Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges

by Keira A. Cohen, Abigail L. Manson, Christopher A. Desjardins, Thomas Abeel, Ashlee M. Earl
Published 2019-07-01

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database.

by João L Reis-Cunha, Daniella C Bartholomeu, Abigail L Manson, Ashlee M Earl, Gustavo C Cerqueira
Published 2019-01-01

QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

by Christine Anyansi, Arlin Keo, Bruce J. Walker, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel
Published 2020-01-01

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data

by Christine Anyansi, Christine Anyansi, Timothy J. Straub, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel, Thomas Abeel
Published 2020-08-01

Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

by Ryan A. Bronson, Chhavi Gupta, Abigail L. Manson, Jan A. Nguyen, Asli Bahadirli-Talbott, Nicole M. Parrish, Ashlee M. Earl, Keira A. Cohen
Published 2021-08-01

Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics

by Nathan L. Bachmann, Nathan L. Bachmann, Rauf Salamzade, Abigail L. Manson, Richard Whittington, Richard Whittington, Vitali Sintchenko, Vitali Sintchenko, Ashlee M. Earl, Ben J. Marais
Published 2020-01-01

Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics

by Peijun Ma, Lorrie L He, Alejandro Pironti, Hannah H Laibinis, Christoph M Ernst, Abigail L Manson, Roby P Bhattacharyya, Ashlee M Earl, Jonathan Livny, Deborah T Hung
Published 2021-04-01

Colon Cancer-Associated Fusobacterium nucleatum May Originate From the Oral Cavity and Reach Colon Tumors via the Circulatory System

by Jawad Abed, Jawad Abed, Naseem Maalouf, Abigail L. Manson, Ashlee M. Earl, Lishay Parhi, Johanna E. M. Emgård, Michael Klutstein, Shay Tayeb, Gideon Almogy, Karine A. Atlan, Stella Chaushu, Eran Israeli, Ofer Mandelboim, Wendy S. Garrett, Wendy S. Garrett, Wendy S. Garrett, Gilad Bachrach
Published 2020-08-01

Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections

by Timothy J. Straub, Wen-Chi Chou, Abigail L. Manson, Henry L. Schreiber, Bruce J. Walker, Christopher A. Desjardins, Sinéad B. Chapman, Kerrie L. Kaspar, Orsalem J. Kahsai, Elizabeth Traylor, Karen W. Dodson, Meredith A. J. Hullar, Scott J. Hultgren, Christina Khoo, Ashlee M. Earl
Published 2021-02-01

Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains

by Arunachalam Ramaiah, Soumya Nayak, Srabanti Rakshit, Abigail L. Manson, Thomas Abeel, Sivakumar Shanmugam, Pravat Nalini Sahoo, Anto Jesuraj Uday Kumar John, Jagadish Chandrabose Sundaramurthi, Sujatha Narayanan, George D'Souza, Paul von Hoegen, Tom H. M. Ottenhoff, Soumya Swaminathan, Ashlee M. Earl, Annapurna Vyakarnam, Annapurna Vyakarnam
Published 2019-02-01