Published in BMC Genomics on March 07, 2006
Experimental evolution of a facultative thermophile from a mesophilic ancestor. Appl Environ Microbiol (2011) 1.02
Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Hum Mutat (2012) 0.85
Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR). PLoS One (2012) 0.81
Validation of an NSP-based (negative selection pattern) gene family identification strategy. BMC Bioinformatics (2008) 0.76
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med (2004) 71.08
EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science (2004) 61.56
SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res (2003) 52.26
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci (1992) 44.38
Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science (1989) 40.22
Identification of the cystic fibrosis gene: genetic analysis. Science (1989) 33.61
Predicting deleterious amino acid substitutions. Genome Res (2001) 28.95
Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins (1997) 26.91
Construction of phylogenetic trees. Science (1967) 23.69
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol (2004) 22.36
Identification of the cystic fibrosis gene: chromosome walking and jumping. Science (1989) 21.46
Prediction of deleterious human alleles. Hum Mol Genet (2001) 21.00
Accounting for human polymorphisms predicted to affect protein function. Genome Res (2002) 14.10
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
A new method of inference of ancestral nucleotide and amino acid sequences. Genetics (1995) 10.23
An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol (1996) 9.31
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83
PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics (2000) 3.66
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62
Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet (2004) 2.38
Planetary biology--paleontological, geological, and molecular histories of life. Science (2002) 2.21
Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci (2002) 1.77
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature (2003) 1.75
Alpha-helical, but not beta-sheet, propensity of proline is determined by peptide environment. Proc Natl Acad Sci U S A (1996) 1.67
Recreating a functional ancestral archosaur visual pigment. Mol Biol Evol (2002) 1.62
Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. Adv Enzyme Regul (1991) 1.44
Angiotensin II-forming activity in a reconstructed ancestral chymase. Science (1996) 1.34
Missense mutations in transmembrane domains of proteins: phenotypic propensity of polar residues for human disease. Proteins (2004) 1.28
Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics. Res Microbiol (2000) 1.13
Interhelical hydrogen bonds in the CFTR membrane domain. Nat Struct Biol (2001) 1.12
Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J Mol Biol (2002) 1.07
Pharmacophylogenomics: genes, evolution and drug targets. Nat Rev Drug Discov (2003) 1.07
Polar mutations in membrane proteins as a biophysical basis for disease. Biopolymers (2002) 0.95
Expression and purification of two hydrophobic double-spanning membrane proteins derived from the cystic fibrosis transmembrane conductance regulator. Protein Expr Purif (2002) 0.95
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
Non-native interhelical hydrogen bonds in the cystic fibrosis transmembrane conductance regulator domain modulated by polar mutations. Biochemistry (2004) 0.93
Bona Fide Predictions of Protein Secondary Structure Using Transparent Analyses of Multiple Sequence Alignments. Chem Rev (1997) 0.91
Polar residues in membrane domains of proteins: molecular basis for helix-helix association in a mutant CFTR transmembrane segment. Biochemistry (2002) 0.90
Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics (2003) 0.90
Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol (2003) 0.89
The planetary biology of cytochrome P450 aromatases. BMC Biol (2004) 0.82
Calculating posterior cystic fibrosis risk with echogenic bowel and one characterized cystic fibrosis mutation: avoiding pitfalls in the risk calculations. Am J Med Genet (1999) 0.81
Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals. Mol Biol Evol (1996) 0.80
The potential and challenges of nanopore sequencing. Nat Biotechnol (2008) 14.24
The challenges of sequencing by synthesis. Nat Biotechnol (2009) 2.89
Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet (2005) 2.68
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
Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci (2002) 1.77
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
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
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
Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society? J Comp Physiol B (2008) 1.23
Synthesis of carbohydrates in mineral-guided prebiotic cycles. J Am Chem Soc (2011) 1.19
In vitro selection with artificial expanded genetic information systems. Proc Natl Acad Sci U S A (2013) 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
Nucleobase pairing in expanded Watson-Crick-like genetic information systems. Structure (2003) 1.04
Experimental evolution of a facultative thermophile from a mesophilic ancestor. Appl Environ Microbiol (2011) 1.02
Theodore E. Woodward award. The evolution of obesity: insights from the mid-Miocene. Trans Am Clin Climatol Assoc (2010) 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
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
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
The NASA Astrobiology Roadmap. Astrobiology (2003) 0.93
Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry (2004) 0.92
Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality. Nucleic Acids Res (2002) 0.91
Conversion strategy using an expanded genetic alphabet to assay nucleic acids. Anal Chem (2013) 0.90
Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics (2003) 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
Dynamic assembly of primers on nucleic acid templates. Nucleic Acids Res (2006) 0.86
2-Hydroxymethylboronate as a reagent to detect carbohydrates: application to the analysis of the formose reaction. J Org Chem (2006) 0.86
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
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
The planetary biology of cytochrome P450 aromatases. BMC Biol (2004) 0.82
Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages. Nucleic Acids Res (2007) 0.81
Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS). Chembiochem (2014) 0.81
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example. BMC Evol Biol (2005) 0.81
Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups. Nucleosides Nucleotides Nucleic Acids (2010) 0.80
Synthesis and properties of 5-cyano-substituted nucleoside analog with a donor-donor-acceptor hydrogen-bonding pattern. J Org Chem (2012) 0.80
Comment on "The silicate-mediated formose reaction: bottom-up synthesis of sugar silicates". Science (2010) 0.80
Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives. J Org Chem (2004) 0.80
Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans. Astrobiology (2015) 0.79
Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure. J Org Chem (2002) 0.78
Self-Avoiding Molecular Recognition Systems (SAMRS). Nucleic Acids Symp Ser (Oxf) (2008) 0.78
Prebiotic glycosylation of uracil with electron-donating substituents. Astrobiology (2015) 0.78
Ribonucleosides for an artificially expanded genetic information system. J Org Chem (2014) 0.77
Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc (2015) 0.77
Abiotic regioselective phosphorylation of adenosine with borate in formamide. Astrobiology (2015) 0.77
C-5 modified nucleosides: direct insertion of alkynyl-thio functionality in pyrimidines. Nucleosides Nucleotides Nucleic Acids (2003) 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
Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. BMC Bioinformatics (2006) 0.75
Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules. Nucleosides Nucleotides Nucleic Acids (2008) 0.75
A convenient synthesis of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-methyl-2'-deoxypseudoisocytidine. Nucleosides Nucleotides Nucleic Acids (2009) 0.75
2'-deoxy-1-methylpseudocytidine, a stable analog of 2'-deoxy-5-methylisocytidine. Bioorg Med Chem (2009) 0.75