Nabil-Fareed Alikhan

Publications

• Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
• Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project [version 2; peer review: 2 approved]
• Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project
• Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
• Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
• Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
• SARS-CoV2 GISAID submission protocol
• SARS-CoV2 GISAID submission protocol
• SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021
• Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
• Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
• Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
• Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru
• Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
• CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes
• SARS-CoV2 GISAID submission protocol
• SARS-CoV-2 EBI submission protocol: ENA, BioSample, and BioProject
• SOP for populating EBI submission templates (ENA)
• SARS-CoV2 EBI assembly submission protocol
• Genomic diversity of Escherichia coli isolates from healthy children in rural Gambia
• GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens
• A genomic overview of the population structure of Salmonella
• GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
• Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
• Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli
• The user’s guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades of Salmonella, the phylogeny of ancient and modern Yersinia pestis genomes, and the core genomic diversity of all Escherichia
• Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
• Principles of Systems Biology, No. 31
• Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak
• The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
• BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
• Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.
• Mechanisms Involved in Acquisition of blaNDM Genes by IncA/C2 and IncFIIY Plasmids.
• Genome sequence of the emerging pathogen Aeromonas caviae.
• Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica
• Comparison Of Multi-locus Sequence Typing software For next generation sequencing data
• Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
• Comparison of classical multi-locus sequence typing software for next-generation sequencing data
• Invasive atypical non-typhoidal Salmonella serovars in The Gambia
• Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package
• PHA4GE contextual metadata SOP v1
• SARS-CoV-2 ENA submission workflow + guidance for structuring and releasing metadata v2
• SARS-CoV2 EBI assembly submission protocol
• SARS-CoV-2 ENA submission workflow + guidance for structuring and releasing metadata v1
• SARS-CoV2 EBI assembly submission protocol
• Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals
• Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health
• SARS-CoV2 EBI assembly submission protocol
• SARS-CoV2 EBI assembly submission protocol
• Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database