Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes von Weaver, Steven, Shank, Stephen D, Spielman, Stephanie J, Li, Michael, Muse, Spencer V, Kosakovsky Pond, Sergei L

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Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection von Smith, Martin D., Wertheim, Joel O., Weaver, Steven, Murrell, Ben, Scheffler, Konrad, Kosakovsky Pond, Sergei L.

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen von MacLean, Oscar A, Lytras, Spyros, Weaver, Steven, Singer, Joshua B, Boni, Maciej F, Lemey, Philippe, Kosakovsky Pond, Sergei L, Robertson, David L

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How a GNSS Receiver Is Held May Affect Static Horizontal Position Accuracy von Weaver, Steven A, Ucar, Zennure, Bettinger, Pete, Merry, Krista

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phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics von Shank, Stephen D, Weaver, Steven, Kosakovsky Pond, Sergei L

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Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes von Lucaci, Alexander G, Wisotsky, Sadie R, Shank, Stephen D, Weaver, Steven, Kosakovsky Pond, Sergei L

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No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics von Baker, Dannon, van den Beek, Marius, Blankenberg, Daniel, Bouvier, Dave, Chilton, John, Coraor, Nate, Coppens, Frederik, Eguinoa, Ignacio, Gladman, Simon, Grüning, Björn, Keener, Nicholas, Larivière, Delphine, Lonie, Andrew, Kosakovsky Pond, Sergei, Maier, Wolfgang, Nekrutenko, Anton, Taylor, James, Weaver, Steven

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A Study of RANS Turbulence Models in Fully Turbulent Jets: A Perspective for CFD-DEM Simulations von Weaver, Dustin Steven, Mišković, Sanja

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Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons von Eren, Kemal, Weaver, Steven, Ketteringham, Robert, Valentyn, Morné, Laird Smith, Melissa, Kumar, Venkatesh, Mohan, Sanjay, Kosakovsky Pond, Sergei L, Murrell, Ben

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An Analysis of CFD-DEM with Coarse Graining for Turbulent Particle-Laden Jet Flows von Weaver, Dustin Steven, Mišković, Sanja

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AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters von Weaver, Steven, Dávila Conn, Vanessa M, Ji, Daniel, Verdonk, Hannah, Ávila-Ríos, Santiago, Leigh Brown, Andrew J, Wertheim, Joel O, Kosakovsky Pond, Sergei L

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IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform von Hepler, N Lance, Scheffler, Konrad, Weaver, Steven, Murrell, Ben, Richman, Douglas D, Burton, Dennis R, Poignard, Pascal, Smith, Davey M, Kosakovsky Pond, Sergei L

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Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa von Tegally, Houriiyah, Moir, Monika, Everatt, Josie, Giovanetti, Marta, Scheepers, Cathrine, Wilkinson, Eduan, Subramoney, Kathleen, Makatini, Zinhle, Moyo, Sikhulile, Amoako, Daniel G., Baxter, Cheryl, Althaus, Christian L., Anyaneji, Ugochukwu J., Kekana, Dikeledi, Viana, Raquel, Giandhari, Jennifer, Lessells, Richard J., Maponga, Tongai, Maruapula, Dorcas, Choga, Wonderful, Matshaba, Mogomotsi, Mbulawa, Mpaphi B., Msomi, Nokukhanya, Naidoo, Yeshnee, Pillay, Sureshnee, Sanko, Tomasz Janusz, San, James E., Scott, Lesley, Singh, Lavanya, Magini, Nonkululeko A., Smith-Lawrence, Pamela, Stevens, Wendy, Dor, Graeme, Tshiabuila, Derek, Wolter, Nicole, Preiser, Wolfgang, Treurnicht, Florette K., Venter, Marietjie, Chiloane, Georginah, McIntyre, Caitlyn, O’Toole, Aine, Ruis, Christopher, Peacock, Thomas P., Roemer, Cornelius, Kosakovsky Pond, Sergei L., Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal N., Glass, Allison, Martin, Darren P., Jackson, Ben, Rambaut, Andrew, Laguda-Akingba, Oluwakemi, Gaseitsiwe, Simani, von Gottberg, Anne, de Oliveira, Tulio

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies von Kosakovsky Pond, Sergei L, Poon, Art F Y, Velazquez, Ryan, Weaver, Steven, Hepler, N Lance, Murrell, Ben, Shank, Stephen D, Magalis, Brittany Rife, Bouvier, Dave, Nekrutenko, Anton, Wisotsky, Sadie, Spielman, Stephanie J, Frost, Simon D W, Muse, Spencer V

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HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens von Kosakovsky Pond, Sergei L, Weaver, Steven, Leigh Brown, Andrew J, Wertheim, Joel O

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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma von Cele, Sandile, Gazy, Inbal, Jackson, Laurelle, Hwa, Shi-Hsia, Tegally, Houriiyah, Lustig, Gila, Giandhari, Jennifer, Pillay, Sureshnee, Wilkinson, Eduan, Naidoo, Yeshnee, Karim, Farina, Ganga, Yashica, Khan, Khadija, Bernstein, Mallory, Balazs, Alejandro B., Gosnell, Bernadett I., Hanekom, Willem, Moosa, Mahomed-Yunus S., Lessells, Richard J., de Oliveira, Tulio, Sigal, Alex

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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages von Martin, Darren P., Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D., Wilkinson, Eduan, Lucaci, Alexander G., Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J., Gupta, Ravindra K., Wertheim, Joel O., Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W., Lemey, Philippe, MacLean, Oscar A., Robertson, David L., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.

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Gene-Wide Identification of Episodic Selection von Murrell, Ben, Weaver, Steven, Smith, Martin D., Wertheim, Joel O., Murrell, Sasha, Aylward, Anthony, Eren, Kemal, Pollner, Tristan, Martin, Darren P., Smith, Davey M., Scheffler, Konrad, Kosakovsky Pond, Sergei L.

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Archaeological Work in Oxfordshire, 2023 von Green, Victoria, Oram, Richard, Weaver, Steven

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Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches von Kosakovsky Pond, Sergei L, Wisotsky, Sadie R, Escalante, Ananias, Magalis, Brittany Rife, Weaver, Steven

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