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Genome Biol. 2004;5(5):R35. Epub 2004 Apr 16.

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Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M.

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Organelle DB: a cross-species database of protein localization and function.

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DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D.

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Comprehensive analysis of orthologous protein domains using the HOPS database.

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Comparative analysis of protein domain organization.

Ye Y, Godzik A.

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AVID: an integrative framework for discovering functional relationships among proteins.

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The COG database: a tool for genome-scale analysis of protein functions and evolution.

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Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness.

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Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach.

Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D.

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DIP: the database of interacting proteins.

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Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps.

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Predicting functional linkages from gene fusions with confidence.

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Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.

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Online predicted human interaction database.

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