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Epidemiologic data and pathogen genome sequences: a powerful synergy for public health

Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local...

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000–2013

Background. Treatment of Neisseria gonorrhoeae infection is empirical and based on population-wide susceptibilities. Increasing antimicrobial resistance underscores the potential importance of rapid diagnostic tests, including sequence-based tests, to guide therapy. However, the usefulness of sequence-based diagnostic tests depends on the prevalence and dynamics of the resistance...

Secular Trends in Helicobacter pylori Seroprevalence in Adults in the United States: Evidence for Sustained Race/Ethnic Disparities

. ACKNOWLEDGMENTS Author affiliations: Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts (Yonatan H. Grad); Center for Communicable Disease Dynamics, Department of Epidemiology ... , Harvard School of Public Health, Harvard University, Boston, Massachusetts (Yonatan H. Grad, Marc Lipsitch); Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard

Bacterial genomes in epidemiology—present and future

Sequence data are well established in the reconstruction of the phylogenetic and demographic scenarios that have given rise to outbreaks of viral pathogens. The application of similar methods to bacteria has been hindered in the main by the lack of high-resolution nucleotide sequence data from quality samples. Developing and already available genomic methods have greatly...

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura

Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but does not directly link DNA sequence with spatio-temporal patterns of expression. The second, based on searches for combinations of transcription factor (TF) binding motifs, has been...