Jonathan E Allen (Jonathan Allen)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 18

Top Topics

Molecular Dynamics Simulations

Respiratory Syndrome Coronavirus

Antimicrobial Resistance

Top Venues

Journal of chemical information and modeling

Bioinformatics (Oxford, England)

This page only lists publications with an associated author ORCID identifier.

Publications

Aram Avila-Herrera, Jeffrey A Kimbrel, Jose Manuel Martí, James Thissen, Edwin A Saada, Tracy Weisenberger, Kathryn T Arrildt, Brent W Segelke, Jonathan E Allen, Adam Zemla, Monica K Borucki
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PloS one 19 (1) (2024)
Aram Avila-Herrera, Jeffrey A Kimbrel, Jose Manuel Martí, James Thissen, Edwin A Saada, Tracy Weisenberger, Kathryn T Arrildt, Brent W Segelke, Jonathan E Allen, Adam Zemla, Monica K Borucki
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PloS one 19 (1) (2024)
Jose Manuel Martí, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski, Hunter Nisonoff, Sean P Leonard, Christina S Kang-Yun, Jennifer L Chlebek, Dante P Ricci, Dan M Park, Harris Wang, Jennifer Listgarten, Yongqin Jiao, Jonathan E Allen
GENTANGLE: integrated computational design of gene entanglements. Bioinformatics (Oxford, England) 40 (7) (2024)
Aram Avila-Herrera, Jeffrey A Kimbrel, Jose Manuel Martí, James Thissen, Edwin A Saada, Tracy Weisenberger, Kathryn T Arrildt, Brent W Segelke, Jonathan E Allen, Adam Zemla, Monica K Borucki
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PloS one 19 (1) (2024)
Jose Manuel Martí, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski, Hunter Nisonoff, Sean P Leonard, Christina S Kang-Yun, Jennifer L Chlebek, Dante P Ricci, Dan M Park, Harris Wang, Jennifer Listgarten, Yongqin Jiao, Jonathan E Allen
GENTANGLE: integrated computational design of gene entanglements. Bioinformatics (Oxford, England) 40 (7) (2024)
Garrett A Stevenson, Dan Kirshner, Brian J Bennion, Yue Yang, Xiaohua Zhang, Adam Zemla, Marisa W Torres, Aidan Epstein, Derek Jones, Hyojin Kim, William F Drew Bennett, Sergio E Wong, Jonathan E Allen, Felice C Lightstone
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. Journal of chemical information and modeling (2023)
Sarah H Sandholtz, Jeffrey A Drocco, Adam T Zemla, Marisa W Torres, Mary S Silva, Jonathan E Allen
A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2. ACS omega 8 (24) (2023)
Jeffrey A Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Christopher Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14 (12) (2022)
Jeffrey A Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Christopher Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14 (12) (2022)
Jeffrey A Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Christopher Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14 (12) (2022)
Vincent Blay, Tijana Radivojevic, Jonathan E Allen, Corey M Hudson, Héctor García Martín
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design. Journal of chemical information and modeling 62 (15) (2022)
Jeffrey A Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Christopher Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14 (12) (2022)
Heesung Shim, Hyojin Kim, Jonathan E Allen, Heike Wulff
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking. Journal of chemical information and modeling 62 (10) (2022)
Jeffrey A Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Christopher Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14 (12) (2022)
Jeffrey A Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Christopher Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14 (12) (2022)
Derek Jones, Jonathan E Allen, Yue Yang, William F Drew Bennett, Maya Gokhale, Niema Moshiri, Tajana S Rosing
Accelerators for Classical Molecular Dynamics Simulations of Biomolecules. Journal of chemical theory and computation 18 (7) (2022)
Heike Sichtig, Timothy Minogue, Yi Yan, Christopher Stefan, Adrienne Hall, Luke Tallon, Lisa Sadzewicz, Suvarna Nadendla, William Klimke, Eneida Hatcher, Martin Shumway, Dayanara Lebron Aldea, Jonathan E Allen, Jeffrey Koehler, Tom Slezak, Stephen Lovell, Randal J Schoepp, Uwe Scherf
FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nature communications 10 (1) (2019)
James B Thissen, Mariko Isshiki, Crystal J Jaing, Yoshiro Nagao, Dayanara Lebron Aldea, Jonathan E Allen, Masafumi Izui, Thomas R Slezak, Takafumi Ishida, Tetsuya Sano
A novel variant of torque teno virus 7 identified in patients with Kawasaki disease. PloS one 13 (12) (2018)