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Steven Weaver

Senior Programming Analyst

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Affiliations

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Prefer not to disclose

Personal Academic Website

Research/Topics of Interest

Pathogens/Diseases of Main Interest/Expertise

COVID-19

Countries of Work/Collaboration

Projects

Papers

Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A, , Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. (2022). Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function. Molecular biology and evolution

Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins G, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A, , Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. (2022). Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function. bioRxiv : the preprint server for biology

Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. (2022). TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics (Oxford, England), 38(10)

Maher MC, Bartha I, Weaver S, di Iulio J, Ferri E, Soriaga L, Lempp FA, Hie BL, Bryson B, Berger B, Robertson DL, Snell G, Corti D, Virgin HW, Kosakovsky Pond SL, Telenti A. (2022). Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science translational medicine, 14(633)

Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. (2022). Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature

Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. (2021). TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. bioRxiv : the preprint server for biology

MacLean OA, Lytras S, Weaver S, Singer JB, Boni MF, Lemey P, Kosakovsky Pond SL, Robertson DL. (2021). Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS biology, 19(3)

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)

Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, , , Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. (2021). The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. medRxiv : the preprint server for health sciences

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San EJ, Msomi N, Mlisana K, von Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass AJ, Engelbrecht S, Van Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies MA, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer CK, Sewell BT, Lourenço J, Alcantara LCJ, Kosakovsky Pond SL, Weaver S, Martin D, Lessells RJ, Bhiman JN, Williamson C, de Oliveira T. (2021). Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein. Nature

Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, , , Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. (2021). The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell

Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. (2021). An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. Molecular biology and evolution

Dávila-Conn V, García-Morales C, Matías-Florentino M, López-Ortiz E, Paz-Juárez HE, Beristain-Barreda Á, Cárdenas-Sandoval M, Tapia-Trejo D, López-Sánchez DM, Becerril-Rodríguez M, García-Esparza P, Macías-González I, Iracheta-Hernández P, Weaver S, Wertheim JO, Reyes-Terán G, González-Rodríguez A, Ávila-Ríos S. (2021). Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020. Journal of the International AIDS Society, 24(11)

MacLean OA, Lytras S, Singer JB, Weaver S, Pond SLK, Robertson DL. (2020). Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans. bioRxiv : the preprint server for biology

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

Kosakovsky Pond SL, Wisotsky SR, Escalante A, Magalis BR, Weaver S. (2020). Contrast-FEL - a test for differences in selective pressures at individual sites among clades and sets of branches. Molecular biology and evolution

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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