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Showing 1–8 of 8 results
Advanced filters: Author: Jennifer L. Gardy Clear advanced filters

  • Summer research programmes are renowned for encouraging underrepresented minorities (URMs) to pursue STEM careers, but COVID-19 left many students in the United States unable to participate. We created the National Summer Undergraduate Research Project to matchmake students with mentors, enabling 250 URM students to do summer research.

    • Michael D. L. Johnson
    • David A. Baltrus
    • Jennifer Gardy
    Comments & Opinion
    Nature Microbiology
    Volume: 5, P: 1311-1313

  • Next-generation sequencing has the potential to support public health surveillance systems to improve the early detection of emerging infectious diseases. This Review delineates the role of genomics in rapid outbreak response and the challenges that need to be tackled for genomics-informed pathogen surveillance to become a global reality.

    • Jennifer L. Gardy
    • Nicholas J. Loman
    Reviews
    Nature Reviews Genetics
    Volume: 19, P: 9-20

  • Maha Farhat, Megan Murray and colleagues report whole-genome sequencing of 116 Mycobacterium tuberculosis strains selected to be representative of both global diversity and drug resistance. The authors develop a new method to search for resistance markers in microbial genomes based on reconstructing a genome-wide phylogeny and identifying regions showing convergent evolution, and they use this method to identify 39 new candidate drug resistance regions in the M. tuberculosis genome.

    • Maha R Farhat
    • B Jesse Shapiro
    • Megan Murray
    Research
    Nature Genetics
    Volume: 45, P: 1183-1189

  • Molecular diagnostics for tuberculosis have focused on predicting drug susceptibilities in a binary manner (i.e., strains are either susceptible or resistant). Here, CRyPTIC Consortium researchers use whole genome sequencing and a quantitative assay to identify associations between genomic mutations and minimum inhibitory concentrations in over 15,000 Mycobacterium tuberculosis clinical isolates.

    • Ivan Barilar
    • Simone Battaglia
    • Baoli Zhu
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-13

  • Sarah Fortune and colleagues report that Mycobacterium tuberculosis strains from lineage 2 acquire drug resistance in vitro more rapidly than strains from lineage 4 and show that this correlates with a higher in vivo mutation rate, as estimated from whole-genome sequencing of clinical isolates. They develop a stochastic mathematical model of the within-host evolution of drug resistance, using these mutation rate estimates to predict the rates of emergence of resistance in individuals with tuberculosis.

    • Christopher B Ford
    • Rupal R Shah
    • Sarah M Fortune
    Research
    Nature Genetics
    Volume: 45, P: 784-790

  • Whole genome sequencing (WGS) offers new opportunities in the clinical management and surveillance of Mycobacterium tuberculosis. In this Review, Meehan and colleagues explore the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

    • Conor J. Meehan
    • Galo A. Goig
    • Annelies Van Rie
    Reviews
    Nature Reviews Microbiology
    Volume: 17, P: 533-545

  • The computational prediction of the particular cellular compartment that a bacterial protein is destined for is an important aspect of microbiological research. This article discusses the methods currently available to predict bacterial protein localization.

    • Jennifer L. Gardy
    • Fiona S. L. Brinkman
    Reviews
    Nature Reviews Microbiology
    Volume: 4, P: 741-751