Julian Parkhill
- Producing polished prokaryotic pangenomes with the Panaroo pipeline
2020/07/22 by Gerry Tonkin‐Hill, Neil MacAlasdair, Christopher Ruis +11 · 58 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
2014/11/20 by Nicholas J. Croucher, Andrew J. Page, Thomas R. Connor +6 · 40 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #Plant Pathogenic Bacteria Studies #Probiotics and Fermented Foods
- Genomic Profiling Reveals Distinct Routes To Complement Resistance in Klebsiella pneumoniae
2020/06/03 by Francesca L. Short, Gianna Di Sario, Nathalie T. Reichmann +3 · 31 citations
Biochemistry, Genetics and Molecular Biology · #Antibiotic Resistance in Bacteria #Bacteria #Bacterial protein #Biology #Computational biology #Enterobacteriaceae and Cronobacter Research #Escherichia coli #Escherichia coli research studies #Gene #Genetics #Klebsiella #Klebsiella pneumoniae #Microbiology #Profiling (computer programming) #Virology
- Guidelines for preventing and reporting contamination in low-biomass microbiome studies
2025/06/20 by Noah Fierer, Pok Man Leung, Rachael Lappan +29 · 1 voice · 32 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Environmental Science · #Bioinformatics #Biology #Biomass (ecology) #Biotechnology #Chemistry #Contamination #Ecology #Environmental chemistry #Environmental science #Gut microbiota and health #Metagenomics #Microbial Community Ecology and Physiology #Microbiome #Molecular Biology Techniques and Applications
- High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
2008/07/20 by Kathryn E. Holt, Kathryn E Holt, Julian Parkhill +14 · 6 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #Salmonella and Campylobacter epidemiology
- Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
2003/08/08 by Julian Parkhill, Mohammed Sebaihia, Andrew Preston +69 · 2 citations
Biochemistry, Genetics and Molecular Biology · Immunology and Microbiology · #Bacteria #Bacterial Infections and Vaccines #Biology #Bordetella #Bordetella bronchiseptica #Bordetella pertussis #Gene #Genetics #Genomics and Phylogenetic Studies #Host adaptation #Microbiology #Virology #Virulence #Whooping cough #Yersinia bacterium, plague, ectoparasites research
- Genome plasticity of BCG and impact on vaccine efficacy
2007/03/19 by Roland Brosch, Stephen V. Gordon, Thierry Garnier +17 · 3 citations
Immunology and Microbiology · Medicine · #BCG vaccine #Biology #Gene #Gene expression #Genetics #Genome #Immune responses and vaccinations #Immune system #Immunodeficiency and Autoimmune Disorders #Immunogenicity #Medicine #Mycobacterium bovis #Mycobacterium tuberculosis #Transcriptome #Tuberculosis #Tuberculosis Research and Epidemiology #Tuberculosis vaccines #Vaccination #Virology
- A lung-specific mutational signature enables inference of viral and bacterial respiratory niche
2023/05/15 by Christopher Ruis, Thomas P. Peacock, Luis Mariano Polo +9 · 1 voice · 4 citations
Biochemistry, Genetics and Molecular Biology · Medicine · #Evolution and Genetic Dynamics #SARS-CoV-2 and COVID-19 Research #SARS-CoV-2 detection and testing
- The mutational landscape of Staphylococcus aureus during colonisation
2025/01/13 by Francesc Coll, Beth Blane, Katie Bellis +9 · 1 voice · 3 citations
Biochemistry, Genetics and Molecular Biology · Medicine · #Antimicrobial Resistance in Staphylococcus #Bacterial biofilms and quorum sensing #Microbial Metabolism and Applications
- What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis
2017/11/13 by Jan Heyckendorf, Sönke Andres, Claudio U. Köser +13 · 1 citation
Medicine · #Tuberculosis Research and Epidemiology #Mycobacterium research and diagnosis #Infectious Diseases and Tuberculosis
- Emergence of methicillin resistance predates the clinical use of antibiotics
2022/01/05 by Jesper Larsen, Claire Raisen, Xiaoliang Ba +61 · 1 citation
Biochemistry, Genetics and Molecular Biology · Medicine · #Antibiotic Resistance in Bacteria #Antimicrobial Resistance in Staphylococcus #Bacterial Identification and Susceptibility Testing
- A decade of advances in transposon-insertion sequencing
2020/06/12 by Amy K. Cain, Lars Barquist, Andrew L. Goodman +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacterial Genetics and Biotechnology #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies
- Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice
2017/07/06 by Catriona P. Harkins, Bruno Pichon, Michel Doumith +7 · 1 citation
Medicine · Biochemistry, Genetics and Molecular Biology · #Antimicrobial Resistance in Staphylococcus #Antibiotic Resistance in Bacteria #Bacterial biofilms and quorum sensing
- Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
2014/08/19 by Kirsten I. Bos, Kelly M. Harkins, Alexander Herbig +33 · 1 citation
Biochemistry, Genetics and Molecular Biology · Medicine · #Ancient DNA #Biology #Comparative genomics #Gene #Genetics #Genome #Genomics #Genomics and Phylogenetic Studies #Human migration #Human pathogen #Medicine #Mycobacterium tuberculosis #Mycobacterium tuberculosis complex #Old World #Population #Tuberculosis #Tuberculosis Research and Epidemiology #Yersinia bacterium, plague, ectoparasites research #Zoology