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Eugene Koonin
Computational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, United States of America

Faculty Member: GENOMICS & GENETICS > Bioinformatics [ since 5 July 2001 ]
[ Evaluations ]
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Evaluations

Universal genome in the origin of metazoa: thoughts about evolution.
Sherman M
Cell Cycle 2007 Aug 1 6(15):1873-7 [abstract on PubMed] [related articles] [order article]
Selected by | Eugene Koonin
Evaluated 8 Feb 2008

Apparent trends of amino Acid gain and loss in protein evolution due to nearly neutral variation.
McDonald JH
Mol Biol Evol 2006 Feb 23(2):240-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Steven Henikoff
Dissenters | Eugene Koonin
Author Response | John McDonald
Evaluated 15 May 2006


A plant vacuolar protease, VPE, mediates virus-induced hypersensitive cell death.
Hatsugai N, Kuroyanagi M, …, Nishimura M, Hara-Nishimura I
Science 2004 Aug 6 305(5685):855-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andrey Rzhetsky / Andrew Bent / Daniel Gallie / Pierre De Wit / Eugene Koonin / Ian Moore
Evaluated 20 Oct 2004

Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step.
Chapman EJ, Prokhnevsky AI, …, Dolja VV, Carrington JC
Genes Dev 2004 May 15 18(10):1179-86 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andy Maule / Eugene Koonin
Evaluated 30 Jul 2004

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
Korbel JO, Jensen LJ, von Mering C, Bork P
Nat Biotechnol 2004 Jul 22(7):911-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Eugene Koonin
Evaluated 30 Jul 2004

Complex molecular architecture of beet yellows virus particles.
Peremyslov VV, Andreev IA, …, Taliansky ME, Dolja VV
Proc Natl Acad Sci U S A 2004 Apr 6 101(14):5030-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin
Evaluated 13 Apr 2004

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection.
Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL
J Mol Evol 2003 57 Suppl 1:S154-64 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Eugene Koonin / Thomas Mitchell-Olds
Evaluated 16 Mar 2004

The origins of genome complexity.
Lynch M, Conery JS
Science 2003 Nov 21 302(5649):1401-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Anna-Louise Reysenbach / Eugene Koonin
Evaluated 16 Mar 2004

Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces?
Gmyl AP, Korshenko SA, …, Khitrina EV, Agol VI
RNA 2003 Oct 9(10):1221-31 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Michael Yarus / Eugene Koonin
Evaluated 16 Mar 2004

Chalcone isomerase family and fold: no longer unique to plants.
Gensheimer M, Mushegian A
Protein Sci 2004 Feb 13(2):540-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin
Evaluated 16 Mar 2004

Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles.
Nesbø CL, Doolittle WF
Proc Natl Acad Sci U S A 2003 Sep 16 100(19):10806-11 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin / Niles Lehman
Evaluated 8 Sep 2003

Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage.
Yuzenkova J, Nechaev S, …, Mushegian A, Severinov K
J Mol Biol 2003 Jul 18 330(4):735-48 [abstract on PubMed] [related articles] [order article]
Selected by | Eugene Koonin
Evaluated 4 Sep 2003

Dosage sensitivity and the evolution of gene families in yeast.
Papp B, Pál C, Hurst LD
Nature 2003 Jul 10 424(6945):194-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Anne Osbourn / Takashi Hirayama / Eugene Koonin
Evaluated 4 Sep 2003

Loop fold structure of proteins: resolution of Levinthas paradox.
Berezovsky IN, Trifonov EN
J Biomol Struct Dyn 2002 Aug 20(1):5-6 [abstract on PubMed] [related articles] [order article]
Selected by | Eugene Koonin
Evaluated 28 Aug 2002

A unifold, mesofold, and superfold model of protein fold use.
Coulson AF, Moult J
Proteins 2002 Jan 1 46(1):61-71 [abstract on PubMed] [related articles] [order article]
Selected by | Eugene Koonin
Evaluated 28 Aug 2002

Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori.
Davids W, Gamieldien J, Liberles DA, Hide W
J Mol Evol 2002 Apr 54(4):458-64 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Eugene Koonin
Evaluated 28 Aug 2002

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
Luscombe NM, Qian J, …, Johnson T, Gerstein M
Genome Biol 2002 Jul 25 3(8):RESEARCH0040 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin
Evaluated 27 Aug 2002

A 'periodic table' for protein structures.
Taylor WR
Nature 2002 Apr 11 416(6881):657-60 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Eugene Koonin / Golan Yona
Evaluated 26 Apr 2002

Genomes in flux: the evolution of archaeal and proteobacterial gene content.
Snel B, Bork P, Huynen MA
Genome Res 2002 Jan 12(1):17-25 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Arcady Mushegian / Christos Ouzounis / Eugene Koonin
Evaluated 25 Apr 2002

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.
Zhaxybayeva O, Gogarten JP
BMC Genomics 2002 3(1):4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin
Evaluated 24 Apr 2002

Positive selection of a gene family during the emergence of humans and African apes.
Johnson ME, Viggiano L, …, Rocchi M, Eichler EE
Nature 2001 Oct 4 413(6855):514-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Eugene Koonin / Yoshiyuki Sakaki
Evaluated 20 Nov 2001

Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias.
Lercher MJ, Williams EJ, Hurst LD
Mol Biol Evol 2001 Nov 18(11):2032-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin
Evaluated 19 Nov 2001

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