Published in Nature on January 19, 2005
Environments shape the nucleotide composition of genomes. EMBO Rep (2005) 2.96
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94
Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc Natl Acad Sci U S A (2008) 2.11
Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol (2007) 2.01
Protein ionizable groups: pK values and their contribution to protein stability and solubility. J Biol Chem (2009) 1.85
Sequence space and the ongoing expansion of the protein universe. Nature (2010) 1.72
Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. Genome Biol (2006) 1.55
Genetic constraints on protein evolution. Crit Rev Biochem Mol Biol (2007) 1.41
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. Proc Natl Acad Sci U S A (2012) 1.34
Analysis and functional prediction of reactive cysteine residues. J Biol Chem (2011) 1.29
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput Biol (2007) 1.26
Cysteine function governs its conservation and degeneration and restricts its utilization on protein surfaces. J Mol Biol (2010) 1.24
Evolution of proteomes: fundamental signatures and global trends in amino acid compositions. BMC Genomics (2006) 1.20
Search for allosteric disulfide bonds in NMR structures. BMC Struct Biol (2007) 1.15
Entropic stabilization of proteins and its proteomic consequences. PLoS Comput Biol (2005) 1.11
On the origin of life in the zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth. Biol Direct (2009) 1.08
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PLoS Comput Biol (2013) 1.07
Divergent evolution within protein superfolds inferred from profile-based phylogenetics. J Mol Biol (2005) 1.04
Evolution of prokaryotic genes by shift of stop codons. J Mol Evol (2010) 0.97
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evol Biol (2006) 0.97
Protein evolution: causes of trends in amino-acid gain and loss. Nature (2006) 0.97
Genetic code ambiguity confers a selective advantage on Acinetobacter baylyi. J Bacteriol (2007) 0.96
Membrane transporters for the special amino acid glutamine: structure/function relationships and relevance to human health. Front Chem (2014) 0.96
Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses. PLoS Comput Biol (2008) 0.95
Adaptive evolution of the Chlamydia trachomatis dominant antigen reveals distinct evolutionary scenarios for B- and T-cell epitopes: worldwide survey. PLoS One (2010) 0.95
Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome. Nucleic Acids Res (2008) 0.94
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Mol Biol Evol (2011) 0.92
Observations of amino acid gain and loss during protein evolution are explained by statistical bias. Mol Biol Evol (2006) 0.92
Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties. PLoS One (2011) 0.90
The universal trend of amino acid gain-loss is caused by CpG hypermutability. J Mol Evol (2008) 0.88
Signature of a primitive genetic code in ancient protein lineages. J Mol Evol (2007) 0.87
Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes. BMC Bioinformatics (2006) 0.86
Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res (2007) 0.85
Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics (2008) 0.84
Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code. Biol Direct (2008) 0.84
Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code. PLoS One (2008) 0.84
Enzyme-driven speciation: crystallizing Archaea via lipid capture. J Mol Evol (2007) 0.82
Genome-wide association study identifies common genetic variants associated with salivary gland carcinoma and its subtypes. Cancer (2015) 0.82
Unassigned codons, nonsense suppression, and anticodon modifications in the evolution of the genetic code. J Mol Evol (2011) 0.82
Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display. PLoS One (2011) 0.81
Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes. BMC Genomics (2010) 0.81
Simplification of the genetic code: restricted diversity of genetically encoded amino acids. Nucleic Acids Res (2012) 0.80
Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One (2012) 0.80
Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis. PLoS One (2011) 0.80
A universal trend among proteomes indicates an oily last common ancestor. PLoS Comput Biol (2012) 0.79
Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins. Front Pharmacol (2015) 0.78
Differences in evolutionary pressure acting within highly conserved ortholog groups. BMC Evol Biol (2008) 0.78
Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution. Genetics (2015) 0.78
Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair. J Am Chem Soc (2016) 0.78
Proteoliposomes as tool for assaying membrane transporter functions and interactions with xenobiotics. Pharmaceutics (2013) 0.78
Evolutionary switches between two serine codon sets are driven by selection. Proc Natl Acad Sci U S A (2016) 0.77
Genome wide exploration of the origin and evolution of amino acids. BMC Evol Biol (2010) 0.77
Strategies of bacterial over expression of membrane transporters relevant in human health: the successful case of the three members of OCTN subfamily. Mol Biotechnol (2013) 0.76
Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy. Biophys J (2014) 0.76
2b or not 2b: Experimental evolution of functional exogenous sequences in a plant RNA virus. Genome Biol Evol (2017) 0.75
From structure to redox: the diverse functional roles of disulfides and implications in disease. Proteomics (2017) 0.75
Features of recent codon evolution: a comparative polymorphism-fixation study. J Biomed Biotechnol (2010) 0.75
A comprehensive software suite for the analysis of cDNAs. Genomics Proteomics Bioinformatics (2005) 0.75
The intrinsic disorder alphabet. III. Dual personality of serine. Intrinsically Disord Proteins (2015) 0.75
A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus. BMC Genomics (2015) 0.75
Prediction of protein amidation sites by feature selection and analysis. Mol Genet Genomics (2013) 0.75
Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code. Life (Basel) (2017) 0.75
Mutations in Cancer Cause Gain of Cysteine, Histidine, and Tryptophan at the Expense of a Net Loss of Arginine on the Proteome Level. Biomolecules (2017) 0.75
Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere. Life (Basel) (2017) 0.75
A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
Small CRISPR RNAs guide antiviral defense in prokaryotes. Science (2008) 17.79
Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (2012) 17.12
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41
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
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res (2002) 6.08
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD. Science (2004) 5.88
Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61
Selection in the evolution of gene duplications. Genome Biol (2002) 5.58
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
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. BMC Evol Biol (2003) 4.70
Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49
The structure of the protein universe and genome evolution. Nature (2002) 4.47
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet (2003) 4.39
The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28
Selection for short introns in highly expressed genes. Nat Genet (2002) 4.04
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res (2003) 3.90
Genome trees and the tree of life. Trends Genet (2002) 3.79
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol (2003) 3.72
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50
Epistasis as the primary factor in molecular evolution. Nature (2012) 3.34
Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci U S A (2002) 3.19
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct (2006) 3.18
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct (2009) 3.17
Introns and the origin of nucleus-cytosol compartmentalization. Nature (2006) 3.16
One-component systems dominate signal transduction in prokaryotes. Trends Microbiol (2005) 3.09
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
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem (2008) 3.00
Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol (2004) 2.78
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol (2008) 2.74
Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A (2007) 2.71
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol (2009) 2.66
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle (2004) 2.65
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res (2004) 2.62
Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct (2007) 2.53
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A (2009) 2.52
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Evolution and classification of P-loop kinases and related proteins. J Mol Biol (2003) 2.52
Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet (2012) 2.50
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res (2005) 2.49
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res (2004) 2.42
New dimensions of the virus world discovered through metagenomics. Trends Microbiol (2009) 2.41
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet (2004) 2.40
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res (2013) 2.35
Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res (2002) 2.35
Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet (2005) 2.34
Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol (2011) 2.32
Sequencing studies in human genetics: design and interpretation. Nat Rev Genet (2013) 2.27
Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol (2002) 2.24
Complete pathway for protein disulfide bond formation encoded by poxviruses. Proc Natl Acad Sci U S A (2002) 2.19
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A (2008) 2.16
Computational methods for Gene Orthology inference. Brief Bioinform (2011) 2.16
Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (2008) 2.15
Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. J Mol Biol (2005) 2.14
Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol (2006) 2.13