Format
Sort by

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 103

1.

Analysis of variation at transcription factor binding sites in Drosophila and humans.

Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E.

Genome Biol. 2012 Sep 28;13(9):R49. doi: 10.1186/gb-2012-13-9-r49.

2.

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.

Polavarapu N, Mariño-Ramírez L, Landsman D, McDonald JF, Jordan IK.

BMC Genomics. 2008 May 17;9:226. doi: 10.1186/1471-2164-9-226.

3.

A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites.

Santolini M, Mora T, Hakim V.

PLoS One. 2014 Jun 13;9(6):e99015. doi: 10.1371/journal.pone.0099015. eCollection 2014.

4.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

5.

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs.

Garcia-Alcalde F, Blanco A, Shepherd AJ.

BMC Bioinformatics. 2010 Nov 8;11:551. doi: 10.1186/1471-2105-11-551.

6.

Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs.

Starr MO, Ho MC, Gunther EJ, Tu YK, Shur AS, Goetz SE, Borok MJ, Kang V, Drewell RA.

Dev Biol. 2011 Nov 15;359(2):290-302. doi: 10.1016/j.ydbio.2011.07.028. Epub 2011 Jul 28.

7.

Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns.

Chan TM, Leung KS, Lee KH, Wong MH, Lau TC, Tsui SK.

Nucleic Acids Res. 2012 Oct;40(19):9392-403. doi: 10.1093/nar/gks749. Epub 2012 Aug 16.

8.

On the identification of potential regulatory variants within genome wide association candidate SNP sets.

Chen CY, Chang IS, Hsiung CA, Wasserman WW.

BMC Med Genomics. 2014 Jun 11;7:34. doi: 10.1186/1755-8794-7-34.

9.

CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing.

Ray P, Shringarpure S, Kolar M, Xing EP.

PLoS Comput Biol. 2008 Jun 6;4(6):e1000090. doi: 10.1371/journal.pcbi.1000090.

10.

P-value-based regulatory motif discovery using positional weight matrices.

Hartmann H, Guthöhrlein EW, Siebert M, Luehr S, Söding J.

Genome Res. 2013 Jan;23(1):181-94. doi: 10.1101/gr.139881.112. Epub 2012 Sep 18.

11.

An information transmission model for transcription factor binding at regulatory DNA sites.

Tan M, Yu D, Jin Y, Dou L, Li B, Wang Y, Yue J, Liang L.

Theor Biol Med Model. 2012 Jun 6;9:19. doi: 10.1186/1742-4682-9-19.

12.

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.

BMC Genomics. 2014 Jun 13;15:472. doi: 10.1186/1471-2164-15-472.

13.

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster.

Marco A, Konikoff C, Karr TL, Kumar S.

Bioinformatics. 2009 Oct 1;25(19):2473-7. doi: 10.1093/bioinformatics/btp462. Epub 2009 Jul 24.

14.

Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

He BZ, Holloway AK, Maerkl SJ, Kreitman M.

PLoS Genet. 2011 Apr;7(4):e1002053. doi: 10.1371/journal.pgen.1002053. Epub 2011 Apr 28.

15.

Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome.

Morozov VY, Ioshikhes IP.

PLoS One. 2013 Aug 6;8(8):e68712. doi: 10.1371/journal.pone.0068712. Print 2013.

16.

Selective constraints in experimentally defined primate regulatory regions.

Gaffney DJ, Blekhman R, Majewski J.

PLoS Genet. 2008 Aug 15;4(8):e1000157. doi: 10.1371/journal.pgen.1000157.

17.

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.

Oh YM, Kim JK, Choi S, Yoo JY.

Nucleic Acids Res. 2012 Mar;40(5):e38. doi: 10.1093/nar/gkr1252. Epub 2011 Dec 19.

18.
19.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

20.

Low nucleosome occupancy is encoded around functional human transcription factor binding sites.

Daenen F, van Roy F, De Bleser PJ.

BMC Genomics. 2008 Jul 15;9:332. doi: 10.1186/1471-2164-9-332.

Items per page

Supplemental Content

Write to the Help Desk