Dr Nabil-Fareed Alikhan


Contact via email

Informatics and bioinformatics support

I am a Bioinformatics Scientific Programmer within the Core Bioinformatics / Page group at the Quadram Institute. I have dedicated my professional life to improving bioinformatic analyses and then using these improvements to find new insight into microbial pathogens.

I completed my doctorate in 2015, which focused on comparative genomics of both O157 and non-O157 Shiga-toxigenic Escherichia coli. I also developed tools and software throughout my PhD, most notably being the the BLAST Ring Image Generator (BRIG). BRIG is a tool for visualizing whole genome comparisons.

I then joined Mark Achtman’s group at the University of Warwick where I was a developer on EnteroBase, a web-resource serving over 250,000 genomes; providing genotyping, genome analysis and curated metadata.

I joined the Quadram Institute in 2018 and my current duties included developing bioinformatics infrastructure and novel algorithms.


Key publications

  • Alikhan, Nabil-Fareed, et al. “A genomic overview of the population structure of Salmonella.” PLoS genetics 14.4 (2018): e1007261.
  • Alikhan, Nabil-Fareed, et al. “BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.” BMC genomics 12.1 (2011): 1.
  • Page, Andrew J., et al. “Comparison of classical multi-locus sequence typing software for next-generation sequencing data.” Microbial genomics 3.8 (2017).
  • Zhou, Zhemin, et al. “Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive para C lineage for millennia.” Current Biology 28.15 (2018): 2420-2428.
  • Zhou, Zhemin, et al. “GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens.” Genome research 28.9 (2018): 1395-1404.

Zhou Z., Alikhan N. F., Mohammed K., Agama Study Group X., Achtman M.. (2019)

The user’s guide to comparative genomics with EnteroBase. Three case studies: micro-clades within Salmonella enterica serovar Agama, ancient and modern populations of Yersinia pestis, and core genomic diversity of all Escherichia

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