Dr Matt Clark

Dr Matthew Clark

Research Leader

Department: Life Sciences
Division: LS Algae, Fungi and Plants Division
Contact: email
Phone: 0207942 6939
Google Scholar publications

Summary

My research is multi-disciplinary: combining molecular biology, genomics, population genetics, and computational biology amongst other disciplines. We have a focus on plant and plant pathogen research, especially for key crops groups such as Triticeae (Wheat, Barley & Rye) and Solanaceae (Potatoes, Tomatoes, Aubergines, Peppers and even Tobacco). 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, and stray outside of plants if an appropriate model or test case presents itself.

Qualifications

Degrees

PhD, Max Planck Institute for Molecular Genetics, Berlin, 1997 - 2002

BSc, imperial College, London, 1990 - 1993

Employment history

Academic

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

McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, et al. (2018) The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nature Ecology & Evolution, 2 (6) : 1000 - 1008. doi: 10.1038/s41559-018-0548-9

Leggett RM, Clark MD (2017) A world of opportunities with nanopore sequencing. Journal of Experimental Botany, 68 (20) : 5419 - 5429. doi: 10.1093/jxb/erx289

Giolai M, Paajanen P, Verweij W, Witek K, Jones JDG, et al. (2017) Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire. BMC Genomics, 18 (1) : doi: 10.1186/s12864-017-3936-7

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, et al. (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 (5) : 885 - 896. doi: 10.1101/gr.217117.116

Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, et al. (2017) Genomic innovation for crop improvement. Nature, 543 (7645) : 346 - 354. doi: 10.1038/nature22011

Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, et al. (2017) Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics. bioRxiv, 180406 - 180406.

Grants

Wheat Pan-Genomics
Role: Principal investigatorClark MD
Funding: BBSRC
Total value £1,355,785 (to Museum £539,000)
Dates: 2018 - 2020

Limits to Evolutionary Adaptation of Phytoplankton in the arctic Ocean
Co-investigator: Clark M
Funding: NERC
Total value £638,621 (to Museum £10,819)
Dates: 2018 - 2020

Publications

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 (2018) The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nature Ecology & Evolution, 2 (6) : 1000 - 1008. doi: 10.1038/s41559-018-0548-9

Claire Armstrong LGS (2018) Genomic associations with bill length and disease reveal drift and selection across island bird populations. Evolution Letters,

Wilson AJ, Nelson TC, Cresko WA, Armstrong C, Richardson DS, Hipperson H, Horsburgh GJ, Küpper C, Percival-Alwyn L, Clark M, others (2018) COMMENTS AND OPINIONS. null,

Leggett RM, Clark MD (2017) A world of opportunities with nanopore sequencing. Journal of Experimental Botany, 68 (20) : 5419 - 5429. doi: 10.1093/jxb/erx289

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 (1) : doi: 10.1186/s12864-017-3936-7

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 (5) : 885 - 896. doi: 10.1101/gr.217117.116

Beier S, Himmelbach A, Colmsee C, Zhang X-Q, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.. Scientific Data, 4 : 170044 - 170044. doi: 10.1038/sdata.2017.44

Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature, 543 (7645) : 346 - 354. doi: 10.1038/nature22011

Hickey JM, Chiurugwi T, Mackay I, Powell W, Hickey JM, Chiurugwi T, Mackay I, Powell W, Eggen A, Kilian A, Jones C, Canales C, Grattapaglia D, Bassi F, Atlin G, Gorjanc G, Dawson I, Rabbi I, Ribaut J-M, Rutkoski J, Benzie J, Lightner J, Mwacharo J, Parmentier J, Robbins K, Skot L, Wolfe M, Rouard M, Clark M, Amer P, Gardiner P, Hendre P, Mrode R, Sivasankar S, Rasmussen S, Groh S, Jackson V, Thomas W, Beyene Y (2017) Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nature Genetics, 49 (9) : 1297 - 1303. doi: 10.1038/ng.3920

Kelly S, Ivens A, Mott GA, O’Neill E, Emms D, Macleod O, Voorheis P, Tyler K, Clark M, Matthews J, Matthews K, Carrington M (2017) An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri. Genome Biology and Evolution, 9 (8) : 2093 - 2109. doi: 10.1093/gbe/evx152

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.

Lu F-H, McKenzie N, Kettleborough G, Heavens D, Clark MD, Bevan MW (2018) Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries. GigaScience, 7 (5) : doi: 10.1093/gigascience/giy053

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, others (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature, 544 : 427 - 427.

McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, others (2017) The ash dieback invasion of Europe was founded by two individuals from a native population with huge adaptive potential. bioRxiv, 146746 - 146746.

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 (7638) : 536 - 540. doi: 10.1038/nature20803

Paajanen P, Kettleborough G, Lopez-Girona E, Giolai M, Heavens D, Baker D, Lister A, Wilde G, Hein I, Macaulay I, others (2017) A critical comparison of technologies for a plant genome sequencing project. bioRxiv, 201830 - 201830.

Paajanen P, Strauss J, van Oosterhout C, McMullan M, Clark MD, Mock T (2017) Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus. Scientific Data, 4 : 170149 - 170149. doi: 10.1038/sdata.2017.149

Zhou J, Reynolds D, Websdale D, Le Cornu T, Gonzalez-Navarro O, Lister C, Orford S, Laycock S, Finlayson G, Stitt T, others (2017) CropQuant: An automated and scalable field phenotyping platform for crop monitoring and trait measurements to facilitate breeding and digital agriculture. bioRxiv, 161547 - 161547.

Giolai M, Paajanen P, Verweij W, Percival-Alwyn L, Baker D, Witek K, Jupe F, Bryan G, Hein I, Jones JD, others (2016) Targeted capture and sequencing of gene-sized DNA molecules. Biotechniques, 61 : 315 - 322.

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 (6) : 656 - 660. doi: 10.1038/nbt.3540

Heavens D, Accinelli GG, Clavijo B, Clark MD (2015) Benchmarks. Biotechniques, 59 : 42 - 45.

Kenyon EJ, Campos I, Bull JC, Williams PH, Stemple DL, Clark MD (2015) Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling. Developmental Biology, 397 (2) : 212 - 224. doi: 10.1016/j.ydbio.2014.11.007

Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP (2015) NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics, 32 : 142 - 144.

Rallapalli G, Saunders DG, Yoshida K, Edwards A, Lugo CA, Collin S, Clavijo B, Corpas M, Swarbreck D, Clark M, Downie JA, Kamoun S, MacLean D (2015) Lessons from Fraxinus, a crowd-sourced citizen science game in genomics. eLife, 4 : doi: 10.7554/eLife.07460

Saunders D, Yoshida K, Sambles C, Glover R, Clavijo B, Corpas M, Bunting D, Dong S, Clark M, Swarbreck D, others (2014) Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community.. BioRxiv, 004564 - 004564.

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, Eliott D, Threadgold G, Harden G, Ware D, Mortimer 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, 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 J, 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, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, 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 (7446) : 498 - 503. doi: 10.1038/nature12111

Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M (2014) NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. Bioinformatics, 30 (4) : 566 - 568. doi: 10.1093/bioinformatics/btt702

MacLean D, Yoshida K, Edwards A, Crossman L, Clavijo B, Clark M, Swarbreck D, Bashton M, Chapman P, Gijzen M, Caccamo M, Downie A, Kamoun S, Saunders DG (2013) Crowdsourcing genomic analyses of ash and ash dieback – power to the people. GigaScience, 2 (1) : doi: 10.1186/2047-217X-2-2

Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher J-P, Clark KJ, Stemple DL, Klee EW, Ekker SC, Scaria V, Sivasubbu S (2013) A Sequence-Based Variation Map of Zebrafish. Zebrafish, 10 (1) : 15 - 20. doi: 10.1089/zeb.2012.0848

Nasiadka A, Clark MD (2012) Zebrafish Breeding in the Laboratory Environment. ILAR Journal, 53 (2) : 161 - 168. doi: 10.1093/ilar.53.2.161

Clark MD, Guryev V, de Bruijn E, Nijman IJ, Tada M, Wilson C, Deloukas P, Postlethwait JH, Cuppen E, Stemple DL (2011) Single Nucleotide Polymorphism (SNP) Panels for Rapid Positional Cloning in Zebrafish, In: null, null : 221 - 235.

Clark MD, Guryev V, de Bruijn E, Nijman IJ, Tada M, Wilson C, Deloukas P, Postlethwait JH, Cuppen E, Stemple DL (2011) Single nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish, In: Methods in cell biology, Academic Press : 219 - 235.

WHITELEY AR, BHAT A, MARTINS EP, MAYDEN RL, ARUNACHALAM M, UUSI-HEIKKILÄ S, AHMED ATA, SHRESTHA J, CLARK M, STEMPLE D, BERNATCHEZ L (2011) Population genomics of wild and laboratory zebrafish (Danio rerio). Molecular Ecology, 20 (20) : 4259 - 4276. doi: 10.1111/j.1365-294X.2011.05272.x

Bennett JT, Joubin K, Cheng S, Aanstad P, Herwig R, Clark M, Lehrach H, Schier AF (2007) Nodal signaling activates differentiation genes during zebrafish gastrulation. Developmental Biology, 304 (2) : 525 - 540. doi: 10.1016/j.ydbio.2007.01.012

Ekker SC, Stemple DL, Clark M, Chien C-B, Rasooly RS, Javois LC (2007) Zebrafish Genome Project: Bringing New Biology to the Vertebrate Genome Field. Zebrafish, 4 (4) : 239 - 251. doi: 10.1089/zeb.2007.9979

Pei W, Williams PH, Clark MD, Stemple DL, Feldman B (2007) Environmental and genetic modifiers of squint penetrance during zebrafish embryogenesis. Developmental biology, 308 : 368 - 378.

Feldman B, Pei W, Williams H, Clark M, Stemple DL (2006) Squint protects early embryos from temperature-induced dysmorphology. Developmental Biology, 295 (1) : 442 - 442. doi: 10.1016/j.ydbio.2006.04.359

Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB (2006) Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS genetics, 2 : e91 - e91.

Clark MDP (2004) Systematic identification of zebrafish transcripts and analysis of their expression.. PhD Thesis.

Dickmeis T, Rastegar S, Lam CS, Aanstad P, Clark M, Fischer N, Rosa F, Korzh V, Strähle U (2002) Expression of the helix-loop-helix gene id3 in the zebrafish embryo. Mechanisms of Development, 113 (1) : 99 - 102. doi: 10.1016/S0925-4773(02)00006-0

Faisst AM, Alvarez-Bolado G, Treichel D, Gruss P, Tadokoro Y, Yomogida K, Ohta H, Tohda A, Nishimune Y, Brody T, others (2002) G. Frazzetto, P. Klingbeil, T. Bouwmeester (Germany) Xenopus marginal coil (Xmc), a novel FGF inducible cytosolic coiled-coil protein regulating gastrulation movements 3. Mechanisms of Development, 113 : 227 - 228.

Wierling CK, Steinfath M, Elge T, Schulze-Kremer S, Aanstad P, Clark M, Lehrach H, Herwig R (2002) Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. BMC BIOINFORMATICS, 3 : doi: 10.1186/1471-2105-3-29

Clark MD (2001) An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library. Genome Research, 11 (9) : 1594 - 1602. doi: 10.1101/gr.186901

Dickmeis T (2001) A crucial component of the endoderm formation pathway, CASANOVA, is encoded by a novel sox-related gene. Genes & Development, 15 (12) : 1487 - 1492. doi: 10.1101/gad.196901

Dickmeis T, Aanstad P, Clark M, Fischer N, Herwig R, Mourrain P, Blader P, Rosa F, Lehrach H, Strähle U (2001) Identification of nodal signaling targets by array analysis of induced complex probes. Developmental Dynamics, 222 (4) : 571 - 580. doi: 10.1002/dvdy.1220

Dickmeis T, Rastegar S, Aanstad P, Clark M, Fischer N, Korzh V, Strähle U (2001) Expression of the anti-dorsalizing morphogenetic protein gene in the zebrafish embryo. Development Genes and Evolution, 211 (11) : 568 - 572. doi: 10.1007/s00427-001-0190-3

Dickmeis T, Rastegar S, Aanstad P, Clark M, Fischer N, Plessy C, Rosa F, Korzh V, Strähle U (2001) Expression of brain subtype creatine kinase in the zebrafish embryo. Mechanisms of Development, 109 (2) : 409 - 412. doi: 10.1016/S0925-4773(01)00536-6

Herwig R, Aanstad P, Clark M, Lehrach H (2001) Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments. Nucleic acids research, 29 : e117 - e117.

Shinya M, Eschbach C, Clark M, Lehrach H, Furutani-Seiki M (2000) Zebrafish Dkk1, induced by the pre-MBT Wnt signaling, is secreted from the prechordal plate and patterns the anterior neural plate. Mechanisms of Development, 98 (1-2) : 3 - 17. doi: 10.1016/S0925-4773(00)00433-0

Boeddrich A, Burgtorf C, Crollius HR, Hennig S, Bernot A, Clark M, Reinhardt R, Lehrach H, Francis F (1999) Analysis of the Spermine Synthase Gene Region inFugu rubripes, Tetraodon fluviatilis,andDanio rerio. Genomics, 57 (1) : 164 - 168. doi: 10.1006/geno.1998.5732

Clark MD, Panopoulou GD, Cahill DJ, Bussow K, Lehrach H (1999) Construction and analysis of arrayed cDNA libraries. CDNA PREPARATION AND CHARACTERIZATION, 303 : 205 - 233.

Clark MD, Panopoulou GD, Cahill DJ, Büssow K, Lehrach H (1999) [13] Construction and analysis of arrayed cDNA libraries, In: Methods in enzymology, Academic Press : 205 - 233.

Dheen T, Sleptsova-Friedrich I, Xu YF, Clark M, Lehrach H, Gong ZY, Korzh V (1999) Zebrafish tbx-c functions during formation of midline structures. DEVELOPMENT, 126 (12) : 2703 - 2713.

Förnzler D, Her H, Knapik EW, Clark M, Lehrach H, Postlethwait JH, Zon LI, Beier DR (1998) Gene mapping in zebrafish using single-strand conformation polymorphism analysis. Genomics, 51 : 216 - 222.

Lehrach H, Meier-Ewert S, Clark M, Panopoulou G, Poustka A, Radelof U, O Brien J, Maier E, Lange J, Schmitt A, others (1998) High throughput tools for gene identification and functional gene analysis. Nucleic Acids Symposium Series 38 : 7 - 10.

Panopoulou GD, Clark MD, Gerst H, Herwig R, Holland LZ, Holland ND, Lehrach H (1998) Large-scale identification of Amphioxus genes from different developmental stages using oligonucleotide fingerprinting. DEVELOPMENTAL BIOLOGY 198 (1) : 200 - 200.

Panopoulou GD, Clark MD, Holland LZ, Lehrach H, Holland ND (1998) AmphiBMP2/4, an amphioxus bone morphogenetic protein closely related to Drosophila decapentaplegic and vertebrate BMP2 and BMP4: Insights into evolution of dorsoventral axis specification. DEVELOPMENTAL DYNAMICS, 213 (1) : 130 - 139. doi: 10.1002/(SICI)1097-0177(199809)213:1<130::AID-AJA13>3.3.CO;2-Z

Holland ND, Zhang SC, Clark M, Panopoulou G (1997) Sequence and developmental expression of AmphiTob, an amphioxus homolog of vertebrate Tob in the PC3/BTG1/Tob family of tumor suppressor genes. DEVELOPMENTAL DYNAMICS, 210 (1) : 11 - 18. doi: 10.1002/(SICI)1097-0177(199709)210:1<11::AID-AJA2>3.0.CO;2-4

Hunter KW, Riba L, Schalkwyk L, Clark M, Resenchuk S, Beeghly A, Su J, Tinkov F, Lee P, Ramu E, Lehrach H, Housman D (1996) Toward the construction of integrated physical and genetic maps of the mouse genome using interspersed repetitive sequence PCR (IRS-PCR) genomics.. Genome Research, 6 (4) : 290 - 299. doi: 10.1101/gr.6.4.290

Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnere G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin A-A, Stein N, Mascher M, Himmelbach A, Choulet F, Keeble-Gagnere G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin A-A, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V, Choulet F, Keeble-Gagnere G, Mascher M, Josselin A-A, Rogers J, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnere G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Simkova H, Wicker T, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L, Appels R, Rimbert H, Choulet F, Juhasz A, Keeble-Gagnere G, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnere G, Mayer KFX, Wicker T, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M, Lang D, Spannagl M, Appels R, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D, Rogers J, Jacobs J, Alaux M, Appels R, Bartos J, Bellec A, Berges H, Dolezel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen O-A, Simkova H, Singh K, Valarik M, van der Vossen E, Vautrin S, Weining S, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J, Tiwari V, Gill B, Paux E, Poland J, Dolezel J, Cihalikova J, Simkova H, Toegelova H, Vrana J, Sourdille P, Darrier B, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G, Small I, Melonek J, Zhou R, Juhasz A, Belova T, Appels R, Olsen O-A, Kanyuka K, King R, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Dolezel J, Cizkova J, Tibbits J, Budak H, Akpinar BA, Biyiklioglu S, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A, Dolezel J, Simkova H, Cihalikova J, Kubalakova M, Safar J, Vrana J, Berges H, Bellec A, Vautrin S, Alaux M, Alfama F, Adam-Blondon A-F, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T, Choulet F, Paux E, Alberti A, Aury J-M, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Gill B, Kaur G, Luo M, Sehgal S, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Dolezel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S, Gill B, Kaur G, Luo M, Sehgal S, Bartos J, Holusova K, Plihal O, Clark MD, Heavens D, Kettleborough G, Wright J, Valarik M, Abrouk M, Balcarkova B, Holusova K, Hu Y, Luo M, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Appels R, Hayden M, Keeble-Gagnere G, Rigault P, Tibbits J, Olsen O-A, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B, Simkova H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelova H, Tulpova Z, Visendi P, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Simkova H, Small I, Spannagl M, Swarbreck D, Uauy C, IWGSC , Principal IWGSCR, Prin IWGSCW-GA, Assembly W-GS, Scaffolding H-CD-B, Quality W-GA, Assembly P, Gene RGS, Annotation A, Curation MG, Anal SC, Elements T, Anal P, Data TAR-S, Methylome W-G, Anal HM, BAC CMTPI-BW, Map CLTCMP, Mapping RH, Mapping O, Anal R, Anal GF, Family CBFG, Family DG, Family NLRG, Family PPRG, Family PG, Family WAKG, Team SSSQTL, Team FICFLCG, Anal GS, Annotation MT, Mapping GM, Sorting BACLC, Repository BACPBACL, Repository IWGSCSD, 1A PMB-BS, Assembly BBACS, Mapping DDDP, Mapping AP, Mapping AP, Wh BDBBDIWGSCB, Mapping AP, BAC DPM, Assembly DBACS, Ass APMBACS, Assembly BBACS, Assembly BBACS, Sequencing APMBAC, Sequencing BPMBAC, Assembly DBACS, Sequencing DPMBAC, Figures , Team MW (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. SCIENCE, 361 (6403) : 661 - +. doi: 10.1126/science.aar7191

EAST ENV (null) General EnvEast enquiries. null,

Finlayson TS, Clark M, Bevan M, Griffiths S (null) CropQuant: An automated and scalable field phenotyping platform for crop 1 monitoring and trait measurements to facilitate breeding and digital agriculture 2. null,

Heavens D, Accinelli GG, Clavijo B, Clark MD (2015) A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost. BioTechniques, 59 (1) : doi: 10.2144/000114310

Mock T, Van Oosterhout C, Moulton V, Clark M (null) Genome editing for the exploration of biotechnological applications and evolutionary potential of microalgae (MOCKUENV18EE). null,

Courses taught

Bioinformatics Tools and Resources
South African Society of Human Genetics, Durban, South Africa
8/2018 - 3/2018.

Professional training: Metagenomics Bioinformatics
European Bioinformatics Institute, Cambridge, United Kingdom
10/2016.

Introduction

Summary

My research is multi-disciplinary: combining molecular biology, genomics, population genetics, and computational biology amongst other disciplines. We have a focus on plant and plant pathogen research, especially for key crops groups such as Triticeae (Wheat, Barley & Rye) and Solanaceae (Potatoes, Tomatoes, Aubergines, Peppers and even Tobacco). 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, and stray outside of plants if an appropriate model or test case presents itself.

Qualifications

Degrees

PhD, Max Planck Institute for Molecular Genetics, Berlin, 1997 - 2002

BSc, imperial College, London, 1990 - 1993

Employment history

Academic

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

McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, et al. (2018) The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nature Ecology & Evolution, 2 (6) : 1000 - 1008. doi: 10.1038/s41559-018-0548-9

Leggett RM, Clark MD (2017) A world of opportunities with nanopore sequencing. Journal of Experimental Botany, 68 (20) : 5419 - 5429. doi: 10.1093/jxb/erx289

Giolai M, Paajanen P, Verweij W, Witek K, Jones JDG, et al. (2017) Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire. BMC Genomics, 18 (1) : doi: 10.1186/s12864-017-3936-7

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, et al. (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 (5) : 885 - 896. doi: 10.1101/gr.217117.116

Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, et al. (2017) Genomic innovation for crop improvement. Nature, 543 (7645) : 346 - 354. doi: 10.1038/nature22011

Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, et al. (2017) Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics. bioRxiv, 180406 - 180406.

Projects

Grants

Wheat Pan-Genomics
Role: Principal investigatorClark MD
Funding: BBSRC
Total value £1,355,785 (to Museum £539,000)
Dates: 2018 - 2020

Limits to Evolutionary Adaptation of Phytoplankton in the arctic Ocean
Co-investigator: Clark M
Funding: NERC
Total value £638,621 (to Museum £10,819)
Dates: 2018 - 2020

Publications

Publications

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 (2018) The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nature Ecology & Evolution, 2 (6) : 1000 - 1008. doi: 10.1038/s41559-018-0548-9

Claire Armstrong LGS (2018) Genomic associations with bill length and disease reveal drift and selection across island bird populations. Evolution Letters,

Wilson AJ, Nelson TC, Cresko WA, Armstrong C, Richardson DS, Hipperson H, Horsburgh GJ, Küpper C, Percival-Alwyn L, Clark M, others (2018) COMMENTS AND OPINIONS. null,

Leggett RM, Clark MD (2017) A world of opportunities with nanopore sequencing. Journal of Experimental Botany, 68 (20) : 5419 - 5429. doi: 10.1093/jxb/erx289

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 (1) : doi: 10.1186/s12864-017-3936-7

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 (5) : 885 - 896. doi: 10.1101/gr.217117.116

Beier S, Himmelbach A, Colmsee C, Zhang X-Q, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.. Scientific Data, 4 : 170044 - 170044. doi: 10.1038/sdata.2017.44

Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature, 543 (7645) : 346 - 354. doi: 10.1038/nature22011

Hickey JM, Chiurugwi T, Mackay I, Powell W, Hickey JM, Chiurugwi T, Mackay I, Powell W, Eggen A, Kilian A, Jones C, Canales C, Grattapaglia D, Bassi F, Atlin G, Gorjanc G, Dawson I, Rabbi I, Ribaut J-M, Rutkoski J, Benzie J, Lightner J, Mwacharo J, Parmentier J, Robbins K, Skot L, Wolfe M, Rouard M, Clark M, Amer P, Gardiner P, Hendre P, Mrode R, Sivasankar S, Rasmussen S, Groh S, Jackson V, Thomas W, Beyene Y (2017) Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nature Genetics, 49 (9) : 1297 - 1303. doi: 10.1038/ng.3920

Kelly S, Ivens A, Mott GA, O’Neill E, Emms D, Macleod O, Voorheis P, Tyler K, Clark M, Matthews J, Matthews K, Carrington M (2017) An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri. Genome Biology and Evolution, 9 (8) : 2093 - 2109. doi: 10.1093/gbe/evx152

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.

Lu F-H, McKenzie N, Kettleborough G, Heavens D, Clark MD, Bevan MW (2018) Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries. GigaScience, 7 (5) : doi: 10.1093/gigascience/giy053

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, others (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature, 544 : 427 - 427.

McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, others (2017) The ash dieback invasion of Europe was founded by two individuals from a native population with huge adaptive potential. bioRxiv, 146746 - 146746.

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 (7638) : 536 - 540. doi: 10.1038/nature20803

Paajanen P, Kettleborough G, Lopez-Girona E, Giolai M, Heavens D, Baker D, Lister A, Wilde G, Hein I, Macaulay I, others (2017) A critical comparison of technologies for a plant genome sequencing project. bioRxiv, 201830 - 201830.

Paajanen P, Strauss J, van Oosterhout C, McMullan M, Clark MD, Mock T (2017) Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus. Scientific Data, 4 : 170149 - 170149. doi: 10.1038/sdata.2017.149

Zhou J, Reynolds D, Websdale D, Le Cornu T, Gonzalez-Navarro O, Lister C, Orford S, Laycock S, Finlayson G, Stitt T, others (2017) CropQuant: An automated and scalable field phenotyping platform for crop monitoring and trait measurements to facilitate breeding and digital agriculture. bioRxiv, 161547 - 161547.

Giolai M, Paajanen P, Verweij W, Percival-Alwyn L, Baker D, Witek K, Jupe F, Bryan G, Hein I, Jones JD, others (2016) Targeted capture and sequencing of gene-sized DNA molecules. Biotechniques, 61 : 315 - 322.

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 (6) : 656 - 660. doi: 10.1038/nbt.3540

Heavens D, Accinelli GG, Clavijo B, Clark MD (2015) Benchmarks. Biotechniques, 59 : 42 - 45.

Kenyon EJ, Campos I, Bull JC, Williams PH, Stemple DL, Clark MD (2015) Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling. Developmental Biology, 397 (2) : 212 - 224. doi: 10.1016/j.ydbio.2014.11.007

Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP (2015) NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics, 32 : 142 - 144.

Rallapalli G, Saunders DG, Yoshida K, Edwards A, Lugo CA, Collin S, Clavijo B, Corpas M, Swarbreck D, Clark M, Downie JA, Kamoun S, MacLean D (2015) Lessons from Fraxinus, a crowd-sourced citizen science game in genomics. eLife, 4 : doi: 10.7554/eLife.07460

Saunders D, Yoshida K, Sambles C, Glover R, Clavijo B, Corpas M, Bunting D, Dong S, Clark M, Swarbreck D, others (2014) Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community.. BioRxiv, 004564 - 004564.

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, Eliott D, Threadgold G, Harden G, Ware D, Mortimer 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, 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 J, 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, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, 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 (7446) : 498 - 503. doi: 10.1038/nature12111

Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M (2014) NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. Bioinformatics, 30 (4) : 566 - 568. doi: 10.1093/bioinformatics/btt702

MacLean D, Yoshida K, Edwards A, Crossman L, Clavijo B, Clark M, Swarbreck D, Bashton M, Chapman P, Gijzen M, Caccamo M, Downie A, Kamoun S, Saunders DG (2013) Crowdsourcing genomic analyses of ash and ash dieback – power to the people. GigaScience, 2 (1) : doi: 10.1186/2047-217X-2-2

Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher J-P, Clark KJ, Stemple DL, Klee EW, Ekker SC, Scaria V, Sivasubbu S (2013) A Sequence-Based Variation Map of Zebrafish. Zebrafish, 10 (1) : 15 - 20. doi: 10.1089/zeb.2012.0848

Nasiadka A, Clark MD (2012) Zebrafish Breeding in the Laboratory Environment. ILAR Journal, 53 (2) : 161 - 168. doi: 10.1093/ilar.53.2.161

Clark MD, Guryev V, de Bruijn E, Nijman IJ, Tada M, Wilson C, Deloukas P, Postlethwait JH, Cuppen E, Stemple DL (2011) Single Nucleotide Polymorphism (SNP) Panels for Rapid Positional Cloning in Zebrafish, In: null, null : 221 - 235.

Clark MD, Guryev V, de Bruijn E, Nijman IJ, Tada M, Wilson C, Deloukas P, Postlethwait JH, Cuppen E, Stemple DL (2011) Single nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish, In: Methods in cell biology, Academic Press : 219 - 235.

WHITELEY AR, BHAT A, MARTINS EP, MAYDEN RL, ARUNACHALAM M, UUSI-HEIKKILÄ S, AHMED ATA, SHRESTHA J, CLARK M, STEMPLE D, BERNATCHEZ L (2011) Population genomics of wild and laboratory zebrafish (Danio rerio). Molecular Ecology, 20 (20) : 4259 - 4276. doi: 10.1111/j.1365-294X.2011.05272.x

Bennett JT, Joubin K, Cheng S, Aanstad P, Herwig R, Clark M, Lehrach H, Schier AF (2007) Nodal signaling activates differentiation genes during zebrafish gastrulation. Developmental Biology, 304 (2) : 525 - 540. doi: 10.1016/j.ydbio.2007.01.012

Ekker SC, Stemple DL, Clark M, Chien C-B, Rasooly RS, Javois LC (2007) Zebrafish Genome Project: Bringing New Biology to the Vertebrate Genome Field. Zebrafish, 4 (4) : 239 - 251. doi: 10.1089/zeb.2007.9979

Pei W, Williams PH, Clark MD, Stemple DL, Feldman B (2007) Environmental and genetic modifiers of squint penetrance during zebrafish embryogenesis. Developmental biology, 308 : 368 - 378.

Feldman B, Pei W, Williams H, Clark M, Stemple DL (2006) Squint protects early embryos from temperature-induced dysmorphology. Developmental Biology, 295 (1) : 442 - 442. doi: 10.1016/j.ydbio.2006.04.359

Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB (2006) Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS genetics, 2 : e91 - e91.

Clark MDP (2004) Systematic identification of zebrafish transcripts and analysis of their expression.. PhD Thesis.

Dickmeis T, Rastegar S, Lam CS, Aanstad P, Clark M, Fischer N, Rosa F, Korzh V, Strähle U (2002) Expression of the helix-loop-helix gene id3 in the zebrafish embryo. Mechanisms of Development, 113 (1) : 99 - 102. doi: 10.1016/S0925-4773(02)00006-0

Faisst AM, Alvarez-Bolado G, Treichel D, Gruss P, Tadokoro Y, Yomogida K, Ohta H, Tohda A, Nishimune Y, Brody T, others (2002) G. Frazzetto, P. Klingbeil, T. Bouwmeester (Germany) Xenopus marginal coil (Xmc), a novel FGF inducible cytosolic coiled-coil protein regulating gastrulation movements 3. Mechanisms of Development, 113 : 227 - 228.

Wierling CK, Steinfath M, Elge T, Schulze-Kremer S, Aanstad P, Clark M, Lehrach H, Herwig R (2002) Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. BMC BIOINFORMATICS, 3 : doi: 10.1186/1471-2105-3-29

Clark MD (2001) An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library. Genome Research, 11 (9) : 1594 - 1602. doi: 10.1101/gr.186901

Dickmeis T (2001) A crucial component of the endoderm formation pathway, CASANOVA, is encoded by a novel sox-related gene. Genes & Development, 15 (12) : 1487 - 1492. doi: 10.1101/gad.196901

Dickmeis T, Aanstad P, Clark M, Fischer N, Herwig R, Mourrain P, Blader P, Rosa F, Lehrach H, Strähle U (2001) Identification of nodal signaling targets by array analysis of induced complex probes. Developmental Dynamics, 222 (4) : 571 - 580. doi: 10.1002/dvdy.1220

Dickmeis T, Rastegar S, Aanstad P, Clark M, Fischer N, Korzh V, Strähle U (2001) Expression of the anti-dorsalizing morphogenetic protein gene in the zebrafish embryo. Development Genes and Evolution, 211 (11) : 568 - 572. doi: 10.1007/s00427-001-0190-3

Dickmeis T, Rastegar S, Aanstad P, Clark M, Fischer N, Plessy C, Rosa F, Korzh V, Strähle U (2001) Expression of brain subtype creatine kinase in the zebrafish embryo. Mechanisms of Development, 109 (2) : 409 - 412. doi: 10.1016/S0925-4773(01)00536-6

Herwig R, Aanstad P, Clark M, Lehrach H (2001) Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments. Nucleic acids research, 29 : e117 - e117.

Shinya M, Eschbach C, Clark M, Lehrach H, Furutani-Seiki M (2000) Zebrafish Dkk1, induced by the pre-MBT Wnt signaling, is secreted from the prechordal plate and patterns the anterior neural plate. Mechanisms of Development, 98 (1-2) : 3 - 17. doi: 10.1016/S0925-4773(00)00433-0

Boeddrich A, Burgtorf C, Crollius HR, Hennig S, Bernot A, Clark M, Reinhardt R, Lehrach H, Francis F (1999) Analysis of the Spermine Synthase Gene Region inFugu rubripes, Tetraodon fluviatilis,andDanio rerio. Genomics, 57 (1) : 164 - 168. doi: 10.1006/geno.1998.5732

Clark MD, Panopoulou GD, Cahill DJ, Bussow K, Lehrach H (1999) Construction and analysis of arrayed cDNA libraries. CDNA PREPARATION AND CHARACTERIZATION, 303 : 205 - 233.

Clark MD, Panopoulou GD, Cahill DJ, Büssow K, Lehrach H (1999) [13] Construction and analysis of arrayed cDNA libraries, In: Methods in enzymology, Academic Press : 205 - 233.

Dheen T, Sleptsova-Friedrich I, Xu YF, Clark M, Lehrach H, Gong ZY, Korzh V (1999) Zebrafish tbx-c functions during formation of midline structures. DEVELOPMENT, 126 (12) : 2703 - 2713.

Förnzler D, Her H, Knapik EW, Clark M, Lehrach H, Postlethwait JH, Zon LI, Beier DR (1998) Gene mapping in zebrafish using single-strand conformation polymorphism analysis. Genomics, 51 : 216 - 222.

Lehrach H, Meier-Ewert S, Clark M, Panopoulou G, Poustka A, Radelof U, O Brien J, Maier E, Lange J, Schmitt A, others (1998) High throughput tools for gene identification and functional gene analysis. Nucleic Acids Symposium Series 38 : 7 - 10.

Panopoulou GD, Clark MD, Gerst H, Herwig R, Holland LZ, Holland ND, Lehrach H (1998) Large-scale identification of Amphioxus genes from different developmental stages using oligonucleotide fingerprinting. DEVELOPMENTAL BIOLOGY 198 (1) : 200 - 200.

Panopoulou GD, Clark MD, Holland LZ, Lehrach H, Holland ND (1998) AmphiBMP2/4, an amphioxus bone morphogenetic protein closely related to Drosophila decapentaplegic and vertebrate BMP2 and BMP4: Insights into evolution of dorsoventral axis specification. DEVELOPMENTAL DYNAMICS, 213 (1) : 130 - 139. doi: 10.1002/(SICI)1097-0177(199809)213:1<130::AID-AJA13>3.3.CO;2-Z

Holland ND, Zhang SC, Clark M, Panopoulou G (1997) Sequence and developmental expression of AmphiTob, an amphioxus homolog of vertebrate Tob in the PC3/BTG1/Tob family of tumor suppressor genes. DEVELOPMENTAL DYNAMICS, 210 (1) : 11 - 18. doi: 10.1002/(SICI)1097-0177(199709)210:1<11::AID-AJA2>3.0.CO;2-4

Hunter KW, Riba L, Schalkwyk L, Clark M, Resenchuk S, Beeghly A, Su J, Tinkov F, Lee P, Ramu E, Lehrach H, Housman D (1996) Toward the construction of integrated physical and genetic maps of the mouse genome using interspersed repetitive sequence PCR (IRS-PCR) genomics.. Genome Research, 6 (4) : 290 - 299. doi: 10.1101/gr.6.4.290

Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnere G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin A-A, Stein N, Mascher M, Himmelbach A, Choulet F, Keeble-Gagnere G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin A-A, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V, Choulet F, Keeble-Gagnere G, Mascher M, Josselin A-A, Rogers J, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnere G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Simkova H, Wicker T, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L, Appels R, Rimbert H, Choulet F, Juhasz A, Keeble-Gagnere G, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnere G, Mayer KFX, Wicker T, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M, Lang D, Spannagl M, Appels R, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D, Rogers J, Jacobs J, Alaux M, Appels R, Bartos J, Bellec A, Berges H, Dolezel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen O-A, Simkova H, Singh K, Valarik M, van der Vossen E, Vautrin S, Weining S, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J, Tiwari V, Gill B, Paux E, Poland J, Dolezel J, Cihalikova J, Simkova H, Toegelova H, Vrana J, Sourdille P, Darrier B, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G, Small I, Melonek J, Zhou R, Juhasz A, Belova T, Appels R, Olsen O-A, Kanyuka K, King R, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Dolezel J, Cizkova J, Tibbits J, Budak H, Akpinar BA, Biyiklioglu S, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A, Dolezel J, Simkova H, Cihalikova J, Kubalakova M, Safar J, Vrana J, Berges H, Bellec A, Vautrin S, Alaux M, Alfama F, Adam-Blondon A-F, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T, Choulet F, Paux E, Alberti A, Aury J-M, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Gill B, Kaur G, Luo M, Sehgal S, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Dolezel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S, Gill B, Kaur G, Luo M, Sehgal S, Bartos J, Holusova K, Plihal O, Clark MD, Heavens D, Kettleborough G, Wright J, Valarik M, Abrouk M, Balcarkova B, Holusova K, Hu Y, Luo M, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Appels R, Hayden M, Keeble-Gagnere G, Rigault P, Tibbits J, Olsen O-A, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B, Simkova H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelova H, Tulpova Z, Visendi P, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Simkova H, Small I, Spannagl M, Swarbreck D, Uauy C, IWGSC , Principal IWGSCR, Prin IWGSCW-GA, Assembly W-GS, Scaffolding H-CD-B, Quality W-GA, Assembly P, Gene RGS, Annotation A, Curation MG, Anal SC, Elements T, Anal P, Data TAR-S, Methylome W-G, Anal HM, BAC CMTPI-BW, Map CLTCMP, Mapping RH, Mapping O, Anal R, Anal GF, Family CBFG, Family DG, Family NLRG, Family PPRG, Family PG, Family WAKG, Team SSSQTL, Team FICFLCG, Anal GS, Annotation MT, Mapping GM, Sorting BACLC, Repository BACPBACL, Repository IWGSCSD, 1A PMB-BS, Assembly BBACS, Mapping DDDP, Mapping AP, Mapping AP, Wh BDBBDIWGSCB, Mapping AP, BAC DPM, Assembly DBACS, Ass APMBACS, Assembly BBACS, Assembly BBACS, Sequencing APMBAC, Sequencing BPMBAC, Assembly DBACS, Sequencing DPMBAC, Figures , Team MW (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. SCIENCE, 361 (6403) : 661 - +. doi: 10.1126/science.aar7191

EAST ENV (null) General EnvEast enquiries. null,

Finlayson TS, Clark M, Bevan M, Griffiths S (null) CropQuant: An automated and scalable field phenotyping platform for crop 1 monitoring and trait measurements to facilitate breeding and digital agriculture 2. null,

Heavens D, Accinelli GG, Clavijo B, Clark MD (2015) A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost. BioTechniques, 59 (1) : doi: 10.2144/000114310

Mock T, Van Oosterhout C, Moulton V, Clark M (null) Genome editing for the exploration of biotechnological applications and evolutionary potential of microalgae (MOCKUENV18EE). null,

Teaching and students

Courses taught

Bioinformatics Tools and Resources
South African Society of Human Genetics, Durban, South Africa
8/2018 - 3/2018.

Professional training: Metagenomics Bioinformatics
European Bioinformatics Institute, Cambridge, United Kingdom
10/2016.