Dr Nabil-Fareed Alikhan

Bioinformatician

Contact via email

Informatics and bioinformatics support

Links/websites:

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

Merhi G, Trotter AJ, de Oliveira Martins L, Koweyes J, Le Viet T, Abou Naja, Al Buaini, Prosolek SJ, Alikhan NF, Lott M, Tohmeh T, Badran B, Jupp OJ, Gardner S, Felgate MW, Makin KA, Wilkinson JM, Stanley R, Sesay AK, Webber MA, Davidson RK, Ghosn N, Pallen M, Hasan H, Page AJ, Tokajian . (2022)

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

Microbial genomics


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Eales O, Walters CW, Wang H, Haw D, Ainslie KEC, Atchison CJ, Page AJ, Prosolek S, Trotter AJ, Le Viet, Alikhan N, Jackson LM, Ludden C, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P, Riley . (2022)

Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2 [version 1; peer review: awaiting peer review]

Wellcome open research


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Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell D. (2022)

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

GigaScience


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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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Foster-Nyarko E,Alikhan NF,Ikumapayi UN,Sarwar G,Okoi C,Tientcheu PM,Defernez M,O J,Antonio M,Pallen MJ. (2021)

Genomic diversity of Escherichia coli from healthy children in rural Gambia.

PeerJ


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Volz E,Hill V,McCrone JT,Price A,Jorgensen D,O'Toole Á,Southgate J,Johnson R,Jackson B,Nascimento FF,Rey SM,Nicholls SM,Colquhoun RM,da Silva,Shepherd J,Pascall DJ,Shah R,Jesudason N,Li K,Jarrett R,Pacchiarini N,Bull M,Geidelberg L,Siveroni I,Goodfellow I,Loman NJ,Pybus OG,Robertson DL,Thomson EC,Rambaut A,Connor TR,Koshy C,Wise E,Cortes N,Lynch J,Kidd S,Mori M,Fairley DJ,Curran T,McKenna JP,Adams H,Fraser C,Golubchik T,Bonsall D,Moore C,Caddy SL,Khokhar FA,Wantoch M,Reynolds N,Warne B,Maksimovic J,Spellman K,McCluggage K,John M,Beer R,Afifi S,Morgan S,Marchbank A,Price A,Kitchen C,Gulliver H,Merrick I,Southgate J,Guest M,Munn R,Workman T,Connor TR,Fuller W,Bresner C,Snell LB,Charalampous T,Nebbia G,Batra R,Edgeworth J,Robson SC,Beckett A,Loveson KF,Aanensen DM,Underwood AP,Yeats CA,Abudahab K,Taylor BEW,Menegazzo M,Clark G,Smith W,Khakh M,Fleming VM,Lister MM,Howson-Wells HC,Berry L,Boswell T,Joseph A,Willingham I,Bird P,Helmer T,Fallon K,Holmes C,Tang J,Raviprakash V,Campbell S,Sheriff N,Loose MW,Holmes N,Moore C,Carlile M,Wright V,Sang F,Debebe J,Coll F,Signell AW,Betancor G,Wilson HD,Feltwell T,Houldcroft CJ,Eldirdiri S,Kenyon A,Davis T,Pybus O,du Plessis,Zarebski A,Raghwani J,Kraemer M,Francois S,Attwood S,Vasylyeva T,Torok ME,Hamilton WL,Goodfellow IG,Hall G,Jahun AS,Chaudhry Y,Hosmillo M,Pinckert ML,Georgana I,Yakovleva A,Meredith LW,Moses S,Lowe H,Ryan F,Fisher CL,Awan AR,Boyes J,Breuer J,Harris KA,Brown JR,Shah D,Atkinson L,Lee JCD,Alcolea-Medina A,Moore N,Cortes N,Williams R,Chapman MR,Levett LJ,Heaney J,Smith DL,Bashton M,Young GR,Allan J,Loh J,Randell PA,Cox A,Madona P,Holmes A,Bolt F,Price J,Mookerjee S,Rowan A,Taylor GP,Ragonnet-Cronin M,Nascimento FF,Jorgensen D,Siveroni I,Johnson R,Boyd O,Geidelberg L,Volz EM,Brunker K,Smollett KL,Loman NJ,Quick J,McMurray C,Stockton J,Nicholls S,Rowe W,Poplawski R,Martinez-Nunez RT,Mason J,Robinson TI,O'Toole E,Watts J,Breen C,Cowell A,Ludden C,Sluga G,Machin NW,Ahmad SSY,George RP,Halstead F,Sivaprakasam V,Thomson EC,Shepherd JG,Asamaphan P,Niebel MO,Li KK,Shah RN,Jesudason NG,Parr YA,Tong L,Broos A,Mair D,Nichols J,Carmichael SN,Nomikou K,Aranday-Cortes E,Johnson N,Starinskij I,da Silva,Robertson DL,Orton RJ,Hughes J,Vattipally S,Singer JB,Hale AD,Macfarlane-Smith LR,Harper KL,Taha Y,Payne BAI,Burton-Fanning S,Waugh S,Collins J,Eltringham G,Templeton KE,McHugh MP,Dewar R,Wastenge E,Dervisevic S,Stanley R,Prakash R,Stuart C,Elumogo N,Sethi DK,Meader EJ,Coupland LJ,Potter W,Graham C,Barton E,Padgett D,Scott G,Swindells E,Greenaway J,Nelson A,Yew WC,Resende Silva,Andersson M,Shaw R,Peto T,Justice A,Eyre D,Crooke D,Hoosdally S,Sloan TJ,Duckworth N,Walsh S,Chauhan AJ,Glaysher S,Bicknell K,Wyllie S,Butcher E,Elliott S,Lloyd A,Impey R,Levene N,Monaghan L,Bradley DT,Allara E,Pearson C,Muir P,Vipond IB,Hopes R,Pymont HM,Hutchings S,Curran MD,Parmar S,Lackenby A,Mbisa T,Platt S,Miah S,Bibby D,Manso C,Hubb J,Chand M,Dabrera G,Ramsay M,Bradshaw D,Thornton A,Myers R,Schaefer U,Groves N,Gallagher E,Lee D,Williams D,Ellaby N,Harrison I,Hartman H,Manesis N,Patel V,Bishop C,Chalker V,Osman H,Bosworth A,Robinson E,Holden MTG,Shaaban S,Birchley A,Adams A,Davies A,Gaskin A,Plimmer A,Gatica-Wilcox B,McKerr C,Moore C,Williams C,Heyburn D,De Lacy,Hilvers E,Downing F,Shankar G,Jones H,Asad H,Coombes J,Watkins J,Evans JM,Fina L,Gifford L,Gilbert L,Graham L,Perry M,Morgan M,Bull M,Cronin M,Pacchiarini N,Craine N,Jones R,Howe R,Corden S,Rey S,Kumziene-Summerhayes S,Taylor S,Cottrell S,Jones S,Edwards S,O'Grady J,Page AJ,Wain J,Webber MA,Mather AE,Baker DJ,Rudder S,Yasir M,Thomson NM,Aydin A,Tedim AP,Kay GL,Trotter AJ,Gilroy RAJ,Alikhan NF,de Oliveira,Le Viet T,Meadows L,Kolyva A,Diaz M,Bell A,Gutierrez AV,Charles IG,Adriaenssens EM,Kingsley RA,Casey A,Simpson DA,Molnar Z,Thompson T,Acheson E,Masoli JAH,Knight BA,Hattersley A,Ellard S,Auckland C,Mahungu TW,Irish-Tavares D,Haque T,Bourgeois Y,Scarlett GP,Partridge DG,Raza M,Evans C,Johnson K,Liggett S,Baker P,Essex S,Lyons RA,Caller LG,Castellano S,Williams RJ,Kristiansen M,Roy S,Williams CA,Dyal PL,Tutill HJ,Panchbhaya YN,Forrest LM,Niola P,Findlay J,Brooks TT,Gavriil A,Mestek-Boukhibar L,Weeks S,Pandey S,Berry L,Jones K,Richter A,Beggs A,Smith CP,Bucca G,Hesketh AR,Harrison EM,Peacock SJ,Palmer S,Churcher CM,Bellis KL,Girgis ST,Naydenova P,Blane B,Sridhar S,Ruis C,Forrest S,Cormie C,Gill HK,Dias J,Higginson EE,Maes M,Young J,Kermack LM,Hadjirin NF,Aggarwal D,Griffith L,Swingler T,Davidson RK,Rambaut A,Williams T,Balcazar CE,Gallagher MD,O'Toole Á,Rooke S,Jackson B,Colquhoun R,Ashworth J,Hill V,McCrone JT,Scher E,Yu X,Williamson KA,Stanton TD,Michell SL,Bewshea CM,Temperton B,Michelsen ML,Warwick-Dugdale J,Manley R,Farbos A,Harrison JW,Sambles CM,Studholme DJ,Jeffries AR,Darby AC,Hiscox JA,Paterson S,Iturriza-Gomara M,Jackson KA,Lucaci AO,Vamos EE,Hughes M,Rainbow L,Eccles R,Nelson C,Whitehead M,Turtle L,Haldenby ST,Gregory R,Gemmell M,Kwiatkowski D,de Silva,Smith N,Angyal A,Lindsey BB,Groves DC,Green LR,Wang D,Freeman TM,Parker MD,Keeley AJ,Parsons PJ,Tucker RM,Brown R,Wyles M,Constantinidou C,Unnikrishnan M,Ott S,Cheng JKJ,Bridgewater HE,Frost LR,Taylor-Joyce G,Stark R,Baxter L,Alam MT,Brown PE,McClure PC,Chappell JG,Tsoleridis T,Ball J,Gramatopoulos D,Buck D,Todd JA,Green A,Trebes A,MacIntyre-Cockett G,de Cesare,Langford C,Alderton A,Amato R,Goncalves S,Jackson DK,Johnston I,Sillitoe J,Palmer S,Lawniczak M,Berriman M,Danesh J,Livett R,Shirley L,Farr B,Quail M,Thurston S,Park N,Betteridge E,Weldon D,Goodwin S,Nelson R,Beaver C,Letchford L,Jackson DA,Foulser L,McMinn L,Prestwood L,Kay S,Kane L,Dorman MJ,Martincorena I,Puethe C,Keatley JP,Tonkin-Hill G,Smith C,Jamrozy D,Beale MA,Patel M,Ariani C,Spencer-Chapman M,Drury E,Lo S,Rajatileka S,Scott C,James K,Buddenborg SK,Berger DJ,Patel G,Garcia-Casado MV,Dibling T,McGuigan S,Rogers HA,Hunter AD,Souster E,Neaverson AS. (2021)

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Cell


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Sarwar M, Yasir M, Alikhan N, Afzal N, de Oliveira, Le Viet, Trotter A, Prosolek S, Kay G, Foster-Nyarko E, Rudder S, Baker D, Roman M, Webber M, Shafiq A, Shabir B, Akram J, Page A, Jahan . (2021)

SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

Microbial Genomics


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Sarwar MB, Yasir M, Alikhan NF, Afzal N, de Oliveira Martins L, Le Viet, Trotter AJ, Prosolek SJ, Kay GL, Foster-Nyarko E, Rudder S, Baker DJ, Muntaha ST, Roman M, Webber MA, Shafiq A, Shabbir B, Akram J, Page AJ, Jahan . (2021)

SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021.

Microbial genomics


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