Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

Keywords

UniProt, Biology, Genome, Proteome, Computational biology

References

• The FlyBase database of the Drosophila genome projects and community literature.The FlyBase Consortium — 2003
• Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resourceMidori A. Harris — 2004
• Automated annotation of microbial proteomes in SWISS-PROTAlexandre Gattiker, Karine Michoud, Catherine Rivoire — 2003
• Announcing the worldwide Protein Data BankHelen M. Berman, Kim Henrick, Haruki Nakamura — 2003
• Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clustersEvgenia V. Kriventseva — 2003
• The HSSP database of protein structure-sequence alignments and family profilesCarol L. Dodge — 1998
• The Eukaryotic Promoter Database EPD: the impact of in silico primer extensionChristof Schmid — 2004
• The International Protein Index: An integrated database for proteomics experimentsPaul Kersey, Jorge Duarte, Allyson L. Williams — 2004
• NCBI Reference Sequence Project: update and current statusKim D. Pruitt — 2003
• The Bio* toolkits--a brief overview.H. Mangalam — 2002
• DBJ in the stream of various biological dataSatoru Miyazaki — 2004
• ArrayExpress—a public repository for microarray gene expression data at the EBIHelen Parkinson — 2004
• UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAsGraziano Pesole — 2000
• The InterPro Database, 2003 brings increased coverage and new featuresNicola Mulder — 2003
• The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene OntologyEvelyn Camon — 2004
• Interactive InterPro-based comparisons of proteins in whole genomesAlexander Kanapin, Rolf Apweiler, Moumita Biswas — 2002
• The complete genome and proteome of Mycoplasma mobile.Jacob D. Jaffe, Nicole Stange-Thomann, Cherylyn Smith — 2004
• E-MSD: the European Bioinformatics Institute Macromolecular Structure DatabaseHarry Boutselakis — 2003
• EnsMart: a generic system for fast and flexible access to biological data.Arek Kasprzyk, Damian Keefe, Damian Smedley — 2003
• UniProt: the Universal Protein knowledgebaseRolf Apweiler — 2004

Cited by

• ROSY – A Flexible and Universal Database and Bioinformatics Tool Platform for Roseobacter Related SpeciesClaudia Pommerenke, Inga Gabriel, Boyke Bunk — 2008
• Gene3D: modelling protein structure, function and evolution山城 康嗣, 細井 昌子, 有村 達之 — 2005
• Biomedical Data Management: A Proposal FrameworkDouglas Teodoro, Choquet Rémy, Emilie Pasche — 2009
• Graph-based methods for large-scale protein classification and orthology inferenceArnold Kuzniar — 2009
• Inference of Synechocystis protein interaction networkMagali Michaut, Samuel Kerrien, Luisa Montecchi‐Palazzi — 2008
• The EMBL Nucleotide Sequence and Genome Reviews Databases.Peter Sterk, Tamara Kulikova, Paul Kersey — 2007
• Bioinformatics for LC-MS/MS-based proteomics.Richard J. Jacob — 2010
• Genómica evolutiva de la regulación transcripcional en las principales familias multigénicas del sistema quimiosensorial de DrosophilaPablo Librado Sanz — 2014
• Recherche de domaines protéiques divergents à l'aide de modèles de Markov cachés : application à Plasmodium falciparum. (Seeking divergent protein domains with Hidden Markov Models: application to Plasmodium falciparum)Nicolas Terrapon — 2010
• Prédiction de réseaux d'interactions biomoléculaires à partir des données de la génomique comparéeFlorian Iragne — 2007
• Inference and validation of Synechocystis protein interaction network using orthologyMagali Michaut, Samuel Kerrien, Luisa Montecchi‐Palazzi — 2007
• LeishBase: Leishmania major structural database.Simranjeet Kaur, Hitesh Patel, Virag Sharma — 2009
• Exploring the function and evolution of proteins using domain familiesAdam J. Reid — 2009
• Creation, evaluation, and use of PSI, a program for identifying protein-phenotype relationships and comparing protein content in groups of organismsBrett Trost — 2009
• Computational approaches to discovering differentiation genes in the peripheral nervous system of Drosophila melanogasterG. Gallone — 2013
• The evolutionary dynamics of biochemical networks in fluctuating environmentsRobert John Platt — 2011
• Development of methods for the automated annotation of prokaryotic proteomesAlexandre Gattiker — 2005
• The Integrated Microbial Genomes (IMG) System: A Case Study in Biological Data ManagementVictor Markowitz, Frank Korzeniewski, Krishna Palaniappan — 2005
• An experimental metagenome data management and analysis systemVictor Markowitz, Natalia Ivanova, Krishna Palaniappan — 2006
• Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implicationsJohn‐Marc Chandonia, Sung‐Hou Kim — 2006

Related papers

• HAMAP in 2013, new developments in the protein family classification and annotation systemIvo Pedruzzi, Catherine Rivoire, Andrea H Auchincloss — 2012
• HAMAP in 2015: updates to the protein family classification and annotation systemIvo Pedruzzi, Catherine Rivoire, Andrea H Auchincloss — 2014
• Computational clustering for viral reference proteomesChuming Chen, Hongzhan Huang, Raja Mazumder — 2016
• Integrating protein annotation resources through the Distributed Annotation SystemPall I. Olason — 2005
• Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase.Sona Vasudevan, C R Vinayaka, Darren A. Natale — 2011
• On the Unknown Proteins of Eukaryotic ProteomesYves‐Henri Sanejouand — 2022
• InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryoticErik L. L. Sonnhammer, Gabriel Östlund — 2014