Dave Baker

Science Support

Contact via email

Core Science Resources - methods development and innovation

Previously to joining the Quadram Institute, I spent 10 months implementing NGS at Food Forensics and prior to that was a team leader in the Genomics Pipelines Group at Earlham Institute (formally TGAC). My primary role was to run and maintain Earlham Institute’s Next Generation Sequencing and Whole Genome Mapping platforms from sample delivery to machine output. I was also involved in outreach activities to both internal and external audiences interacting with individuals from a range of backgrounds and scientific understanding and for this was awarded the Cue East Award in 2011.

I have worked with DNA Sequencing technologies for more than 20 years. Graduating with a Mechanical Engineering first degree from Oxford Brookes University I moved to Norfolk and started at The Sainsbury Laboratory running their DNA Sequencers in 1995. In 2002 I moved over to the John Innes Centre to develop TILLING on the ABI3730 capillary sequencing platform. In the summer of 2009 I became one of the first members of TGAC.

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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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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Webber M., Yasir M., Turner K., Bastkowski S., Baker D., Page A., Telatin A., Savva G., Charles I.. (2020)

TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance.

Genome Research, 30, 239-249


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Isaacs A., Echeandia M., Moreno-Gonzalez M., Brion A., Goldson A., Philo M., Patterson A. M., Parker A., Galduroz M., Baker D., Rushbrook S. M., Hildebrand F., Beraza N.. (2020)

Intestinal microbiome-macrophage crosstalk contributes to cholestatic liver disease by promoting intestinal permeability.

Hepatology (Baltimore, Md.)


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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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James S,Phillips S,Telatin A,Baker D,Ansorge R,Clarke P,Hall LJ,Carding S. (2020)

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts

Journal of Fungi, 6, 273


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Rasheed F,Saeed M,Alikhan NF,Baker D,Khurshid M,Ainsworth EV,Turner AK,Imran AA,Rasool MH,Saqalein M,Nisar MA,Fayyaz Ur,Wain J,Yasir M,Langridge GC,Ikram A. (2020)

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan.

Microorganisms


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