Spencer Muse

Mannino, F., Wisotsky, S., Pond, S. L. K., & Muse, S. V. (2020). Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability. PLOS ONE, 15(3). https://doi.org/10.1371/journal.pone.0229493

Pond, S. L. K., Poon, A. F. Y., Velazquez, R., Weaver, S., Hepler, N. L., Murrell, B., … Muse, S. V. (2020). HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 295–299. https://doi.org/10.1093/molbev/msz197

Wisotsky, S. R., Pond, S. L. K., Shank, S. D., & Muse, S. V. (2020). 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. https://doi.org/10.1093/molbev/msaa037

Weaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., & Pond, S. L. K. (2018). Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes. MOLECULAR BIOLOGY AND EVOLUTION, 35(3), 773–777. https://doi.org/10.1093/molbev/msx335

Katz, L. A., DeBerardinis, J., Hall, M. S., Kovner, A. M., Dunthorn, M., & Muse, S. V. (2011). Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata. JOURNAL OF MOLECULAR EVOLUTION, 73(5-6), 266–272. https://doi.org/10.1007/s00239-011-9468-x

Delport, W., Scheffler, K., Gravenor, M. B., Muse, S. V., & Pond, S. K. (2010). Benchmarking multi-rate codon models. PLoS One, 5(7).

Delport, W., Scheffler, K., Botha, G., Gravenor, M. B., Muse, S. V., & Pond, S. L. K. (2010). Codontest: modeling amino acid substitution preferences in coding sequences. PLoS Computational Biology, 6(8).

Pond, S. K., Delport, W., Muse, S. V., & Scheffler, K. (2010). Correcting the bias of empirical frequency parameter estimators in codon models. PLoS One, 5(7).

Strain, E., Kelley, L. A., Schultz-Cherry, S., Muse, S. V., & Koci, M. D. (2008). Genomic analysis of closely related astroviruses. JOURNAL OF VIROLOGY, 82(10), 5099–5103. https://doi.org/10.1128/JVI.01993-07

Kosakovsky Pond, S. L., Mannino, F. V., Gravenor, M. B., Muse, S. V., & Frost, S. D. W. (2007). Evolutionary model selection with a genetic algorithm: A case study using stem RNA. MOLECULAR BIOLOGY AND EVOLUTION, 24(1), 159–170. https://doi.org/10.1093/molbev/msl144

Zufall, R. A., McGrath, C. L., Muse, S. V., & Katz, L. A. (2006). Genome architecture drives protein evolution in ciliates. MOLECULAR BIOLOGY AND EVOLUTION, 23(9), 1681–1687. https://doi.org/10.1093/molbev/msl032

Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2005). HyPhy: hypothesis testing using phylogenies. BIOINFORMATICS, 21(5), 676–679. https://doi.org/10.1093/bioinformatics/bti079

Strain, E., & Muse, S. V. (2005). Positively selected sites in the Arabidopsis receptor-like kinase gene family. JOURNAL OF MOLECULAR EVOLUTION, 61(3), 325–332. https://doi.org/10.1007/s00239-004-0308-0

Liu, K. J., & Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. BIOINFORMATICS, 21(9), 2128–2129. https://doi.org/10.1093/bioinformatics/bti282

Pond, S. K., & Muse, S. V. (2005). Site-to-site variation of synonymous substitution rates. MOLECULAR BIOLOGY AND EVOLUTION, 22(12), 2375–2385. https://doi.org/10.1093/molbev/msi232

Gibson, G., & Muse, S. V. (2004). A primer of genome science (2nd ed.). Sunderland, MA: Sinauer Associates.

Pond, S. L. K., & Muse, S. V. (2004). Column sorting: Rapid calculation of the phylogenetic likelihood function. SYSTEMATIC BIOLOGY, 53(5), 685–692. https://doi.org/10.1080/10635150490522269

Katz, L. A., Bornstein, J. G., Lasek-Nesselquist, E., & Muse, S. V. (2004). 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. https://doi.org/10.1093/molbev.msh048

Du, C. G., Buckler, E., & Muse, S. (2003, April). Development of a maize molecular evolutionary genomic database. COMPARATIVE AND FUNCTIONAL GENOMICS, Vol. 4, pp. 246–249. https://doi.org/10.1002/cfg.282

Liu, K. J., Goodman, M., Muse, S., Smith, J. S., Buckler, E., & Doebley, J. (2003). Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics, 165(4), 2117–2128.

Gibson, G., & Muse, S. V. (2002). A primer of genome science. Sunderland, MA: Sinauer.

Israel, R. L., Pond, S. L. K., Muse, S. V., & Katz, L. A. (2002). Evolution of duplicated alpha-tubulin genes in ciliates. Evolution, 56(6), 1110–1122. https://doi.org/10.1111/j.0014-3820.2002.tb01425.x

Buckler, E., Doebley, J., Gaut, B., Goodman, M., Kresovich, S., Muse, S., & Weir, B. (2002). Evolutionary genomics of maize. Maize Genetics Cooperation Newsletter, (76), 86.

Muse, S. V. (2000). Examining rates and patterns of nucleotide substitution in plants. PLANT MOLECULAR BIOLOGY, 42(1), 25–43. https://doi.org/10.1023/A:1006319803002

Muse, S. V., & Gaut, B. S. (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution, 11(5), 715.