Professor Matt Clark
Research Leader
Summary
My research is multi-disciplinary: combining molecular biology, genomics, population genetics, and computational biology amongst other disciplines. The strong theme of technology cuts through most projects, as my team often adopts, or develops, novel techniques which allow us to tackle biological problems that were previously seen as intractable. We are big users of next generation sequencing, which as a rapidly evolving technology presents many such opportunities. Beyond technology development my research largely involves collection genomics (historical DNA sequencing) and environmental DNA (especially AirSeq).
Qualifications
Degrees
- BSc, imperial College, United Kingdom, 1990 - 1993
- PhD, Max Planck Institute for Molecular Genetics, Germany, 1997 - 2002
Academic
- Merit Reseacher, Natural History Museum, Research, United Kingdom, 2025 - 2030
- Honorary Professor, University of East Anglia, Environmental Sciences, United Kingdom, 2019 - ongoing
- Research Leader, Natural History Museum, Life Sciences, United Kingdom, 2018 - ongoing
- Principal Research leader, National Institute of Agricultural Botany, Genomics, Genetics and Breeding, United Kingdom, 2017 - 2018
- Head of Technology Development, Earlham Institute, Faculty, United Kingdom, 2015 - 2017
- Plant and Microbial Genomics Group leader, The Genome Analysis Centre (TGAC), Faculty, United Kingdom, 2013 - 2015
- Sequencing Technology Development Team leader, The Genome Analysis Centre (TGAC), Genomics, United Kingdom, 2010 - 2013
- Staff Scientist, Wellcome Trust Sanger Institute (WT), Vertebrate Development and Genetics, United Kingdom, 2006 - 2010
- Postdoctoral Fellow, Wellcome Trust Sanger Institute, Vertebrate Development and Genetics, CB10 1SA, 2003 - 2006
Highlighted publications
- Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 543, 346 - 354. doi: 10.1038/nature22011
- Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu F-H, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD (2017) An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research 27, 885 - 896. doi: 10.1101/gr.217117.116
- Giolai M, Paajanen P, Verweij W, Witek K, Jones JDG, Clark MD (2017) Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire. BMC Genomics 18, doi: 10.1186/s12864-017-3936-7
- Leggett RM, Clark MD (2017) A world of opportunities with nanopore sequencing. Journal of Experimental Botany 68, 5419 - 5429. doi: 10.1093/jxb/erx289
- Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Hoyles L, Clarke P, Hall L, Clark MD (2017) Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics. bioRxiv 180406 - 180406.
- Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, Van Oosterhout C, Grigoriev IV (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536 - 540. doi: 10.1038/nature20803
- Witek K, Jupe F, Witek AI, Baker D, Clark MD, Jones JDG (2016) Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing. Nature Biotechnology 34, 656 - 660. doi: 10.1038/nbt.3540
- Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch G-J, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel J-H, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper JD, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SMJ, Enright A, Geisler R, Plasterk RHA, Lee C, Westerfield M, De Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJP, Crollius HR, Rogers J, Stemple DL (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498 - 503. doi: 10.1038/nature12111
- McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, Garcia Accinelli G, Wright J, Verweij W, Koutsovoulos G, Yoshida K, Hosoya T, Williamson L, Jennings P, Ioos R, Husson C, Hietala AM, Vivian-Smith A, Solheim H, MaClean D, Fosker C, Hall N, Brown JKM, Swarbreck D, Blaxter M, Downie JA, Clark MD The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nature Ecology & Evolution 2, 1000 - 1008. doi: 10.1038/s41559-018-0548-9
Highlighted publications
- Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 543, 346 - 354. doi: 10.1038/nature22011
- Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu F-H, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD (2017) An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research 27, 885 - 896. doi: 10.1101/gr.217117.116
- Giolai M, Paajanen P, Verweij W, Witek K, Jones JDG, Clark MD (2017) Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire. BMC Genomics 18, doi: 10.1186/s12864-017-3936-7
- Leggett RM, Clark MD (2017) A world of opportunities with nanopore sequencing. Journal of Experimental Botany 68, 5419 - 5429. doi: 10.1093/jxb/erx289
- Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Hoyles L, Clarke P, Hall L, Clark MD (2017) Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics. bioRxiv 180406 - 180406.
- Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, Van Oosterhout C, Grigoriev IV (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536 - 540. doi: 10.1038/nature20803
- Witek K, Jupe F, Witek AI, Baker D, Clark MD, Jones JDG (2016) Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing. Nature Biotechnology 34, 656 - 660. doi: 10.1038/nbt.3540
- Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch G-J, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel J-H, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper JD, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SMJ, Enright A, Geisler R, Plasterk RHA, Lee C, Westerfield M, De Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJP, Crollius HR, Rogers J, Stemple DL (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498 - 503. doi: 10.1038/nature12111
- McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, Garcia Accinelli G, Wright J, Verweij W, Koutsovoulos G, Yoshida K, Hosoya T, Williamson L, Jennings P, Ioos R, Husson C, Hietala AM, Vivian-Smith A, Solheim H, MaClean D, Fosker C, Hall N, Brown JKM, Swarbreck D, Blaxter M, Downie JA, Clark MD The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nature Ecology & Evolution 2, 1000 - 1008. doi: 10.1038/s41559-018-0548-9