Spencer V Muse

Works (25)

Updated: July 17th, 2023 21:17
Download BibTeX Download Plain Text View JSON

2020 journal article

Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability

PLOS ONE, 15(3).

By: F. Mannino n, S. Wisotsky n, S. Pond * & S. Muse n

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Amino Acid Substitution; Evolution, Molecular; Likelihood Functions; Models, Genetic; Mutation Rate; Phylogeny; Sequence Alignment; Sequence Analysis, DNA / methods
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.

By: S. Pond *, A. Poon*, R. Velazquez *, S. Weaver *, N. Hepler*, B. Murrell *, S. Shank*, B. Magalis * ...

co-author countries: Canada 🇨🇦 United Kingdom of Great Britain and Northern Ireland 🇬🇧 Sweden 🇸🇪 United States of America 🇺🇸
author keywords: evolutionary analysis; natural selection; hypothesis testing; statistical inference; software engineering
MeSH headings : Genetic Techniques; Phylogeny; Software
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.

By: S. Wisotsky n, S. Pond *, S. Shank* & S. Muse n

co-author countries: United States of America 🇺🇸
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
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.

By: S. Weaver *, S. Shank*, S. Spielman *, M. Li *, S. Muse n & S. Pond *

co-author countries: United States of America 🇺🇸
author keywords: natural selection; statistical methods; web application; recombination; evolutionary inference
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.

By: L. Katz *, J. DeBerardinis*, M. Hall*, A. Kovner*, M. Dunthorn* & S. Muse n

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
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
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Benchmarking multi-rate codon models

PLoS One, 5(7).

By: W. Delport, K. Scheffler, M. Gravenor, S. Muse & S. Pond

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).

By: W. Delport, K. Scheffler, G. Botha, M. Gravenor, S. Muse & S. Pond

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).

By: S. Pond, W. Delport, S. Muse & K. Scheffler

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.

By: E. Strain*, L. Kelley *, S. Schultz-Cherry *, S. Muse* & M. Koci n 

co-author countries: United States of America 🇺🇸

Contributors: E. Strain*, L. Kelley *, S. Schultz-Cherry *, S. Muse* & 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
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.

By: S. Kosakovsky Pond *, F. Mannino n, M. Gravenor *, S. Muse n & S. Frost *

co-author countries: United Kingdom of Great Britain and Northern Ireland 🇬🇧 United States of America 🇺🇸
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
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.

By: R. Zufall, C. McGrath, S. Muse* & L. Katz

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
Source: Web Of Science
Added: August 6, 2018

2005 journal article

HyPhy: hypothesis testing using phylogenies

BIOINFORMATICS, 21(5), 676–679.

By: S. Pond, S. Frost & S. Muse*

MeSH headings : Algorithms; Computer Simulation; Evolution, Molecular; Models, Genetic; Phylogeny; Sequence Alignment / methods; Sequence Analysis, Protein / methods; Software; User-Computer Interface
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.

By: E. Strain n & S. Muse n

co-author countries: United States of America 🇺🇸
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
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.

By: K. Liu n & S. Muse n

co-author countries: United States of America 🇺🇸
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
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.

By: S. Pond * & S. Muse*

co-author countries: United States of America 🇺🇸
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
Source: Web Of Science
Added: August 6, 2018

2004 book

A primer of genome science (2nd ed.)

Sunderland, MA: Sinauer Associates.

By: G. Gibson & S. Muse

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.

By: S. Pond * & S. Muse n

co-author countries: United States of America 🇺🇸
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
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.

By: L. Katz, J. Bornstein, E. Lasek-Nesselquist & S. Muse

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.

By: C. Du*, E. Buckler n & S. Muse n

co-author countries: United States of America 🇺🇸
author keywords: database; maize; genome; evolution; germplasm; phenotype; SSR; DNA sequence
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.

By: K. Liu, M. Goodman, S. Muse, J. Smith, E. Buckler & J. Doebley

Source: NC State University Libraries
Added: August 6, 2018

2002 book

A primer of genome science

Sunderland, MA: Sinauer.

By: G. Gibson & S. Muse

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.

By: R. Israel*, S. Pond *, S. Muse n & L. Katz*

co-author countries: United States of America 🇺🇸
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
Source: NC State University Libraries
Added: August 6, 2018

2002 journal article

Evolutionary genomics of maize

Maize Genetics Cooperation Newsletter, (76), 86.

By: E. Buckler, J. Doebley, B. Gaut, M. Goodman, S. Kresovich, S. Muse, B. Weir

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.

By: S. Muse n

co-author countries: United States of America 🇺🇸
author keywords: chloroplast genes; maximum likelihood; molecular clocks; nucleotide substitution models; rates of molecular evolution
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.

By: S. Muse & B. Gaut

Source: NC State University Libraries
Added: August 6, 2018