Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
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* Corresponding author: Eugene V Koonin koonin@ncbi.nlm.nih.gov
BMC Evolutionary Biology 2003, 3:2 doi:10.1186/1471-2148-3-2
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BioMed Central: 25 citations
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Natalya Yutin, Eugene V Koonin Biology Direct 2009, 4:51 (18 December 2009) |
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Research article
Search for a 'Tree of Life' in the thicket of the phylogenetic forest Pere Puigbò, Yuri I Wolf, Eugene V Koonin Journal of Biology 2009, 8:59 (13 July 2009) Koonin and colleagues, comparing a forest of 7000 phylogenetic trees, discern vertical inheritance even at the earliest stages of prokaryotic evolution, despite horizontal gene transfer, but the branching order of the earliest radiations may never be resolved.
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ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets Guan Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu BMC Bioinformatics 2009, 10(Suppl 1):S5 (30 January 2009) |
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The evolution of domain-content in bacterial genomes Nacho Molina, Erik van Nimwegen Biology Direct 2008, 3:51 (11 December 2008) |
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Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin, Kira S Makarova, Yuri I Wolf, Daniel J Rigden, Peter F Dunfield, Lei Wang, Maqsudul Alam Genome Biology 2008, 9:R161 (17 November 2008) Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation. |
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A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans Mircea Podar, Iain Anderson, Kira S Makarova, James G Elkins, Natalia Ivanova, Mark A Wall, Athanasios Lykidis, Kostantinos Mavromatis, Hui Sun, Matthew E Hudson, Wenqiong Chen, Cosmin Deciu, Don Hutchison, Jonathan R Eads, Abraham Anderson, Fillipe Fernandes, Ernest Szeto, Alla Lapidus, Nikos C Kyrpides, Milton H Saier, Paul M Richardson, Reinhard Rachel, Harald Huber, Jonathan A Eisen, Eugene V Koonin, Martin Keller, Karl O Stetter Genome Biology 2008, 9:R158 (10 November 2008) Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans. |
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Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe, Angela V Smirnova, Peter F Dunfield, Lu Feng, Lei Wang, Maqsudul Alam Biology Direct 2008, 3:26 (1 July 2008) Genome sequence of a methanotrophic member of the bacterial phylum Verrucomicrobia reveals adaptations to the methane utilization under acidic conditions and supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a superphylum
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Research article
Uncovering rate variation of lateral gene transfer during bacterial genome evolution Weilong Hao, G Brian Golding BMC Genomics 2008, 9:235 (20 May 2008) |
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Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli Morgan N Price, Paramvir S Dehal, Adam P Arkin Genome Biology 2008, 9:R4 (7 January 2008) Most Escherichia coli transcription factors have paralogs, but these usually arose by horizontal gene transfer rather than by duplication within the E. coli lineage, as previously believed. |
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Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:33 (27 November 2007) |
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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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Research article
Raja Jothi, Teresa M Przytycka, L Aravind BMC Bioinformatics 2007, 8:173 (23 May 2007) |
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Correspondence
Systematic overestimation of gene gain through false diagnosis of gene absence Olga Zhaxybayeva, Camilla L Nesbø, W Ford Doolittle Genome Biology 2007, 8:402 (26 February 2007) Usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer. |
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The role of laterally transferred genes in adaptive evolution Pradeep Marri, Weilong Hao, G Brian Golding BMC Evolutionary Biology 2007, 7(Suppl 1):S8 (8 February 2007) |
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Opinion
Tal Dagan, William Martin Genome Biology 2006, 7:118 (1 November 2006) As lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes are fundamentally not tree-like in nature, biologists need to depart from the notion that all genomes are related by a single bifurcating tree.
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Phylogenomic analysis of the GIY-YIG nuclease superfamily Stanislaw Dunin-Horkawicz, Marcin Feder, Janusz M Bujnicki BMC Genomics 2006, 7:98 (28 April 2006) |
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Research article
Natural history of S-adenosylmethionine-binding proteins Piotr Z Kozbial, Arcady R Mushegian BMC Structural Biology 2005, 5:19 (14 October 2005) Analysis of the phyletic distribution and structural similarities of S-adenosylmethionine-binding proteins indicate that two widespread folds, the Rossman fold and TIM barrel, have repeatedly evolved for diverse types of reactions that require S-adenosylmethionine.
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Jing-Ke Weng, Milos Tanurdzic, Clint Chapple BMC Genomics 2005, 6:85 (6 June 2005) |
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Do orthologous gene phylogenies really support tree-thinking? E Bapteste, E Susko, J Leigh, D MacLeod, RL Charlebois, WF Doolittle BMC Evolutionary Biology 2005, 5:33 (24 May 2005) |
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Galina V Glazko, Arcady R Mushegian Genome Biology 2004, 5:R32 (27 April 2004) A hierarchy of 3,688 phyletic patterns was characterized encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes. The results indicate that gene loss and displacement has occurred in the evolution of most pathways. |
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Research
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale Genome Biology 2004, 5:R7 (15 January 2004) We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. |
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Research article
The COG database: an updated version includes eukaryotes Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale BMC Bioinformatics 2003, 4:41 (11 September 2003) |
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Research article
Colin R Jackson, Sandra L Dugas BMC Evolutionary Biology 2003, 3:18 (23 July 2003) |
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Opinion
Comparative genomics of archaea: how much have we learned in six years, and what's next? Kira S Makarova, Eugene V Koonin Genome Biology 2003, 4:115 (16 July 2003) With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange. |
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Research
Eugene V Koonin, Kira S Makarova, Igor B Rogozin, Laetitia Davidovic, Marie-Claude Letellier, Luca Pellegrini Genome Biology 2003, 4:R19 (28 February 2003) The near-universal presence of the rhomboid family in bacteria, archaea and eukaryotes appears to suggest that this protein is part of the heritage of the last universal common ancestor, phylogenetic tree analysis indicates a likely bacterial origin with subsequent dissemination by horizontal gene transfer. |