Julian Parkhill

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BamView: viewing mapped read alignment data in the context of the reference sequence

Matthew Berriman, Thomas D. Otto, Tim J. Carver, 2010, Bioinform..

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

Nigel J. Martin, Francesc Coll, Stephen D. Bentley, 2012, Bioinform..

DNAPlotter: circular and linear interactive genome visualization

Matthew Berriman, Tim J. Carver, Julian Parkhill, 2008, Bioinform..

Artemis: sequence visualization and annotation

Kim Rutherford, Peter Rice, Julian Parkhill, 2000, Bioinform..

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

Andrew J. Page, Lars Barquist, Julian Parkhill, 2016, Bioinform..

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

Martin C. J. Maiden, Keith A. Jolley, James E. Bray, 2014, PLoS Comput. Biol..

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

Georgios S. Vernikos, Julian Parkhill, J. Parkhill, 2006, Bioinform..

BamView: visualizing and interpretation of next-generation sequencing read alignments

Matthew Berriman, Thomas D. Otto, Tim J. Carver, 2012, Briefings Bioinform..

GeneDB—an annotation database for pathogens

Haiming Wang, Andrew Jackson, Brian P. Brunk, 2011, Nucleic Acids Res..

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page, Daniel Falush, Julian Parkhill, 2015, bioRxiv.

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

Matthew Berriman, Tim J. Carver, Julian Parkhill, 2011, Bioinform..

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

Heng Li, Julian Parkhill, Kathryn E. Holt, 2009, Bioinform..

ACT: the Artemis comparison tool

Matthew Berriman, Kim Rutherford, Tim J. Carver, 2005, Bioinform..

GeneDB: a resource for prokaryotic and eukaryotic organisms

Matthew Berriman, Neil Hall, Kim Rutherford, 2004, Nucleic Acids Res..

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Julian Parkhill, Michelle Kendall, Caroline Colijn, 2018, Wellcome open research.

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

Matthew Berriman, Tim J. Carver, Ulrike Böhme, 2008, Bioinform..

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Julian Parkhill, Simon R. Harris, Martin Hunt, 2016, bioRxiv.

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology

Julian Parkhill, Martin Hunt, Kim Judge, 2016, bioRxiv.

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease

Julian Parkhill, Alan W Walker, Miles Parkes, 2018, Inflammatory bowel diseases.

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

Julian Parkhill, Stephen D Bentley, Rodney Dawson, 2013, The Lancet. Respiratory medicine.

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

Julian Parkhill, Nicholas J Croucher, Stephen D Bentley, 2012, The New England journal of medicine.

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus

Julian Parkhill, Andrew Rambaut, Edward J Feil, 2012, Proceedings of the National Academy of Sciences.

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.

Kim Rutherford, Julian Parkhill, Ben Crossett, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Jukka Corander, Paul Turner, 2016, bioRxiv.

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Julian Parkhill, Keith A Jolley, J. Parkhill, 2014, BMC Genomics.

Strains: Insights into the Pneumococcal Supragenome

Julian Parkhill, Garth D. Ehrlich, Justin S. Hogg, 2007 .

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?

Daniel Falush, Julian Parkhill, Xavier Didelot, 2006, Genome research.

Reagent contamination can critically impact sequence-based microbiome analyses

Paul Turner, Julian Parkhill, Nicholas J. Loman, 2014, bioRxiv.

Microevolution of extensively drug-resistant tuberculosis in Russia.

Stephen D. Bentley, Julian Parkhill, Simon R. Harris, 2012, Genome research.

Genomic information infrastructure after the deluge

Ewan Birney, Julian Parkhill, Paul Kersey, 2010, Genome Biology.

Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

Julian Parkhill, Peter Gilligan, R. Andres Floto, 2015, Journal of Clinical Microbiology.

Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis

Johannes Trück, Julian Parkhill, Gerton Lunter, 2015, The Journal of Immunology.

Evidence for several waves of global transmission in the seventh cholera pandemic

Julian Parkhill, Nicholas J. Croucher, Simon R. Harris, 2011, Nature.

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Mihai Pop, Julian Parkhill, Hector Corrada Bravo, 2014, Genome Biology.

Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination

Anna E. Sheppard, Julian Parkhill, David M. Aanensen, 2019, bioRxiv.

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

Daniel J. Wilson, Julian Parkhill, A Sarah Walker, 2013, The Lancet. Infectious diseases.

Recognizing the reagent microbiome

Julian Parkhill, Josef Wagner, Sharon J. Peacock, 2018, Nature Microbiology.

Complete Genome Sequence of Uropathogenic Proteus mirabilis, a Master of both Adherence and Motility

Nicholas M. Luscombe, Julian Parkhill, Michael A. Quail, 2008, Journal of bacteriology.

Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens

Julian Parkhill, Andrew Barron, Matthew Mayho, 2009, BMC Genomics.

Identification, variation and transcription of pneumococcal repeat sequences

Georgios S. Vernikos, Julian Parkhill, Nicholas J Croucher, 2011, BMC Genomics.

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

Julian Parkhill, Bart Barrell, Paul Davis, 2006, Nature Genetics.

Microbial genome-wide association studies: lessons from human GWAS

Tulio de Oliveira, Julian Parkhill, J. Parkhill, 2016, Nature Reviews Genetics.

Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

Raphael Lamed, Edward A. Bayer, Julian Parkhill, 2013, PloS one.

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

Keith A. Jolley, Daniel Falush, Stephen D. Bentley, 2013, Proceedings of the National Academy of Sciences.

The complete genome sequence of Mycobacterium bovis

Julian Parkhill, Stewart T. Cole, Paul R. Wheeler, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens

Julian Parkhill, Sharon J. Peacock, J. Parkhill, 2018, Microbiology.

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

Julian Parkhill, Gemma G. R. Murray, Sharon J Peacock, 2015, Nature Communications.

Microbial Genome-Wide Association Studies: Lessons from Human GWAS

Julian Parkhill, Tulio de Oliveira, Robert A. Power, 2016 .

Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

Keith A. Jolley, Stephen D. Bentley, Julian Parkhill, 2013, Journal of Clinical Microbiology.

The extant World War 1 dysentery bacillus NCTC1: a genomic analysis

Julian Parkhill, Julie E Russell, Gemma C. Langridge, 2014, The Lancet.

Rapid Whole-Genome Sequencing for Investigation of a Suspected Tuberculosis Outbreak

Stephen D. Bentley, Julian Parkhill, Sandra Reuter, 2012, Journal of Clinical Microbiology.

Microevolution and history of the plague bacillus, Yersinia pestis.

Giovanna Morelli, Julian Parkhill, Paul Keim, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Resolution of a Meningococcal Disease Outbreak from Whole-Genome Sequence Data with Rapid Web-Based Analysis Methods

Keith A. Jolley, Julian Parkhill, J. Parkhill, 2012, Journal of Clinical Microbiology.

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

Eduardo P C Rocha, Adam Baldwin, Julian Parkhill, 2008, Journal of bacteriology.

Whole genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

Julian Parkhill, Rosanna W. Peeling, Simon R. Harris, 2012, Nature Genetics.

Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community

Julian Parkhill, Sharon J Peacock, F. Lowy, 2014, Proceedings of the National Academy of Sciences.

Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus

Julian Parkhill, Stephen D Bentley, Simon R Harris, 2015, BMC Genomics.

Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

Julian Parkhill, Danesh Moradigaravand, Sharon J. Peacock, 2017, Genome Medicine.

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

Jukka Corander, Julian Parkhill, Marco Galardini, 2020, mBio.

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

Julian Parkhill, Stephen D Bentley, Sharon J Peacock, 2011, The Lancet. Infectious diseases.

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

Julian Parkhill, Pham Van Minh, D. W. Kim, 2013, Proceedings of the National Academy of Sciences.

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Alex Bateman, Paul P. Gardner, Lars Barquist, 2013, Nucleic acids research.

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

Julian Parkhill, Magnus Unemo, Paul Scott, 2013, Genome research.

Parallel independent evolution of pathogenicity within the genus Yersinia

Jukka Corander, Lars Barquist, Julian Parkhill, 2014, Proceedings of the National Academy of Sciences.

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks

Stephen D. Bentley, Julian Parkhill, David M. Aanensen, 2016, mBio.

Evolution and transmission of drug resistant tuberculosis in a Russian population

Jukka Corander, Julian Parkhill, Sergey Nejentsev, 2014, Nature Genetics.

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

Kim Rutherford, Anders Krogh, Stephen D. Bentley, 2001, Nature.

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Georgios S. Vernikos, Julian Parkhill, Konstantinos Mavromatis, 2009, Genome Biology.

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

Julian Parkhill, Brian White, Gemma C. Langridge, 2009, BMC Genomics.

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

Phelim Bradley, Zamin Iqbal, Daniel J. Wilson, 2015, The Lancet. Infectious diseases.

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

Julian Parkhill, Simon R. Harris, Kim Judge, 2015, The Journal of antimicrobial chemotherapy.

Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

Julian Parkhill, Stephen D Bentley, J. Parkhill, 2007, BMC Genomics.

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

Jukka Corander, Julian Parkhill, Nicholas J. Croucher, 2019, mBio.

A High-Resolution View of Genome-Wide Pneumococcal Transformation

Lars Barquist, Stephen D. Bentley, Julian Parkhill, 2012, PLoS pathogens.

The importance of complete genome sequences.

Julian Parkhill, 2002, Trends in microbiology.

Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study

Julian Parkhill, Timothy Brown, Agnieszka Broda, 2016, PLoS medicine.

A Novel Linear Plasmid Mediates Flagellar Variation in Salmonella Typhi

Julian Parkhill, Michael Quail, Robert A Kingsley, 2007, PLoS pathogens.

Bacterial epidemiology and biology - lessons from genome sequencing

Julian Parkhill, J. Parkhill, B. Wren, 2011, Genome Biology.

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

Julian Parkhill, Michael A Quail, Stephen D Bentley, 2013, The Lancet. Infectious Diseases.

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants.

Leopold Parts, Julian Parkhill, Gemma C. Langridge, 2009, Genome research.

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

Keith Dobney, Julian Parkhill, Grant Townsend, 2013, Nature Genetics.

Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370.

Julian Parkhill, Frank Desiere, J. Parkhill, 2002, Virology.

Towards richer descriptions of our collection of genomes andmetagenomes

Robert Stevens, Victor Markowitz, James R. Cole, 2006 .

Resolving the structural features of genomic islands: a machine learning approach.

Georgios S. Vernikos, Julian Parkhill, J. Parkhill, 2008, Genome research.

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

Julian Parkhill, Simon R. Harris, Martin Aslett, 2016, Journal of Clinical Microbiology.

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks

Julian Parkhill, Michael A Quail, Sharon J Peacock, 2013 .

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

Julian Parkhill, Alan W Walker, Gordon Dougan, 2011, BMC Microbiology.

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

Rick Stevens, Folker Meyer, Victor Markowitz, 2014, PLoS biology.

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

Jukka Corander, Antti Honkela, Niko Välimäki, 2016, Nature Communications.

The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay

Julian Parkhill, Erik Hjerde, Michael A Quail, 2008, BMC Genomics.

A Shared Population of Epidemic Methicillin-Resistant Staphylococcus aureus 15 Circulates in Humans and Companion Animals

Julian Parkhill, Sharon J Peacock, John J Welch, 2014, mBio.

Dense genomic sampling identifies highways of pneumococcal recombination

Jukka Corander, David Goldblatt, Paul Turner, 2014, Nature Genetics.

The genome of the blood fluke Schistosoma mansoni

John P. Overington, Adhemar Zerlotini, Anna V. Protasio, 2009, Nature.

Genome Evolution and Plasticity of Serratia marcescens, an Important Multidrug-Resistant Nosocomial Pathogen

Julian Parkhill, Masahira Hattori, Ken Kurokawa, 2014, Genome biology and evolution.

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

Julian Parkhill, Vanya Gant, Zhemin Zhou, 2013, Genome research.

Genome plasticity of BCG and impact on vaccine efficacy

Julian Parkhill, Stewart T. Cole, Stephen V. Gordon, 2007, Proceedings of the National Academy of Sciences.

Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens

Keith A. Jolley, Stephen D. Bentley, Julian Parkhill, 2009, PLoS pathogens.

Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community

Francesc Coll, Julian Parkhill, Ewan M. Harrison, 2017, Science Translational Medicine.

The Citrobacter rodentium Genome Sequence Reveals Convergent Evolution with Human Pathogenic Escherichia coli

Julian Parkhill, Andrew Barron, Michael A. Quail, 2009, Journal of bacteriology.

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

Julian Parkhill, Michael A Quail, Edward J Feil, 2010, Science.

Selective and Genetic Constraints on Pneumococcal Serotype Switching

Stephen D. Bentley, Julian Parkhill, Nicholas J. Croucher, 2015, PLoS genetics.

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

Julian Parkhill, Marc Lipsitch, Yonatan H Grad, 2014, The Lancet. Infectious diseases.

Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes

Julian Parkhill, Paul Davis, Michael A. Quail, 2004, Journal of bacteriology.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Jukka Corander, Pekka Marttinen, Julian Parkhill, 2014, Molecular ecology.

Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes

Julian Parkhill, Bart Barrell, Michael A Quail, 2006, PLoS genetics.

Roary: Rapid large-scale prokaryote pan genome analysis

Julian Parkhill, Martin Hunt, Jacqueline A. Keane, 2015, bioRxiv.

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

David Goldblatt, Paul Turner, Julian Parkhill, 2017, bioRxiv.

Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

Julian Parkhill, Stephen D Bentley, Anita C Schürch, 2013, BMC Infectious Diseases.

A Comprehensive Survey of Single Nucleotide Polymorphisms (SNPs) across Mycobacterium bovis Strains and M. bovis BCG Vaccine Strains Refines the Genealogy and Defines a Minimal Set of SNPs That Separate Virulent M. bovis Strains and M. bovis BCG Strains

Julian Parkhill, Stewart T. Cole, Stephen V. Gordon, 2009, Infection and Immunity.

Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Julian Parkhill, Simon R. Harris, Martin Hunt, 2016, bioRxiv.

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

Taane G. Clark, Julian Parkhill, Roland Rad, 2012, PLoS pathogens.

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.

Georgios S. Vernikos, Julian Parkhill, Michael A Quail, 2008, Genome research.

A Very Early-Branching Staphylococcus aureus Lineage Lacking the Carotenoid Pigment Staphyloxanthin

Stephen D. Bentley, Julian Parkhill, Philip M. Giffard, 2011, Genome biology and evolution.

1 The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge,

Mark J. Pallen, Julian Parkhill, Roy R. Chaudhuri, 2010 .

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

Paul Turner, Julian Parkhill, Jacqueline A. Keane, 2015, Nature Genetics.

EPIGENETIC REGULATION OF CELLULAR MEMORY BY THE POLYCOMB AND TRITHORAX GROUP PROTEINS

Jo Handelsman, Julian Parkhill, David Haig, 2008 .

Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt

Stephen D. Bentley, Julian Parkhill, Simon R. Harris, 2017, Microbial genomics.

Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

Julian Parkhill, J. Parkhill, A. Walker, 2013, PloS one.

Genome‐wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

Keith A. Jolley, James E. Bray, Stephen D. Bentley, 2017, Environmental microbiology.

Single-cell genomics

Julian Parkhill, J. Parkhill, Alan Walker, 2008, Nature Reviews Microbiology.

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

Jukka Corander, Stephen D. Bentley, Julian Parkhill, 2016, mBio.

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

Omar Salim, Julian Parkhill, Andrew Barron, 2009, BMC Genomics.

Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

Stephen D. Bentley, Julian Parkhill, Nicholas J. Croucher, 2017, Microbial genomics.

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

Julian Parkhill, Marc Lipsitch, Nicholas J Croucher, 2015, Scientific Data.

Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland

Julian Parkhill, Christine J. Boinett, Danesh Moradigaravand, 2016, Genome research.

Genomic history of the seventh pandemic of cholera in Africa

Julian Parkhill, Roland Grunow, Christiane Bouchier, 2017, Science.

Complete Genome of Acute Rheumatic Fever-Associated Serotype M5 Streptococcus pyogenes Strain Manfredo

Julian Parkhill, Michael A. Quail, Ann Cronin, 2006, Journal of bacteriology.

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

Jukka Corander, Julian Parkhill, Sharon J Peacock, 2017, Genome research.

Genome-wide epistasis and co-selection study using mutual information

Jukka Corander, Johan Pensar, Julian Parkhill, 2019 .

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.

Julian Parkhill, Michael A Quail, Alexandra Bignell, 2008, Genome research.

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

Karen P. Scott, Julian Parkhill, Paul Scott, 2015, Microbiome.

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis

Stephen D. Bentley, Julian Parkhill, Andrew Barron, 2010, Microbiology.

The Burkholderia cepacia Epidemic Strain Marker Is Part of a Novel Genomic Island Encoding Both Virulence and Metabolism-Associated Genes in Burkholderia cenocepacia

Adam Baldwin, Julian Parkhill, Eshwar Mahenthiralingam, 2004, Infection and Immunity.

Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion

Julian Parkhill, Thomas R Connor, Stephen D Bentley, 2014, mBio.

Microbiology in the post-genomic era

Julian Parkhill, Claudio Donati, David A. Relman, 2008, Nature Reviews Microbiology.

Armed to the teeth.

Julian Parkhill, J. Parkhill, N. Thomson, 2002, Trends in microbiology.

Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome

Evan Powell, Stephen D. Bentley, Julian Parkhill, 2007, Journal of bacteriology.

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.

Julian Parkhill, Torsten Seemann, Brian White, 2008, Genome research.

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Paul Turner, Julian Parkhill, Nicholas J Loman, 2014, BMC Biology.

Brothers in arms

Julian Parkhill, J. Parkhill, N. Thomson, 2005, Nature Reviews Microbiology.

Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals

Julian Parkhill, Gemma C. Langridge, Roy R. Chaudhuri, 2013, PLoS genetics.

Characterisation and distribution of a cryptic Salmonella typhi plasmid pHCM2.

Julian Parkhill, Gordon Dougan, Jeremy Farrar, 2002, Plasmid.

Yersinia pestis pFra Shows Biovar-Specific Differences and Recent Common Ancestry with aSalmonella enterica Serovar Typhi Plasmid

Julian Parkhill, Richard W. Titball, Karen L. Mungall, 2001, Journal of bacteriology.

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Julian Parkhill, Martin Hunt, Leonor Sánchez-Busó, 2017, bioRxiv.

Complete Genome Sequence and Lytic Phase Transcription Profile of a Coccolithovirus

Julian Parkhill, Peter Ghazal, Michael A Quail, 2005, Science.

The Flag-2 Locus, an Ancestral Gene Cluster, Is Potentially Associated with a Novel Flagellar System from Escherichia coli

Mark J. Pallen, Julian Parkhill, Scott A. Beatson, 2005, Journal of bacteriology.