Researcher profile · Semantic Scholar

S. Muse

h-index: 24
Works: 40
Citations: 12K

Most-cited papers

PowerMarker: an integrated analysis environment for genetic marker analysis
Kejun Liu, S. Muse
2005Bioinform.4,348 citations
Semantic Scholar
BIOINFORMATICS APPLICATIONS
Sergei L. Kosakovsky Pond, S. Frost, S. Muse
2,518 citations
Semantic Scholar
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
S. Muse, B. Gaut
1994Molecular biology and evolution955 citations Open access
Semantic Scholar
Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.
S. Weaver, S. Shank, S. Spielman, Michael Li +2 more
2018Molecular biology and evolution905 citations Open access
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HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.
Sergei L. Kosakovsky Pond, A. Poon, Ryan Velazquez, S. Weaver +10 more
2019Molecular biology and evolution678 citations Open access
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Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites.
Kejun Liu, M. Goodman, S. Muse, J. S. Smith +2 more
2003Genetics566 citations
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Site-to-site variation of synonymous substitution rates.
Sergei L. Kosakovsky Pond, S. Muse
2005Molecular biology and evolution253 citations
Semantic Scholar
Testing for equality of evolutionary rates.
S. Muse, B. Weir
1992Genetics219 citations
Semantic Scholar
Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants
B. Gaut, S. Muse, W. Clark, M. Clegg
1992Journal of Molecular Evolution196 citations
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Examining rates and patterns of nucleotide substitution in plants
S. Muse
2004Plant Molecular Biology162 citations
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Estimating synonymous and nonsynonymous substitution rates.
S. Muse
1996Molecular biology and evolution152 citations Open access
Semantic Scholar
Evolutionary analyses of DNA sequences subject to constraints of secondary structure.
S. Muse
1995Genetics141 citations
Semantic Scholar
Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae).
B. Gaut, L. Clark, J. Wendel, S. Muse
1997Molecular biology and evolution120 citations Open access
Semantic Scholar
Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
S. Wisotsky, Sergei L. Kosakovsky Pond, S. Shank, S. Muse
2020Molecular biology and evolution82 citations Open access
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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
W. Delport, K. Scheffler, Gordon Botha, M. Gravenor +2 more
2010PLoS Comput. Biol.79 citations Open access
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Genome architecture drives protein evolution in ciliates.
Rebecca A. Zufall, Casey McGrath, S. Muse, L. A. Katz
2006Molecular biology and evolution76 citations Open access
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Genomic Analysis of Closely Related Astroviruses
E. Strain, Laura A. Kelley, S. Schultz-Cherry, S. Muse +1 more
2008Journal of Virology71 citations Open access
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Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models
Sergei L. Kosakovsky Pond, W. Delport, S. Muse, K. Scheffler
2010PLoS ONE59 citations Open access
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Molecular evolution of type 1 serine/threonine protein phosphatases.
Q. Lin, E. Buckler, S. Muse, John C. Walker
1999Molecular Phylogenetics and Evolution58 citations
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Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes.
L. A. Katz, J. Bornstein, E. Lasek-Nesselquist, S. Muse
2004Molecular biology and evolution47 citations Open access
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Heterogeneous rates of molecular evolution among cryptic species of the ciliate morphospecies Chilodonella uncinata
L. A. Katz, Jennifer DeBerardinis, Meaghan S. Hall, Alexandra M. Kovner +2 more
2011Journal of Molecular Evolution46 citations Open access
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Column sorting: rapid calculation of the phylogenetic likelihood function.
Sergei L. Kosakovsky Pond, S. Muse
2004Systematic Biology32 citations
Semantic Scholar
EVOLUTION OF DUPLICATED ALPHA-TUBULIN GENES IN CILIATES
Rachel L Israel, Sergei L. Kosakovsky Pond, S. Muse, L. A. Katz
200226 citations
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Evolutionary model selection with a genetic algorithm: a case study using stem RNA.
Sergei L. Kosakovsky Pond, Frank Mannino, M. Gravenor, S. Muse +1 more
2007Molecular biology and evolution23 citations Open access
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EVOLUTION OF DUPLICATED ALPHα‐TUBULIN GENES IN CILIATES
Rachel L Israel, Sergei L. Kosakovsky Pond, S. Muse, L. A. Katz
2002Evolution; international journal of organic evolution17 citations
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Benchmarking Multi-Rate Codon Models
W. Delport, K. Scheffler, M. Gravenor, S. Muse +1 more
2010PLoS ONE13 citations Open access
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Positively Selected Sites in the Arabidopsis Receptor-Like Kinase Gene Family
E. Strain, S. Muse
2005Journal of Molecular Evolution13 citations
Semantic Scholar
Comparisons of the Nucleotide Substitution Process Among Repetitive Segments of the α- and β-Spectrin Genes
S. Muse, A. Clark, G. Thomas
1997Journal of Molecular Evolution10 citations
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Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
Avery G. Selberg, Nathan L. Clark, Timothy B. Sackton, S. Muse +5 more
2024bioRxiv9 citations Open access
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Development of a Maize Molecular Evolutionary Genomic Database
C. Du, E. Buckler, S. Muse
2003Comparative and Functional Genomics8 citations Open access
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Classical Statistical Approaches to Molecular Classification of Cancer from Gene Expression Profiling
Jun Lu, S. Hardy, Wen-Hui Tao, S. Muse +2 more
20026 citations
Semantic Scholar
Training the Next Generation of Quantitative Biologists in the Era of Big Data
K. Pattin, A. C. Greene, R. Altman, K. Cohen +6 more
2014Pacific Symposium on Biocomputing5 citations
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Comparisons of the nucleotide substitution process among repetitive segments of the alpha- and beta-spectrin genes.
S. Muse, A. Clark, G. Thomas
1997Journal of Molecular Evolution4 citations
Semantic Scholar
Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability
Frank Mannino, S. Wisotsky, Sergei L. Kosakovsky Pond, S. Muse
2020PLoS ONE2 citations Open access
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GENOMICS AND BIOINFORMATICS
S. Muse
2012Introduction to Biomedical Engineering1 citations
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Peer Review #1 of "Evolutionary history of the vertebrate Piwi gene family (v0.1)"
Javier Gutiérrez, R. Platt, J. Opazo, D. Ray +374 more
20210 citations Open access
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Peer Review #1 of "Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) (v0.1)"
F. Mehmood, Abdullah Abdullah, Zartasha Ubaid, I. Shahzadi +496 more
20200 citations Open access
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The Computational Phyloinformatics Summer Course wikis
R. Vos, B. O'Meara, J. Balhoff, K. Cranston +10 more
20150 citations
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Correction: Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models
Sergei L. Kosakovsky Pond, W. Delport, S. Muse, K. Scheffler
2014PLoS ONE0 citations Open access
Semantic Scholar
Minus the Error: Estimating d N / d S and Testing for Natural Selection in the Presence of Residual Alignment Errors.
Authors Avery, G. Selberg, Maria Chikina, Timothy B. Sackton +6 more
0 citations
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K. Scheffler

×4

P. Poczai×4

S. Frost×3

B. Gaut×3

S. Spielman×3

B. Murrell×3

S. Wisotsky×3

M. Gravenor×3