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Works (25)
Updated: April 3rd, 2024 20:19
2020 journal article
Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability
PLOS ONE, 15(3).
MeSH headings : Algorithms; Amino Acid Substitution; Evolution, Molecular; Likelihood Functions; Models, Genetic; Mutation Rate; Phylogeny; Sequence Alignment; Sequence Analysis, DNA / methods
TL;DR:
It is demonstrated that the variance of this discretized distribution has an upper bound determined solely by the choice of K and the mean of the distribution, which can introduce biases into statistical inference when estimating parameters governing site-to-site variability of substitution rates.
(via Semantic Scholar)
journals.plos.org (publisher PDF)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: June 15, 2020
2020 journal article
HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 295–299.
author keywords: evolutionary analysis; natural selection; hypothesis testing; statistical inference; software engineering
MeSH headings : Genetic Techniques; Phylogeny; Software
TL;DR:
The 2.5 release of Hyphy includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backwards compatible with previous HyPhy releases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: March 10, 2020
2020 journal article
Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
MOLECULAR BIOLOGY AND EVOLUTION, 37(8), 2430–2439.
author keywords: evolutionary model; synonymous rate variation; codon model; episodic selection
MeSH headings : Animals; Models, Genetic; Phylogeny; Rhodopsin / genetics; Selection, Genetic; Silent Mutation; Vertebrates / genetics
TL;DR:
It is found that failing to account for even moderate levels of SRV in selection testing is likely to produce intolerably high false positive rates and add to a growing literature establishing that tests of selection are much more sensitive to certain model assumptions than previously believed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: October 19, 2020
2018 journal article
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes
MOLECULAR BIOLOGY AND EVOLUTION, 35(3), 773–777.
author keywords: natural selection; statistical methods; web application; recombination; evolutionary inference
TL;DR:
The release ofDatamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data, and HyPhy Vision, an accompanying JavaScript application for visualizing analysis results.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2011 journal article
Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata
JOURNAL OF MOLECULAR EVOLUTION, 73(5-6), 266–272.
author keywords: Cryptic species; Molecular evolution; Genome architecture; Ciliate
MeSH headings : Ciliophora / classification; Ciliophora / genetics; DNA, Ribosomal / genetics; Evolution, Molecular; Genome; Mitochondrial Proteins / genetics; Nuclear Proteins / genetics; Phylogeny; Recombination, Genetic / genetics; Species Specificity; Tubulin / genetics
TL;DR:
Describing the diversity of several nuclear protein-coding genes plus both nSSU-rDNA and mitochondrial small subunit rDNA of five isolates of the ciliate morphospecies Chilodonella uncinata indicates that C. uncInata lineages are able to maintain both highly divergent and highly conserved genes within a rapidly evolving germline genome.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2010 journal article
Benchmarking multi-rate codon models
PLoS One, 5(7).
Source: NC State University Libraries
Added: August 6, 2018
2010 journal article
Codontest: modeling amino acid substitution preferences in coding sequences
PLoS Computational Biology, 6(8).
Source: NC State University Libraries
Added: August 6, 2018
2010 journal article
Correcting the bias of empirical frequency parameter estimators in codon models
PLoS One, 5(7).
Source: NC State University Libraries
Added: August 6, 2018
2008 journal article
Genomic analysis of closely related astroviruses
JOURNAL OF VIROLOGY, 82(10), 5099–5103.
Contributors: E. Strain*, L. Kelley *, S. Schultz-Cherry *, * & M. Koci n
MeSH headings : Animals; Astroviridae Infections / virology; Avastrovirus / genetics; Avastrovirus / isolation & purification; Genome, Viral; Phylogeny; Poultry Diseases / virology; RNA, Viral / genetics; Recombination, Genetic; Sequence Analysis, DNA; Sequence Homology; Turkeys; United States
TL;DR:
The analysis of the capsid gene demonstrated evidence for both site-specific positive selection and purifying selection, and suggests that the TAstV species contains multiple subtypes and that recombination events have occurred across the astrovirus genome.
(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, ORCID
Added: August 6, 2018
2007 journal article
Evolutionary model selection with a genetic algorithm: A case study using stem RNA
MOLECULAR BIOLOGY AND EVOLUTION, 24(1), 159–170.
author keywords: RNA sequence evolution; secondary structure; model selection; genetic algorithms; multimodel inference
MeSH headings : Algorithms; Animals; Computational Biology; Evolution, Molecular; HIV / genetics; Invertebrates / genetics; Likelihood Functions; Mammals / genetics; Models, Genetic; Nucleic Acid Conformation; RNA / chemistry; RNA / genetics; Response Elements; Sequence Alignment
TL;DR:
This work describes a likelihood-based approach for evolutionary model selection that allows, for the first time, to evaluate the performance of existing RNA evolutionary models by comparing them with a large pool of candidate models and to validate common modeling assumptions.
(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
Genome architecture drives protein evolution in ciliates
MOLECULAR BIOLOGY AND EVOLUTION, 23(9), 1681–1687.
author keywords: genome evolution; genome architecture; protein evolution; ciliate evolution
MeSH headings : Animals; Ciliophora / genetics; Evolution, Molecular; Genetic Variation; Genome, Protozoan; Selection, Genetic; Species Specificity
TL;DR:
A model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner is proposed, predicting that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
HyPhy: hypothesis testing using phylogenies
BIOINFORMATICS, 21(5), 676–679.
MeSH headings : Algorithms; Computer Simulation; Evolution, Molecular; Models, Genetic; Phylogeny; Sequence Alignment / methods; Sequence Analysis, Protein / methods; Software; User-Computer Interface
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
Positively selected sites in the Arabidopsis receptor-like kinase gene family
JOURNAL OF MOLECULAR EVOLUTION, 61(3), 325–332.
author keywords: receptor-like kinase; positive selection; gene family; leucine-rich repeat
MeSH headings : Arabidopsis / classification; Arabidopsis / enzymology; Arabidopsis / genetics; Arabidopsis Proteins / classification; Arabidopsis Proteins / genetics; Leucine / genetics; Phosphotransferases / classification; Phosphotransferases / genetics; Phylogeny
TL;DR:
Analysis of members of the receptor-like kinase (RLK) gene family in Arabidopsis thaliana finds evidence for positive selection in 12 of the 52 RLK family sequences groups, raising the possibility that some RLK genes function in a similar role.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
PowerMarker: an integrated analysis environment for genetic marker analysis
BIOINFORMATICS, 21(9), 2128–2129.
MeSH headings : Algorithms; Computer Graphics; DNA Mutational Analysis / methods; Gene Frequency; Genetic Markers / genetics; Genetics, Population / methods; Linkage Disequilibrium / genetics; Oligonucleotide Array Sequence Analysis / methods; Polymorphism, Single Nucleotide / genetics; Software; User-Computer Interface
TL;DR:
PowerMarker delivers a data-driven, integrated analysis environment (IAE) for genetic data that accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process.
(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)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
Site-to-site variation of synonymous substitution rates
MOLECULAR BIOLOGY AND EVOLUTION, 22(12), 2375–2385.
author keywords: synonymous substitution rate; positive selection; molecular evolution; codon model; model selection
MeSH headings : Amino Acid Substitution; Amino Acids / genetics; Codon; Evolution, Molecular; Genetic Variation; Humans; Models, Genetic; Mutation; Open Reading Frames; Phylogeny; Selection, Genetic
TL;DR:
It is demonstrated that within-gene heterogeneity of synonymous substitution rates appears to be common, and how failure to model synonymous rate variation in the model can lead to misidentification of sites as positively selected is 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 book
A primer of genome science (2nd ed.)
Sunderland, MA: Sinauer Associates.
Source: NC State University Libraries
Added: August 6, 2018
2004 journal article
Column sorting: Rapid calculation of the phylogenetic likelihood function
SYSTEMATIC BIOLOGY, 53(5), 685–692.
author keywords: DNA sequence; graph theory; likelihood; phylogeny; traveling salesman problem
MeSH headings : Algorithms; Base Sequence / genetics; Classification / methods; Evolution, Molecular; Likelihood Functions; Models, Genetic; Phylogeny
TL;DR:
An algorithm for exploiting this speed improvement via an application of graph theory to provide faster likelihood algorithms, which will allow likelihood methods to be applied to larger sets of taxa and to include more thorough searches of the tree topology space.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2004 journal article
Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes
Molecular Biology and Evolution, 21(3), 555–562.
MeSH headings : Amino Acid Substitution; Animals; Ciliophora / genetics; Evolution, Molecular; Genealogy and Heraldry; Genetic Variation; Histones / genetics
Source: NC State University Libraries
Added: August 6, 2018
2003 article
Development of a maize molecular evolutionary genomic database
Du, C. G., Buckler, E., & Muse, S. (2003, April). COMPARATIVE AND FUNCTIONAL GENOMICS, Vol. 4, pp. 246–249.
author keywords: database; maize; genome; evolution; germplasm; phenotype; SSR; DNA sequence
TL;DR:
PANZEA is the first public database for studying maize genomic diversity and has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data.
(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)
Source: Web Of Science
Added: August 6, 2018
2003 journal article
Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites
Genetics, 165(4), 2117–2128.
Source: NC State University Libraries
Added: August 6, 2018
2002 book
A primer of genome science
Sunderland, MA: Sinauer.
Source: NC State University Libraries
Added: August 6, 2018
2002 journal article
Evolution of duplicated alpha-tubulin genes in ciliates
Evolution, 56(6), 1110–1122.
MeSH headings : Amino Acid Sequence; Animals; Base Sequence; Ciliophora / genetics; Cloning, Molecular; Evolution, Molecular; Gene Duplication; Genetic Variation; Molecular Sequence Data; Phylogeny; Sequence Alignment; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Tubulin / genetics
TL;DR:
The topology of ciliate α‐tubulin genealogies are inconsistent with taxonomy based on morphology and other molecular markers, which may be due to taxonomic sampling, gene conversion, unequal rates of evolution, or asymmetric patterns of gene duplication and loss.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: NC State University Libraries
Added: August 6, 2018
2002 journal article
Evolutionary genomics of maize
Maize Genetics Cooperation Newsletter, (76), 86.
Source: NC State University Libraries
Added: August 6, 2018
2000 journal article
Examining rates and patterns of nucleotide substitution in plants
PLANT MOLECULAR BIOLOGY, 42(1), 25–43.
author keywords: chloroplast genes; maximum likelihood; molecular clocks; nucleotide substitution models; rates of molecular evolution
TL;DR:
In this chapter, a review of recent literature focusing on rates and patterns of nucleotide substitution rates in the nuclear, chloroplast, and mitochondrial genomes of plants demonstrates the power and flexibility of these new methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1994 journal article
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
Molecular Biology and Evolution, 11(5), 715.
Source: NC State University Libraries
Added: August 6, 2018
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