Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes S Weaver, SD Shank, SJ Spielman, M Li, SV Muse, SL Kosakovsky Pond Molecular biology and evolution 35 (3), 773-777, 2018 | 692 | 2018 |
Maximum allowed solvent accessibilites of residues in proteins MZ Tien, AG Meyer, DK Sydykova, SJ Spielman, CO Wilke PloS one 8 (11), e80635, 2013 | 412 | 2013 |
HyPhy 2.5—a customizable platform for evolutionary hypothesis testing using phylogenies SL Kosakovsky Pond, AFY Poon, R Velazquez, S Weaver, NL Hepler, ... Molecular biology and evolution 37 (1), 295-299, 2020 | 346 | 2020 |
Causes of evolutionary rate variation among protein sites J Echave, SJ Spielman, CO Wilke Nature Reviews Genetics 17 (2), 109-121, 2016 | 271 | 2016 |
Regulation of clathrin-mediated endocytosis by hierarchical allosteric activation of AP2 Z Kadlecova, SJ Spielman, D Loerke, A Mohanakrishnan, DK Reed, ... Journal of Cell Biology 216 (1), 167-179, 2017 | 183 | 2017 |
The Relationship between dN/dS and Scaled Selection Coefficients SJ Spielman, CO Wilke Molecular biology and evolution 32 (4), 1097-1108, 2015 | 122 | 2015 |
Pyvolve: a flexible Python module for simulating sequences along phylogenies SJ Spielman, CO Wilke PloS one 10 (9), e0139047, 2015 | 96 | 2015 |
Evolution of viral genomes: interplay between selection, recombination, and other forces SJ Spielman, S Weaver, SD Shank, BR Magalis, M Li, ... Evolutionary genomics: statistical and computational methods, 427-468, 2019 | 55 | 2019 |
Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design A Shahmoradi, DK Sydykova, SJ Spielman, EL Jackson, ET Dawson, ... Journal of molecular evolution 79, 130-142, 2014 | 51 | 2014 |
Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak AG Meyer, SJ Spielman, T Bedford, CO Wilke Virus Evolution 1 (1), vev006, 2015 | 32 | 2015 |
Kosakovsky Pond, SL Evolution of viral genomes: Interplay between selection, recombination, and other forces SJ Spielman, S Weaver, SD Shank, BR Magalis, M Li Methods Mol. Biol 1910, 427-468, 2019 | 28 | 2019 |
Relative model fit does not predict topological accuracy in single-gene protein phylogenetics SJ Spielman Molecular biology and evolution 37 (7), 2110-2123, 2020 | 26 | 2020 |
Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors SJ Spielman, CO Wilke Journal of Molecular Evolution 76, 172-182, 2013 | 26 | 2013 |
The evolving redox chemistry and bioavailability of vanadium in deep time EK Moore, J Hao, SJ Spielman, N Yee Geobiology 18 (2), 127-138, 2020 | 25 | 2020 |
Extensively parameterized mutation–selection models reliably capture site-specific selective constraint SJ Spielman, CO Wilke Molecular biology and evolution 33 (11), 2990-3002, 2016 | 24 | 2016 |
Measuring evolutionary rates of proteins in a structural context DK Sydykova, BR Jack, SJ Spielman, CO Wilke F1000Research 6, 2017 | 22 | 2017 |
Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors SJ Spielman, K Kumar, CO Wilke PeerJ 3, e773, 2015 | 21 | 2015 |
Relative evolutionary rate inference in HyPhy with LEISR SJ Spielman, SL Kosakovsky Pond PeerJ 6, e4339, 2018 | 20 | 2018 |
Relative evolutionary rates in proteins are largely insensitive to the substitution model SJ Spielman, SL Kosakovsky Pond Molecular Biology and Evolution, 2018 | 19 | 2018 |
A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation SJ Spielman, S Wan, CO Wilke Genetics 204 (2), 499-511, 2016 | 18* | 2016 |