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Obituary: Walter Fitch and the orthology paradigm.
Eugene V. Koonin Briefings in Bioinformatics 12(5):377-378 (2011)
to dblp by dblp on Sep 23, 2011, 12:00 AM
URL | BibTeX
Computational methods for Gene Orthology inference.
David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, and Eugene V. Koonin Briefings in Bioinformatics 12(5):379-391 (2011)
to dblp by dblp on Sep 23, 2011, 12:00 AM
URL | BibTeX
Initial sequencing and analysis of the human genome
E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J. P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J. C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R. H. Waterston, R. K. Wilson, L. W. Hillier, J. D. McPherson, M. A. Marra, E. R. Mardis, L. A. Fulton, A. T. Chinwalla, K. H. Pepin, W. R. Gish, S. L. Chissoe, M. C. Wendl, K. D. Delehaunty, T. L. Miner, A. Delehaunty, J. B. Kramer, L. L. Cook, R. S. Fulton, D. L. Johnson, P. J. Minx, S. W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J. F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R. A. Gibbs, D. M. Muzny, S. E. Scherer, J. B. Bouck, E. J. Sodergren, K. C. Worley, C. M. Rives, J. H. Gorrell, M. L. Metzker, S. L. Naylor, R. S. Kucherlapati, D. L. Nelson, G. M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D. R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H. M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R. W. Davis, N. A. Federspiel, A. P. Abola, M. J. Proctor, R. M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D. R. Cox, M. V. Olson, R. Kaul, C. Raymond, N. Shimizu, K. Kawasaki, S. Minoshima, G. A. Evans, M. Athanasiou, R. Schultz, B. A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W. R. McCombie, M. de la Bastide, N. Dedhia, H. Blocker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J. A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D. G. Brown, C. B. Burge, L. Cerutti, H. C. Chen, D. Church, M. Clamp, R. R. Copley, T. Doerks, S. R. Eddy, E. E. Eichler, T. S. Furey, J. Galagan, J. G. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjakob, K. Hokamp, W. Jang, L. S. Johnson, T. A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W. J. Kent, P. Kitts, E. V. Koonin, I. Korf, D. Kulp, D. Lancet, T. M. Lowe, A. McLysaght, T. Mikkelsen, J. V. Moran, N. Mulder, V. J. Pollara, C. P. Ponting, G. Schuler, J. Schultz, G. Slater, A. F. Smit, E. Stupka, J. Szustakowski, D. Thierry-Mieg, J. Thierry-Mieg, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y. I. Wolf, K. H. Wolfe, S. P. Yang, R. F. Yeh, F. Collins, M. S. Guyer, J. Peterson, A. Felsenfeld, K. A. Wetterstrand, A. Patrinos, M. J. Morgan, P. de Jong, J. J. Catanese, K. Osoegawa, H. Shizuya, S. Choi, Y. J. Chen, and J. Szustakowki Nature (February 2001)
to imported by jschultz on Jul 21, 2011, 4:10 PM
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Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
C. P. Ponting, L. Aravind, J. Schultz, P. Bork, and E. V. Koonin J. Mol. Biol. (June 1999)
to imported by jschultz on Jul 21, 2011, 4:10 PM
BibTeX
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.
Igor B. Rogozin, Kira S. Makarova, Yuri I. Wolf, and Eugene V. Koonin Briefings in Bioinformatics 5(2):131-149 (2004)
to dblp by dblp on Jun 29, 2011, 12:00 AM
URL | BibTeX
Analysis of evolution of exon-intron structure of eukaryotic genes.
Igor B. Rogozin, Alexander V. Sverdlov, Vladimir N. Babenko, and Eugene V. Koonin Briefings in Bioinformatics 6(2):118-134 (2005)
to dblp by dblp on Jun 29, 2011, 12:00 AM
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The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome November 15-18, 2001, Atlanta, Georgia, USA.
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, and Igor B. Zhulin Bioinformatics 17(10):859-861 (2001)
to dblp by dblp on Jun 29, 2011, 12:00 AM
URL | BibTeX
Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve?
Georgy P. Karev, Yuri I. Wolf, and Eugene V. Koonin Bioinformatics 19(15):1889-1900 (2003)
to dblp by dblp on Jun 29, 2011, 12:00 AM
URL | BibTeX
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a `weak' context of the start codon.
Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, and Luciano Milanesi Bioinformatics 17(10):890-900 (2001)
to dblp by dblp on Jun 29, 2011, 12:00 AM
URL | BibTeX
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, and Stephen F. Altschul Bioinformatics 15(12):1000-1011 (1999)
to dblp by dblp on Jun 29, 2011, 12:00 AM
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A simple tool to search for sequence motifs that are conserved in BLAST outputs.
Roman L. Tatusov, and Eugene V. Koonin Computer Applications in the Biosciences 10(4):457-459 (1994)
to dblp by dblp on Jun 29, 2011, 12:00 AM
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Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria.
Tatyana V. Ilyina, and Eugene V. Koonin Nucleic Acids Research 20(13):3279-3285 (1992)
to dblp by dblp on Jun 29, 2011, 12:00 AM
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Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120.
Eugene V. Koonin Nucleic Acids Research 22(13):2476-2478 (1994)
to dblp by dblp on Jun 29, 2011, 12:00 AM
URL | BibTeX
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Roman L. Tatusov, Michael Y. Galperin, Darren A. Natale, and Eugene V. Koonin Nucleic Acids Research 28(1):33-36 (2000)
to dblp by dblp on Jun 29, 2011, 12:00 AM
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The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Roman L. Tatusov, Darren A. Natale, Igor V. Garkavtsev, Tatiana A. Tatusova, Uma T. Shankavaram, Bachoti S. Rao, Boris Kiryutin, Michael Y. Galperin, Natalie D. Fedorova, and Eugene V. Koonin Nucleic Acids Research 29(1):22-28 (2001)
to dblp by dblp on Jun 29, 2011, 12:00 AM
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EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.
Liran Carmel, Yuri I. Wolf, Igor B. Rogozin, and Eugene V. Koonin Adv. Bioinformatics (2010)
to dblp by dblp on Feb 28, 2011, 12:00 AM
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Orthologs, Paralogs, and Evolutionary Genomics
E. V. Koonin Genetics 39(1):309 (2005)
to bioinformatics homology orthology paralogy by ytyoun on Nov 21, 2010, 1:27 PM
DOI | BibTeX
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.
David M. Kristensen, Lavanya Kannan, Michael K. Coleman, Yuri I. Wolf, Alexander Sorokin, Eugene V. Koonin, and Arcady R. Mushegian Bioinformatics 26(12):1481-1487 (2010)
to dblp by dblp on Aug 11, 2010, 12:00 AM
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The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode
Jeremy Foster, Mehul Ganatra, Ibrahim Kamal, Jennifer Ware, Kira Makarova, Natalia Ivanova, Anamitra Bhattacharyya, Vinayak Kapatral, Sanjay Kumar, Janos Posfai, Tamas Vincze, Jessica Ingram, Laurie Moran, Alla Lapidus, Marina Omelchenko, Nikos Kyrpides, Elodie Ghedin, Shiliang Wang, Eugene Goltsman, Victor Joukov, Olga Ostrovskaya, Kiryl Tsukerman, Mikhail Mazur, Donald Comb, Eugene Koonin, and Barton Slatko PLoS Biology 3(4):e121 EP -- (April 2005)
to imported by derele on Dec 9, 2009, 5:59 PM
DOI | BibTeX
On the origin of genomes and cells within inorganic compartments
E. V. Koonin, and W. Martin Trends in Genetics 21(12):647--654 (December 2005)
to imported by svance and 1 other user on Nov 3, 2009, 8:21 PM
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