A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
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* Corresponding author: Eugene V Koonin koonin@ncbi.nlm.nih.gov
Genome Biology 2004, 5:R7 doi:
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Research
Energetics and genetics across the prokaryote-eukaryote divide Nick Lane Biology Direct 2011, 6:35 (30 June 2011) This article is part of a collection on Beyond the tree of life |
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Research article
Aminael Sánchez-Rodríguez, Cindy Martens, Kristof Engelen, Yves Van de Peer, Kathleen Marchal BMC Evolutionary Biology 2010, 10:318 (21 October 2010) |
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Review
The origin and early evolution of eukaryotes in the light of phylogenomics Eugene V Koonin Genome Biology 2010, 11:209 (5 May 2010) This article is part of a collection on 10th Anniversary... Comparative genomics and new phylogenies of eukaryote groups suggest a scenario in which the mitochondrial endosymbiosis triggered the origin of eukaryotes. |
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Research article
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods Valentín Ruano-Rubio, Olivier Poch, Julie D Thompson BMC Bioinformatics 2009, 10:383 (24 November 2009) |
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Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE Xin Wang, Yongjun Zhao, Kim Wong, Peter Ehlers, Yuji Kohara, Steven J Jones, Marco A Marra, Robert A Holt, Donald G Moerman, Dave Hansen BMC Genomics 2009, 10:213 (9 May 2009) |
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Research
Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin Biology Direct 2008, 3:40 (7 October 2008) |
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Methodology article
Conserved co-expression for candidate disease gene prioritization Martin Oti, Jeroen van Reeuwijk, Martijn A Huynen, Han G Brunner BMC Bioinformatics 2008, 9:208 (23 April 2008) |
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Research
Quantification of ortholog losses in insects and vertebrates Stefan Wyder, Evgenia V Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M Zdobnov Genome Biology 2007, 8:R242 (16 November 2007) Comparison of the gene repertoires of 5 vertebrates and 5 insects showed that the rate of losses correlates well with the species' rates of molecular evolution and radiation times and suggests that the Urbilateria genome contained more than 7,000 genes. |
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Research article
Poly-G/poly-C tracts in the genomes of Caenorhabditis Yang Zhao, Nigel J O'Neil, Ann M Rose BMC Genomics 2007, 8:403 (7 November 2007) |
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Research article
Manuel Irimia, Jakob Rukov, David Penny, Scott Roy BMC Evolutionary Biology 2007, 7:188 (4 October 2007) |
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Research article
Diego Miranda-Saavedra, Michael JR Stark, Jeremy C Packer, Christian P Vivares, Christian Doerig, Geoffrey J Barton BMC Genomics 2007, 8:309 (4 September 2007) |
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Research article
Johann Wägele, Christoph Mayer BMC Evolutionary Biology 2007, 7:147 (28 August 2007) |
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Research
Masumi Itoh, Jose C Nacher, Kei-ichi Kuma, Susumu Goto, Minoru Kanehisa Genome Biology 2007, 8:R121 (25 June 2007) A rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no similar trends were observed in other clades of eukaryotes. |
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Methodology article
Orthology prediction at scalable resolution by phylogenetic tree analysis René TJM van der Heijden, Berend Snel, Vera van Noort, Martijn A Huynen BMC Bioinformatics 2007, 8:83 (8 March 2007) |
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Hypothesis
Pavel V Baranov, Bente Vestergaard, Thomas Hamelryck, Raymond F Gesteland, Jens Nyborg, John F Atkins Biology Direct 2006, 1:28 (13 September 2006) |
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Research
Julia Tischler, Ben Lehner, Nansheng Chen, Andrew G Fraser Genome Biology 2006, 7:R69 (2 August 2006) High-throughput combinatorial RNAi demonstrates that many duplicated genes in |
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Research article
Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413 Juan Vizcaíno, Francisco González, M Belén Suárez, José Redondo, Julian Heinrich, Jesús Delgado-Jarana, Rosa Hermosa, Santiago Gutiérrez, Enrique Monte, Antonio Llobell, Manuel Rey BMC Genomics 2006, 7:193 (27 July 2006) |
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Research article
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers Journal of Biology 2006, 5:11 (8 June 2006) A new literature-based yeast database documents over 33,000 biological interactions, manually curated from the primary literature, and provides an invaluable resource to benchmark high-throughput methods in the study of complex networks.
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Research
The gain and loss of genes during 600 million years of vertebrate evolution Tine Blomme, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere, Yves Van de Peer Genome Biology 2006, 7:R43 (24 May 2006) Phylogenetic analysis of gene gain and loss during vertebrate evolution provides evidence for the importance of early gene or genome duplication events in evolution of complex vertebrates. |
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Method
Identifying repeat domains in large genomes Degui Zhi, Benjamin J Raphael, Alkes L Price, Haixu Tang, Pavel A Pevzner Genome Biology 2006, 7:R7 (31 January 2006) A graph-based method for the analysis of repeat families in a repeat library is presented that helps elucidating the evolutionary history of repeats. |
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Research article
Bas E Dutilh, Martijn A Huynen, Berend Snel BMC Genomics 2006, 7:10 (19 January 2006) |
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Research article
Etienne GJ Danchin, Philippe Gouret, Pierre Pontarotti BMC Evolutionary Biology 2006, 6:5 (18 January 2006) The absence of certain gene families that are conserved throughout other eukaryotes suggests that the human genome, which is generally considered to have evolved to high levels of complexity, has also undergone simplification and specific gene loss.
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Research article
Emmanuel G Reynaud, Miguel A Andrade, Fabien Bonneau, Thi Ly, Michael Knop, Klaus Scheffzek, Rainer Pepperkok BMC Biology 2005, 3:21 (7 October 2005) The expansion of a unique family of essential circularly permuted GTPases related to the human Lsg1 correlates with the evolution of compartmentalization of eukaryotic cells.
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Database
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis Alexander Sczyrba, Michael Beckstette, Ali H Brivanlou, Robert Giegerich, Curtis R Altmann BMC Genomics 2005, 6:123 (14 September 2005) XenDB is a database of clustered EST and cDNA sequences from Xenopus laevis; ESTs are identified by a suffix array-based clustering approach and will be useful for researchers working on comparative genome analysis.
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Software
Philippe Gouret, Vérane Vitiello, Nathalie Balandraud, André Gilles, Pierre Pontarotti, Etienne GJ Danchin BMC Bioinformatics 2005, 6:198 (5 August 2005) |
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Research article
Evolutionary sequence analysis of complete eukaryote genomes Jaime E Blair, Prachi Shah, S Blair Hedges BMC Bioinformatics 2005, 6:53 (11 March 2005) An evolutionary analysis based only on 'panorthologs' - genes that are found as a single copy among divergent species - matches up well to slower methods in indicating a divergence of deuterostomes and arthropods 400 million years before the Cambrian explosion of fossils.
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Research article
Gary W Stuart, Michael W Berry BMC Bioinformatics 2004, 5:204 (17 December 2004) |
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Research
A Drosophila protein-interaction map centered on cell-cycle regulators Clement A Stanyon, Guozhen Liu, Bernardo A Mangiola, Nishi Patel, Loic Giot, Bing Kuang, Huamei Zhang, Jinhui Zhong, Russell L Finley Genome Biology 2004, 5:R96 (26 November 2004) A |
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Research article
Georgy P Karev, Yuri I Wolf, Faina S Berezovskaya, Eugene V Koonin BMC Evolutionary Biology 2004, 4:32 (9 September 2004) |
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Method
Jeanne Boyer, Gwenaël Badis, Cécile Fairhead, Emmanuel Talla, Florence Hantraye, Emmanuelle Fabre, Gilles Fischer, Christophe Hennequin, Romain Koszul, Ingrid Lafontaine, Odile Ozier-Kalogeropoulos, Miria Ricchetti, Guy-Franck Richard, Agnès Thierry, Bernard Dujon Genome Biology 2004, 5:R72 (31 August 2004) A screen of the |
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Research article
Duplicated genes evolve slower than singletons despite the initial rate increase I King Jordan, Yuri I Wolf, Eugene V Koonin BMC Evolutionary Biology 2004, 4:22 (6 July 2004) Following gene duplication there is a period of rapid evolution, which then slows down in cases where the original gene has an important biological function and the duplicate is retained.
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