Dr Nabil-Fareed Alikhan

Bioinformatician

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Informatics and bioinformatics support

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Biography

Recent Publications

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. https://doi.org/10.1371/journal.pgen.1007261

Alikhan, Nabil-Fareed, et al. “BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.” BMC genomics 12.1 (2011): 1. https://doi.org/10.1186/1471-2164-12-402

Page, Andrew J., et al. “Comparison of classical multi-locus sequence typing software for next-generation sequencing data.” Microbial genomics 3.8 (2017). https://doi.org/10.1099/mgen.0.000124

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. https://doi.org/10.1016/j.cub.2018.05.058

Zhou, Zhemin, et al. “GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens.” Genome research 28.9 (2018): 1395-1404. https://doi.org/10.1101/gr.232397.117

Baker DJ,Aydin A,Le Viet T,Kay GL,Rudder S,de Oliveira Martins L,Tedim AP,Kolyva A,Diaz M,Alikhan NF,Meadows L,Bell A,Gutierrez AV,Trotter AJ,Thomson NM,Gilroy R,Griffith L,Adriaenssens EM,Stanley R,Charles IG,Elumogo N,Wain J,Prakash R,Meader E,Mather AE,Webber M,Dervisevic S,Page AJ,O J. (2021)

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.

Genome medicine

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Gold Lock

Barylski J., Kropinski A. M., Alikhan N., Adriaenssens E. M.. (2020)

ICTV Virus Taxonomy Profile: Herelleviridae

Journal of General Virology, jgv001392

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Gold Lock

Key F. M., Posth C., Esquivel-Gomez L. R., Hübler R., Spyrou M. A., Neumann G. U., Furtwängler A., Sabin S., Burri M., Wissgott A., Lankapalli A. K., Vågene A. J., Meyer M., Nagel S., Tukhbatova R., Khokhlov A., Chizhevsky A., Hansen S., Belinsky A. B., Kalmykov A., Kantorovich A. R., Maslov V. E., Vai S., Zavattaro M., Riga A., Skeates R., Beckett J., Gradoli M. G., Steuri N., Hafner A., Ramstein M., Siebke I., Erdal Y. S., Alikhan N., Zhou Z., Achtman M., Bos K., Reinhold S., Haak W., Kühnert D., Herbig A., Krause J.. (2020)

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

Nature Ecology and Evolutiion

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Gold Lock

Bawn M,Alikhan N,Thilliez G,Adriaenssens E,Hall N,Kingsley R. (2020)

Evolution of Salmonella enterica serotypeTyphimurium driven by anthropogenicselection and niche adaptation

PLoS Genetics

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Gold Lock

Achtman M,Zhou Z,Alikhan N,Tyne W,Parkhill J,Cormican M,Chiou CS,Torpdahl M,Litrup E,Prendergast DM,Moore JE,Strain S,Kornschober C,Meinersmann R,Uesbeck A,Weill FX,Coffey A,Andrews-Polymenis H,Curtis R,Fanning S. (2020)

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project [version 1; peer review: awaiting peer review]

Wellcome Open Res

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Foster-Nyarko E,Alikhan NF,Ravi A,Thilliez G,Thomson N,Baker D,Kay G,Antonio M,O J,Pallen MJ. (2020)

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

Microbial Genomics, 6

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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

Chen L., Song N., Liu B., Zhang N., Alikhan N., Zhou Z., Zhou Y., Zhou S., Zheng D., Chen M., Hapeshi A., Healey J., Waterfield N. R., Yang J., Yang G.. (2019)

Genome-wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems

Cell Reports, 29, 511-521

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