Published in Bioinformatics on September 12, 2013
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics (2014) 0.93
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Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol (2007) 1.51
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Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathog (2009) 1.45
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Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol (2001) 1.15
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Bringing molecules back into molecular evolution. PLoS Comput Biol (2012) 1.10
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Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds. Protein Eng Des Sel (2005) 1.06
Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci U S A (2013) 1.06
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The evolution and evolutionary consequences of marginal thermostability in proteins. Proteins (2011) 1.02
Mutation bias favors protein folding stability in the evolution of small populations. PLoS Comput Biol (2010) 1.00
Engineering by homologous recombination: exploring sequence and function within a conserved fold. Curr Opin Struct Biol (2007) 1.00
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
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Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity. J Mol Biol (2004) 0.95
Estimating selection pressures on HIV-1 using phylogenetic likelihood models. Stat Med (2008) 0.92
The effect of branch length variation on the selection of models of molecular evolution. J Mol Evol (2001) 0.91
Quantifying the impact of dependent evolution among sites in phylogenetic inference. Syst Biol (2010) 0.89
Trade-off between positive and negative design of protein stability: from lattice models to real proteins. PLoS Comput Biol (2009) 0.86
Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context. Syst Biol (2012) 0.85
Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophys Chem (2006) 0.84
Protein conformational diversity modulates sequence divergence. Mol Biol Evol (2012) 0.84
Protein conformational diversity correlates with evolutionary rate. Mol Biol Evol (2013) 0.83
Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles. Gene (2005) 0.82
Detecting selection for negative design in proteins through an improved model of the misfolded state. Proteins (2013) 0.82
Computer programs and methodologies for the simulation of DNA sequence data with recombination. Front Genet (2013) 0.81
Divergence, recombination and retention of functionality during protein evolution. Hum Genomics (2005) 0.79
jModelTest: phylogenetic model averaging. Mol Biol Evol (2008) 44.78
jModelTest 2: more models, new heuristics and parallel computing. Nat Methods (2012) 27.83
ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
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Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A (2003) 4.88
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Pharmacogenetic study of statin therapy and cholesterol reduction. JAMA (2004) 4.47
The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34
An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics (2004) 1.87
Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol (2006) 1.85
Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution (2002) 1.62
A coalescent model of recombination hotspots. Genetics (2003) 1.60
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J Mol Evol (2013) 1.45
A comparison of phylogenetic network methods using computer simulation. PLoS One (2008) 1.40
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics (2007) 1.27
MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol (2006) 1.27
Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries? Environ Microbiol (2006) 1.26
The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26
The effect of recombination on the reconstruction of ancestral sequences. Genetics (2010) 1.25
Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol (2006) 1.23
Coalescent simulation of intracodon recombination. Genetics (2009) 1.20
Analysing recombination in nucleotide sequences. Mol Ecol Resour (2011) 1.18
Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PLoS Comput Biol (2009) 1.14
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11
Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora). BMC Evol Biol (2003) 1.10
SABERTOOTH: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics (2007) 1.07
Reconstruction of protein structures from a vectorial representation. Phys Rev Lett (2004) 1.06
Mutation bias favors protein folding stability in the evolution of small populations. PLoS Comput Biol (2010) 1.00
Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect Genet Evol (2007) 1.00
Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol (2005) 1.00
Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution (2007) 0.97
Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol Biol (2013) 0.96
GenDecoder: genetic code prediction for metazoan mitochondria. Nucleic Acids Res (2006) 0.95
Characterization of phylogenetic networks with NetTest. BMC Bioinformatics (2010) 0.95
Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. Mol Biol Evol (2004) 0.94
Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation. Proteins (2010) 0.94
Inverted replication of vertebrate mitochondria. Mol Biol Evol (2008) 0.93
Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology (2009) 0.93
Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba. J Acquir Immune Defic Syndr (2007) 0.92
Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba. AIDS (2005) 0.91
Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins. Phys Rev Lett (2010) 0.91
jmodeltest.org: selection of nucleotide substitution models on the cloud. Bioinformatics (2014) 0.89
High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins. EMBO J (2013) 0.88
Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. J Mol Evol (2009) 0.87
Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infect Genet Evol (2007) 0.87
Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America. Mol Biol Evol (2009) 0.87
Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients. Virology (2007) 0.87
Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol (2014) 0.87
Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol (2011) 0.86
Computational design of centralized HIV-1 genes. Curr HIV Res (2010) 0.85
Characterization of reticulate networks based on the coalescent with recombination. Mol Biol Evol (2008) 0.84
Testing similarity measures with continuous and discrete protein models. Proteins (2003) 0.84
Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. AIDS Res Hum Retroviruses (2006) 0.82
Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates. Dev Comp Immunol (2010) 0.82
Structure and non-structure of centrosomal proteins. PLoS One (2013) 0.82
Detecting selection for negative design in proteins through an improved model of the misfolded state. Proteins (2013) 0.82
Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations. Mol Phylogenet Evol (2006) 0.81
Proving universal common ancestry with similar sequences. Trends Evol Biol (2012) 0.81
HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol (2011) 0.81
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH. BMC Bioinformatics (2010) 0.81
New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex. Mycologia (2010) 0.80
The evolution of the mitochondrial genetic code in arthropods revisited. Mitochondrial DNA (2012) 0.80
Novel HLA-B27-restricted epitopes from Chlamydia trachomatis generated upon endogenous processing of bacterial proteins suggest a role of molecular mimicry in reactive arthritis. J Biol Chem (2013) 0.79
An efficient conformational sampling method for homology modeling. Proteins (2008) 0.79
On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy. Infect Genet Evol (2005) 0.79
Detection and reduction of microaggregates in insulin preparations. Biotechnol Bioeng (2011) 0.78
Comparison of translation loads for standard and alternative genetic codes. BMC Evol Biol (2010) 0.78
Origin and length distribution of unidirectional prokaryotic overlapping genes. G3 (Bethesda) (2014) 0.77
Protein evolution in viral quasispecies under selective pressure: a thermodynamic and phylogenetic analysis. Gene (2005) 0.77
Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada. Infect Genet Evol (2012) 0.77
Characterizing conformation changes in proteins through the torsional elastic response. Biochim Biophys Acta (2013) 0.76
CRDOCK: an ultrafast multipurpose protein-ligand docking tool. J Chem Inf Model (2012) 0.76
Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae). Mol Phylogenet Evol (2009) 0.76
Genetic code prediction for metazoan mitochondria with GenDecoder. Methods Mol Biol (2009) 0.76
The emerging dynamic view of proteins: protein plasticity in allostery, evolution and self-assembly. Biochim Biophys Acta (2013) 0.75
Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes. PLoS One (2012) 0.75
Grid selection of models of nucleotide substitution. Stud Health Technol Inform (2010) 0.75
Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis. PLoS One (2016) 0.75
In memoriam. Angel Ramírez Ortiz (1966-2008). Proteins (2010) 0.75
The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network models. Integr Biol (Camb) (2017) 0.75
Flow-induced 2D protein crystallization: characterization of the coupled interfacial and bulk flows. Soft Matter (2015) 0.75