Jeffrey L Thorne
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Works (45)
Updated: April 6th, 2024 05:04
2023 journal article
Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization
MOLECULAR BIOLOGY AND EVOLUTION, 40(9).
author keywords: interlocus gene conversion; paralog homogenization; teleost genome duplication
academic.oup.com (publisher PDF)
Sources: Web Of Science, NC State University Libraries
Added: April 1, 2024
2023 article
Scalable Bayesian Divergence Time Estimation With Ratio Transformations
Ji, X., Fisher, A. A., Su, S., Thorne, J. L., Potter, B., Lemey, P., … Suchard, M. A. (2023, July 17). SYSTEMATIC BIOLOGY.
author keywords: Bayesian inference; divergence time estimation; effective sample size; Hamiltonian Monte Carlo; pathogens; phylogenetics; ratio transformation
TL;DR:
A ratio transformation is explored that maps the original N-1 internal node heights into a space of one height parameter and N-2 ratio parameters and improves inference efficiency by at least 5-fold and makes it computationally feasible to incorporate mixed-effects molecular clock models for the Ebola virus example.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: September 5, 2023
2022 article
Convergent evolution of polyploid genomes from across the eukaryotic tree of life
Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P. P., Pires, J. C., … Conant, G. C. (2022, May 10). G3-GENES GENOMES GENETICS, Vol. 5.
author keywords: polyploidy; convergent evolution; reciprocal gene loss; evolutionary model
MeSH headings : Diploidy; Eukaryota; Evolution, Molecular; Humans; Phylogeny; Polyploidy
TL;DR:
By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, it is shown that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 23, 2022
2022 journal article
Correlations between alignment gaps and nucleotide substitution or amino acid replacement
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(34).
TL;DR:
A test of the null hypothesis that nucleotide substitution or amino acid replacement processes are independent of gap locations within sequence alignments is introduced, demonstrating the need for modifying the conventional approach of basing evolutionary inferences upon single optimal alignments.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: July 31, 2023
2022 journal article
Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers A pilot study
EVOLUTION MEDICINE AND PUBLIC HEALTH, 10(1), 221–230.
author keywords: liver cancer; mutation; prosimians; non-human primates; TP53; ARID1A; CTNNB1
TL;DR:
This pilot study suggests that human exome capture reagents are a promising tool for genomic studies of cancer in lemurs and other non-human primates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: May 23, 2022
2021 article
Measuring Phylogenetic Information of Incomplete Sequence Data
Seo, T.-K., Gascuel, O., & Thorne, J. L. (2021, September 1). SYSTEMATIC BIOLOGY.
MeSH headings : Evolution, Molecular; INDEL Mutation; Models, Genetic; Models, Statistical; Phylogeny; Sequence Alignment
TL;DR:
A new test for model adequacy is developed by comparing the Fisher information of actual and simulated sequences and identifying which alignment sites and tree branches are most affected by gaps and model misspecification.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: March 14, 2022
2021 article
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
Campbell, C. R., Tiley, G. P., Poelstra, J. W., Hunnicutt, K. E., Larsen, P. A., Lee, H.-J., … Yoder, A. D. (2021, July 16). HEREDITY.
MeSH headings : Animals; Cheirogaleidae / genetics; Genome; Mice; Mutation Rate; Pedigree; Phylogeny
TL;DR:
This study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade, and finds both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: Web Of Science
Added: August 2, 2021
2020 journal article
Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life
MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 11–17.
author keywords: veterinary oncology; cross-species studies; cancer drug discovery; evolutionary biology
MeSH headings : Animals; Drug Discovery; Humans; Neoplasms / drug therapy; Neoplasms / veterinary
TL;DR:
Clinical trials in veterinary patients with cancer provide an opportunity to evaluate a novel therapeutic in a setting that recapitulates many of the key features of human cancers, including key genomic aberrations that underly tumor development, response and resistance to treatment, and the presence of comorbidities that can affect outcomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 10, 2020
2020 journal article
Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models
JOURNAL OF COMPUTATIONAL BIOLOGY, 27(3), 361–375.
author keywords: diffusion process; dynamic programming; evolution; phylogeny; protein structure
MeSH headings : Computational Biology / methods; Evolution, Molecular; Models, Statistical; Proteins / chemistry; Proteins / metabolism; Sequence Alignment; Sequence Analysis, Protein; Structural Homology, Protein
TL;DR:
This work develops a simple model of site-dependent sequence evolution, which is used to demonstrate the bias resulting from the application of standard site-independent sequence evolution models and yields a significant reduction of bias in estimated evolutionary distances.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: April 20, 2020
2018 article
Modeling Dependence in Evolutionary Inference for Proteins
RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB 2018, Vol. 10812, pp. 122–137.
author keywords: Protein structure; Evolution; Dynamic programming; Phylogeny; Diffusion process
TL;DR:
It is demonstrated that this extended, site-dependent model (SDM), extended to account for correlated evolutionary drift among neighboring amino acid positions, yields a significant reduction of bias in estimated evolutionary distances and helps further improve phylogenetic tree reconstruction.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: March 18, 2019
2016 journal article
A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast
MOLECULAR BIOLOGY AND EVOLUTION, 33(9), 2469–2476.
author keywords: interlocus gene conversion; multigene family evolution
MeSH headings : Base Sequence / genetics; Biological Evolution; Evolution, Molecular; Gene Conversion; Models, Genetic; Multigene Family; Nucleotides / genetics; Phylogeny; Point Mutation; Saccharomyces cerevisiae; Sequence Analysis, DNA / methods; Yeasts / genetics
TL;DR:
This work estimated the percentage of nucleotide substitutions that originate with an IGC event rather than a point mutation in 14 groups of yeast ribosomal protein-coding genes, and found values ranging from 20% to 38%.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Grouping substitution types into different relaxed molecular clocks
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species
Current Genetics, 61(4), 567–577.
Contributors: E. Lassiter n, C. Russ *, C. Nusbaum*, Q. Zeng *, A. Saville n, R. Olarte n, I. Carbone n , C. Hu n
author keywords: Phytophthora 1 c clade; Mitochondria; Late blight; Phylogenetics
MeSH headings : Biological Evolution; Chimera / microbiology; Colombia; DNA, Mitochondrial / genetics; Ecuador; Genome, Mitochondrial; Solanum lycopersicum / microbiology; Mitochondria / genetics; Peru; Phylogeny; Phylogeography; Phytophthora / classification; Phytophthora / genetics; Phytophthora infestans / classification; Phytophthora infestans / genetics; Plant Diseases / microbiology; Sequence Analysis, DNA; Solanum tuberosum / microbiology
TL;DR:
The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2015 journal article
Relaxing the Molecular Clock to Different Degrees for Different Substitution Types
MOLECULAR BIOLOGY AND EVOLUTION, 32(8), 1948–1961.
author keywords: CpG transition rate; context-dependent substitution; relaxed molecular clock; divergence time estimation
MeSH headings : Animals; Biological Clocks / physiology; CpG Islands / physiology; DNA, Intergenic / genetics; Evolution, Molecular; Humans; Models, Biological
TL;DR:
Through stochastic mapping of sequence histories from context-independent substitution models, this approach allows for context-dependent nucleotide substitutions to change their relative rates over time, and finds comparatively little rate variation over time for CpG to TpG substitutions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution
EVOLUTIONARY BIOINFORMATICS, 11.
author keywords: protein evolution; protein structure; gene expression; codon usage; scaled selection coefficient; solvent accessibility
TL;DR:
It is come to the biologically plausible conclusion that both RSA and gene expression are related to amino acid frequencies, but, among synonymous codons, the relative probability of a particular codon is more closely related to gene expression than RSA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution
Bayesian Phylogenetics: Methods, Algorithms, and Applications, 247–275.
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
The interface of protein structure, protein biophysics, and molecular evolution
Protein Science, 21(6), 769–785.
author keywords: evolutionary modeling; domain evolution; sequence-structure-function relationships; protein dynamics; protein thermodynamics; gene duplication; protein expression; ancestral sequence reconstruction
MeSH headings : Amino Acid Sequence; Animals; Evolution, Molecular; Humans; Models, Molecular; Molecular Sequence Data; Protein Conformation; Protein Folding; Proteins / chemistry; Proteins / genetics; RNA, Messenger / genetics; Sequence Alignment
TL;DR:
The relationship between modeling and needed high‐throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: August 28, 2020
2012 review
The interface of protein structure, protein biophysics, and molecular evolution
[Review of ]. Protein Science, 21(6), 769–785.
Source: NC State University Libraries
Added: August 6, 2018
2011 journal article
Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution
GENOME BIOLOGY AND EVOLUTION, 3, 66–74.
author keywords: gene expression; transcriptional regulation; protein-DNA coevolution; cis-regulatory evolution
MeSH headings : Animals; Evolution, Molecular; Gene Expression; Genome; Humans; Mice; Models, Genetic; Models, Statistical; Phylogeny; Promoter Regions, Genetic; Regulatory Sequences, Nucleic Acid; Transcriptional Activation; Vertebrates / genetics
TL;DR:
It is found that a surprisingly large number of cis-regulatory elements have been subject to coordinated genome-wide modifications during vertebrate evolution, such that the motif frequency changes on a single branch of vertebrate phylogeny.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2011 journal article
History Can Matter: Non-Markovian Behavior of Ancestral Lineages
SYSTEMATIC BIOLOGY, 60(3), 276–290.
author keywords: Ancestral lineage; ancestral process; Hill-Robertson effect; population genetics
MeSH headings : Computer Simulation; Evolution, Molecular; Genetic Fitness; Genetic Variation; Markov Chains; Models, Genetic; Polymorphism, Genetic; Selection, Genetic
TL;DR:
This work used the Wright-Fisher model of population genetics to simulate very many generations of mutation, natural selection, and genetic drift to show that the process by which a nonrecombining sequence changes over time can markedly deviate from the Markov assumption that is ubiquitous in molecular phylogenetics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2009 journal article
Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci
Gene, 441(1-2), 45–52.
MeSH headings : Evolution, Molecular; Gene Frequency; Humans; Polymorphism, Single Nucleotide; Protein Structure, Tertiary; Proteins / genetics; Selection, Genetic
TL;DR:
This work focuses on 140 nonsynonymous single nucleotide polymorphisms of humans that are in proteins with known tertiary structures and finds that the technique for employing protein tertiary structure information yields some biologically plausible results but that it does not substantially improve the inference of ancestral human allele types.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: NC State University Libraries
Added: August 6, 2018
2008 journal article
Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 363(1512), 3931–3939.
author keywords: variable-length Markov model; profile hidden Markov model; insertion-deletion model; scaled selection coefficient; fitness; Pfam
MeSH headings : Computer Simulation; DNA / genetics; Evolution, Molecular; Genetics, Population; INDEL Mutation / genetics; Markov Chains; Models, Genetic; Population Density; Proteins / genetics; Selection, Genetic
TL;DR:
This work explores how to construct time-reversible evolutionary models that yield stationary distributions of sequences that match given target distributions, and introduces an insertion–deletion model that describes selectively neutral evolutionary changes to DNA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2008 journal article
Rates of nucleotide substitution in Cornaceae (Cornales)—Pattern of variation and underlying causal factors
Molecular Phylogenetics and Evolution, 49(1), 327–342.
author keywords: Comus; Cornaceae; Divergence time; Rate of molecular evolution; Rate of morphological evolution; Speciation
MeSH headings : Bayes Theorem; Chloroplasts / genetics; Cornus / anatomy & histology; Cornus / classification; Cornus / genetics; DNA, Chloroplast / genetics; DNA, Plant / genetics; Evolution, Molecular; Fossils; Genes, Plant; Genetic Speciation; Genome, Chloroplast; Models, Genetic; Nucleotides / genetics; Phylogeny; Sequence Analysis, DNA
TL;DR:
This study examined the rate and pattern of molecular evolution for five DNA regions over a phylogeny of Cornus, the single genus of Cornaceae, and suggested a possible localized link between species richness and rate of nonsynonymous nucleotide substitution for the combined cpDNA regions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2007 journal article
A tabu search algorithm for maximum parsimony phylogeny inference
EUROPEAN JOURNAL OF OPERATIONAL RESEARCH, 176(3), 1908–1917.
author keywords: tabu search; OR in biology; bioinformatics; phylogeny inference; maximum parsimony
TL;DR:
The parsimony principle is adopted and a tabu search algorithm is designed for finding a most parsimonious phylogeny tree and it generates much more accurate results than the default options of the program “dnapars” (heuristic search based).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2007 journal article
Population genetics without intraspecific data
MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1667–1677.
author keywords: dependence among sites; fixation probability; protein structure; RNA structure
MeSH headings : Animals; Annexin A5 / genetics; Computational Biology; Computer Simulation; Evolution, Molecular; Genetic Variation; Genetics, Population; Likelihood Functions; Mice; Models, Biological; Models, Genetic; Nucleic Acid Conformation; Phenotype; Phylogeny; RNA / chemistry; RNA / genetics; Rats; Selection, Genetic
TL;DR:
It is argued that statistical fit to data should not be the sole criterion for assessing models of sequence change, and a good interspecific model should also yield a clear and biologically plausible population genetic interpretation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Protein evolution constraints and model-based techniques to study them
CURRENT OPINION IN STRUCTURAL BIOLOGY, 17(3), 337–341.
MeSH headings : Evolution, Molecular; Models, Molecular; Protein Folding; Proteins / chemistry; Proteins / genetics
TL;DR:
Although statistical tools for characterizing protein evolution are improving, the list of candidate phenomena that can affect rates of protein evolution is long and the relative contributions of these phenomena are only beginning to be disentangled.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Quantifying the impact of protein tertiary structure on molecular evolution
MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1769–1782.
author keywords: molecular evolution; protein structure impact; Gene Ontology; MCMC; Bayes factor
MeSH headings : Bayes Theorem; Computational Biology; Computer Simulation; Data Interpretation, Statistical; Evolution, Molecular; Protein Structure, Tertiary; Proteins / chemistry; Proteins / genetics; Sequence Alignment
TL;DR:
Although their influences on rates of evolution vary among protein families, it is found that the mean impacts of solvent accessibility and pairwise interactions are about the same.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2006 journal article
Dependence among sites in RNA evolution
MOLECULAR BIOLOGY AND EVOLUTION, 23(8), 1525–1537.
author keywords: RNA secondary structure; dependence among sites; substitution rate
MeSH headings : Animals; Computer Simulation; Evolution, Molecular; Markov Chains; Nucleic Acid Conformation; Phylogeny; RNA / chemistry; RNA / genetics; RNA, Ribosomal / chemistry; RNA, Ribosomal / genetics; Sequence Analysis, RNA
TL;DR:
An evolutionary model and a Bayesian inference procedure that are aimed at filling the gap in probabilistic models of genotype evolution are proposed and potential applications, including improved ancestral sequence inference and location of functionally interesting sites, are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2006 journal article
Testing for spatial clustering of amino acid replacements within protein tertiary structure
JOURNAL OF MOLECULAR EVOLUTION, 62(6), 682–692.
author keywords: protein tertiary structure; protein evolution; spatial clustering
MeSH headings : Amino Acid Substitution; Cluster Analysis; Evolution, Molecular; Protein Structure, Tertiary; Statistics, Nonparametric
TL;DR:
Two simple and not very parametric hypothesis tests are introduced that help distinguish three possibilities of spatial clustering of amino acid replacements during evolution and these findings need to be reconciled with the common practice of basing evolutionary inferences on models that assume independent change among sites.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(12), 4436–4441.
MeSH headings : Biological Evolution; Databases, Genetic; Genetic Techniques; Genetic Variation; Likelihood Functions; Models, Genetic; Phylogeny
TL;DR:
Two criteria for inferring the optimal tree topology from data sets with multiple genes and a two-stage bootstrap procedure that involves resampling genes and then resamplings alignment columns within resampled genes are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2004 article
A Bayesian approach to DNA sequence segmentation - Discussion
Thorne, J. L. (2004, September). BIOMETRICS, Vol. 60, pp. 584–585.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2004 journal article
Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
MOLECULAR BIOLOGY AND EVOLUTION, 21(7), 1201–1213.
author keywords: Bayesian method; Markov chain Monte Carlo (MCMC); rate change model; lognormal; evolutionary rate; selection; synonymous rate; nonsynonymous rate
MeSH headings : Animals; Base Sequence / genetics; Bayes Theorem; Electron Transport Complex IV / genetics; Evolution, Molecular; Genetic Variation; Nucleotides / genetics; Polymorphism, Genetic; Primates / genetics; Rodentia / genetics; Selection, Genetic; Sequence Analysis, DNA / methods
TL;DR:
This work analyzes cytochrome oxidase subunit I evolution in primates and infer that nonsynonymous rates have a greater tendency to change over time than do synonymous rates, and suggests that rates have been positively correlated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2004 review
Molecular evidence on plant divergence times
[Review of ]. AMERICAN JOURNAL OF BOTANY, 91(10), 1656–1665.
author keywords: adaptive radiation; biogeography; divergence time; molecular clock; phylogeny; rates
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2003 journal article
Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach
Genome Biology, 4(6), R39–1.
Source: NC State University Libraries
Added: August 6, 2018
2003 journal article
Protein evolution with dependence among codons due to tertiary structure
MOLECULAR BIOLOGY AND EVOLUTION, 20(10), 1692–1704.
author keywords: protein structure; evolution; Markov chain Monte Carlo; Bayesian
MeSH headings : Annexin A5 / chemistry; Annexin A5 / genetics; Codon; Computational Biology; Computer Simulation; Data Interpretation, Statistical; Evolution, Molecular; Markov Chains; Muramidase / chemistry; Muramidase / genetics; Protein Structure, Tertiary; Proteins / chemistry; Proteins / genetics
TL;DR:
The focus here is evolutionary dependence among codons that is associated with protein structure and could be applied to diverse cases of evolutionary dependence where surrogates for sequence fitness can be measured or modeled.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2003 journal article
Time flies, a new molecular time-scale for brachyceran fly evolution without a clock
Systematic Biology, 52(6), 745–756.
Source: NC State University Libraries
Added: August 6, 2018
2003 review
Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution
[Review of ]. GENES & GENETIC SYSTEMS, 78(4), 267–283.
author keywords: Bayesian method; divergence times; variation of evolutionary
MeSH headings : Animals; Bayes Theorem; Evolution, Molecular; Fossils; Genetic Variation; Humans; Mathematics; Models, Biological; Models, Genetic; Phylogeny; Probability; Time Factors
TL;DR:
This Bayesian method not only takes account of the variation of molecular evolutionary rate among lineages and among genes, but it also incorporates fossil evidence via constraints on node times and is expected to increase the accuracy of divergence time estimates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2002 journal article
A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
BIOINFORMATICS, 18(1), 115–123.
MeSH headings : Computational Biology; Evolution, Molecular; HIV-1 / genetics; HIV-1 / isolation & purification; Humans; Models, Genetic; Models, Statistical; Time Factors; Viruses / genetics; Viruses / isolation & purification
TL;DR:
Variation in sequence isolation times can be intentionally adjusted to increase the power of hypothesis tests and to reduce the uncertainty of evolutionary parameter estimates, but this fact has received little previous attention.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2002 journal article
Divergence time and evolutionary rate estimation with multilocus data
SYSTEMATIC BIOLOGY, 51(5), 689–702.
author keywords: Markov chain Monte Carlo; Metropolis-Hastings algorithm; molecular clock; phylogeny
MeSH headings : Algorithms; Bayes Theorem; Biological Evolution; Evolution, Molecular; Markov Chains; Models, Genetic; Monte Carlo Method; Phylogeny; Plants / genetics; Time Factors
TL;DR:
Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2002 journal article
Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach
Genetics, 160(4), 1283–1293.
Source: NC State University Libraries
Added: August 6, 2018
2001 journal article
Performance of a divergence time estimation method under a probabilistic model of rate evolution
MOLECULAR BIOLOGY AND EVOLUTION, 18(3), 352–361.
author keywords: molecular clock; phylogeny; Markov chain Monte Carlo; Metropolis-Hastings algorithm
MeSH headings : Bayes Theorem; Biological Evolution; Fossils; Models, Genetic; Probability
TL;DR:
Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included and new parameterization more effectively captures the phylogenetic structure of rate evolution on a tree.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2000 journal article
Models of protein sequence evolution and their applications
CURRENT OPINION IN GENETICS & DEVELOPMENT, 10(6), 602–605.
MeSH headings : Amino Acid Sequence; Animals; Codon; Evolution, Molecular; Genetic Variation; Models, Genetic; Mutagenesis, Insertional; Point Mutation; Protein Structure, Secondary; Proteins / genetics; Sequence Deletion
TL;DR:
Notable recent advances have been made in the treatment of insertion and deletion events, the estimation of amino-acid replacement rates, and the detection of positive selection.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1998 journal article
Assessing the impact of secondary structure and solvent accessibility on protein evolution
Genetics, 149(1), 445–458.
Source: NC State University Libraries
Added: August 6, 2018
1998 journal article
Estimating the rate of evolution of the rate of molecular evolution
MOLECULAR BIOLOGY AND EVOLUTION, 15(12), 1647–1657.
author keywords: molecular clock; phylogeny; Markov chain Monte Carlo; Metropolis-Hastings algorithm
MeSH headings : Algorithms; Biological Evolution; Evolution, Molecular; Models, Genetic; Models, Statistical; Phylogeny; Plant Proteins / genetics; Plants / classification; Plants / genetics; Ribulose-Bisphosphate Carboxylase; Time
TL;DR:
A simple model for the evolution of the rate of molecular evolution with a Bayesian approach can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1998 journal article
PASSML: combining evolutionary inference and protein secondary structure prediction
BIOINFORMATICS, 14(8), 726–733.
MeSH headings : Adenylate Kinase / genetics; Algorithms; Amino Acid Sequence; Animals; Cattle; Databases, Factual; Escherichia coli / genetics; Evolution, Molecular; Humans; Neisseria meningitidis / genetics; Phylogeny; Protein Structure, Secondary; Rats; Saccharomyces cerevisiae / genetics; Schizosaccharomyces / genetics; Sequence Alignment; Software
TL;DR:
The PASSML software is described and it is illustrated how it allows both the reconstruction of phylogenies and prediction of secondary structure from aligned amino acid sequences.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
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