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NAR Genomics and Bioinformatics|December 20, 2024
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomesJalees A Nasir, Finlay Maguire, Kendrick M Smith, et al.
Med (New York, N.Y.)|April 19, 2022
Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variantsArinjay Banerjee, Jocelyne Lew, Andrea Kroeker, et al.
Iscience|November 29, 2023
Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (<i>Odocoileus virginianus</i>)Jonathon D Kotwa, Briallen Lobb, Ariane Massé, et al.
Microbial Genomics|June 11, 2024
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and trainingEmma J Griffiths, Inês Mendes, Finlay Maguire, et al.
Microbial Genomics|September 21, 2022
Exploring the mobilome and resistome of <i>Enterococcus faecium</i> in a One Health context across two continentsHaley Sanderson, Kristen L Gray, Alexander Manuele, et al.
BMC Infectious Diseases|January 28, 2025
Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter studyKuganya Nirmalarajah, Patryk Aftanas, Shiva Barati, et al.
Microbial Genomics|December 12, 2023
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applicationsRuth E Timme, Ilene Karsch-Mizrachi, Zahra Waheed, et al.
The Journal of Infectious Diseases|June 3, 2025
Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals a Unique Evolutionary Route for SARS-CoV-2 to Gain ResistanceNatalie M Deschenes, Jimena Pérez-Vargas, Zoe Zhong, et al.
Heliyon|January 4, 2023
Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factorsKatherine Chan, Adrian Granda Farias, Hunsang Lee, et al.
Npj Viruses|April 28, 2025
Pathogenesis and transmission of SARS-CoV-2 D614G, Alpha, Gamma, Delta, and Omicron variants in golden hamstersAndra Banete, Bryan D Griffin, Juan C Corredor, et al.
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