Julian Parkhill

Research interests

Publications

• Producing polished prokaryotic pangenomes with the Panaroo pipeline

  Genome biology · 2020 · https://doi.org/10.1186/s13059-020-02090-4

• Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium

  Science · 2016 · 10.1126/science.aaf8156

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

  The Lancet Infectious Diseases · 2015 · https://doi.org/10.1016/s1473-3099(15)00062-6

• Roary: rapid large-scale prokaryote pan genome analysis

  Bioinformatics · 2015 · https://doi.org/10.1093/bioinformatics/btv421

• Circlator: automated circularization of genome assemblies using long sequencing reads

  Genome biology · 2015 · 10.1186/s13059-015-0849-0

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

  Nature Genetics · 2015 · https://doi.org/10.1038/ng.3281

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

  BMC Biology · 2014 · https://doi.org/10.1186/s12915-014-0087-z

• Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

  Nucleic Acids Research · 2014 · 10.1093/nar/gku1196

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

  Nature Genetics · 2013 · 10.1038/ng.2744

• Richness of human gut microbiome correlates with metabolic markers

  Nature · 2013 · https://doi.org/10.1038/nature12506

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

  The Lancet Infectious Diseases · 2012 · 10.1016/s1473-3099(12)70277-3

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

  Bioinformatics · 2011 · 10.1093/bioinformatics/btr703

• Evolution of MRSA During Hospital Transmission and Intercontinental Spread

  Science · 2010 · 10.1126/science.1182395

• Dominant and diet-responsive groups of bacteria within the human colonic microbiota

  The ISME Journal · 2010 · 10.1038/ismej.2010.118

• A human gut microbial gene catalogue established by metagenomic sequencing

  Nature · 2010 · https://doi.org/10.1038/nature08821

• The genome of the blood fluke Schistosoma mansoni

  Nature · 2009 · 10.1038/nature08160

• The minimum information about a genome sequence (MIGS) specification

  Nature Biotechnology · 2008 · 10.1038/nbt1360

• Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota

  PLoS Biology · 2007 · 10.1371/journal.pbio.0050244

• ACT: the Artemis comparison tool

  Computer applications in the biosciences · 2005 · 10.1093/bioinformatics/bti553

• The complete genome sequence of Mycobacterium bovis

  Proceedings of the National Academy of Sciences · 2003 · 10.1073/pnas.1130426100

• Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

  Nature Genetics · 2003 · 10.1038/ng1227

• Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

  Nature · 2002 · 10.1038/417141a

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

  Nature · 2001 · 10.1038/35101607

• Massive gene decay in the leprosy bacillus

  Nature · 2001 · 10.1038/35059006

• Genome sequence of Yersinia pestis, the causative agent of plague

  Nature · 2001 · 10.1038/35097083

• The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

  Nature · 2000 · 10.1038/35001088

• Artemis: sequence visualization and annotation

  Bioinformatics · 2000 · 10.1093/bioinformatics/16.10.944

• Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

  Nature · 1998 · https://doi.org/10.1038/31159

Current projects

No projects listed.