المؤلفون: Melissa Rincon-Sandoval, Rishi De-Kayne, Stephen D. Shank, Stacy Pirro, Alfred Ko’ou, Linelle Abueg, Alan Tracey, Jackie Mountcastle, Brian O’Toole, Jennifer Balacco, Giulio Formenti, Erich D. Jarvis, Dahiana Arcila, Sergei L. Kosakovsky Pond, Aaron Davis, Devin D. Bloom, Ricardo Betancur-R

المصدر: Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)

مصطلحات موضوعية: Science

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2041-1723

URL الوصول: https://doaj.org/article/94d7d6badae4477888b08089ebcb2c77

المؤلفون: Jordan D. Zehr, Sergei L. Kosakovsky Pond, Stephen D. Shank, Holly McQueary, Jennifer K. Grenier, Gary R. Whittaker, Michael J. Stanhope, Laura B. Goodman

المصدر: Microbiology Spectrum, Vol 12, Iss 11 (2024)

مصطلحات موضوعية: equine coronavirus, natural selection, coronavirus, tropism shift, Microbiology, QR1-502

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2165-0497

URL الوصول: https://doaj.org/article/9314bfd05ef54dbb8ff850dff370a0ea

المؤلفون: Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko

المصدر: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-13 (2023)

مصطلحات موضوعية: Protein–protein interactions, Structural modeling, Galaxy workflow, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1471-2105

URL الوصول: https://doaj.org/article/02770213d40246049a08d1048a98d4a6

المؤلفون: Joel O. Wertheim, Jade C. Wang, Mindy Leelawong, Darren P. Martin, Jennifer L. Havens, Moinuddin A. Chowdhury, Jonathan E. Pekar, Helly Amin, Anthony Arroyo, Gordon A. Awandare, Hoi Yan Chow, Edimarlyn Gonzalez, Elizabeth Luoma, Collins M. Morang’a, Anton Nekrutenko, Stephen D. Shank, Stefan Silver, Peter K. Quashie, Jennifer L. Rakeman, Victoria Ruiz, Lucia V. Torian, Tetyana I. Vasylyeva, Sergei L. Kosakovsky Pond, Scott Hughes

المصدر: Nature Communications, Vol 13, Iss 1, Pp 1-11 (2022)

مصطلحات موضوعية: Science

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2041-1723

URL الوصول: https://doaj.org/article/c258b0e47c8e46188ea0732ebd024c24

المؤلفون: David E. Northover, Stephen D. Shank, David A. Liberles

المصدر: BMC Evolutionary Biology, Vol 20, Iss 1, Pp 1-20 (2020)

مصطلحات موضوعية: Comparative genomics, Molecular evolution, Gene duplication, Pathway evolution, Protein structure, Evolution, QH359-425

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1471-2148

URL الوصول: https://doaj.org/article/533c346eef7c4160ba034af1d99b1a83

المؤلفون: Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond

المصدر: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-5 (2018)

مصطلحات موضوعية: Phylogenetics, JavaScript, Data visualization, D3, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2283-2; https://doaj.org/toc/1471-2105

URL الوصول: https://doaj.org/article/083f58dada73412a8e1b4a574bdb7584

المؤلفون: Alexander G Lucaci, Jordan D Zehr, Stephen D Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P Martin, Sergei L Kosakovsky Pond

المصدر: PLoS ONE, Vol 17, Iss 11, p e0275623 (2022)

مصطلحات موضوعية: Medicine, Science

Relation: https://doi.org/10.1371/journal.pone.0275623; https://doaj.org/toc/1932-6203; https://doaj.org/article/bca1a56d05294988afd66598cded39bb

الاتاحة: https://doi.org/10.1371/journal.pone.0275623
https://doaj.org/article/bca1a56d05294988afd66598cded39bb

المؤلفون: Alexander G. Lucaci (10296991), Sadie R. Wisotsky (10296994), Stephen D. Shank (5560244), Steven Weaver (634651), Sergei L. Kosakovsky Pond (8321352)

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Molecular Biology, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Biological Sciences not elsewhere classified, alignment errors, codons encoding serine, 3 H signal, Extra base hits, model misspecification

Relation: https://figshare.com/articles/journal_contribution/Estimated_i_i_rate_distributions_for_benchmark_datasets_for_different_models_on_the_benchmark_datasets_/14208775

الاتاحة: https://doi.org/10.1371/journal.pone.0248337.s001

المؤلفون: Alexander G Lucaci, Sadie R Wisotsky, Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond

المصدر: PLoS ONE, Vol 16, Iss 3, p e0248337 (2021)

مصطلحات موضوعية: Medicine, Science

Relation: https://doi.org/10.1371/journal.pone.0248337; https://doaj.org/toc/1932-6203; https://doaj.org/article/8c1c63c09e00483a8808e2e2339075da

الاتاحة: https://doi.org/10.1371/journal.pone.0248337
https://doaj.org/article/8c1c63c09e00483a8808e2e2339075da

المؤلفون: Jordan D Zehr, Sergei L Kosakovsky Pond, Jean K Millet, Ximena A Olarte-Castillo, Alexander G Lucaci, Stephen D Shank, Kristina M Ceres, Annette Choi, Gary R Whittaker, Laura B Goodman, Michael J Stanhope

مصطلحات موضوعية: Virology, Microbiology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d683545c570de0086cf6f6aec59fbbf6
https://doi.org/10.1101/2023.01.11.523607

المؤلفون: Lauren E Droske, Stephen D. Shank, Melanie N Cash, Sergei L Kosakovsky Pond, Marco Salemi, Brittany Rife Magalis

مصطلحات موضوعية: History, Polymers and Plastics, Business and International Management, Industrial and Manufacturing Engineering

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d937d6b07df7511e09c5eb306661b44
https://doi.org/10.1101/2022.05.04.490630

المؤلفون: Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, Maciej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio de Oliveira, Sergei L. Kosakovsky Pond

المساهمون: Wellcome Trust

مصطلحات موضوعية: epistasis, Evolutionary Biology, 0604 Genetics, SARS-CoV-2, negative selection, COVID-19, NGS-SA, 0601 Biochemistry and Cell Biology, 0603 Evolutionary Biology, positive selection, coevolution, Mutation, Spike Glycoprotein, Coronavirus, Genetics, Humans, Molecular Biology, Ecology, Evolution, Behavior and Systematics

وصف الملف: Print; application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4bd9d9cee7a0bc6864e95f20126e07fd
https://lirias.kuleuven.be/handle/20.500.12942/694602

المؤلفون: Joel O. Wertheim, Jade C. Wang, Mindy Leelawong, Darren P. Martin, Jennifer L. Havens, Moinuddin A. Chowdhury, Jonathan Pekar, Helly Amin, Anthony Arroyo, Gordon A. Awandare, Hoi Yan Chow, Edimarlyn Gonzalez, Elizabeth Luoma, Collins M. Morang’a, Anton Nekrutenko, Stephen D. Shank, Peter K. Quashie, Jennifer L. Rakeman, Victoria Ruiz, Lucia V. Torian, Tetyana I. Vasylyeva, Sergei L. Kosakovsky Pond, Scott Hughes

مصطلحات موضوعية: viruses

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::832e44cf4bde58349f198196dba79635
https://doi.org/10.1101/2022.01.18.22269300

المؤلفون: Brittany Rife Magalis, Stephanie J. Spielman, Ben Murrell, Sadie R Wisotsky, Simon D. W. Frost, Dave Bouvier, Ryan Velazquez, Art F. Y. Poon, Spencer V. Muse, N. Lance Hepler, Sergei L Kosakovsky Pond, Stephen D. Shank, Anton Nekrutenko, Steven Weaver

المصدر: Mol Biol Evol

مصطلحات موضوعية: Natural selection, Estimation theory, business.industry, Stability (learning theory), Usability, Biology, Machine learning, computer.software_genre, Resources, Backward compatibility, Genetic Techniques, Genetics, Statistical inference, Artificial intelligence, business, Molecular Biology, computer, Phylogeny, Software, Ecology, Evolution, Behavior and Systematics, Coevolution, Statistical hypothesis testing

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7f2726ff45bdf76bef80d72b39b3f6c4
https://doi.org/10.1093/molbev/msz197

المؤلفون: Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko

مصطلحات موضوعية: chemistry.chemical_classification, chemistry, Spike Protein, Experimental validation, Computational biology, Experimental methods, Biology, Glycoprotein, Interactome, Genome, Disease treatment, Protein–protein interaction

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::84e4889522ad941a983235bb520f4410
https://doi.org/10.1101/2021.03.17.435706

المؤلفون: Darren P, Martin, Steven, Weaver, Houryiah, Tegally, Emmanuel James, San, Stephen D, Shank, Eduan, Wilkinson, Alexander G, Lucaci, Jennifer, Giandhari, Sureshnee, Naidoo, Yeshnee, Pillay, Lavanya, Singh, Richard J, Lessells, Ravindra K, Gupta, Joel O, Wertheim, Anton, Nekturenko, Ben, Murrell, Gordon W, Harkins, Philippe, Lemey, Oscar A, MacLean, David L, Robertson, Tulio, de Oliveira, Sergei L, Kosakovsky Pond

المصدر: Cell
medRxiv

مصطلحات موضوعية: transmission advantage, Genes, Viral, convergent mutations, SARS-CoV-2, viruses, Genetic Drift, lineage-defining mutations, COVID-19, directional selection, diversifying selection, Host Adaptation, Article, Evolution, Molecular, positive selection, Mutation, recurrent mutations, evolutionary adaptation, Humans, Amino Acid Sequence, Public Health, Codon, Pandemics, COVID 19, Phylogeny, immune evasion

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::01702bbc675ce676d46c9e51075b09e9
https://pubmed.ncbi.nlm.nih.gov/34537136

المؤلفون: Stephen D. Shank, Valeria Simoncini, Daniel B. Szyld, Daniel, B. Szyld

المساهمون: The Pennsylvania State University CiteSeerX Archives

المصدر: https://math.temple.edu/%7Eszyld/reports/efficientLyap.rev.report.pdf.

وصف الملف: application/pdf

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.698.2848

الاتاحة: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.698.2848

المؤلفون: Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, Sergei L. Kosakovsky Pond

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::005c10a93a2521c980a7b3219e006d78
https://doi.org/10.17504/protocols.io.brcwm2xe

المؤلفون: Alexander G. Lucaci, Sergei L Kosakovsky Pond, Steven Weaver, Stephen D. Shank, Sadie R Wisotsky

المصدر: PLoS ONE, Vol 16, Iss 3, p e0248337 (2021)
PLoS ONE

مصطلحات موضوعية: Topography, Computer science, Biochemistry, Serine, Database and Informatics Methods, Empirical research, Nucleotide, Amino Acids, Phylogeny, Islands, chemistry.chemical_classification, Multidisciplinary, Hierarchy (mathematics), Nucleotides, Organic Compounds, Simulation and Modeling, Eukaryota, Chemistry, Physical Sciences, Vertebrates, Medicine, Sequence Analysis, Research Article, Multiple Alignment Calculation, Bioinformatics, Science, Sequence alignment, Computational biology, Research and Analysis Methods, Evolution, Molecular, Phylogenetics, Hydroxyl Amino Acids, Computational Techniques, Animals, Codon, Evolutionary dynamics, Landforms, Evolutionary Biology, Models, Genetic, Organic Chemistry, Chemical Compounds, Organisms, Biology and Life Sciences, Proteins, Geomorphology, Base (topology), Split-Decomposition Method, chemistry, Earth Sciences, Sequence Alignment, Zoology, Software

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::73bc5592da41806663c3db1506593ff4
https://doi.org/10.1101/2020.05.13.091652

المؤلفون: Alexander G. Lucaci (10296991), Sadie R. Wisotsky (10296994), Stephen D. Shank (5560244), Steven Weaver (634651), Sergei L. Kosakovsky Pond (8321352)

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Molecular Biology, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Biological Sciences not elsewhere classified, alignment errors, codons encoding serine, 3 H signal, Extra base hits, model misspecification

Relation: https://figshare.com/articles/figure/The_effect_of_model_choice_on_rate_estimates_/14208778

الاتاحة: https://doi.org/10.1371/journal.pone.0248337.s002