A survey of motif discovery methods in an integrated framework.

Sandve GK, Drabløs F.

Biol Direct. 2006 Apr 6;1:11.

PMID: 16600018 [PubMed]

Related Articles Free article in PMC

Discovering motifs in ranked lists of DNA sequences.

Eden E, Lipson D, Yogev S, Yakhini Z.

PLoS Comput Biol. 2007 Mar 23;3(3):e39.

PMID: 17381235 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Improved benchmarks for computational motif discovery.

Sandve GK, Abul O, Walseng V, Drabløs F.

BMC Bioinformatics. 2007 Jun 8;8:193.

PMID: 17559676 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.

Wei W, Yu XD.

Genomics Proteomics Bioinformatics. 2007 May;5(2):131-42.

PMID: 17893078 [PubMed - indexed for MEDLINE]

Related Articles

Computational identification of transcriptional regulatory elements in DNA sequence.

GuhaThakurta D.

Nucleic Acids Res. 2006 Jul 19;34(12):3585-98. Print 2006. Review.

PMID: 16855295 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

How to reduce false positive results when undertaking in vitro genotoxicity testing and thus avoid unnecessary follow-up animal tests: Report of an ECVAM Workshop.

Kirkland D, Pfuhler S, Tweats D, Aardema M, Corvi R, Darroudi F, Elhajouji A, Glatt H, Hastwell P, Hayashi M, Kasper P, Kirchner S, Lynch A, Marzin D, Maurici D, Meunier JR, Müller L, Nohynek G, Parry J, Parry E, Thybaud V, Tice R, van Benthem J, Vanparys P, White P.

Mutat Res. 2007 Mar 30;628(1):31-55. Epub 2007 Jan 13.

PMID: 17293159 [PubMed - indexed for MEDLINE]

Related Articles

MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs.

Kato M, Tsunoda T.

BMC Bioinformatics. 2007 Mar 22;8:100.

PMID: 17378935 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves.

Berendzen KW, Stüber K, Harter K, Wanke D.

BMC Bioinformatics. 2006 Nov 30;7:522.

PMID: 17137509 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

[Development of antituberculous drugs: current status and future prospects]

Tomioka H, Namba K.

Kekkaku. 2006 Dec;81(12):753-74. Review. Japanese.

PMID: 17240921 [PubMed - indexed for MEDLINE]

Related Articles

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

PMID: 16716228 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Finding regulatory elements and regulatory motifs: a general probabilistic framework.

van Nimwegen E.

BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S4. Review.

PMID: 17903285 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

A classification-based framework for predicting and analyzing gene regulatory response.

Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C.

BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S5.

PMID: 16723008 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Cost-effectiveness of using prognostic information to select women with breast cancer for adjuvant systemic therapy.

Williams C, Brunskill S, Altman D, Briggs A, Campbell H, Clarke M, Glanville J, Gray A, Harris A, Johnston K, Lodge M.

Health Technol Assess. 2006 Sep;10(34):iii-iv, ix-xi, 1-204. Review.

PMID: 16959170 [PubMed - indexed for MEDLINE]

Related Articles

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.

PMID: 17683565 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Kernel-imbedded Gaussian processes for disease classification using microarray gene expression data.

Zhao X, Cheung LW.

BMC Bioinformatics. 2007 Feb 28;8:67.

PMID: 17328811 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Method of predicting splice sites based on signal interactions.

Churbanov A, Rogozin IB, Deogun JS, Ali H.

Biol Direct. 2006 Apr 3;1:10.

PMID: 16584568 [PubMed]

Related Articles Free article in PMC

A computational analysis of the three isoforms of glutamate dehydrogenase reveals structural features of the isoform EC 1.4.1.4 supporting a key role in ammonium assimilation by plants.

Jaspard E.

Biol Direct. 2006 Dec 15;1:38.

PMID: 17173671 [PubMed]

Related Articles Free article in PMC

CoMoDis: composite motif discovery in mammalian genomes.

Donaldson IJ, Göttgens B.

Nucleic Acids Res. 2007;35(1):e1. Epub 2006 Nov 27.

PMID: 17130158 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Analysis of computational approaches for motif discovery.

Li N, Tompa M.

Algorithms Mol Biol. 2006 May 19;1:8.

PMID: 16722558 [PubMed]

Related Articles Free article in PMC

Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples.

Novak JP, Miller MC 3rd, Bell DA.

Biol Direct. 2006 Jun 20;1:18.

PMID: 16787528 [PubMed]

Related Articles Free article in PMC