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2020 journal article
Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability
PLOS ONE, 15(3).
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.
2019 journal article
HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 295–299.
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.
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.
2010 journal article
Benchmarking multi-rate codon models
PLoS One, 5(7).
2010 journal article
Codontest: modeling amino acid substitution preferences in coding sequences
PLoS Computational Biology, 6(8).
2010 journal article
Correcting the bias of empirical frequency parameter estimators in codon models
PLoS One, 5(7).
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
2006 journal article
Evolutionary model selection with a genetic algorithm: A case study using stem RNA
MOLECULAR BIOLOGY AND EVOLUTION, 24(1), 159–170.
2006 journal article
Genome architecture drives protein evolution in ciliates
MOLECULAR BIOLOGY AND EVOLUTION, 23(9), 1681–1687.
2005 journal article
Positively selected sites in the Arabidopsis receptor-like kinase gene family
JOURNAL OF MOLECULAR EVOLUTION, 61(3), 325–332.
2005 journal article
PowerMarker: an integrated analysis environment for genetic marker analysis
BIOINFORMATICS, 21(9), 2128–2129.
2005 journal article
Site-to-site variation of synonymous substitution rates
MOLECULAR BIOLOGY AND EVOLUTION, 22(12), 2375–2385.
2004 book
A primer of genome science (2nd ed.)
Sunderland, MA: Sinauer Associates.
2004 journal article
Column sorting: Rapid calculation of the phylogenetic likelihood function
SYSTEMATIC BIOLOGY, 53(5), 685–692.
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.
2004 journal article
HyPhy: hypothesis testing using phylogenies
BIOINFORMATICS, 21(5), 676–679.
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.
2003 journal article
Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites
Genetics, 165(4), 2117–2128.
2002 book
A primer of genome science
Sunderland, MA: Sinauer.
2002 journal article
Evolution of duplicated alpha-tubulin genes in ciliates
Evolution, 56(6), 1110–1122.
2002 journal article
Evolutionary genomics of maize
Maize Genetics Cooperation Newsletter, (76), 86.
2000 journal article
Examining rates and patterns of nucleotide substitution in plants
PLANT MOLECULAR BIOLOGY, 42(1), 25–43.
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.
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