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
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
Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein
Zehr, Jordan D, Pond, Sergei L Kosakovsky, Martin, Darren P, Ceres, Kristina, Whittaker, Gary R, Millet, Jean K, Goodman, Laura B, Stanhope, Michael J
Published in Viruses (21.04.2022)
Published in Viruses (21.04.2022)
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Journal Article
Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead
Stanhope, Michael J., Ceres, Kristina M., Sun, Qi, Wang, Minghui, Zehr, Jordan D., Marra, Nicholas J., Wilder, Aryn P., Zou, Cheng, Bernard, Andrea M., Pavinski-Bitar, Paulina, Lokey, Mitchell G., Shivji, Mahmood S.
Published in iScience (20.01.2023)
Published in iScience (20.01.2023)
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Journal Article
Evolutionary genomic analyses of canine E. coli infections identify a relic capsular locus associated with resistance to multiple classes of antimicrobials
Ceres, Kristina, Zehr, Jordan D, Murrell, Chloe, Millet, Jean K, Sun, Qi, McQueary, Holly C, Horton, Alanna, Cazer, Casey, Sams, Kelly, Reboul, Guillaume, Andreopoulos, William B, Mitchell, Patrick K, Anderson, Renee, Franklin-Guild, Rebecca, Cronk, Brittany D, Stanhope, Bryce J, Burbick, Claire R, Wolking, Rebecca, Peak, Laura, Zhang, Yan, McDowall, Rebeccah, Krishnamurthy, Aparna, Slavic, Durda, Sekhon, Prabhjot Kaur, Tyson, Gregory H, Ceric, Olgica, Stanhope, Michael J, Goodman, Laura B
Published in Applied and environmental microbiology (21.08.2024)
Published in Applied and environmental microbiology (21.08.2024)
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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
Conserved recombination patterns across coronavirus subgenera
de Klerk, Arné, Swanepoel, Phillip, Lourens, Rentia, Zondo, Mpumelelo, Abodunran, Isaac, Lytras, Spyros, MacLean, Oscar A, Robertson, David, Kosakovsky Pond, Sergei L, Zehr, Jordan D, Kumar, Venkatesh, Stanhope, Michael J, Harkins, Gordon, Murrell, Ben, Martin, Darren P
Published in Virus evolution (2022)
Published in Virus evolution (2022)
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Journal Article
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes
Zehr, Jordan D, Kosakovsky Pond, Sergei L, Millet, Jean K, Olarte-Castillo, Ximena A, Lucaci, Alexander G, Shank, Stephen D, Ceres, Kristina M, Choi, Annette, Whittaker, Gary R, Goodman, Laura B, Stanhope, Michael J
Published in Virus evolution (2023)
Published in Virus evolution (2023)
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Journal Article
Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead
Stanhope, Michael J., Ceres, Kristina M., Sun, Qi, Wang, Minghui, Zehr, Jordan D., Marra, Nicholas J., Wilder, Aryn P., Zou, Cheng, Bernard, Andrea M., Pavinski-Bitar, Paulina, Lokey, Mitchell G., Shivji, Mahmood S.
Published in iScience (20.01.2023)
Published in iScience (20.01.2023)
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Journal Article
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic Feline Coronavirus phenotypes
Zehr, Jordan D, Kosakovsky Pond, Sergei L, Millet, Jean K, Olarte-Castillo, Ximena Adrea, Lucaci, Alexander G, Stephen Shank D, Ceres, Kristina, Choi, Annette, Whittaker, Gary, Laura Brunengraber Goodman, Stanhope, Michael J
Published in bioRxiv (11.01.2023)
Published in bioRxiv (11.01.2023)
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Paper
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic Feline Coronavirus phenotypes
Zehr, Jordan D, Pond, Sergei L Kosakovsky, Millet, Jean K, Olarte-Castillo, Ximena A, Lucaci, Alexander G, Shank, Stephen D, Ceres, Kristina M, Choi, Annette, Whittaker, Gary R, Goodman, Laura B, Stanhope, Michael J
Published in bioRxiv : the preprint server for biology (11.01.2023)
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Published in bioRxiv : the preprint server for biology (11.01.2023)
Journal Article
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Lucaci, Alexander G, Zehr, Jordan D, Shank, Stephen D, Bouvier, Dave, Mei, Han, Nekrutenko, Anton, Martin, Darren P, Kosakovsky Pond, Sergei L
Published in bioRxiv (18.01.2022)
Published in bioRxiv (18.01.2022)
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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 bioRxiv (14.04.2021)
Published in bioRxiv (14.04.2021)
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Paper
Conserved recombination patterns across coronavirus subgenera
De Klerk, Arne, Swanepoel, Phillip Ivan, Lourens, Rentia Francis, Zondo, Mpumelelo, Abodunran, Isaac, Lytras, Spyros, Maclean, Oscar, Robertson, David L, Kosakovsky Pond, Sergei L, Zehr, Jordan D, Kumar, Venkatesh, Stanhope, Michael J, Harkins, Gordon, Murrell, Ben, Martin, Darren
Published in bioRxiv (23.11.2021)
Published in bioRxiv (23.11.2021)
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