Who's your neighbor? New computational approaches for functional genomics

By Michael Y. Galperin, Eugene V. Koonin. Nature Biotechnology, 2000

337 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ff583fbb57f8f085fd42101b0c2d07166f78ba08

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Citations in the corpus

Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network (2003, background): “In fact, the function of 30-35% of encoded proteins per completely sequenced genome remains unknown [1].”
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. (2001, background): “Conservation of operon organization is one of the principal types of context information, which appears to become increasingly important with the growth of the collection of completely sequenced genomes (Galperin and Koonin 2000; Huynen and Snel 2000a; Huynen et al. 2000).”
Protein interaction networks from yeast to human. (2004, background): “fusion, neighborhood and phylogenetic profile) to predict functional relations between gene products [1–3] and the respective networks of such associations.”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “fo rm atio n leading to concrete functional predictions [42,59-61].”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “Despite many efforts to classify and organize proteins [1–6] from both structural and functional perspectives, we are far from a clear understanding of the size and diversity of the protein universe [7–9].”
Novel domains of the prokaryotic two-component signal transduction systems. (2001, background): “In the absence of direct experimental data, some clues to the range of functions of these newly described domains could be revealed by their genomic context, including operon structures and conserved domain fusions [5].”
Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners (2007, methodology): “additional evidence about functional linkage between their constituent genes [2,7–10].”
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis (2016, methodology): “, operons in bacteria) (5, 6), the Rosetta stone method (domains fused to a single protein in some genome are expected to interact in other genomes) (7, 8), and also coevolutionary techniques like phylogenetic profiling (correlated presence or absence of interacting proteins in genomes) (9) or simil”
Evolution of proteins and proteomes: a phylogenetics approach (2005, background): “Moreover, the detection of proteins with complementary phylogenetic patterns might indicate a nonorthologous gene displacement and thus a similar function for both protein families (Galperin and Koonin 2000).”