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MOPED: Model Organism Protein Expression Database.

Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1093-9. doi: 10.1093/nar/gkr1177. Epub 2011 Dec 1.


MOPED enables discoveries through consistently processed proteomics data.

Higdon R, Stewart E, Stanberry L, Haynes W, Choiniere J, Montague E, Anderson N, Yandl G, Janko I, Broomall W, Fishilevich S, Lancet D, Kolker N, Kolker E.

J Proteome Res. 2014 Jan 3;13(1):107-13. doi: 10.1021/pr400884c. Epub 2013 Dec 18.


SPIRE: Systematic protein investigative research environment.

Kolker E, Higdon R, Morgan P, Sedensky M, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N.

J Proteomics. 2011 Dec 10;75(1):122-6. doi: 10.1016/j.jprot.2011.05.009. Epub 2011 May 13. Erratum in: J Proteomics. 2012 Jun 27;75(12):3789. Morgan, Phil [added]; Sedensky, Margaret [added].


MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data.

Montague E, Stanberry L, Higdon R, Janko I, Lee E, Anderson N, Choiniere J, Stewart E, Yandl G, Broomall W, Kolker N, Kolker E.

OMICS. 2014 Jun;18(6):335-43. doi: 10.1089/omi.2014.0061.


Beyond protein expression, MOPED goes multi-omics.

Montague E, Janko I, Stanberry L, Lee E, Choiniere J, Anderson N, Stewart E, Broomall W, Higdon R, Kolker N, Kolker E.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1145-51. doi: 10.1093/nar/gku1175. Epub 2014 Nov 17.


Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Schaab C, Geiger T, Stoehr G, Cox J, Mann M.

Mol Cell Proteomics. 2012 Mar;11(3):M111.014068. doi: 10.1074/mcp.M111.014068. Epub 2012 Feb 2.


An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

Zhang C, Crasta O, Cammer S, Will R, Kenyon R, Sullivan D, Yu Q, Sun W, Jha R, Liu D, Xue T, Zhang Y, Moore M, McGarvey P, Huang H, Chen Y, Zhang J, Mazumder R, Wu C, Sobral B.

Nucleic Acids Res. 2008 Jan;36(Database issue):D884-91. Epub 2007 Nov 4.


EPIC-DB: a proteomics database for studying Apicomplexan organisms.

Madrid-Aliste CJ, Dybas JM, Angeletti RH, Weiss LM, Kim K, Simon I, Fiser A.

BMC Genomics. 2009 Jan 21;10:38. doi: 10.1186/1471-2164-10-38.


2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.

Allmer J, Kuhlgert S, Hippler M.

BMC Bioinformatics. 2008 Jul 7;9:302. doi: 10.1186/1471-2105-9-302.


Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Haw R, Hermjakob H, D'Eustachio P, Stein L.

Proteomics. 2011 Sep;11(18):3598-613. doi: 10.1002/pmic.201100066.


The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data.

Häkkinen J, Vincic G, Månsson O, Wårell K, Levander F.

J Proteome Res. 2009 Jun;8(6):3037-43. doi: 10.1021/pr900189c.


ApoptoProteomics, an integrated database for analysis of proteomics data obtained from apoptotic cells.

Arntzen MØ, Thiede B.

Mol Cell Proteomics. 2012 Feb;11(2):M111.010447. doi: 10.1074/mcp.M111.010447. Epub 2011 Nov 8.


Human Proteinpedia: a unified discovery resource for proteomics research.

Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D773-81. doi: 10.1093/nar/gkn701. Epub 2008 Oct 23.


The PRIDE proteomics identifications database: data submission, query, and dataset comparison.

Jones P, Côté R.

Methods Mol Biol. 2008;484:287-303. doi: 10.1007/978-1-59745-398-1_19.


LMPD: LIPID MAPS proteome database.

Cotter D, Maer A, Guda C, Saunders B, Subramaniam S.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D507-10.


The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.


PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Vizcaíno JA, Reisinger F, Côté R, Martens L.

Methods Mol Biol. 2011;696:93-105. doi: 10.1007/978-1-60761-987-1_6.


BNDb--Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database.

Faria-Campos AC, Gomes RR, Moratelli FS, Rausch-Fernandes H, Franco GR, Campos SV.

Genet Mol Res. 2007 Oct 5;6(4):937-45.


PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations.

Rappoport N, Fromer M, Schweiger R, Linial M.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W84-9. doi: 10.1093/nar/gkq320. Epub 2010 May 5.


Liverbase: a comprehensive view of human liver biology.

Sun A, Jiang Y, Wang X, Liu Q, Zhong F, He Q, Guan W, Li H, Sun Y, Shi L, Yu H, Yang D, Xu Y, Song Y, Tong W, Li D, Lin C, Hao Y, Geng C, Yun D, Zhang X, Yuan X, Chen P, Zhu Y, Li Y, Liang S, Zhao X, Liu S, He F.

J Proteome Res. 2010 Jan;9(1):50-8. doi: 10.1021/pr900191p.

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