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Your search keyword '"Alcock, Brian P"' showing total 14 results
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14 results on '"Alcock, Brian P"'

1. SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes.

Author

Nasir, Jalees A, Maguire, Finlay, Smith, Kendrick M, Panousis, Emily M, Baker, Sheridan J C, Aftanas, Patryk, Raphenya, Amogelang R, Alcock, Brian P, Maan, Hassaan, Knox, Natalie C, Banerjee, Arinjay, Mossman, Karen, Wang, Bo, Simpson, Jared T, Kozak, Robert A, Mubareka, Samira, and McArthur, Andrew G

Published
2024
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2. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline

Author

Lu, Dan, primary, Kalantar, Katrina L., additional, Chu, Victoria T., additional, Glascock, Abigail L., additional, Guerrero, Estella S., additional, Bernick, Nina, additional, Butcher, Xochitl, additional, Ewing, Kirsty, additional, Fahsbender, Elizabeth, additional, Holmes, Olivia, additional, Hoops, Erin, additional, Jones, Ann E., additional, Lim, Ryan, additional, McCanny, Suzette, additional, Reynoso, Lucia, additional, Rosario, Karyna, additional, Tang, Jennifer, additional, Valenzuela, Omar, additional, Mourani, Peter M., additional, Pickering, Amy J., additional, Raphenya, Amogelang R., additional, Alcock, Brian P., additional, McArthur, Andrew G., additional, and Langelier, Charles R., additional

Published
2024
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5. The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T., Klunk, Jennifer, Porter, Ashleigh F., Dhody, Anna N., Hicks, Robert, Smith, Geoffrey L., Humphreys, Margaret, McCollum, Andrea M., Davidson, Whitni B., Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Raphenya, Amogelang R., Lau, Tammy T. Y., Alcock, Brian, McArthur, Andrew G., Golding, G. Brian, Holmes, Edward C., and Poinar, Hendrik N.

Published
2020
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6. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Author

Alcock, Brian P, primary, Huynh, William, additional, Chalil, Romeo, additional, Smith, Keaton W, additional, Raphenya, Amogelang R, additional, Wlodarski, Mateusz A, additional, Edalatmand, Arman, additional, Petkau, Aaron, additional, Syed, Sohaib A, additional, Tsang, Kara K, additional, Baker, Sheridan J C, additional, Dave, Mugdha, additional, McCarthy, Madeline C, additional, Mukiri, Karyn M, additional, Nasir, Jalees A, additional, Golbon, Bahar, additional, Imtiaz, Hamna, additional, Jiang, Xingjian, additional, Kaur, Komal, additional, Kwong, Megan, additional, Liang, Zi Cheng, additional, Niu, Keyu C, additional, Shan, Prabakar, additional, Yang, Jasmine Y J, additional, Gray, Kristen L, additional, Hoad, Gemma R, additional, Jia, Baofeng, additional, Bhando, Timsy, additional, Carfrae, Lindsey A, additional, Farha, Maya A, additional, French, Shawn, additional, Gordzevich, Rodion, additional, Rachwalski, Kenneth, additional, Tu, Megan M, additional, Bordeleau, Emily, additional, Dooley, Damion, additional, Griffiths, Emma, additional, Zubyk, Haley L, additional, Brown, Eric D, additional, Maguire, Finlay, additional, Beiko, Robert G, additional, Hsiao, William W L, additional, Brinkman, Fiona S L, additional, Van Domselaar, Gary, additional, and McArthur, Andrew G, additional

Published
2022
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7. Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Author

Sanderson, Haley, primary, Gray, Kristen L., additional, Manuele, Alexander, additional, Maguire, Finlay, additional, Khan, Amjad, additional, Liu, Chaoyue, additional, Navanekere Rudrappa, Chandana, additional, Nash, John H. E., additional, Robertson, James, additional, Bessonov, Kyrylo, additional, Oloni, Martins, additional, Alcock, Brian P., additional, Raphenya, Amogelang R., additional, McAllister, Tim A., additional, Peacock, Sharon J., additional, Raven, Kathy E., additional, Gouliouris, Theodore, additional, McArthur, Andrew G., additional, Brinkman, Fiona S. L., additional, Fink, Ryan C., additional, Zaheer, Rahat, additional, and Beiko, Robert G., additional

Published
2022
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8. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

Author

Alcock, Brian P, Huynh, William, Chalil, Romeo, Smith, Keaton W, Raphenya, Amogelang R, Wlodarski, Mateusz A, Edalatmand, Arman, Petkau, Aaron, Syed, Sohaib A, Tsang, Kara K, Baker, Sheridan J C, Dave, Mugdha, McCarthy, Madeline C, Mukiri, Karyn M, Nasir, Jalees A, Golbon, Bahar, Imtiaz, Hamna, Jiang, Xingjian, Kaur, Komal, and Kwong, Megan

Published
2023
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9. A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture

Author

Nasir, Jalees A., primary, Kozak, Robert A., additional, Aftanas, Patryk, additional, Raphenya, Amogelang R., additional, Smith, Kendrick M., additional, Maguire, Finlay, additional, Maan, Hassaan, additional, Alruwaili, Muhannad, additional, Banerjee, Arinjay, additional, Mbareche, Hamza, additional, Alcock, Brian P., additional, Knox, Natalie C., additional, Mossman, Karen, additional, Wang, Bo, additional, Hiscox, Julian A., additional, McArthur, Andrew G., additional, and Mubareka, Samira, additional

Published
2020
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10. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

Author

Alcock, Brian P, primary, Raphenya, Amogelang R, additional, Lau, Tammy T Y, additional, Tsang, Kara K, additional, Bouchard, Mégane, additional, Edalatmand, Arman, additional, Huynh, William, additional, Nguyen, Anna-Lisa V, additional, Cheng, Annie A, additional, Liu, Sihan, additional, Min, Sally Y, additional, Miroshnichenko, Anatoly, additional, Tran, Hiu-Ki, additional, Werfalli, Rafik E, additional, Nasir, Jalees A, additional, Oloni, Martins, additional, Speicher, David J, additional, Florescu, Alexandra, additional, Singh, Bhavya, additional, Faltyn, Mateusz, additional, Hernandez-Koutoucheva, Anastasia, additional, Sharma, Arjun N, additional, Bordeleau, Emily, additional, Pawlowski, Andrew C, additional, Zubyk, Haley L, additional, Dooley, Damion, additional, Griffiths, Emma, additional, Maguire, Finlay, additional, Winsor, Geoff L, additional, Beiko, Robert G, additional, Brinkman, Fiona S L, additional, Hsiao, William W L, additional, Domselaar, Gary V, additional, and McArthur, Andrew G, additional

Published
2019
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11. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.

Author

Alcock, Brian P, Raphenya, Amogelang R, Lau, Tammy T Y, Tsang, Kara K, Bouchard, Mégane, Edalatmand, Arman, Huynh, William, Nguyen, Anna-Lisa V, Cheng, Annie A, Liu, Sihan, Min, Sally Y, Miroshnichenko, Anatoly, Tran, Hiu-Ki, Werfalli, Rafik E, Nasir, Jalees A, Oloni, Martins, Speicher, David J, Florescu, Alexandra, Singh, Bhavya, and Faltyn, Mateusz

Published
2020
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13. Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Author

Guitor, Allison K., Raphenya, Amogelang R., Klunk, Jennifer, Kuch, Melanie, Alcock, Brian, Surette, Michael G., McArthur, Andrew G., Poinar, Hendrik N., and Wright, Gerard D.

Abstract

Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations.

Published
2019
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14. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Author

Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, and Langelier CR

Abstract

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR., Competing Interests: Competing interests The authors declare that they have no competing interests.

Published
2024
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