Steven Weaver

Senior Programming Analyst





Lucaci AG, Wisotsky SR, Shank SD, Weaver S, Kosakovsky Pond SL. (2021). Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes. PloS one, 16(3)

Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. (2020). An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. bioRxiv : the preprint server for biology

Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, Nekrutenko A, Taylor J, Weaver S. (2020). No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS pathogens, 16(8)

Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, Murrell B, Shank SD, Magalis BR, Bouvier D, Nekrutenko A, Wisotsky S, Spielman SJ, Frost SDW, Muse SV. (2020). HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Molecular biology and evolution, 37(1)

Spielman SJ, Weaver S, Shank SD, Magalis BR, Li M, Kosakovsky Pond SL. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces. Methods in molecular biology (Clifton, N.J.), (1910)

Shank SD, Weaver S, Kosakovsky Pond SL. (2018). phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC bioinformatics, 19(1)

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. (2018). HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Molecular biology and evolution, 35(7)

Weaver S, Shank SD, Spielman SJ, Li M, Muse SV, Kosakovsky Pond SL. (2018). Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Molecular biology and evolution, 35(3)

Eren K, Weaver S, Ketteringham R, Valentyn M, Laird Smith M, Kumar V, Mohan S, Kosakovsky Pond SL, Murrell B. (2018). Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS computational biology, 14(12)

Weaver SA, Ucar Z, Bettinger P, Merry K. (2015). How a GNSS Receiver Is Held May Affect Static Horizontal Position Accuracy. PLoS One, 10(4)

Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. (2015). Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Molecular biology and evolution, 32(5)

Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. (2015). Gene-wide identification of episodic selection. Molecular biology and evolution, 32(5)

Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL. (2014). IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS computational biology, 10(9)

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