Published in Trends Biochem Sci on June 01, 2002
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics (2006) 2.39
Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol (2007) 2.01
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci (2004) 1.91
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol (2004) 1.70
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res (2004) 1.57
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha. Protein Sci (2004) 1.33
A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha. Proc Natl Acad Sci U S A (2004) 1.32
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. Nucleic Acids Res (2005) 1.27
Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria. Nucleic Acids Res (2003) 1.09
FamClash: a method for ranking the activity of engineered enzymes. Proc Natl Acad Sci U S A (2004) 1.06
Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res (2003) 1.06
Evolutionary proteomics identifies amino acids essential for ligand-binding of the cytokinin receptor CHASE domain. BMC Evol Biol (2007) 1.05
Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol (2011) 1.04
The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. PLoS One (2012) 0.99
Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr Opin Chem Biol (2011) 0.99
Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics (2009) 0.98
Phylogenetic analysis of the cytochrome P450 3 (CYP3) gene family. J Mol Evol (2003) 0.97
Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints. J Mol Evol (2007) 0.96
Horizontal gene transfer of "prototype" Nramp in bacteria. J Mol Evol (2003) 0.94
Evolutionary origin of the mitochondrial cholesterol transport machinery reveals a universal mechanism of steroid hormone biosynthesis in animals. PLoS One (2013) 0.93
Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics (2007) 0.93
Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family. BMC Evol Biol (2006) 0.92
SPEER-SERVER: a web server for prediction of protein specificity determining sites. Nucleic Acids Res (2012) 0.88
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. Mol Biol Evol (2010) 0.87
Variability-based sequence alignment identifies residues responsible for functional differences in alpha and beta tubulin. Protein Sci (2004) 0.86
Exploiting models of molecular evolution to efficiently direct protein engineering. J Mol Evol (2010) 0.85
Recombination detection under evolutionary scenarios relevant to functional divergence. J Mol Evol (2012) 0.83
The planetary biology of cytochrome P450 aromatases. BMC Biol (2004) 0.82
Deep phylogeny--how a tree can help characterize early life on Earth. Cold Spring Harb Perspect Biol (2010) 0.82
Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family. BMC Genomics (2006) 0.82
Delineation of plant caleosin residues critical for functional divergence, positive selection and coevolution. BMC Evol Biol (2014) 0.81
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evol Bioinform Online (2008) 0.81
Inference of functional divergence among proteins when the evolutionary process is non-stationary. J Mol Evol (2013) 0.80
UVPAR: fast detection of functional shifts in duplicate genes. BMC Bioinformatics (2006) 0.80
Unravelling selection shifts among foot-and-mouth disease virus (FMDV) serotypes. Evol Bioinform Online (2007) 0.80
Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PLoS Comput Biol (2009) 0.79
Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses. BMC Evol Biol (2012) 0.79
Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa). Front Plant Sci (2016) 0.78
Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L. PLoS One (2015) 0.77
Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation. BMC Evol Biol (2014) 0.77
Interchanging functionality among homologous elongation factors using signatures of heterotachy. J Mol Evol (2013) 0.76
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. J Mol Biol (2012) 0.76
Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics. BMC Evol Biol (2006) 0.76
Coevolution of URAT1 and Uricase during Primate Evolution: Implications for Serum Urate Homeostasis and Gout. Mol Biol Evol (2016) 0.76
Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. PLoS Comput Biol (2016) 0.75
The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana. BMC Plant Biol (2016) 0.75
Evolution of the 3R-MYB Gene Family in Plants. Genome Biol Evol (2017) 0.75
Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis. BMC Evol Biol (2016) 0.75
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. Genetics (2017) 0.75
The potential and challenges of nanopore sequencing. Nat Biotechnol (2008) 14.24
Role of duplicate genes in genetic robustness against null mutations. Nature (2003) 7.81
Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat Rev Genet (2007) 3.48
The challenges of sequencing by synthesis. Nat Biotechnol (2009) 2.89
Expression divergence between duplicate genes. Trends Genet (2005) 2.69
Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet (2005) 2.68
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
A three-stage colonization model for the peopling of the Americas. PLoS One (2008) 2.40
Induced gene expression in human brain after the split from chimpanzee. Trends Genet (2003) 2.19
Enzymatic incorporation of a third nucleobase pair. Nucleic Acids Res (2007) 1.79
Amplification, mutation, and sequencing of a six-letter synthetic genetic system. J Am Chem Soc (2011) 1.78
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature (2003) 1.75
Signatures of a shadow biosphere. Astrobiology (2009) 1.65
The role of medical libraries in undergraduate education: a case study in genetics. J Med Libr Assoc (2002) 1.60
Evolution of alternative splicing after gene duplication. Genome Res (2005) 1.55
PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1. Nucleic Acids Res (2004) 1.52
Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol (2004) 1.51
Locked nucleic acid molecular beacons. J Am Chem Soc (2005) 1.51
The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Res (2005) 1.49
Intron gain and loss in segmentally duplicated genes in rice. Genome Biol (2006) 1.48
Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biol (2004) 1.48
Updated three-stage model for the peopling of the Americas. PLoS One (2008) 1.45
How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet (2004) 1.38
Expanded genetic alphabets in the polymerase chain reaction. Angew Chem Int Ed Engl (2010) 1.38
Multiplexed genetic analysis using an expanded genetic alphabet. Clin Chem (2004) 1.37
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res (2006) 1.32
Sequence alignments and pair hidden Markov models using evolutionary history. J Mol Biol (2003) 1.30
Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol Biol (2010) 1.28
Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society? J Comp Physiol B (2008) 1.23
Characterization of paralogous protein families in rice. BMC Plant Biol (2008) 1.19
Synthesis of carbohydrates in mineral-guided prebiotic cycles. J Am Chem Soc (2011) 1.19
Lamprey type II collagen and Sox9 reveal an ancient origin of the vertebrate collagenous skeleton. Proc Natl Acad Sci U S A (2006) 1.17
The origin and evolution of enamel mineralization genes. Cells Tissues Organs (2007) 1.12
Predicting the proportion of essential genes in mouse duplicates based on biased mouse knockout genes. J Mol Evol (2008) 1.11
In vitro selection with artificial expanded genetic information systems. Proc Natl Acad Sci U S A (2013) 1.10
Accurate and fast methods to estimate the population mutation rate from error prone sequences. BMC Bioinformatics (2009) 1.10
Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine. Nucleic Acids Res (2004) 1.09
Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proc Natl Acad Sci U S A (2010) 1.09
Redesigning a library-based genetics class research project through instructional theory and authentic experience. J Med Libr Assoc (2012) 1.08
Identification of copy number variation hotspots in human populations. Am J Hum Genet (2010) 1.08
Ordered origin of the typical two- and three-repeat Myb genes. Gene (2004) 1.04
Nucleobase pairing in expanded Watson-Crick-like genetic information systems. Structure (2003) 1.04
Comment on "Population size does not influence mitochondrial genetic diversity in animals". Science (2006) 1.04
A preliminary analysis of gene pleiotropy estimated from protein sequences. J Exp Zool B Mol Dev Evol (2010) 1.03
Experimental evolution of a facultative thermophile from a mesophilic ancestor. Appl Environ Microbiol (2011) 1.02
Utility of DNA viruses for studying human host history: case study of JC virus. Mol Phylogenet Evol (2007) 1.02
Theodore E. Woodward award. The evolution of obesity: insights from the mid-Miocene. Trans Am Clin Climatol Assoc (2010) 1.01
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics (2004) 1.01
Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern. J Org Chem (2003) 0.99
The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. PLoS One (2012) 0.99
A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol Phylogenet Evol (2005) 0.99
The "strong" RNA world hypothesis: fifty years old. Astrobiology (2013) 0.99
A review: synthesis of aryl C-glycosides via the heck coupling reaction. Nucleosides Nucleotides Nucleic Acids (2006) 0.98
A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs. BMC Genomics (2007) 0.96
Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulation. Genome Res (2002) 0.96
Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints. J Mol Evol (2007) 0.96
The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors. Mol Biol Evol (2002) 0.94
The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease. Med Hypotheses (2008) 0.94
Natural history and functional divergence of protein tyrosine kinases. Gene (2003) 0.93
The NASA Astrobiology Roadmap. Astrobiology (2003) 0.93
Cross-correlation frequency resolved optical gating analysis of broadband continuum generation in photonic crystal fiber: simulations and experiments. Opt Express (2002) 0.92
Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits. J Exp Zool B Mol Dev Evol (2007) 0.92
Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry (2004) 0.92
Time squared: repeated measures on phylogenies. Mol Biol Evol (2006) 0.91
Incorporating experimental design and error into coalescent/mutation models of population history. Genetics (2007) 0.91
Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality. Nucleic Acids Res (2002) 0.91
Identification of functional mutations in GATA4 in patients with congenital heart disease. PLoS One (2013) 0.91
Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics (2003) 0.90
Conversion strategy using an expanded genetic alphabet to assay nucleic acids. Anal Chem (2013) 0.90
Unique structure and regulation of the nematode detoxification gene regulator, SKN-1: implications to understanding and controlling drug resistance. Drug Metab Rev (2012) 0.90
The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events? Mol Biol Evol (2007) 0.89
Artificial genetic systems: self-avoiding DNA in PCR and multiplexed PCR. Angew Chem Int Ed Engl (2010) 0.89
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. Nucleic Acids Res (2011) 0.89
Extremely simple single-prism ultrashort- pulse compressor. Opt Express (2006) 0.88
Carrier-envelope-phase-stable, 1.2 mJ, 1.5 cycle laser pulses at 2.1 μm. Opt Lett (2012) 0.87
Dynamic assembly of primers on nucleic acid templates. Nucleic Acids Res (2006) 0.86
Evolution of RNases in leaf monkeys: being parallel gene duplications or parallel gene conversions is a problem of molecular phylogeny. Mol Phylogenet Evol (2008) 0.86
Genome factor and gene pleiotropy hypotheses in protein evolution. Biol Direct (2010) 0.86
2-Hydroxymethylboronate as a reagent to detect carbohydrates: application to the analysis of the formose reaction. J Org Chem (2006) 0.86
Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Mol Phylogenet Evol (2007) 0.85
2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymerase. Org Lett (2004) 0.85
Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure. Nucleosides Nucleotides Nucleic Acids (2008) 0.85
Synthetic biology. Expert Opin Biol Ther (2005) 0.84
Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet. Chem Commun (Camb) (2008) 0.84
Maximum likelihood for genome phylogeny on gene content. Stat Appl Genet Mol Biol (2004) 0.84
Revisit on the evolutionary relationship between alternative splicing and gene duplication. Gene (2012) 0.84
Pulse-front tilt caused by spatial and temporal chirp. Opt Express (2004) 0.84
Fourier transform-ion cyclotron resonance mass spectrometric resolution, identification, and screening of non-covalent complexes of Hck Src homology 2 domain receptor and ligands from a 324-member peptide combinatorial library. J Am Soc Mass Spectrom (2002) 0.83
Frequency-resolved optical gating and single-shot spectral measurements reveal fine structure in microstructure-fiber continuum. Opt Lett (2002) 0.83
A simple method for phylogenomic inference using the information of gene content of genomes. Gene (2008) 0.83
Algorithms for multiple genome rearrangement by signed reversals. Pac Symp Biocomput (2003) 0.82
Multiple genome rearrangement by reversals. Pac Symp Biocomput (2002) 0.82
Experimental studies of the coherence of microstructure-fiber supercontinuum. Opt Express (2003) 0.82
Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family. BMC Genomics (2006) 0.82
Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes. J Mol Evol (2002) 0.82
Primate DNA suggests long-term stability of an African rainforest. Ecol Evol (2012) 0.82
Tissue-driven hypothesis with Gene Ontology (GO) analysis. Ann Biomed Eng (2007) 0.82
The planetary biology of cytochrome P450 aromatases. BMC Biol (2004) 0.82