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Items: 1 to 20 of 33


A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors.

Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ.

Cell. 2009 Jul 23;138(2):314-27. doi: 10.1016/j.cell.2009.04.058.


Biofilm matrix regulation by Candida albicans Zap1.

Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault JS, Nantel A, Andes DR, Johnson AD, Mitchell AP.

PLoS Biol. 2009 Jun;7(6):e1000133. doi: 10.1371/journal.pbio.1000133. Epub 2009 Jun 16.


Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.


High-resolution DNA-binding specificity analysis of yeast transcription factors.

Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML.

Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21.


A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.


An integrated software system for analyzing ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.

Nat Biotechnol. 2008 Nov;26(11):1293-300. doi: 10.1038/nbt.1505. Epub 2008 Nov 2.


UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Newburger DE, Bulyk ML.

Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82. doi: 10.1093/nar/gkn660. Epub 2008 Oct 8.


MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.

Wijaya E, Yiu SM, Son NT, Kanagasabai R, Sung WK.

Bioinformatics. 2008 Oct 15;24(20):2288-95. doi: 10.1093/bioinformatics/btn420. Epub 2008 Aug 12.


BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.


Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.


An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.

Casimiro AC, Vinga S, Freitas AT, Oliveira AL.

BMC Bioinformatics. 2008 Feb 7;9:89. doi: 10.1186/1471-2105-9-89.


JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6. Epub 2007 Nov 15.


Quantifying similarity between motifs.

Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS.

Genome Biol. 2007;8(2):R24.


SwissRegulon: a database of genome-wide annotations of regulatory sites.

Pachkov M, Erb I, Molina N, van Nimwegen E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D127-31. Epub 2006 Nov 27.


Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML.

Nat Biotechnol. 2006 Nov;24(11):1429-35. Epub 2006 Sep 24.


Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

Foat BC, Morozov AV, Bussemaker HJ.

Bioinformatics. 2006 Jul 15;22(14):e141-9.


MEME: discovering and analyzing DNA and protein sequence motifs.

Bailey TL, Williams N, Misleh C, Li WW.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73.


What are DNA sequence motifs?

D'haeseleer P.

Nat Biotechnol. 2006 Apr;24(4):423-5.


An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E.

BMC Bioinformatics. 2006 Mar 7;7:113.

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