E-Predict: a computational strategy for species id...[Genome Biol. 2005]

SearchDatabase nameforSearch term

Advanced Search

Your browser version may not work well with NCBI's Web applications. More information here...

Display Show

All: 1

Review: 0

Click to change filter selection through MyNCBI.

1: Genome Biol. 2005;6(9):R78. Epub 2005 Aug 30. Links

E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.

Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.

Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA. anatoly@derisilab.ucsf.edu

DNA microarrays may be used to identify microbial species present in environmental and clinical samples. However, automated tools for reliable species identification based on observed microarray hybridization patterns are lacking. We present an algorithm, E-Predict, for microarray-based species identification. E-Predict compares observed hybridization patterns with theoretical energy profiles representing different species. We demonstrate the application of the algorithm to viral detection in a set of clinical samples and discuss its relevance to other metagenomic applications.

PMID: 16168085 [PubMed - indexed for MEDLINE]

PMCID: PMC1242213

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data.
Genome Biol. 2007; 8(9):R190.

[Genome Biol. 2007]
FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data.
BMC Bioinformatics. 2007 Jan 4; 8:3. Epub 2007 Jan 4.

[BMC Bioinformatics. 2007]
Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.
Bioinformatics. 2006 Jul 1; 22(13):1665-7. Epub 2006 May 3.

[Bioinformatics. 2006]
ReviewComparative environmental genomics in non-model species: using heterologous hybridization to DNA-based microarrays.
J Exp Biol. 2007 May; 210(Pt 9):1602-6.

[J Exp Biol. 2007]
ReviewMicroarrays--identifying molecular portraits for prostate tumors with different Gleason patterns.
Methods Mol Med. 2008; 141:131-51.

[Methods Mol Med. 2008]
» See reviews... | » See all...

Cited by 11 PubMed Central articles

Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.
Liu Y, Sam L, Li J, Lussier YA. BMC Bioinformatics. 2009 Feb 5; 10 Suppl 2:S11. Epub 2009 Feb 5.

[BMC Bioinformatics. 2009]
Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections.
Chiu CY, Greninger AL, Kanada K, Kwok T, Fischer KF, Runckel C, Louie JK, Glaser CA, Yagi S, Schnurr DP, et al. Proc Natl Acad Sci U S A. 2008 Sep 16; 105(37):14124-9. Epub 2008 Sep 3.

[Proc Natl Acad Sci U S A. 2008]
Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.
Kistler AL, Gancz A, Clubb S, Skewes-Cox P, Fischer K, Sorber K, Chiu CY, Lublin A, Mechani S, Farnoushi Y, et al. Virol J. 2008 Jul 31; 5:88. Epub 2008 Jul 31.

[Virol J. 2008]
» See all...

Recent Activity

Clear Turn Off Turn On

E-Predict: a computational strategy for species identification based on observed DNA micro...E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Display Show

E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.

Related articles

Cited by 11 PubMed Central articles

Recent Activity