Spencer V Muse

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).

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

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)
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15. Life on Land (Web of Science)
Source: Web Of Science
Added: June 15, 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

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)
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UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: October 19, 2020

2019 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 * ...

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)
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UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: March 10, 2020

2017 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 *

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)
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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.

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

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).

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 

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
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)
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UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2006 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 *

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)
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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.

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
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

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

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)
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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.

By: K. Liu n & S. Muse n

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 Goals Color Wheel
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.

By: S. Pond * & S. Muse*

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 Goals Color Wheel
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.

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

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)
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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.

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

2004 journal article

HyPhy: hypothesis testing using phylogenies

BIOINFORMATICS, 21(5), 676–679.

By: S. Pond *, S. Frost * & S. Muse n

MeSH headings : Algorithms; Computer Simulation; Evolution, Molecular; Models, Genetic; Phylogeny; Sequence Alignment / methods; Sequence Analysis, Protein / methods; Software; User-Computer Interface
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
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

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 Goals Color Wheel
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.

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 *

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 Goals Color Wheel
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.

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

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 Goals Color Wheel
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.

By: S. Muse & B. Gaut

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

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