| 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 | 798 | 2018 |
| 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 | 436 | 2020 |
| The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages DP Martin, S Weaver, H Tegally, EJ San, SD Shank, E Wilkinson, ... Cell, 2021 | 272 | 2021 |
| Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA. 1 that likely impact Spike function DP Martin, S Lytras, AG Lucaci, W Maier, B Grüning, SD Shank, S Weaver, ... Molecular Biology and Evolution, 2022 | 81 | 2022 |
| Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces SJ Spielman, S Weaver, SD Shank, BR Magalis, M Li, SLK Pond Evolutionary Genomics, 427-468, 2019 | 68 | 2019 |
| Efficient low-rank solution of generalized Lyapunov equations SD Shank, V Simoncini, DB Szyld Numerische Mathematik 134 (2), 327-342, 2016 | 59 | 2016 |
| Synonymous site-to-site substitution rate variation dramatically inflates false positive rates of selection analyses: ignore at your own peril SR Wisotsky, SL Kosakovsky Pond, SD Shank, SV Muse Molecular Biology and Evolution, 2020 | 55 | 2020 |
| phylotree. js-a JavaScript library for application development and interactive data visualization in phylogenetics SD Shank, S Weaver, SLK Pond BMC bioinformatics 19 (1), 276, 2018 | 51 | 2018 |
| Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City JO Wertheim, JC Wang, M Leelawong, DP Martin, JL Havens, ... Nature Communications 13 (1), 1-11, 2022 | 31 | 2022 |
| Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes AG Lucaci, SR Wisotsky, SD Shank, S Weaver, SL Kosakovsky Pond PloS one 16 (3), e0248337, 2021 | 24 | 2021 |
| Krylov subspace methods for large-scale constrained Sylvester equations SD Shank, V Simoncini SIAM Journal on Matrix Analysis and Applications 34 (4), 1448-1463, 2013 | 13 | 2013 |
| Overlapping blocks by growing a partition with applications to preconditioning D Fritzsche, A Frommer, SD Shank, DB Szyld SIAM Journal on Scientific Computing 35 (1), A453-A473, 2013 | 12 | 2013 |
| The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates RA Hermansen, BP Oswald, S Knight, SD Shank, D Northover, ... Journal of Molecular Evolution 85 (1-2), 46-56, 2017 | 10 | 2017 |
| Natural selection differences detected in key protein domains between non-pathogenic and pathogenic Feline Coronavirus phenotypes JD Zehr, SL Kosakovsky Pond, JK Millet, XA Olarte-Castillo, AG Lucaci, ... Virus Evolution 9 (1), vead019, 2023 | 8 | 2023 |
| RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis AG Lucaci, JD Zehr, SD Shank, D Bouvier, A Ostrovsky, H Mei, ... Plos one 17 (11), e0275623, 2022 | 7 | 2022 |
| A short note on rank-2 relaxation for waveform inversion A Cosse*, SD Shank, L Demanet SEG Technical Program Expanded Abstracts 2015, 1344-1350, 2015 | 7 | 2015 |
| Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host B RifeMagalis, SL Strickland, SD Shank, P Autissier, A Schuetz, ... Virus Evolution 6 (1), veaa005, 2020 | 6 | 2020 |
| Low-rank Solution Methods for Large-scale Linear Matrix Equations SD Shank Temple University Libraries, 2014 | 5 | 2014 |
| Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates DE Northover, SD Shank, DA Liberles BMC Evolutionary Biology 20 (1), 24, 2020 | 3 | 2020 |
| Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus JD Zehr, SL Kosakovsky Pond, SD Shank, H McQueary, JK Grenier, ... Microbiology Spectrum 12 (11), e00867-24, 2024 | | 2024 |