PubRank

Yuri I Wolf

Author PubWeight™ 278.26‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003 60.98
2 Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011 17.11
3 A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 2006 11.31
4 Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol 2002 6.85
5 The ecoresponsive genome of Daphnia pulex. Science 2011 6.55
6 Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002 6.08
7 Selection in the evolution of gene duplications. Genome Biol 2002 5.58
8 A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 2004 4.94
9 Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008 4.78
10 The structure of the protein universe and genome evolution. Nature 2002 4.47
11 The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 2002 4.28
12 Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 2011 3.92
13 Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 2003 3.90
14 The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A 2002 3.72
15 Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 2003 3.72
16 Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A 2003 3.55
17 Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct 2009 3.17
18 No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol 2003 3.07
19 A universal trend of amino acid gain and loss in protein evolution. Nature 2005 2.81
20 Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol 2004 2.78
21 The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 2008 2.74
22 Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 2009 2.66
23 Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2007 2.53
24 Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res 2002 2.35
25 Computational methods for Gene Orthology inference. Brief Bioinform 2011 2.16
26 Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J 2009 2.13
27 The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A 2006 2.11
28 Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem 2006 2.10
29 Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res 2007 2.06
30 Microevolutionary genomics of bacteria. Theor Popul Biol 2002 1.95
31 Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 2004 1.95
32 The deep archaeal roots of eukaryotes. Mol Biol Evol 2008 1.90
33 Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol Biol 2002 1.86
34 Phylogenomics of prokaryotic ribosomal proteins. PLoS One 2012 1.82
35 Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res 2013 1.82
36 Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol 2008 1.79
37 Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 2008 1.78
38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res 2005 1.77
39 Arginyltransferase is an ATP-independent self-regulating enzyme that forms distinct functional complexes in vivo. Chem Biol 2011 1.76
40 Global analysis of posttranslational protein arginylation. PLoS Biol 2007 1.75
41 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct 2013 1.75
42 Purifying and directional selection in overlapping prokaryotic genes. Trends Genet 2002 1.74
43 Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol 2006 1.68
44 A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 2010 1.67
45 Is evolution Darwinian or/and Lamarckian? Biol Direct 2009 1.67
46 Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol Biol 2005 1.63
47 Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A 2004 1.62
48 Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol 2003 1.62
49 Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol 2002 1.60
50 Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol 2012 1.59
51 Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 2004 1.58
52 Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct 2009 1.58
53 The tree and net components of prokaryote evolution. Genome Biol Evol 2010 1.55
54 Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. Nucleic Acids Res 2002 1.54
55 Potential genomic determinants of hyperthermophily. Trends Genet 2003 1.54
56 Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol 2011 1.53
57 Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2007 1.52
58 The origins of phagocytosis and eukaryogenesis. Biol Direct 2009 1.49
59 Patterns of intron gain and conservation in eukaryotic genes. BMC Evol Biol 2007 1.42
60 Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet 2010 1.41
61 Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol 2008 1.39
62 Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct 2010 1.35
63 Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J Virol 2012 1.33
64 Universal pacemaker of genome evolution. PLoS Comput Biol 2012 1.31
65 ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res 2008 1.30
66 A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes. Genome Biol Evol 2012 1.25
67 Evolutionarily conserved genes preferentially accumulate introns. Genome Res 2007 1.25
68 The basic building blocks and evolution of CRISPR-CAS systems. Biochem Soc Trans 2013 1.23
69 Evolutionary primacy of sodium bioenergetics. Biol Direct 2008 1.23
70 Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol 2014 1.21
71 Small proteins can no longer be ignored. Annu Rev Biochem 2014 1.21
72 Universal distribution of protein evolution rates as a consequence of protein folding physics. Proc Natl Acad Sci U S A 2010 1.20
73 Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. Mol Biol Evol 2007 1.19
74 Viral diversity threshold for adaptive immunity in prokaryotes. MBio 2012 1.17
75 Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform 2004 1.16
76 Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol Direct 2008 1.15
77 Predictability of evolutionary trajectories in fitness landscapes. PLoS Comput Biol 2011 1.12
78 Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol 2012 1.11
79 The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol Direct 2009 1.09
80 Nature and intensity of selection pressure on CRISPR-associated genes. J Bacteriol 2011 1.08
81 Differential translation tunes uneven production of operon-encoded proteins. Cell Rep 2013 1.06
82 Evolutionary plasticity of protein families: coupling between sequence and structure variation. Proteins 2005 1.06
83 Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin. PLoS Curr 2009 1.06
84 Analysis of rare amino acid replacements supports the Coelomata clade. Mol Biol Evol 2007 1.06
85 Seeing the Tree of Life behind the phylogenetic forest. BMC Biol 2013 1.04
86 Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve? Bioinformatics 2003 1.02
87 Role of hypermutability in the evolution of the genus Oenococcus. J Bacteriol 2007 0.99
88 Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol Biol 2004 0.99
89 An insertion in the catalytic trigger loop gates the secondary channel of RNA polymerase. J Mol Biol 2012 0.98
90 Comparison of phylogenetic trees and search for a central trend in the "forest of life". J Comput Biol 2011 0.98
91 Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. Biol Direct 2007 0.96
92 Gene frequency distributions reject a neutral model of genome evolution. Genome Biol Evol 2013 0.94
93 Drastic neofunctionalization associated with evolution of the timezyme AANAT 500 Mya. Proc Natl Acad Sci U S A 2013 0.92
94 Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles 2014 0.92
95 The common ancestry of life. Biol Direct 2010 0.92
96 The vast, conserved mammalian lincRNome. PLoS Comput Biol 2013 0.91
97 Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context. J Bacteriol 2013 0.89
98 Estimation of prokaryotic supergenome size and composition from gene frequency distributions. BMC Genomics 2014 0.82
99 Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. Methods Mol Biol 2012 0.81
100 EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution. Adv Bioinformatics 2010 0.81
101 A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure. Methods Mol Biol 2009 0.79
102 Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution. Mol Biosyst 2014 0.79
103 Virus-host arms race at the joint origin of multicellularity and programmed cell death. Cell Cycle 2014 0.78
104 Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes. Mol Biosyst 2013 0.77
105 Reply to "codon usage frequency of RNA virus genomes from high-temperature acidic-environment metagenomes". J Virol 2013 0.77
106 Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis. Biol Direct 2014 0.75
107 Microbial genome analysis: the COG approach. Brief Bioinform 2017 0.75