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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA
Genome Biol 2004, 5:R7
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Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?
Stiller JW, Huang J, Ding Q, Tian J, Goodwillie C
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Wang X, Zhao Y, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D
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Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
Wolf MY, Wolf YI, Koonin EV
Biology Direct 2008, 3:40 (7 October 2008)
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Methodology article    
Conserved co-expression for candidate disease gene prioritization
Oti M, van Reeuwijk J, Huynen MA, Brunner HG
BMC Bioinformatics 2008, 9:208 (23 April 2008)
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Quantification of ortholog losses in insects and vertebrates
Wyder S, Kriventseva EV, Schröder R, Kadowaki T, Zdobnov EM
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Poly-G/poly-C tracts in the genomes of Caenorhabditis
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BMC Genomics 2007, 8:403 (7 November 2007)
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Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
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Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
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Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
Itoh M, Nacher JC, Kuma K, Goto S, Kanehisa M
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Orthology prediction at scalable resolution by phylogenetic tree analysis
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BMC Bioinformatics 2007, 8:83 (8 March 2007)
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Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons
Baranov PV, Vestergaard B, Hamelryck T, Gesteland RF, Nyborg J, Atkins JF
Biology Direct 2006, 1:28 (13 September 2006)
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Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution
Tischler J, Lehner B, Chen N, Fraser AG
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Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413
Vizcaíno JA, González FJ, Suárez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutiérrez S, Monte E, Llobell A, Rey M
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Method    
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Danchin EGJ, Gouret P, Pontarotti P
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Reynaud EG, Andrade MA, Bonneau F, Ly TBN, Knop M, Scheffzek K, Pepperkok R
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Database    
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR
BMC Genomics 2005, 6:123 (14 September 2005)
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Software    
FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform
Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin EGJ
BMC Bioinformatics 2005, 6:198 (5 August 2005)
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Research article    
Evolutionary sequence analysis of complete eukaryote genomes
Blair JE, Shah P, Hedges SB
BMC Bioinformatics 2005, 6:53 (11 March 2005)
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Research article    
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Research    
A Drosophila protein-interaction map centered on cell-cycle regulators
Stanyon CA, Liu G, Mangiola BA, Patel N, Giot L, Kuang B, Zhang H, Zhong J, Finley RL
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Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models
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Method    
Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae
Boyer J, Badis G, Fairhead C, Talla E, Hantraye F, Fabre E, Fischer G, Hennequin C, Koszul R, Lafontaine I, Ozier-Kalogeropoulos O, Ricchetti M, Richard GF, Thierry A, Dujon B
Genome Biology 2004, 5:R72 (31 August 2004)
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Research article    
Duplicated genes evolve slower than singletons despite the initial rate increase
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