PubMed

GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data.

Carvalho PC, Fischer JS, Chen EI, Domont GB, Carvalho MG, Degrave WM, Yates JR 3rd, Barbosa VC.

Proteome Sci. 2009 Feb 24;7:6.PMID: 19239707 [PubMed]Related articlesFree article

PatternLab for proteomics: a tool for differential shotgun proteomics.

Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC.

BMC Bioinformatics. 2008 Jul 21;9:316.PMID: 18644148 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol.

Fischer JD, Liao L, Carvalho PC, Barbosa VC, Domont GB, Carvalho MD, Yates JR 3rd.

J Proteomics. 2010 Mar 10;73(5):1018-1027. Epub 2010 Jan 18.PMID: 20083244 [PubMed - as supplied by publisher]Related articles

GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data.

Sun H, Fang H, Chen T, Perkins R, Tong W.

BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S23.PMID: 17118145 [PubMed - in process]Related articlesFree article

PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison.

Kim T, Kim E, Park SJ, Joo H.

Comput Biol Med. 2009 Aug;39(8):689-96. Epub 2009 Jun 21.PMID: 19541297 [PubMed - indexed for MEDLINE]Related articles

Identifying differences in protein expression levels by spectral counting and feature selection.

Carvalho PC, Hewel J, Barbosa VC, Yates JR 3rd.

Genet Mol Res. 2008 Apr 15;7(2):342-56.PMID: 18551400 [PubMed - indexed for MEDLINE]Related articlesFree article

GOGrapher: A Python library for GO graph representation and analysis.

Muller B, Richards AJ, Jin B, Lu X.

BMC Res Notes. 2009 Jul 7;2:122.PMID: 19583843 [PubMed]Related articlesFree article

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae.

Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA.

BMC Microbiol. 2009 Feb 19;9 Suppl 1:S8. Review.PMID: 19278556 [PubMed - indexed for MEDLINE]Related articlesFree article

Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis.

White CA, Oey N, Emili A.

J Proteome Res. 2009 Jul;8(7):3653-65.PMID: 19400582 [PubMed - indexed for MEDLINE]Related articles

Computational annotation of genes differentially expressed along olive fruit development.

Galla G, Barcaccia G, Ramina A, Collani S, Alagna F, Baldoni L, Cultrera NG, Martinelli F, Sebastiani L, Tonutti P.

BMC Plant Biol. 2009 Oct 24;9:128.PMID: 19852839 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology.

Xu T, Gu J, Zhou Y, Du L.

BMC Bioinformatics. 2009 Aug 5;10:240.PMID: 19653916 [PubMed - indexed for MEDLINE]Related articlesFree article

Introducing the CPL/MUW proteome database: interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells.

Wimmer H, Gundacker NC, Griss J, Haudek VJ, Stättner S, Mohr T, Zwickl H, Paulitschke V, Baron DM, Trittner W, Kubicek M, Bayer E, Slany A, Gerner C.

Electrophoresis. 2009 Jun;30(12):2076-89.PMID: 19582709 [PubMed - indexed for MEDLINE]Related articles

Shotgun proteomics approach to characterizing the embryonic proteome of the silkworm, Bombyx mori, at labrum appearance stage.

Li JY, Chen X, Hosseini Moghaddam SH, Chen M, Wei H, Zhong BX.

Insect Mol Biol. 2009 Oct;18(5):649-60.PMID: 19754742 [PubMed - indexed for MEDLINE]Related articles

EGOMiner: a comprehensive genomics and proteomics data analysis and biological function interpretation system.

Feng W, Henning P, Wang MD.

Conf Proc IEEE Eng Med Biol Soc. 2004;4:2809-12.PMID: 17270861 [PubMed]Related articles

Mapping the lung proteome in cystic fibrosis.

Gharib SA, Vaisar T, Aitken ML, Park DR, Heinecke JW, Fu X.

J Proteome Res. 2009 Jun;8(6):3020-8.PMID: 19354268 [PubMed - indexed for MEDLINE]Related articles

Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors.

Zybailov BL, Florens L, Washburn MP.

Mol Biosyst. 2007 May;3(5):354-60. Epub 2007 Apr 10.PMID: 17460794 [PubMed - indexed for MEDLINE]Related articles

Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability.

Park JC, Kim TE, Park J.

BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S7.PMID: 18426552 [PubMed - indexed for MEDLINE]Related articlesFree article

KAIKObase: an integrated silkworm genome database and data mining tool.

Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, Antonio B, Nagamura Y, Kadono-Okuda K, Kajiwara H, Sezutsu H, Nagaraju J, Goldsmith MR, Xia Q, Yamamoto K, Mita K.

BMC Genomics. 2009 Oct 21;10:486.PMID: 19843344 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating shotgun proteomics and mRNA expression data to improve protein identification.

Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R.

Bioinformatics. 2009 Jun 1;25(11):1397-403. Epub 2009 Mar 24.PMID: 19318424 [PubMed - indexed for MEDLINE]Related articlesFree article

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function.

Grobei MA, Qeli E, Brunner E, Rehrauer H, Zhang R, Roschitzki B, Basler K, Ahrens CH, Grossniklaus U.

Genome Res. 2009 Oct;19(10):1786-800. Epub 2009 Jun 22.PMID: 19546170 [PubMed - indexed for MEDLINE]Related articles