PubMed

Similarity searches in genome-wide numerical data sets.

Glazko G, Coleman M, Mushegian A.

Biol Direct. 2006 May 30;1:13.PMID: 16734895 [PubMed]Related articlesFree article

Evaluating the protein coding potential of exonized transposable element sequences.

Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK.

Biol Direct. 2007 Nov 26;2:31.PMID: 18036258 [PubMed - indexed for MEDLINE]Related articlesFree article

Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data.

Gilchrist MJ, Christensen MB, Harland R, Pollet N, Smith JC, Ueno N, Papalopulu N.

BMC Bioinformatics. 2008 Oct 17;9:442.PMID: 18928517 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of biochemical pathways by probabilistic matching of phyletic vectors.

Li H, Kristensen DM, Coleman MK, Mushegian A.

PLoS One. 2009;4(4):e5326. Epub 2009 Apr 24.PMID: 19390636 [PubMed - indexed for MEDLINE]Related articlesFree article

A search engine to identify pathway genes from expression data on multiple organisms.

Chen C, Weirauch MT, Powell CC, Zambon AC, Stuart JM.

BMC Syst Biol. 2007 May 4;1:20.PMID: 17477880 [PubMed - indexed for MEDLINE]Related articlesFree article

Database similarity searches.

Plewniak F.

Methods Mol Biol. 2008;484:361-78.PMID: 18592192 [PubMed - indexed for MEDLINE]Related articles

Sequence context-specific profiles for homology searching.

Biegert A, Söding J.

Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3770-5. Epub 2009 Feb 20.PMID: 19234132 [PubMed - indexed for MEDLINE]Related articlesFree article

Relative avidity, specificity, and sensitivity of transcription factor-DNA binding in genome-scale experiments.

Kuznetsov VA.

Methods Mol Biol. 2009;563:15-50.PMID: 19597778 [PubMed - indexed for MEDLINE]Related articles

The BioPrompt-box: an ontology-based clustering tool for searching in biological databases.

Corsi C, Ferragina P, Marangoni R.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S8.PMID: 17430575 [PubMed - indexed for MEDLINE]Related articlesFree article

A new probabilistic database search algorithm for ETD spectra.

Sadygov RG, Good DM, Swaney DL, Coon JJ.

J Proteome Res. 2009 Jun;8(6):3198-205.PMID: 19354237 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments.

Tanner SW, Agarwal P.

BMC Bioinformatics. 2008 Aug 22;9:348.PMID: 18721468 [PubMed - indexed for MEDLINE]Related articlesFree article

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 articlesFree article

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.

Xie L, Xie L, Bourne PE.

Bioinformatics. 2009 Jun 15;25(12):i305-12.PMID: 19478004 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene-based bin analysis of genome-wide association studies.

Omont N, Forner K, Lamarine M, Martin G, Képès F, Wojcik J.

BMC Proc. 2008 Dec 17;2 Suppl 4:S6.PMID: 19091053 [PubMed]Related articlesFree article

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

Redhead E, Bailey TL.

BMC Bioinformatics. 2007 Oct 15;8:385.PMID: 17937785 [PubMed - indexed for MEDLINE]Related articlesFree article

Tracing globin phylogeny using PSIBLAST searches based on groups of sequences.

Vinogradov SN.

Methods Enzymol. 2008;436:571-83.PMID: 18237654 [PubMed - indexed for MEDLINE]Related articles

ESG: extended similarity group method for automated protein function prediction.

Chitale M, Hawkins T, Park C, Kihara D.

Bioinformatics. 2009 Jul 15;25(14):1739-45. Epub 2009 May 12.PMID: 19435743 [PubMed - indexed for MEDLINE]Related articles

Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.

Yan B, Lovley DR, Krushkal J.

Biosystems. 2007 Sep-Oct;90(2):421-41. Epub 2006 Oct 26.PMID: 17184904 [PubMed - indexed for MEDLINE]Related articles

Strategies and issues in the detection of pathway enrichment in genome-wide association studies.

Hong MG, Pawitan Y, Magnusson PK, Prince JA.

Hum Genet. 2009 Aug;126(2):289-301. Epub 2009 May 1.PMID: 19408013 [PubMed - indexed for MEDLINE]Related articles

How to decide which are the most pertinent overly-represented features during gene set enrichment analysis.

Barriot R, Sherman DJ, Dutour I.

BMC Bioinformatics. 2007 Sep 11;8:332.PMID: 17848190 [PubMed - indexed for MEDLINE]Related articlesFree article