Eugene V. Koonin

Liran Carmel, Eugene V. Koonin, Stella Dracheva: Dependencies among Editing Sites in Serotonin 2C Receptor mRNA. PLoS Computational Biology 8(9) (2012)

Eugene V. Koonin: Obituary: Walter Fitch and the orthology paradigm. Briefings in Bioinformatics 12(5): 377-378 (2011)

David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin: Computational methods for Gene Orthology inference. Briefings in Bioinformatics 12(5): 379-391 (2011)

Eugene V. Koonin, Pere Puigbò, Yuri I. Wolf: Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life". Journal of Computational Biology 18(7): 917-924 (2011)

Nobuto Takeuchi, Paulien Hogeweg, Eugene V. Koonin: On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems. PLoS Computational Biology 7(3) (2011)

Eugene V. Koonin: Are There Laws of Genome Evolution? PLoS Computational Biology 7(8) (2011)

Miklós Csürös, Igor B. Rogozin, Eugene V. Koonin: A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes. PLoS Computational Biology 7(9) (2011)

Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin: Predictability of Evolutionary Trajectories in Fitness Landscapes. PLoS Computational Biology 7(12) (2011)

Liran Carmel, Yuri I. Wolf, Igor B. Rogozin, Eugene V. Koonin: EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution. Adv. Bioinformatics 2010 (2010)

David M. Kristensen, Lavanya Kannan, Michael K. Coleman, Yuri I. Wolf, Alexander Sorokin, Eugene V. Koonin, Arcady R. Mushegian: A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26(12): 1481-1487 (2010)

Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, Inna Dubchak: ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Research 37(Database-Issue): 448-454 (2009)

Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka: A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals. RECOMB-CG 2007: 177-191

Artem S. Novozhilov, Georgy P. Karev, Eugene V. Koonin: Biological applications of the theory of birth-and-death processes. Briefings in Bioinformatics 7(1): 70-85 (2006)

Kira S. Makarova, Eugene V. Koonin, Robert Haselkorn, Michael Y. Galperin: Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion. Bioinformatics 22(11): 1297-1301 (2006)

Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin: The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics 22(21): 2581-2584 (2006)

Igor B. Rogozin, Alexander V. Sverdlov, Vladimir N. Babenko, Eugene V. Koonin: Analysis of evolution of exon-intron structure of eukaryotic genes. Briefings in Bioinformatics 6(2): 118-134 (2005)

Georgy P. Karev, Faina S. Berezovskaya, Eugene V. Koonin: Modeling genome evolution with a diffusion approximation of a birth-and-death process. Bioinformatics 21(S3): 19 (2005)

Liran Carmel, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin: An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes. Comparative Genomics 2005: 35-46

Igor B. Rogozin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin: Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Briefings in Bioinformatics 5(2): 131-149 (2004)

Georgy P. Karev, Yuri I. Wolf, Eugene V. Koonin: Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve? Bioinformatics 19(15): 1889-1900 (2003)

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: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41 (2003)

Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin: The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinformatics 17(10): 859-861 (2001)

Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi: Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a `weak' context of the start codon. Bioinformatics 17(10): 890-900 (2001)

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, Eugene V. Koonin: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research 29(1): 22-28 (2001)

Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller: Winnowing Sequences from a Database Search. Journal of Computational Biology 7(1-2): 293-302 (2000)

Roman L. Tatusov, Michael Y. Galperin, Darren A. Natale, Eugene V. Koonin: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research 28(1): 33-36 (2000)

Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul: IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15(12): 1000-1011 (1999)

Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller: Winnowing sequences from a database search. RECOMB 1999: 50-58

Michael Y. Galperin, Eugene V. Koonin: Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption. In Silico Biology 1: 7 (1998)

Eugene V. Koonin, Roman L. Tatusov, Michael Y. Galperin, Michael N. Rosanov: Genome analysis using clusters of orthologous groups (COGs). RECOMB 1998: 135-139

Eugene V. Koonin, Roman L. Tatusov, David J. Lipman: A natural taxonomy of gene families from complete genomes. German Conference on Bioinformatics 1997: 13-14

D. Roland Walker, Eugene V. Koonin: SEALS: A System for Easy Analysis of Lots of Sequences. ISMB 1997: 333-339

Roman L. Tatusov, Eugene V. Koonin: A simple tool to search for sequence motifs that are conserved in BLAST outputs. Computer Applications in the Biosciences 10(4): 457-459 (1994)

Eugene V. Koonin: Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120. Nucleic Acids Research 22(13): 2476-2478 (1994)

Tatyana V. Ilyina, Eugene V. Koonin: Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Research 20(13): 3279-3285 (1992)