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Results: 1 to 20 of 257

1.

Re-annotation is an essential step in systems biology modeling of functional genomics data.

van den Berg BH, McCarthy FM, Lamont SJ, Burgess SC.

PLoS One. 2010 May 14;5(5):e10642. doi: 10.1371/journal.pone.0010642.

PMID:
20498845
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.

van den Berg BH, Konieczka JH, McCarthy FM, Burgess SC.

BMC Bioinformatics. 2009 Jan 23;10:30. doi: 10.1186/1471-2105-10-30.

PMID:
19166590
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Structural and functional-annotation of an equine whole genome oligoarray.

Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S8. doi: 10.1186/1471-2105-10-S11-S8.

PMID:
19811692
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

MILANO--custom annotation of microarray results using automatic literature searches.

Rubinstein R, Simon I.

BMC Bioinformatics. 2005 Jan 20;6:12.

PMID:
15661078
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Where are we in genomics?

Hocquette JF.

J Physiol Pharmacol. 2005 Jun;56 Suppl 3:37-70. Review.

PMID:
16077195
[PubMed - indexed for MEDLINE]
Free Article
6.

Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology.

Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G.

BMC Genomics. 2008 Jul 24;9:347. doi: 10.1186/1471-2164-9-347.

PMID:
18652646
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Facilitating functional annotation of chicken microarray data.

Buza TJ, Kumar R, Gresham CR, Burgess SC, McCarthy FM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S2. doi: 10.1186/1471-2105-10-S11-S2.

PMID:
19811685
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA.

BMC Bioinformatics. 2007 Nov 2;8:426.

PMID:
17980028
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

GOing from functional genomics to biological significance.

McCarthy FM, Bridges SM, Burgess SC.

Cytogenet Genome Res. 2007;117(1-4):278-87.

PMID:
17675869
[PubMed - indexed for MEDLINE]
10.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6. Epub 2007 May 3.

PMID:
17478504
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Practical applications of structural genomics technologies for mutagen research.

Zemla A, Segelke BW.

Mutat Res. 2011 Jun 17;722(2):165-70. doi: 10.1016/j.mrgentox.2010.12.006. Epub 2010 Dec 21.

PMID:
21182983
[PubMed - indexed for MEDLINE]
12.

[Transcriptomes for serial analysis of gene expression].

Marti J, Piquemal D, Manchon L, Commes T.

J Soc Biol. 2002;196(4):303-7. Review. French.

PMID:
12645300
[PubMed - indexed for MEDLINE]
13.

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data.

van den Berg BH, Thanthiriwatte C, Manda P, Bridges SM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S9. doi: 10.1186/1471-2105-10-S11-S9.

PMID:
19811693
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.

Paschall JE, Oleksiak MF, VanWye JD, Roach JL, Whitehead JA, Wyckoff GJ, Kolell KJ, Crawford DL.

BMC Genomics. 2004 Dec 20;5(1):96.

PMID:
15610557
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Microarray annotation and biological information on function.

Brors B.

Methods Inf Med. 2005;44(3):468-72.

PMID:
16113775
[PubMed - indexed for MEDLINE]
16.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6.

PMID:
16845052
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes.

Cogburn LA, Wang X, Carre W, Rejto L, Porter TE, Aggrey SE, Simon J.

Poult Sci. 2003 Jun;82(6):939-51.

PMID:
12817449
[PubMed - indexed for MEDLINE]
18.

A procedure for assessing GO annotation consistency.

Dolan ME, Ni L, Camon E, Blake JA.

Bioinformatics. 2005 Jun;21 Suppl 1:i136-43.

PMID:
15961450
[PubMed - indexed for MEDLINE]
Free Article
19.

Gene Ontology annotation quality analysis in model eukaryotes.

Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC.

Nucleic Acids Res. 2008 Feb;36(2):e12. doi: 10.1093/nar/gkm1167. Epub 2008 Jan 10.

PMID:
18187504
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Modeling of gene regulatory network dynamics using threshold logic.

Gowda T, Vrudhula S, Kim S.

Ann N Y Acad Sci. 2009 Mar;1158:71-81. doi: 10.1111/j.1749-6632.2008.03754.x.

PMID:
19348633
[PubMed - indexed for MEDLINE]

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