Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes
Weaver, Steven, Shank, Stephen D, Spielman, Stephanie J, Li, Michael, Muse, Spencer V, Kosakovsky Pond, Sergei L
Published in Molecular biology and evolution (01.03.2018)
Published in Molecular biology and evolution (01.03.2018)
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Journal Article
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
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.
Published in Cell (30.09.2021)
Published in Cell (30.09.2021)
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Journal Article
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
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
Published in Molecular biology and evolution (01.01.2020)
Published in Molecular biology and evolution (01.01.2020)
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Journal Article
Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
Guerler, Aysam, Baker, Dannon, van den Beek, Marius, Gruening, Bjoern, Bouvier, Dave, Coraor, Nate, Shank, Stephen D, Zehr, Jordan D, Schatz, Michael C, Nekrutenko, Anton
Published in BMC bioinformatics (23.06.2023)
Published in BMC bioinformatics (23.06.2023)
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Journal Article
Multicenter Evaluation of the Clinical Performance and the Neutralizing Antibody Activity Prediction Properties of 10 High-Throughput Serological Assays Used in Clinical Laboratories
Therrien, C, Serhir, B, Bélanger-Collard, M, Skrzypczak, J, Shank, D K, Renaud, C, Girouard, J, Loungnarath, V, Carrier, M, Brochu, G, Tourangeau, F, Gilfix, B, Piche, A, Bazin, R, Guérin, R, Lavoie, M, Martel-Laferrière, V, Fortin, C, Benoit, A, Marcoux, D, Gauthier, N, Laumaea, A M, Gasser, R, Finzi, A, Roger, M
Published in Journal of clinical microbiology (18.02.2021)
Published in Journal of clinical microbiology (18.02.2021)
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Journal Article
Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes
Lucaci, Alexander G, Wisotsky, Sadie R, Shank, Stephen D, Weaver, Steven, Kosakovsky Pond, Sergei L
Published in PloS one (12.03.2021)
Published in PloS one (12.03.2021)
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Journal Article
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Wertheim, Joel O., Wang, Jade C., Leelawong, Mindy, Martin, Darren P., Havens, Jennifer L., Chowdhury, Moinuddin A., Pekar, Jonathan E., Amin, Helly, Arroyo, Anthony, Awandare, Gordon A., Chow, Hoi Yan, Gonzalez, Edimarlyn, Luoma, Elizabeth, Morang’a, Collins M., Nekrutenko, Anton, Shank, Stephen D., Silver, Stefan, Quashie, Peter K., Rakeman, Jennifer L., Ruiz, Victoria, Torian, Lucia V., Vasylyeva, Tetyana I., Kosakovsky Pond, Sergei L., Hughes, Scott
Published in Nature communications (25.06.2022)
Published in Nature communications (25.06.2022)
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Journal Article
RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis
Lucaci, Alexander G, Zehr, Jordan D, Shank, Stephen D, Bouvier, Dave, Ostrovsky, Alexander, Mei, Han, Nekrutenko, Anton, Martin, Darren P, Kosakovsky Pond, Sergei L
Published in PloS one (02.11.2022)
Published in PloS one (02.11.2022)
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Journal Article
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function
Martin, Darren P., Lytras, Spyros, Lucaci, Alexander G., Maier, Wolfgang, Grüning, Björn, Shank, Stephen D., Weaver, Steven, MacLean, Oscar A., Orton, Richard J., Lemey, Philippe, Boni, Maciej F., Tegally, Houriiyah, Harkins, Gordon W., Scheepers, Cathrine, Bhiman, Jinal N., Everatt, Josie, Amoako, Daniel G., San, James Emmanuel, Giandhari, Jennifer, Sigal, Alex, Williamson, Carolyn, Hsiao, Nei-yuan, von Gottberg, Anne, De Klerk, Arne, Shafer, Robert W., Robertson, David L., Wilkinson, Robert J., Sewell, B. Trevor, Lessells, Richard, Nekrutenko, Anton, Greaney, Allison J., Starr, Tyler N., Bloom, Jesse D., Murrell, Ben, Wilkinson, Eduan, Gupta, Ravindra K., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.
Published in Molecular biology and evolution (2022)
Published in Molecular biology and evolution (2022)
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Journal Article
Dewpoint Temperature Prediction Using Artificial Neural Networks
Shank, D. B., Hoogenboom, G., McClendon, R. W.
Published in Journal of applied meteorology and climatology (01.06.2008)
Published in Journal of applied meteorology and climatology (01.06.2008)
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Journal Article
Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus
Zehr, Jordan D, Kosakovsky Pond, Sergei L, Shank, Stephen D, McQueary, Holly, Grenier, Jennifer K, Whittaker, Gary R, Stanhope, Michael J, Goodman, Laura B
Published in Microbiology spectrum (07.10.2024)
Published in Microbiology spectrum (07.10.2024)
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Journal Article
Differential expression of p16(INK4A) and cyclin D1 in benign and malignant salivary gland tumors: a study of 44 Cases
Jour, G, West, K, Ghali, V, Shank, D, Ephrem, G, Wenig, B M
Published in Head & neck pathology (Totowa, N.J.) (01.09.2013)
Published in Head & neck pathology (Totowa, N.J.) (01.09.2013)
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Journal Article
Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
Wisotsky, Sadie R, Kosakovsky Pond, Sergei L, Shank, Stephen D, Muse, Spencer V
Published in Molecular biology and evolution (01.08.2020)
Published in Molecular biology and evolution (01.08.2020)
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Journal Article
Current Topics in the Management of Acute Traumatic Spinal Cord Injury
Shank, Christopher D., Walters, Beverly C., Hadley, Mark N.
Published in Neurocritical care (01.04.2019)
Published in Neurocritical care (01.04.2019)
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Journal Article
Efficient low-rank solution of generalized Lyapunov equations
Shank, Stephen D., Simoncini, Valeria, Szyld, Daniel B.
Published in Numerische Mathematik (01.10.2016)
Published in Numerische Mathematik (01.10.2016)
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