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Results: 15

1.

uORFdb--a comprehensive literature database on eukaryotic uORF biology.

Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D60-7. doi: 10.1093/nar/gkt952. Epub 2013 Oct 24.

PMID:
24163100
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Preimplantation development regulatory pathway construction through a text-mining approach.

Donnard E, Barbosa-Silva A, Guedes RL, Fernandes GR, Velloso H, Kohn MJ, Andrade-Navarro MA, Ortega JM.

BMC Genomics. 2011 Dec 22;12 Suppl 4:S3. doi: 10.1186/1471-2164-12-S4-S3. Epub 2011 Dec 22.

PMID:
22369103
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Caipirini: using gene sets to rank literature.

Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R.

BioData Min. 2012 Feb 1;5(1):1. doi: 10.1186/1756-0381-5-1.

PMID:
22297131
[PubMed]
Free PMC Article
4.

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.

Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA.

BMC Bioinformatics. 2011 Nov 9;12:435. doi: 10.1186/1471-2105-12-435.

PMID:
22070195
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Génie: literature-based gene prioritization at multi genomic scale.

Fontaine JF, Priller F, Barbosa-Silva A, Andrade-Navarro MA.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W455-61. doi: 10.1093/nar/gkr246. Epub 2011 May 23.

PMID:
21609954
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A reference guide for tree analysis and visualization.

Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R.

BioData Min. 2010 Feb 22;3(1):1. doi: 10.1186/1756-0381-3-1.

PMID:
20175922
[PubMed]
Free PMC Article
7.

LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships.

Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM.

BMC Bioinformatics. 2010 Feb 1;11:70. doi: 10.1186/1471-2105-11-70.

PMID:
20122157
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Martini: using literature keywords to compare gene sets.

Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R.

Nucleic Acids Res. 2010 Jan;38(1):26-38. doi: 10.1093/nar/gkp876. Epub 2009 Oct 25.

PMID:
19858102
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

MedlineRanker: flexible ranking of biomedical literature.

Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W141-6. doi: 10.1093/nar/gkp353. Epub 2009 May 8.

PMID:
19429696
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model.

Fernandes GR, Barbosa DV, Prosdocimi F, Pena IA, Santana-Santos L, Coelho Junior O, Barbosa-Silva A, Velloso HM, Mudado MA, Natale DA, Faria-Campos AC, Aguiar SC, Ortega JM.

Genet Mol Res. 2008 Sep 30;7(3):910-24.

PMID:
18949709
[PubMed - indexed for MEDLINE]
Free Article
11.

Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence.

Barbosa-Silva A, Satagopam VP, Schneider R, Ortega JM.

BMC Bioinformatics. 2008 Mar 5;9:141. doi: 10.1186/1471-2105-9-141.

PMID:
18321373
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

Barbosa-Silva A, Pafilis E, Ortega JM, Schneider R.

Genet Mol Res. 2007 Dec 11;6(4):1142-50.

PMID:
18273808
[PubMed - indexed for MEDLINE]
Free Article
13.

Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis.

Wanderley-Nogueira AC, Soares-Cavalcanti NM, Morais DA, Belarmino LC, Barbosa-Silva A, Benko-Iseppon AM.

Genet Mol Res. 2007 Oct 5;6(4):866-89.

PMID:
18058709
[PubMed - indexed for MEDLINE]
Free Article
14.

Moving pieces in a taxonomic puzzle: venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones).

Nascimento DG, Rates B, Santos DM, Verano-Braga T, Barbosa-Silva A, Dutra AA, Biondi I, Martin-Eauclaire MF, De Lima ME, Pimenta AM.

Toxicon. 2006 May;47(6):628-39. Epub 2006 Mar 23.

PMID:
16551474
[PubMed - indexed for MEDLINE]
15.

PROTOGIM: a novel tool to search motifs and domains in hypothetical proteins of protozoan genomes.

Cestari IS, Haver NJ, Barbosa-Silva A, Ramirez MI.

Parasitol Res. 2006 Mar;98(4):375-7. Epub 2005 Dec 13.

PMID:
16362340
[PubMed - indexed for MEDLINE]

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