: 10.1042/BJ20111942.

18.

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

Wallerman O, Motallebipour M, Enroth S, Patra K, Bysani MS, Komorowski J, Wadelius C.

Nucleic Acids Res. 2009 Dec;37(22):7498-508. doi: 10.1093/nar/gkp823.

19.

Gene trapping uncovers sex-specific mechanisms for upstream stimulatory factors 1 and 2 in angiotensinogen expression.

Park S, Liu X, Davis DR, Sigmund CD.

Hypertension. 2012 Jun;59(6):1212-9. doi: 10.1161/HYPERTENSIONAHA.112.192971. Epub 2012 Apr 30.

20.

Human prolyl-4-hydroxylase alpha(I) transcription is mediated by upstream stimulatory factors.

Chen L, Shen YH, Wang X, Wang J, Gan Y, Chen N, Wang J, LeMaire SA, Coselli JS, Wang XL.

J Biol Chem. 2006 Apr 21;281(16):10849-55. Epub 2006 Feb 17.

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