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List of works by Nabil-Fareed Alikhan

A genomic overview of the population structure of Salmonella.

scientific article

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons ⬇️

scientific article published on August 8, 2011

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

scientific article published on 28 February 2018

Comparison Of Multi-locus Sequence Typing Software For Next Generation Sequencing Data

article published in 2017

Comparison of classical multi-locus sequence typing software for next-generation sequencing data

scientific article published on 4 July 2017

Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health

scientific article published on 02 June 2022

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

scientific article published on 08 June 2020

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

scientific article published on 06 April 2021

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

scientific article published in 2022

Genome sequence of the emerging pathogen Aeromonas caviae.

scientific article

Genomic diversity of <i>Escherichia coli</i> isolates from backyard chickens and guinea fowl in the Gambia

scientific article published on 30 November 2020

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

scientific article published on 26 July 2018

Mechanisms Involved in Acquisition of blaNDM Genes by IncA/C2 and IncFIIY Plasmids.

scientific article published on 25 April 2016

Millennia of genomic stability within the invasive Para C Lineage ofSalmonella enterica

article published in 2017

Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition

scientific article

Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli

scholarly article published 19 February 2019

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database ⬇️

scientific article published in 2022

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

scientific article published on 19 July 2018

Principles of Systems Biology, No. 31

scientific article published on 01 August 2018

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

scientific article published on 06 December 2019

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