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Urhan, A. (author), Cosma, Bianca-Maria (author), Earl, Ashlee M. (author), Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author)Motivation: Today, we know the function of only a small fraction of the protein sequences predicted from genomic data. This problem is even more salient for bacteria, which represent some of the most phylogenetically and metabolically diverse taxa on Earth. This low rate of bacterial gene annotation is compounded by the fact that most...journal article 2024
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StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communitiesvan Dijk, L.R. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Worby, Colin J. (author), Grote, Alexandra (author), Schreiber, Henry L. (author), Anyansi, C.A. (author), Pickering, Amy J. (author), Hultgren, Scott J. (author), Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Earl, Ashlee M. (author)Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which...journal article 2022
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Anyansi, C.A. (author), Straub, Timothy J. (author), Manson, Abigail L. (author), Earl, Ashlee M. (author), Abeel, T.E.P.M.F. (author)Metagenomic sequencing is a powerful tool for examining the diversity and complexity of microbial communities. Most widely used tools for taxonomic profiling of metagenomic sequence data allow for a species-level overview of the composition. However, individual strains within a species can differ greatly in key genotypic and phenotypic...review 2020
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Anyansi, C.A. (author), Keo, D. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Manson, Abigail L. (author), Earl, Ashlee M. (author), Abeel, T.E.P.M.F. (author)Background: Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In...journal article 2020
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Cohen, Keira A. (author), Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Desjardins, Christopher A. (author), Chapman, Sinead B. (author), Hoffner, Sven (author), Birren, Bruce W. (author), Earl, Ashlee M. (author)Background: While the international spread of multidrug-resistant (MDR) Mycobacterium tuberculosis strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed. Methods: In a global dataset of 5310 M....journal article 2019
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Cohen, Keira A. (author), Manson, Abigail L. (author), Desjardins, Christopher A. (author), Abeel, T.E.P.M.F. (author), Earl, Ashlee M. (author)Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998...review 2019
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Georgescu, C.H. (author), Manson McGuire, Abigail L. (author), Griggs, Alexander D. (author), Desjardins, Christopher A. (author), Pironti, Alejandro (author), Wapinski, Ilan (author), Abeel, T.E.P.M.F. (author), Haas, Brian J. (author), Earl, Ashlee M. (author)Accurate orthologue identification is a vital component of bacterial comparative genomic studies, but many popular sequence-similarity-based approaches do not scale well to the large numbers of genomes that are now generated routinely. Furthermore, most approaches do not take gene synteny into account, which is useful information for...journal article 2018
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- Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Galagan, James (author), Chandrabose Sundaramurthi, Jagadish (author), Shanmugam, Siva Kumar (author), Palaniyandi, Kannan (author), Narayanan, Sujatha (author), Swaminathan, Soumya (author), Earl, Ashlee M. (author) journal article 2018
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Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Galagan, James E. (author), Chandrabose Sundaramurthi, Jagadish (author), Salazar, A.N. (author), Gehrmann, T. (author), Shanmugam, Siva Kumar (author), Palaniyandi, Kannan (author), Narayanan, Sujatha (author), Swaminathan, Soumya (author), Earl, Ashlee M. (author)Background.<br/><br/>India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3.<br/>Methods.<br/>...journal article 2017