Benchmarking ortholog identification methods using functional genomics data
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* Corresponding author: Peter MA Groenen peter.groenen@organon.com
Genome Biology 2006, 7:R31 doi:10.1186/gb-2006-7-4-r31
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Proceedings
ApicoAlign: an alignment and sequence search tool for apicomplexan proteins Jamshaid Ali, Umadevi Paila, Akash Ranjan BMC Genomics 2011, 12(Suppl 3):S6 (30 November 2011) |
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Research
Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar, Jaime Mora Biology Direct 2011, 6:48 (4 October 2011) Diversification of orthologous genes provokes specific physico-chemical changes in proteins of related species, revealing particular trends required to perform their functional roles in the adaptation to niche and intra-cellular conditions.
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Research article
An integrative approach to ortholog prediction for disease-focused and other functional studies Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E Mohr BMC Bioinformatics 2011, 12:357 (31 August 2011) |
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Research article
Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera) Stephen L Cameron, Kazunori Yoshizawa, Atsushi Mizukoshi, Michael F Whiting, Kevin P Johnson BMC Genomics 2011, 12:394 (4 August 2011) Mitochondrial genomes in several louse species form multiple, minicircular genomes each containing a subset of mitochondrial genes which may be due to loss of the mitochondrial single-stranded binding protein of the mtDNA replisome.
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Correspondence
Joining forces in the quest for orthologs Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis Genome Biology 2009, 10:403 (29 September 2009) Building momentum to coordinate and leverage community orthology prediction resources. |
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Research article
Evolutionary flexibility of protein complexes Michael F Seidl, Jörg Schultz BMC Evolutionary Biology 2009, 9:155 (7 July 2009) |
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Software
EDGAR: A software framework for the comparative analysis of prokaryotic genomes Jochen Blom, Stefan P Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski, Alexander Goesmann BMC Bioinformatics 2009, 10:154 (20 May 2009) |
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Review
Large-scale assignment of orthology: back to phylogenetics? Toni Gabaldón Genome Biology 2008, 9:235 (30 October 2008) Automated use of phylogenetic trees to deduce orthology relationships in proteins. |
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Database
Automatically extracting functionally equivalent proteins from SwissProt Lisa EM McMillan, Andrew CR Martin BMC Bioinformatics 2008, 9:418 (6 October 2008) |
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Methodology article
Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants Matthieu G Conte, Sylvain Gaillard, Gaetan Droc, Christophe Perin BMC Genomics 2008, 9:183 (21 April 2008) |
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Research article
Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data Frédéric Lemoine, Olivier Lespinet, Bernard Labedan BMC Evolutionary Biology 2007, 7:237 (29 November 2007) |
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Research article
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome Teresia J Buza, Fiona M McCarthy, Shane C Burgess BMC Genomics 2007, 8:425 (19 November 2007) |
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Research
Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón Genome Biology 2007, 8:R109 (13 June 2007) The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed. |
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Database
PlnTFDB: an integrative plant transcription factor database Diego Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer, Bernd Mueller-Roeber BMC Bioinformatics 2007, 8:42 (7 February 2007) |
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Research article
Testing statistical significance scores of sequence comparison methods with structure similarity Tim Hulsen, Jacob de Vlieg, Jack AM Leunissen, Peter MA Groenen BMC Bioinformatics 2006, 7:444 (12 October 2006) |
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Database
PhyloPat: phylogenetic pattern analysis of eukaryotic genes Tim Hulsen, Jacob de Vlieg, Peter MA Groenen BMC Bioinformatics 2006, 7:398 (1 September 2006) |