相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
Emmanuel Paradis et al.
BIOINFORMATICS (2019)
Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions
James Stimson et al.
MOLECULAR BIOLOGY AND EVOLUTION (2019)
Best practices for benchmarking germline small-variant calls in human genomes
Peter Krusche et al.
NATURE BIOTECHNOLOGY (2019)
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Alexey M. Kozlov et al.
BIOINFORMATICS (2019)
Role and value of whole genome sequencing in studying tuberculosis transmission
V. Nikolayevskyy et al.
CLINICAL MICROBIOLOGY AND INFECTION (2019)
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
Conor J. Meehan et al.
NATURE REVIEWS MICROBIOLOGY (2019)
Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting
Avika Dixit et al.
SCIENTIFIC REPORTS (2019)
The molecular clock of Mycobacterium tuberculosis
Fabrizio Menardo et al.
PLOS PATHOGENS (2019)
Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Rana Jajou et al.
EUROSURVEILLANCE (2019)
Genetic Clustering of Tuberculosis in an Indigenous Community of Brazil
Flavia Patussi Correia Sacchi et al.
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE (2018)
Identification of missing variants by combining multiple analytic pipelines
Yingxue Ren et al.
BMC BIOINFORMATICS (2018)
Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis
Joshua L. Warren et al.
BMC MEDICINE (2018)
Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis
Chongguang Yang et al.
LANCET INFECTIOUS DISEASES (2018)
Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam
Kathryn E. Holt et al.
NATURE GENETICS (2018)
When are pathogen genome sequences informative of transmission events?
Finlay Campbell et al.
PLOS PATHOGENS (2018)
Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase
Matthew Ezewudo et al.
SCIENTIFIC REPORTS (2018)
Genomic sequencing is required for identification of tuberculosis transmission in Hawaii
Kent J. Koster et al.
BMC INFECTIOUS DISEASES (2018)
MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates
Thomas Andreas Kohl et al.
PEERJ (2018)
China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis
Qingyun Liu et al.
NATURE ECOLOGY & EVOLUTION (2018)
Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population
Diepreye Ayabina et al.
MICROBIAL GENOMICS (2018)
Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission
Michael A. Martin et al.
MICROBIAL GENOMICS (2018)
Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks
Xavier Didelot et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
treespace: Statistical exploration of landscapes of phylogenetic trees
Thibaut Jombart et al.
MOLECULAR ECOLOGY RESOURCES (2017)
Transmission of Extensively Drug-Resistant Tuberculosis in South Africa
N. Sarita Shah et al.
NEW ENGLAND JOURNAL OF MEDICINE (2017)
Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola
Joao Perdigao et al.
SCIENTIFIC REPORTS (2017)
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
Jody E. Phelan et al.
BMC GENOMICS (2016)
Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review
Hollie-Ann Hatherell et al.
BMC MEDICINE (2016)
Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis
Robyn S. Lee et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2016)
Within-Host Heterogeneity of Mycobacterium tuberculosis Infection Is Associated With Poor Early Treatment Response: A Prospective Cohort Study
Ted Cohen et al.
JOURNAL OF INFECTIOUS DISEASES (2016)
Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
Michelle Kendall et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Declaring a tuberculosis outbreak over with genomic epidemiology
Hollie-Ann Hatherell et al.
MICROBIAL GENOMICS (2016)
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Andrew J. Page et al.
MICROBIAL GENOMICS (2016)
PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data
Silke Feuerriegel et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2015)
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study
Timothy M. Walker et al.
LANCET INFECTIOUS DISEASES (2015)
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
Phelim Bradley et al.
NATURE COMMUNICATIONS (2015)
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
Francesc Coll et al.
GENOME MEDICINE (2015)
Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome
Vinita Periwal et al.
PLOS ONE (2015)
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
Stephanie J. Spielman et al.
PLOS ONE (2015)
Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data
Xavier Didelot et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Thibaut Jombart et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study
Timothy M. Walker et al.
LANCET RESPIRATORY MEDICINE (2014)
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data
Josephine M. Bryant et al.
BMC INFECTIOUS DISEASES (2013)
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
Timothy M. Walker et al.
LANCET INFECTIOUS DISEASES (2013)
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
Christopher B. Ford et al.
NATURE GENETICS (2013)
Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study
Andreas Roetzer et al.
PLOS MEDICINE (2013)
ART: a next-generation sequencing read simulator
Weichun Huang et al.
BIOINFORMATICS (2012)
Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control
Ted Cohen et al.
CLINICAL MICROBIOLOGY REVIEWS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Heng Li
BIOINFORMATICS (2011)
How Many Bootstrap Replicates Are Necessary?
Nicholas D. Pattengale et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2010)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Molecular epidemiology of tuberculosis: Current insights
Barun Mathema et al.
CLINICAL MICROBIOLOGY REVIEWS (2006)
Versatile and open software for comparing large genomes
S Kurtz et al.
GENOME BIOLOGY (2004)
Molecular epidemiology of tuberculosis
PF Barnes et al.
NEW ENGLAND JOURNAL OF MEDICINE (2003)
分享论文
