Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

By Yuri I. Wolf, Igor B. Rogozin, Alexey S. Kondrashov, Eugene V. Koonin. Genome Research, 2001

357 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b058ee380a8b479c0eb35e1776b5ea6f92aa659d

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Citations in the corpus

Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application (2017, background): “Functional genomics (Pevsner 2009), genome sequence annotation (Ouzounis and Karp 2002; Wolf et al. 2001) and high-resolution phenotyping (Crowell et al. 2016) can be useful for characterising the roles of genotypes and environments in driving G×E. Developing environment-specific genomic breeding…”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “2708 Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [124] Putative complex involved in translation regulation [125] O Represented by orthologs in all archaea and bacteria (COG0533) 0 X One of the few remaining uncharacterized proteins that are universally conserved in all cel”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “The most striking illustration of this trend is the ribosomal superoperon that includes over 50 genes of ribosomal proteins that are found in different combinations and arrangements in all sequenced archaeal and bacterial genomes (86,87).”
The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode (2005, methodology): “Gene orders in bacterial genomes were compared using the Lamarck program [179].”
The COG database: an updated version includes eukaryotes (2003, background): “…were made on a case by case basis through a combination of published data on C/KOG members and their homologs, protein domain analysis and different types of context analysis, particularly phyletic patterns and, in prokaryotes, conservation of gene strings which comprise putative operons [46–48].”
A novel method for accurate operon predictions in all sequenced prokaryotes (2005, background): “We suspect that this is because many operons are evolutionarily new [(8); M.”
Prokaryotic evolution in light of gene transfer. (2002, background): “Many careful studies show, not unexpectedly, that the ease with which genes recombine declines dramatically as their sequences diverge (Zawadzki, Roberts, and Cohan 1995; Majewski and Cohan 1998, 1999; Wolf et al. 2001).”
The MiST2 database: a comprehensive genomics resource on microbial signal transduction (2009, background): “Because gene rearrangements and reshuffling frequently occur between species (26), our approach permits neighboring twocomponent genes in the same set to be separated by up to two intervening genes.”
Orthologs, Paralogs, and Evolutionary Genomics 1 (2005, background): “, primates and rodents or different enterobacterial species), a conserved synteny block may include hundreds or even thousands of genes, whereas in distantly related genomes, there is very little conservation of gene order (7, 99).”