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High-throughput sequencing for the study of bacterial pathogen biology
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1001/jama.2013.3231openalex-snapshot
A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
inferredcites →https://doi.org/10.1002/emmm.201202413openalex-snapshot
Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC
inferredcites →https://doi.org/10.1016/j.chom.2009.08.003openalex-snapshot
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
inferredcites →https://doi.org/10.1016/j.jhin.2010.01.012openalex-snapshot
High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak
inferredcites →https://doi.org/10.1016/j.mib.2010.09.009openalex-snapshot
Studying bacterial transcriptomes using RNA-seq
inferredcites →https://doi.org/10.1016/j.mib.2011.07.023openalex-snapshot
Progress in prokaryotic transcriptomics
inferredcites →https://doi.org/10.1016/j.tim.2006.06.003openalex-snapshot
Genome-wide association mapping in bacteria?
inferredcites →https://doi.org/10.1016/j.ymed.2012.08.011openalex-snapshot
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
inferredcites →https://doi.org/10.1016/s0140-6736(13)60632-7openalex-snapshot
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study
inferredcites →https://doi.org/10.1016/s1473-3099(12)70268-2openalex-snapshot
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
inferredcites →https://doi.org/10.1038/nature10392openalex-snapshot
Evidence for several waves of global transmission in the seventh cholera pandemic
inferredcites →https://doi.org/10.1038/nature12212openalex-snapshot
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
inferredcites →https://doi.org/10.1038/nbt.2198openalex-snapshot
Performance comparison of benchtop high-throughput sequencing platforms
inferredcites →https://doi.org/10.1038/ng.1072openalex-snapshot
Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event
inferredcites →https://doi.org/10.1038/ng.2369openalex-snapshot
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
inferredcites →https://doi.org/10.1038/ng.2423openalex-snapshot
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa
inferredcites →https://doi.org/10.1038/ng.2625openalex-snapshot
Population genomics of post-vaccine changes in pneumococcal epidemiology
inferredcites →https://doi.org/10.1038/ng.2848openalex-snapshot
Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
inferredcites →https://doi.org/10.1038/ng.811openalex-snapshot
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
inferredcites →https://doi.org/10.1038/ng.997openalex-snapshot
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
inferredcites →https://doi.org/10.1038/nmeth.1377openalex-snapshot
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
inferredcites →https://doi.org/10.1038/nrmicro2850openalex-snapshot
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity
inferredcites →https://doi.org/10.1038/nrmicro2852openalex-snapshot
Dual RNA-seq of pathogen and host
inferredcites →https://doi.org/10.1038/nrmicro2880openalex-snapshot
From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence?
inferredcites →https://doi.org/10.1038/nrmicro3033openalex-snapshot
Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms
inferredcites →https://doi.org/10.1056/nejmoa1003176openalex-snapshot
Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak
inferredcites →https://doi.org/10.1056/nejmoa1106483openalex-snapshot
Epidemic Profile of Shiga-Toxin–ProducingEscherichia coliO104:H4 Outbreak in Germany
inferredcites →https://doi.org/10.1056/nejmoa1106920openalex-snapshot
Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany
inferredcites →https://doi.org/10.1056/nejmoa1107643openalex-snapshot
Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4
inferredcites →https://doi.org/10.1056/nejmoa1109910openalex-snapshot
Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak
inferredcites →https://doi.org/10.1073/pnas.0609839104openalex-snapshot
Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing
inferredcites →https://doi.org/10.1073/pnas.0906627106openalex-snapshot
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
inferredcites →https://doi.org/10.1073/pnas.0909285106openalex-snapshot
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus
inferredcites →https://doi.org/10.1073/pnas.1000087107openalex-snapshot
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
inferredcites →https://doi.org/10.1073/pnas.1113219109openalex-snapshot
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
inferredcites →https://doi.org/10.1073/pnas.1202869109openalex-snapshot
Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus
inferredcites →https://doi.org/10.1073/pnas.1305559110openalex-snapshot
Genome-wide association study identifies vitamin B 5 biosynthesis as a host specificity factor in Campylobacter
inferredcites →https://doi.org/10.1073/pnas.1308632110openalex-snapshot
Tracking the establishment of local endemic populations of an emergent enteric pathogen
inferredcites →https://doi.org/10.1073/pnas.1311217110openalex-snapshot
Genome-wide fitness profiling reveals adaptations required by Haemophilus in coinfection with influenza A virus in the murine lung
inferredcites →https://doi.org/10.1093/jac/dkr315openalex-snapshot
Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota
inferredcites →https://doi.org/10.1093/molbev/msq319openalex-snapshot
Testing Spatiotemporal Hypothesis of Bacterial Evolution Using Methicillin-Resistant Staphylococcus aureus ST239 Genome-wide Data within a Bayesian Framework
inferredcites →https://doi.org/10.1093/nar/gkt148openalex-snapshot
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
inferredcites →https://doi.org/10.1098/rsob.110008openalex-snapshot
Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission
inferredcites →https://doi.org/10.1101/gr.097097.109openalex-snapshot
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
inferredcites →https://doi.org/10.1101/gr.137430.112openalex-snapshot
A fine scale phenotype–genotype virulence map of a bacterial pathogen
inferredcites →https://doi.org/10.1101/gr.147710.112openalex-snapshot
A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic
inferredcites →https://doi.org/10.1101/gr.150037.112openalex-snapshot
Whole-genome sequences ofChlamydia trachomatisdirectly from clinical samples without culture
inferredcites →https://doi.org/10.1101/gr.165415.113openalex-snapshot
Predicting the virulence of MRSA from its genome sequence
inferredcites →https://doi.org/10.1111/mmi.12111openalex-snapshot
ChIP ‐seq and transcriptome analysis of the OmpR regulon of S almonella enterica serovars T yphi and T yphimurium reveals accessory genes implicated in host colonization
inferredcites →https://doi.org/10.1111/mmi.12387openalex-snapshot
Identification and characterization of the genetic changes responsible for the characteristic smooth‐to‐rough morphotype alterations of clinically persistent M ycobacterium abscessus
inferredcites →https://doi.org/10.1126/science.1198545openalex-snapshot
Rapid Pneumococcal Evolution in Response to Clinical Interventions
inferredcites →https://doi.org/10.1126/science.1240578openalex-snapshot
Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts
inferredcites →https://doi.org/10.1126/scitranslmed.3004458openalex-snapshot
Quantitative Analysis of the Human Airway Microbial Ecology Reveals a Pervasive Signature for Cystic Fibrosis
inferredcites →https://doi.org/10.1128/jb.00875-13openalex-snapshot
Probing Bacterial Metabolism during Infection Using High-Resolution Transcriptomics
inferredcites →https://doi.org/10.1128/jb.01870-12openalex-snapshot
Nontypeable Haemophilus influenzae Carbonic Anhydrase Is Important for Environmental and Intracellular Survival
inferredcites →https://doi.org/10.1128/mbio.00157-11openalex-snapshot
Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak
inferredcites →https://doi.org/10.1128/mbio.00305-11openalex-snapshot
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
inferredcites →https://doi.org/10.1128/mbio.00356-13openalex-snapshot
Livestock Origin for a Human Pandemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus
inferredcites →https://doi.org/10.1128/mbio.00398-13openalex-snapshot
Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti
inferredcites →https://doi.org/10.1128/mbio.00534-13openalex-snapshot
Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains
inferredcites →https://doi.org/10.1128/mbio.00565-13openalex-snapshot
Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar
inferredcites →https://doi.org/10.1136/bmjopen-2012-001124openalex-snapshot
A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance
inferredcites →https://doi.org/10.1136/bmjopen-2012-002175openalex-snapshot
A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak
inferredcites →https://doi.org/10.1371/journal.pcbi.1003059openalex-snapshot
Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission
inferredcites →https://doi.org/10.1371/journal.pgen.1003456openalex-snapshot
Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals
inferredcites →https://doi.org/10.1371/journal.pone.0007370openalex-snapshot
Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals
inferredcites →https://doi.org/10.1371/journal.pone.0024301openalex-snapshot
Adaptive Evolution of Staphylococcus aureus during Chronic Endobronchial Infection of a Cystic Fibrosis Patient
inferredcites →https://doi.org/10.1371/journal.pone.0061319openalex-snapshot
Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage
inferredcites →https://doi.org/10.1371/journal.pone.0063237openalex-snapshot
Molecular Longitudinal Tracking of Mycobacterium abscessus spp. during Chronic Infection of the Human Lung
inferredcites →https://doi.org/10.1371/journal.pone.0065226openalex-snapshot
Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
inferredcites →https://doi.org/10.1371/journal.pone.0065466openalex-snapshot
Global Transcriptional and Phenotypic Analyses of Escherichia coli O157:H7 Strain Xuzhou21 and Its pO157_Sal Cured Mutant
inferredcites →https://doi.org/10.1371/journal.pone.0072193openalex-snapshot
Characterization of the Molecular Interplay between Moraxella catarrhalis and Human Respiratory Tract Epithelial Cells
inferredcites →https://doi.org/10.1371/journal.ppat.1001078openalex-snapshot
Host Imprints on Bacterial Genomes—Rapid, Divergent Evolution in Individual Patients
inferredcites →https://doi.org/10.1371/journal.ppat.1002359openalex-snapshot
Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR
inferredcites →https://doi.org/10.1371/journal.ppat.1002824openalex-snapshot
Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
inferredcites →https://doi.org/10.4161/rna.24765openalex-snapshot
Approaches to querying bacterial genomes with transposon-insertion sequencing
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1186/s13358-024-00324-7zenodo-depositor-declared
The effects of clays on bacterial community composition during arthropod decay
inferred← citeshttps://doi.org/10.1007/s12155-021-10290-4openalex-snapshot
Biomethanation of Napier Grass Mono-digestion in Single-Stage Anaerobic Completely Stirred Tank Reactors Seeded with Cow Manure and Anaerobic Sludge
inferred← citeshttps://doi.org/10.1016/b978-0-12-397188-3.00001-9openalex-snapshot
General Principles
inferred← citeshttps://doi.org/10.1016/b978-0-12-410530-0.00005-3openalex-snapshot
Genomics, Genetic Variation, and Regions of Differences
inferred← citeshttps://doi.org/10.1016/j.aca.2026.345963openalex-snapshot
Highly sensitive and precise SERS quantification of P. gingivalis in complex saliva matrices via AgNPs@4-MPBA substrates coupled with the NiPLS-AMLP algorithm
inferred← citeshttps://doi.org/10.1016/j.aquaculture.2022.738529openalex-snapshot
Effects of water temperature on the gut microbiome and physiology of Chinook salmon (Oncorhynchus tshawytscha) reared in a freshwater recirculating system
inferred← citeshttps://doi.org/10.1016/j.jhazmat.2025.139625openalex-snapshot
Rapid identification of metal resistance genes using an enhanced ResNet deep learning model trained on a largely expanded BacMet-based database
inferred← citeshttps://doi.org/10.1016/j.mib.2015.06.007openalex-snapshot
Experimental approaches to phenotypic diversity in infection
inferred← citeshttps://doi.org/10.1016/j.tim.2014.10.005openalex-snapshot
Diversity and disease pathogenesis in Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1016/j.ymeth.2017.04.016openalex-snapshot
Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics
inferred← citeshttps://doi.org/10.1021/acs.est.2c04943openalex-snapshot
Coexistence of Synechococcus and Microcystis Blooms in a Tropical Urban Reservoir and Their Links with Microbiomes
inferred← citeshttps://doi.org/10.1038/s41576-018-0032-zopenalex-snapshot
Population genomics of bacterial host adaptation
inferred← citeshttps://doi.org/10.1038/s41598-026-53668-0openalex-snapshot
Intestinal colonization of weaner pigs by extended-spectrum-β-lactamase-encoding Escherichia coli classified for differential host-association using a phylogenetics-based approach
inferred← citeshttps://doi.org/10.1073/pnas.1908858116openalex-snapshot
Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast
inferred← citeshttps://doi.org/10.1080/09593330.2020.1754924openalex-snapshot
Study of enhanced nitrogen removal efficiency and microbial characteristics of an improved two-stage A/O process
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab363openalex-snapshot
PaIntDB: network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.1099/mgen.0.000146openalex-snapshot
MentaLiST – A fast MLST caller for large MLST schemes
inferred← citeshttps://doi.org/10.1101/140194openalex-snapshot
The resistome of common human pathogens
inferred← citeshttps://doi.org/10.1101/2024.02.19.580992openalex-snapshot
The effects of clay minerals on bacterial community composition during arthropod decay
inferred← citeshttps://doi.org/10.1101/403824openalex-snapshot
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
inferred← citeshttps://doi.org/10.1111/jam.14903openalex-snapshot
Genomics informed design of a suite of real‐time PCR assays for the specific detection of each Xylella fastidiosa subspecies
inferred← citeshttps://doi.org/10.1111/tbed.12698openalex-snapshot
Knowledge gaps and research priorities inStaphylococcus aureusmastitis control
inferred← citeshttps://doi.org/10.1128/msystems.00378-22openalex-snapshot
Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches
inferred← citeshttps://doi.org/10.1146/annurev-genet-112414-054804openalex-snapshot
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies
inferred← citeshttps://doi.org/10.1186/s12864-015-1555-8openalex-snapshot
An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data
inferred← citeshttps://doi.org/10.1186/s12866-022-02743-3openalex-snapshot
Oropharyngeal, proximal colonic, and vaginal microbiomes of healthy Korean native black pig gilts
inferred← citeshttps://doi.org/10.1186/s12915-020-0748-zopenalex-snapshot
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
inferred← citeshttps://doi.org/10.1186/s13059-014-0514-zopenalex-snapshot
Translating genomics research into control of tuberculosis: lessons learned and future prospects
inferred← citeshttps://doi.org/10.1371/journal.pone.0128036openalex-snapshot
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
inferred← citeshttps://doi.org/10.1371/journal.pone.0176191openalex-snapshot
Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure
inferred← citeshttps://doi.org/10.3389/fbinf.2022.813599openalex-snapshot
Detecting Genetic Variation of Colonizing Streptococcus agalactiae Genomes in Humans: A Precision Protocol
inferred← citeshttps://doi.org/10.3389/fmicb.2015.01032openalex-snapshot
Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1267395openalex-snapshot
Characterization of Pseudomonas capsici strains from pepper and tomato
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1543610openalex-snapshot
Comparative genomics reveals key adaptive mechanisms in pathogen host-niche specialization
inferred← citeshttps://doi.org/10.3389/fpls.2022.855262openalex-snapshot
Editorial: Genome-Wide Analyses of Pectobacterium and Dickeya Species
inferred← citeshttps://doi.org/10.3390/jof4030108openalex-snapshot
Standardization of G. mellonella Larvae to Provide Reliable and Reproducible Results in the Study of Fungal Pathogens
inferred← citeshttps://doi.org/10.3390/life12111893openalex-snapshot
The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research
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Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium
inferred← citeshttps://doi.org/10.3390/w14111769openalex-snapshot
Monitoring Bacterial Community Dynamics in Abalone (Haliotis discus hannai) and the Correlations Associated with Aquatic Diseases
inferred← citeshttps://doi.org/10.3410/f.736556232.793564850openalex-snapshot
Faculty Opinions recommendation of Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast.
inferred← citeshttps://doi.org/10.3920/jiff2020.0135openalex-snapshot
Application of laboratory methods for understanding fish responses to black soldier fly (Hermetia illucens) based diets
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Molecular mechanisms of Methicillin-Resistant Staphylococcus Aureus (MRSA) pathogenesis and colonisation: community-versus hospital-acquired strains
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High-Throughput Screening for Drug Discovery toward Infectious Diseases: Options and Challenges
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High-Throughput Screening for Drug Discovery
inferred← citeshttps://doi.org/10.6084/m9.figshare.22615244openalex-snapshot
Additional file 6 of Oropharyngeal, proximal colonic, and vaginal microbiomes of healthy Korean native black pig gilts
inferred← citeshttps://doi.org/10.6084/m9.figshare.22615247openalex-snapshot
Additional file 7 of Oropharyngeal, proximal colonic, and vaginal microbiomes of healthy Korean native black pig gilts
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Analyse métabolomique de S. aureus par chromatographie liquide couplée à la spectrométrie de masse à haute résolution : Développements analytiques et applications à l’étude de la résistance à la méticilline
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Changes in the genetic requirements for microbial interactions with increasing community complexity
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