Lista de obras - Kat Holt - Dominio Público Uruguay

A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.

artículo científico publicado en 2013

A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo

artículo científico publicado en 2011

A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters

artículo científico publicado en 2012

A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate

artículo científico publicado en 2014

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

artículo científico publicado en 2021

A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

artículo científico publicado en 2007

A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.

artículo científico publicado en 2010

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307

artículo científico publicado en 2022

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

artículo científico publicado en 2016

A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji

artículo científico publicado en 2017

A platform for leveraging next generation sequencing for routine microbiology and public health use.

artículo científico publicado en 2015

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant

artículo científico publicado en 2015

A type 2 A/C2 plasmid carrying the aacC4 apramycin resistance gene and the erm(42) erythromycin resistance gene recovered from two Salmonella enterica serovars.

artículo científico publicado en 2014

Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus

artículo científico publicado en 2014

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

artículo científico publicado en 2016

An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution

artículo científico publicado en 2014

Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons

artículo científico publicado en 2014

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

artículo científico publicado en 2018

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

artículo científico publicado en 2016

Bandage: interactive visualization of de novo genome assemblies

artículo científico publicado en 2015

Beginner's guide to comparative bacterial genome analysis using next-generation sequence data

artículo científico publicado en 2013

Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study

artículo científico publicado en 2021

Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.

artículo científico publicado en 2014

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

artículo científico publicado en 2013

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii

artículo científico publicado en 2019

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia

article

Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission

artículo científico publicado en 2011

Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City

scientific article published on 01 March 2019

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

artículo científico publicado en 2016

Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece

scientific article published on 10 October 2019

Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage

article

Completing bacterial genome assemblies with multiplex MinION sequencing.

artículo científico publicado en 2017

Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus.

artículo científico publicado en 2015

Cord blood hemopoietic progenitor profiles predict acute respiratory symptoms in infancy

artículo científico publicado en 2008

Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1

artículo científico publicado en 2019

Cross-validation to select Bayesian hierarchical models in phylogenetics

artículo científico publicado en 2016

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

artículo científico publicado en 2018

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

artículo científico publicado en 2011

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

artículo científico publicado en 2009

Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.

artículo científico publicado en 2016

Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

scientific article published on 23 October 2019

Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China

artículo científico publicado en 2022

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

scientific article published on 06 April 2020

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

article

Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.

artículo científico publicado en 2015

Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants ⬇️

artículo científico publicado el 27 de junio de 2013

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

article

Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy

artículo científico publicado en 2014

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

artículo científico publicado en 2019

Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid

artículo científico publicado en 2011

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

scientific article published on 29 May 2019

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

artículo científico publicado en 2009

Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

artículo científico publicado en 2013

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1

article

Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants

artículo científico publicado en 2016

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

artículo científico publicado en 2018

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

artículo científico publicado en 2017

Evolutionary dynamics of Clostridium difficile over short and long time scales

artículo científico publicado en 2010

Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.

artículo científico publicado en 2015

FastSpar: rapid and scalable correlation estimation for compositional data

artículo científico publicado en 2019

Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.

artículo científico publicado en 2016

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

article

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

artículo científico publicado en 2017

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

scientific article published on 09 July 2018

Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.

artículo científico publicado en 2015

Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1

artículo científico publicado en 2015

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

artículo científico publicado en 2013

Genome-scale rates of evolutionary change in bacteria.

artículo científico publicado en 2016

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

artículo científico publicado en 2015

Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

artículo científico publicado en 2022

Genomic history of the seventh pandemic of cholera in Africa.

artículo científico publicado en 2017

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

artículo científico publicado en 2018

Genomic insights to control the emergence of vancomycin-resistant enterococci

artículo científico publicado en 2013

Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate

artículo científico publicado en 2015

Global expansion of lineage 4 shaped by colonial migration and local adaptation

article

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

scientific article published on 20 May 2019

Global phylogeny of Shigella sonnei strains from limited single nucleotide polymorphisms (SNPs) and development of a rapid and cost-effective SNP-typing scheme for strain identification by high-resolution melting analysis.

artículo científico publicado en 2012

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

artículo científico publicado en 2016

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

artículo científico publicado en 2021

High-resolution genotyping of the endemic Salmonella Typhi population during a Vi (typhoid) vaccination trial in Kolkata.

artículo científico publicado en 2012

High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children

artículo científico publicado en 2010

High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia

artículo científico publicado en 2008

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

artículo científico publicado en 2008

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

artículo científico publicado en 2015

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

artículo científico publicado en 2020

Identification of Klebsiella capsule synthesis loci from whole genome data

artículo científico publicado en 2016

Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification

artículo científico publicado en 2013

Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii

artículo científico publicado en 2013

Identifying adaptive differences could provide insight.

artículo científico publicado en 2009

Impact of insertion sequences on convergent evolution of Shigella species

scientific article published on 09 July 2020

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.

artículo científico publicado en 2016

Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate

artículo científico publicado en 2016

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

artículo científico publicado en 2018

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

scientific article published on 12 September 2019

Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides

artículo científico publicado en 2014

Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2

artículo científico publicado en 2019

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan

scientific article published on 24 December 2015

Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933.

artículo científico publicado en 2012

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.

artículo científico publicado en 2018

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones

artículo científico publicado en 2016

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

artículo científico publicado en 2018

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

artículo científico publicado en 2018

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

artículo científico publicado en 2021

Microbial mercury methylation in Antarctic sea ice.

artículo científico publicado en 2016

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants

artículo científico publicado en 2006

Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa

artículo científico publicado en 2016

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

artículo científico publicado en 2018

Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.

artículo científico publicado en 2015

Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.

artículo científico publicado en 2007

Multidrug-resistant Shigella sonnei carrying plasmid-mediated mcr-1 gene in China

artículo científico publicado en 2018

Multiple Genetic Mutations Associated with Polymyxin Resistance in Acinetobacter baumannii

artículo científico publicado en 2015

Navigating the future of bacterial molecular epidemiology.

artículo científico publicado en 2010

Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk

artículo científico publicado en 2020

On the origin of mycobacterium ulcerans, the causative agent of buruli ulcer

artículo científico publicado en 2012

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

artículo científico publicado en 2011

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

artículo científico publicado en 2013

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

artículo científico publicado en 2015

Polypolish: Short-read polishing of long-read bacterial genome assemblies

artículo científico publicado en 2022

Population genomics of Klebsiella pneumoniae

artículo científico publicado en 2020

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

artículo científico publicado en 2018

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016

scientific article published on 27 February 2020

Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS.

artículo científico publicado en 2016

Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata

scientific article published on 17 August 2020

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

artículo científico publicado en 2009

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward

artículo científico publicado en 2016

Shigella sonnei

artículo científico publicado en 2020

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

artículo científico publicado en 2012

Short read sequence typing (SRST): multi-locus sequence types from short reads

artículo científico publicado en 2012

Small IncQ1 and Col-Like Plasmids Harboring bla KPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258

artículo científico publicado en 2019

South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study

artículo científico publicado en 2016

Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community

artículo científico publicado en 2022

Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam

artículo científico publicado en 2011

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia

artículo científico publicado en 2016

The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys

artículo científico publicado en 2017

The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu

artículo científico publicado en 2010

The complete sequence of Salmonella genomic island SGI1-K.

artículo científico publicado en 2014

The complete sequence of Salmonella genomic island SGI2.

artículo científico publicado en 2014

The diversity of Klebsiella pneumoniae surface polysaccharides

scientific article published on 25 August 2016

The genomic signatures of Shigella evolution, adaptation and geographical spread

artículo científico publicado en 2016

The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development

artículo científico publicado en 2015

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

artículo científico publicado en 2018

The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens

artículo científico publicado en 2010

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

artículo científico publicado en 2018

Tracking the establishment of local endemic populations of an emergent enteric pathogen

artículo científico publicado en 2013

Trajectories of childhood immune development and respiratory health relevant to asthma and allergy

artículo científico publicado en 2018

Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia

artículo científico publicado en 2010

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

artículo científico publicado en 2017

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore

artículo científico publicado en 2017

Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever

artículo científico publicado en 2008

Vitamin D over the first decade and susceptibility to childhood allergy and asthma

artículo científico publicado en 2016

WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?

artículo científico publicado en 2014

Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program

artículo científico publicado en 2017

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus.

artículo científico publicado en 2019

pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron.

artículo científico publicado en 2016

wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations

artículo científico publicado en 2021

Lista de obras de Kat Holt

A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.

A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo

A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters

A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji

A platform for leveraging next generation sequencing for routine microbiology and public health use.

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant

A type 2 A/C2 plasmid carrying the aacC4 apramycin resistance gene and the erm(42) erythromycin resistance gene recovered from two Salmonella enterica serovars.

Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution

Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

Bandage: interactive visualization of de novo genome assemblies

Beginner's guide to comparative bacterial genome analysis using next-generation sequence data

Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study

Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia

Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission

Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece

Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage

Completing bacterial genome assemblies with multiplex MinION sequencing.

Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus.

Cord blood hemopoietic progenitor profiles predict acute respiratory symptoms in infancy

Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1

Cross-validation to select Bayesian hierarchical models in phylogenetics

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.

Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.

Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants ⬇️

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1

Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

Evolutionary dynamics of Clostridium difficile over short and long time scales

Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.

FastSpar: rapid and scalable correlation estimation for compositional data

Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.

Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

Genome-scale rates of evolutionary change in bacteria.

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

Genomic history of the seventh pandemic of cholera in Africa.

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

Genomic insights to control the emergence of vancomycin-resistant enterococci

Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate

Global expansion of lineage 4 shaped by colonial migration and local adaptation

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Global phylogeny of Shigella sonnei strains from limited single nucleotide polymorphisms (SNPs) and development of a rapid and cost-effective SNP-typing scheme for strain identification by high-resolution melting analysis.

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei