Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data
Authors
Keywords
-
Journal
Frontiers in Microbiology
Volume 11, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2020-08-18
DOI
10.3389/fmicb.2020.01925
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data
- (2020) Christine Anyansi et al. BMC GENOMICS
- Assembly of long, error-prone reads using repeat graphs
- (2019) Mikhail Kolmogorov et al. NATURE BIOTECHNOLOGY
- Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
- (2019) Vincent Somerville et al. BMC MICROBIOLOGY
- Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance
- (2019) Kimberley V. Sukhum et al. CLINICAL PHARMACOLOGY & THERAPEUTICS
- Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
- (2019) Denis Bertrand et al. NATURE BIOTECHNOLOGY
- Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
- (2019) Alexander T. Dilthey et al. Nature Communications
- GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
- (2019) Pierre-Alain Chaumeil et al. BIOINFORMATICS
- Comparison of normalization methods for the analysis of metagenomic gene abundance data
- (2018) Mariana Buongermino Pereira et al. BMC GENOMICS
- Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation
- (2018) Christopher S. Smillie et al. Cell Host & Microbe
- Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality
- (2018) John P. Dekker JOURNAL OF CLINICAL MICROBIOLOGY
- On the Road to Strain-Resolved Comparative Metagenomics
- (2018) Nicola Segata mSystems
- Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data
- (2018) Benjamin Sobkowiak et al. BMC GENOMICS
- Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
- (2018) Daniela S. Aliaga Goltsman et al. GENOME RESEARCH
- Strain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions
- (2018) Francesca De Filippis et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient
- (2018) Xin Fang et al. Frontiers in Microbiology
- Microbial strain-level population structure and genetic diversity from metagenomes
- (2017) Duy Tin Truong et al. GENOME RESEARCH
- Application of next generation sequencing in clinical microbiology and infection prevention
- (2017) Ruud H. Deurenberg et al. JOURNAL OF BIOTECHNOLOGY
- Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
- (2017) Antonina A. Votintseva et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Short Read Mapping: An Algorithmic Tour
- (2017) Stefan Canzar et al. PROCEEDINGS OF THE IEEE
- MetaSort untangles metagenome assembly by reducing microbial community complexity
- (2017) Peifeng Ji et al. Nature Communications
- Strain profiling and epidemiology of bacterial species from metagenomic sequencing
- (2017) Davide Albanese et al. Nature Communications
- Massively parallel digital transcriptional profiling of single cells
- (2017) Grace X. Y. Zheng et al. Nature Communications
- metaSNV: A tool for metagenomic strain level analysis
- (2017) Paul Igor Costea et al. PLoS One
- Clostridium butyricum : from beneficial to a new emerging pathogen
- (2016) N. Cassir et al. CLINICAL MICROBIOLOGY AND INFECTION
- An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
- (2016) Stephen Nayfach et al. GENOME RESEARCH
- Near-optimal probabilistic RNA-seq quantification
- (2016) Nicolas L Bray et al. NATURE BIOTECHNOLOGY
- Microbiology: the road to strain-level identification
- (2016) Vivien Marx NATURE METHODS
- Strain-level microbial epidemiology and population genomics from shotgun metagenomics
- (2016) Matthias Scholz et al. NATURE METHODS
- Targeted treatment for bacterial infections: prospects for pathogen-specific antibiotics coupled with rapid diagnostics
- (2016) Tucker Maxson et al. TETRAHEDRON
- Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing
- (2016) Yu-Chih Tsai et al. mBio
- Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants
- (2016) Doyle V. Ward et al. Cell Reports
- Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
- (2016) John D. O’Brien et al. PLoS Computational Biology
- Diversity of Saccharomyces cerevisiae Strains Isolated from Two Italian Wine-Producing Regions
- (2016) Angela Capece et al. Frontiers in Microbiology
- MetaPalette: a k -mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
- (2016) David Koslicki et al. mSystems
- Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis
- (2016) Mingyu Gan et al. PLoS One
- Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
- (2015) Evan Z. Macosko et al. CELL
- Antimicrobial Heteroresistance: an Emerging Field in Need of Clarity
- (2015) Omar M. El-Halfawy et al. CLINICAL MICROBIOLOGY REVIEWS
- Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection
- (2015) Giacomo Plazzotta et al. JOURNAL OF THEORETICAL BIOLOGY
- ConStrains identifies microbial strains in metagenomic datasets
- (2015) Chengwei Luo et al. NATURE BIOTECHNOLOGY
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
- (2015) Tracey Allen K. Freitas et al. NUCLEIC ACIDS RESEARCH
- Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations
- (2015) Sergio Pulido-Tamayo et al. NUCLEIC ACIDS RESEARCH
- Application of metagenomics in the human gut microbiome
- (2015) Wei-Lin Wang et al. WORLD JOURNAL OF GASTROENTEROLOGY
- Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data
- (2015) Jason W. Sahl et al. Genome Medicine
- estMOI: estimating multiplicity of infection using parasite deep sequencing data
- (2014) Samuel A. Assefa et al. BIOINFORMATICS
- Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
- (2014) Tae-Hyuk Ahn et al. BIOINFORMATICS
- Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data
- (2014) Allyson L Byrd et al. BMC BIOINFORMATICS
- Making sense of deep sequencing
- (2014) D. Goldman et al. INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY
- Strain/species identification in metagenomes using genome-specific markers
- (2014) Qichao Tu et al. NUCLEIC ACIDS RESEARCH
- Clinical detection and characterization of bacterial pathogens in the genomics era
- (2014) Pierre-Edouard Fournier et al. Genome Medicine
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples
- (2014) Changjin Hong et al. Microbiome
- Multiple infections and the evolution of virulence
- (2013) Samuel Alizon et al. ECOLOGY LETTERS
- Pathoscope: Species identification and strain attribution with unassembled sequencing data
- (2013) O. E. Francis et al. GENOME RESEARCH
- Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission
- (2013) David W. Eyre et al. PLoS Computational Biology
- Identifying differentially expressed transcripts from RNA-seq data with biological variation
- (2012) Peter Glaus et al. BIOINFORMATICS
- Metagenomic analysis: the challenge of the data bonanza
- (2012) C. I. Hunter et al. BRIEFINGS IN BIOINFORMATICS
- Classification of metagenomic sequences: methods and challenges
- (2012) S. S. Mande et al. BRIEFINGS IN BIOINFORMATICS
- Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
- (2012) H. Teeling et al. BRIEFINGS IN BIOINFORMATICS
- Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control
- (2012) T. Cohen et al. CLINICAL MICROBIOLOGY REVIEWS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- Grinder: a versatile amplicon and shotgun sequence simulator
- (2012) Florent E. Angly et al. NUCLEIC ACIDS RESEARCH
- Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome
- (2012) Sanqing Yuan et al. PLoS One
- ART: a next-generation sequencing read simulator
- (2011) Weichun Huang et al. BIOINFORMATICS
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
- (2011) H. Li BIOINFORMATICS
- ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
- (2011) Osvaldo Zagordi et al. BMC BIOINFORMATICS
- Clostridium difficile Mixed Infection and Reinfection: Fig 1
- (2011) David W. Eyre et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Systematic Survey of Clonal Complexity in Tuberculosis at a Populational Level and Detailed Characterization of the Isolates Involved
- (2011) Y. Navarro et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Prevalence and implications of multiple-strain infections
- (2011) Oliver Balmer et al. LANCET INFECTIOUS DISEASES
- TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
- (2011) Daehwan Kim et al. GENOME BIOLOGY
- A survey of sequence alignment algorithms for next-generation sequencing
- (2010) H. Li et al. BRIEFINGS IN BIOINFORMATICS
- Heteroresistance: a concern of increasing clinical significance?
- (2010) M.E. Falagas et al. CLINICAL MICROBIOLOGY AND INFECTION
- Mixed Infection with Beijing and Non-Beijing Strains and Drug Resistance Pattern ofMycobacterium tuberculosis
- (2010) Han-Yu Huang et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
- (2010) Jenna L. Morgan et al. PLoS One
- The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
- (2009) Nathan L. Clement et al. BIOINFORMATICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started