@article{mannino_wisotsky_pond_muse_2020, title={Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability}, volume={15}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0229493}, number={3}, journal={PLOS ONE}, author={Mannino, Frank and Wisotsky, Sadie and Pond, Sergei L. Kosakovsky and Muse, Spencer V}, year={2020}, month={Mar} }
 @article{pond_poon_velazquez_weaver_hepler_murrell_shank_magalis_bouvier_nekrutenko_et al._2020, title={HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies}, volume={37}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msz197}, number={1}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Pond, Sergei L. Kosakovsky and Poon, Art F. Y. and Velazquez, Ryan and Weaver, Steven and Hepler, N. Lance and Murrell, Ben and Shank, Stephen D. and Magalis, Brittany Rife and Bouvier, Dave and Nekrutenko, Anton and et al.}, year={2020}, month={Jan}, pages={295–299} }
 @article{wisotsky_pond_shank_muse_2020, title={Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril}, volume={37}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msaa037}, number={8}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Wisotsky, Sadie R. and Pond, Sergei L. Kosakovsky and Shank, Stephen D. and Muse, Spencer V}, year={2020}, month={Aug}, pages={2430–2439} }
 @article{weaver_shank_spielman_li_muse_pond_2018, title={Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes}, volume={35}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msx335}, number={3}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Weaver, Steven and Shank, Stephen D. and Spielman, Stephanie J. and Li, Michael and Muse, Spencer V. and Pond, Sergei L. Kosakovsky}, year={2018}, month={Mar}, pages={773–777} }
 @article{katz_deberardinis_hall_kovner_dunthorn_muse_2011, title={Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata}, volume={73}, ISSN={["1432-1432"]}, DOI={10.1007/s00239-011-9468-x}, number={5-6}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Katz, Laura A. and DeBerardinis, Jennifer and Hall, Meaghan S. and Kovner, Alexandra M. and Dunthorn, Micah and Muse, Spencer V.}, year={2011}, month={Dec}, pages={266–272} }
 @article{delport_scheffler_gravenor_muse_pond_2010, title={Benchmarking multi-rate codon models}, volume={5}, number={7}, journal={PLoS One}, author={Delport, W. and Scheffler, K. and Gravenor, M. B. and Muse, S. V. and Pond, S. K.}, year={2010} }
 @article{delport_scheffler_botha_gravenor_muse_pond_2010, title={Codontest: modeling amino acid substitution preferences in coding sequences}, volume={6}, number={8}, journal={PLoS Computational Biology}, author={Delport, W. and Scheffler, K. and Botha, G. and Gravenor, M. B. and Muse, S. V. and Pond, S. L. K.}, year={2010} }
 @article{pond_delport_muse_scheffler_2010, title={Correcting the bias of empirical frequency parameter estimators in codon models}, volume={5}, number={7}, journal={PLoS One}, author={Pond, S. K. and Delport, W. and Muse, S. V. and Scheffler, K.}, year={2010} }
 @article{strain_kelley_schultz-cherry_muse_koci_2008, title={Genomic analysis of closely related astroviruses}, volume={82}, ISSN={["0022-538X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-43249085073&partnerID=MN8TOARS}, DOI={10.1128/JVI.01993-07}, number={10}, journal={JOURNAL OF VIROLOGY}, author={Strain, Errol and Kelley, Laura A. and Schultz-Cherry, Stacey and Muse, Spencer V. and Koci, Matthew D.}, year={2008}, month={May}, pages={5099–5103} }
 @article{kosakovsky pond_mannino_gravenor_muse_frost_2007, title={Evolutionary model selection with a genetic algorithm: A case study using stem RNA}, volume={24}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msl144}, number={1}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Kosakovsky Pond, Sergei L. and Mannino, Frank V. and Gravenor, Michael B. and Muse, Spencer V. and Frost, Simon D. W.}, year={2007}, month={Jan}, pages={159–170} }
 @article{zufall_mcgrath_muse_katz_2006, title={Genome architecture drives protein evolution in ciliates}, volume={23}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msl032}, number={9}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Zufall, Rebecca A. and McGrath, Casey L. and Muse, Spencer V. and Katz, Laura A.}, year={2006}, month={Sep}, pages={1681–1687} }
 @article{pond_frost_muse_2005, title={HyPhy: hypothesis testing using phylogenies}, volume={21}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/bti079}, number={5}, journal={BIOINFORMATICS}, author={Pond, SLK and Frost, SDW and Muse, SV}, year={2005}, month={Mar}, pages={676–679} }
 @article{strain_muse_2005, title={Positively selected sites in the Arabidopsis receptor-like kinase gene family}, volume={61}, ISSN={["1432-1432"]}, DOI={10.1007/s00239-004-0308-0}, number={3}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Strain, E and Muse, SV}, year={2005}, month={Sep}, pages={325–332} }
 @article{liu_muse_2005, title={PowerMarker: an integrated analysis environment for genetic marker analysis}, volume={21}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/bti282}, number={9}, journal={BIOINFORMATICS}, author={Liu, KJ and Muse, SV}, year={2005}, month={May}, pages={2128–2129} }
 @article{pond_muse_2005, title={Site-to-site variation of synonymous substitution rates}, volume={22}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msi232}, number={12}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Pond, SK and Muse, SV}, year={2005}, month={Dec}, pages={2375–2385} }
 @book{gibson_muse_2004, title={A primer of genome science (2nd ed.)}, ISBN={0878932321}, publisher={Sunderland, MA: Sinauer Associates}, author={Gibson, G. and Muse, S. V.}, year={2004} }
 @article{pond_muse_2004, title={Column sorting: Rapid calculation of the phylogenetic likelihood function}, volume={53}, ISSN={["1076-836X"]}, DOI={10.1080/10635150490522269}, number={5}, journal={SYSTEMATIC BIOLOGY}, author={Pond, SLK and Muse, SV}, year={2004}, month={Oct}, pages={685–692} }
 @article{katz_bornstein_lasek-nesselquist_muse_2004, title={Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes}, volume={21}, DOI={10.1093/molbev.msh048}, number={3}, journal={Molecular Biology and Evolution}, author={Katz, L. A. and Bornstein, J. G. and Lasek-Nesselquist, E. and Muse, S. V.}, year={2004}, pages={555–562} }
 @article{du_buckler_muse_2003, title={Development of a maize molecular evolutionary genomic database}, volume={4}, ISSN={["1531-6912"]}, DOI={10.1002/cfg.282}, number={2}, journal={COMPARATIVE AND FUNCTIONAL GENOMICS}, author={Du, CG and Buckler, E and Muse, S}, year={2003}, month={Apr}, pages={246–249} }
 @article{liu_goodman_muse_smith_buckler_doebley_2003, title={Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites}, volume={165}, number={4}, journal={Genetics}, author={Liu, K. J. and Goodman, M. and Muse, S. and Smith, J. S. and Buckler, E. and Doebley, J.}, year={2003}, pages={2117–2128} }
 @book{gibson_muse_2002, title={A primer of genome science}, ISBN={0878932348}, publisher={Sunderland, MA: Sinauer}, author={Gibson, G. and Muse, S. V.}, year={2002} }
 @article{israel_pond_muse_katz_2002, title={Evolution of duplicated alpha-tubulin genes in ciliates}, volume={56}, DOI={10.1111/j.0014-3820.2002.tb01425.x}, number={6}, journal={Evolution}, author={Israel, R. L. and Pond, S. L. K. and Muse, S. V. and Katz, L. A.}, year={2002}, pages={1110–1122} }
 @article{buckler_doebley_gaut_goodman_kresovich_muse_weir_2002, title={Evolutionary genomics of maize}, number={76}, journal={Maize Genetics Cooperation Newsletter}, author={Buckler, E. and Doebley, J. and Gaut, B. and Goodman, M. and Kresovich, S. and Muse, S. and Weir, B.}, year={2002}, pages={86} }
 @article{muse_2000, title={Examining rates and patterns of nucleotide substitution in plants}, volume={42}, ISSN={["1573-5028"]}, DOI={10.1023/A:1006319803002}, number={1}, journal={PLANT MOLECULAR BIOLOGY}, author={Muse, SV}, year={2000}, month={Jan}, pages={25–43} }
 @article{muse_gaut_1994, title={A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome}, volume={11}, number={5}, journal={Molecular Biology and Evolution}, author={Muse, S. V. and Gaut, B. S.}, year={1994}, pages={715} }