An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes
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Title
An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes
Authors
Keywords
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Journal
Frontiers in Microbiology
Volume 8, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2017-11-29
DOI
10.3389/fmicb.2017.02351
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Note: Only part of the references are listed.- Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States
- (2017) Yi Chen et al. PLoS One
- Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes
- (2016) Yi Chen et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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- (2016) Yi Chen et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing
- (2016) Clémentine Henri et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Whole-genome Sequencing Used to Investigate a Nationwide Outbreak of Listeriosis Caused by Ready-to-eat Delicatessen Meat, Denmark, 2014
- (2016) Anne Kvistholm Jensen et al. CLINICAL INFECTIOUS DISEASES
- Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation
- (2016) Brendan R. Jackson et al. CLINICAL INFECTIOUS DISEASES
- Whole genome sequence-based serogrouping of Listeria monocytogenes isolates
- (2016) Patrick Hyden et al. JOURNAL OF BIOTECHNOLOGY
- An Outbreak of Human Listeriosis in England between 2010 and 2012 Associated with the Consumption of Pork Pies
- (2016) A. AWOFISAYO-OKUYELU et al. JOURNAL OF FOOD PROTECTION
- Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity
- (2016) Mylène M Maury et al. NATURE GENETICS
- Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
- (2016) Alexandra Moura et al. Nature Microbiology
- dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
- (2015) Tal Galili BIOINFORMATICS
- PFGE Standard Operating Procedures forListeria monocytogenes: Harmonizing the Typing of Food and Clinical Strains in Europe
- (2015) Damien Michelon et al. Foodborne Pathogens and Disease
- Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes
- (2015) Werner Ruppitsch et al. JOURNAL OF CLINICAL MICROBIOLOGY
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
- (2015) Xavier Didelot et al. PLoS Computational Biology
- An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food
- (2015) Jodi Woan-Fei Law et al. Frontiers in Microbiology
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA
- (2014) D. Weller et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Listeria monocytogenes Persistence in Food-Associated Environments: Epidemiology, Strain Characteristics, and Implications for Public Health
- (2014) V. FERREIRA et al. JOURNAL OF FOOD PROTECTION
- The global burden of listeriosis: a systematic review and meta-analysis
- (2014) Charline Maertens de Noordhout et al. LANCET INFECTIOUS DISEASES
- Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads
- (2014) Frederic Bertels et al. MOLECULAR BIOLOGY AND EVOLUTION
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
- (2014) Nicholas J. Croucher et al. NUCLEIC ACIDS RESEARCH
- Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
- (2014) Pimlapas Leekitcharoenphon et al. PLoS One
- Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses
- (2014) Arthur W. Pightling et al. PLoS One
- Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
- (2014) Rolf S. Kaas et al. PLoS One
- Comparison of Widely Used Listeria monocytogenes Strains EGD, 10403S, and EGD-e Highlights Genomic Differences Underlying Variations in Pathogenicity
- (2014) C. Becavin et al. mBio
- Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not
- (2014) Jessica Hedge et al. mBio
- A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
- (2014) Francesc Coll et al. Nature Communications
- Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf
- (2013) Gabriel Cardona et al. BMC BIOINFORMATICS
- “Epidemic Clones” of Listeria monocytogenes Are Widespread and Ancient Clonal Groups
- (2013) Thomas Cantinelli et al. JOURNAL OF CLINICAL MICROBIOLOGY
- MLST revisited: the gene-by-gene approach to bacterial genomics
- (2013) Martin C. J. Maiden et al. NATURE REVIEWS MICROBIOLOGY
- snpTree - a web-server to identify and construct SNP trees from whole genome sequence data
- (2012) Pimlapas Leekitcharoenphon et al. BMC GENOMICS
- Genomic variation in Salmonella enterica core genes for epidemiological typing
- (2012) Pimlapas Leekitcharoenphon et al. BMC GENOMICS
- Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
- (2012) Rolf S Kaas et al. BMC GENOMICS
- BIGSdb: Scalable analysis of bacterial genome variation at the population level
- (2011) Keith A Jolley et al. BMC BIOINFORMATICS
- Revival of Seeliger's historical ‘Special Listeria Culture Collection’
- (2011) Jana K. Haase et al. ENVIRONMENTAL MICROBIOLOGY
- Review — Persistence of Listeria monocytogenes in food industry equipment and premises
- (2011) Brigitte Carpentier et al. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
- The Salmonella enterica Pan-genome
- (2011) Annika Jacobsen et al. MICROBIAL ECOLOGY
- Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera
- (2011) Oksana Lukjancenko et al. MICROBIAL ECOLOGY
- phytools: an R package for phylogenetic comparative biology (and other things)
- (2011) Liam J. Revell Methods in Ecology and Evolution
- phangorn: phylogenetic analysis in R
- (2010) Klaus Peter Schliep BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
- (2010) Xiangyu Deng et al. BMC GENOMICS
- Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics
- (2010) Renato H. Orsi et al. INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY
- Comparison of 61 Sequenced Escherichia coli Genomes
- (2010) Oksana Lukjancenko et al. MICROBIAL ECOLOGY
- Genomic Characterization of Campylobacter jejuni Strain M1
- (2010) Carsten Friis et al. PLoS One
- Standard operating procedure for computing pangenome trees
- (2010) Lars Snipen et al. Standards in Genomic Sciences
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- On the Origins of a Vibrio Species
- (2009) Tammi Vesth et al. MICROBIAL ECOLOGY
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- A New Perspective on Listeria monocytogenes Evolution
- (2008) Marie Ragon et al. PLoS Pathogens
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