Zobrazeno 1 - 10
of 31
pro vyhledávání: '"Stephen D. Shank"'
Autor:
Jordan D. Zehr, Sergei L. Kosakovsky Pond, Stephen D. Shank, Holly McQueary, Jennifer K. Grenier, Gary R. Whittaker, Michael J. Stanhope, Laura B. Goodman
Publikováno v:
Microbiology Spectrum, Vol 12, Iss 11 (2024)
ABSTRACT There are several examples of coronaviruses in the Betacoronavirus subgenus Embecovirus that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the
Externí odkaz:
https://doaj.org/article/9314bfd05ef54dbb8ff850dff370a0ea
Autor:
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
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-13 (2023)
Abstract Background Protein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a pu
Externí odkaz:
https://doaj.org/article/02770213d40246049a08d1048a98d4a6
Autor:
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
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-11 (2022)
Here, the authors characterize a case of SARS-CoV-2 superinfection with Alpha and Epsilon variants, in which, via full genome sequencing analyses, they identify recombinant haplotypes in the spike, nucleocapsid, and ORF 8 coding regions, suggesting r
Externí odkaz:
https://doaj.org/article/c258b0e47c8e46188ea0732ebd024c24
Publikováno v:
BMC Evolutionary Biology, Vol 20, Iss 1, Pp 1-20 (2020)
Abstract Background Understanding the origins of genome content has long been a goal of molecular evolution and comparative genomics. By examining genome evolution through the guise of lineage-specific evolution, it is possible to make inferences abo
Externí odkaz:
https://doaj.org/article/533c346eef7c4160ba034af1d99b1a83
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-5 (2018)
Abstract Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not availa
Externí odkaz:
https://doaj.org/article/083f58dada73412a8e1b4a574bdb7584
Autor:
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
Feline coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed feline enteric coronavirus [FECV]), with around 12 per cent developing into deadly feline infectious peritonitis (FIP; feline infectious peritonitis viru
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d683545c570de0086cf6f6aec59fbbf6
https://doi.org/10.1101/2023.01.11.523607
https://doi.org/10.1101/2023.01.11.523607
Autor:
Lauren E Droske, Stephen D. Shank, Melanie N Cash, Sergei L Kosakovsky Pond, Marco Salemi, Brittany Rife Magalis
During the course of infection, human immunodeficiency virus (HIV) maintains a stably integrated reservoir of replication-competent proviruses within the host genome that are unaffected by antiretroviral therapy. Curative advancements rely heavily on
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d937d6b07df7511e09c5eb306661b44
https://doi.org/10.1101/2022.05.04.490630
https://doi.org/10.1101/2022.05.04.490630
Autor:
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
Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likel
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4bd9d9cee7a0bc6864e95f20126e07fd
https://lirias.kuleuven.be/handle/20.500.12942/694602
https://lirias.kuleuven.be/handle/20.500.12942/694602
Autor:
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
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses con
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::832e44cf4bde58349f198196dba79635
https://doi.org/10.1101/2022.01.18.22269300
https://doi.org/10.1101/2022.01.18.22269300
Autor:
Alexander G. Lucaci, Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P. Martin, Sergei L. Kosakovsky Pond
Publikováno v:
bioRxiv
article-version (status) pre
article-version (number) 1
article-version (status) pre
article-version (number) 1
An important unmet need revealed by the COVID-19 pandemic is the near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::553c95069d89d8075999c87e4675d759
https://doi.org/10.1371/journal.pone.0275623
https://doi.org/10.1371/journal.pone.0275623