Dr Matt Clark

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

Giolai M, Verweij W, Pearson N, Nicholson P, Leggett RM, Clark MD (null) Air-seq: Measuring air metagenomic diversity in an agricultural ecosystem. null, doi: 10.1101/2022.12.13.520298

Jackson HA, Percival‐Alwyn L, Ryan C, Albeshr MF, Venturi L, Morales HE, Mathers TC, Cocker J, Speak SA, Accinelli GG, Barker T, Heavens D, Willman F, Dawson D, Ward L, Tatayah V, Zuël N, Young R, Concannon L, Whitford H, Clavijo B, Bunbury N, Tyler KM, Ruhomaun K, Grace MK, Bruford MW, Jones CG, Tollington S, Bell DJ, Groombridge JJ, Clark M, Van Oosterhout C (2022) Genomic erosion in a demographically recovered bird species during conservation rescue. Conservation Biology, 36 (4) : doi: 10.1111/cobi.13918

Heavens D, Chooneea D, Giolai M, Cuber P, Aanstad P, Martin S, Alston M, Misra R, Clark MD, Leggett RM (null) How low can you go? Driving down the DNA input requirements for nanopore sequencing. null, doi: 10.1101/2021.10.15.464554

Martin S, Heavens D, Lan Y, Horsfield S, Clark MD, Leggett RM (null) Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples. null, doi: 10.1101/2021.05.07.443191

Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo D-H, Ens J, Wiebe K, N’Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnère G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, Pozniak CJ (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature, 588 (7837) : 277 - 283. doi: 10.1038/s41586-020-2961-x

Bollmann‐Giolai A, Giolai M, Heavens D, Macaulay I, Malone J, Clark MD (2020) A low‐cost pipeline for soil microbiome profiling. MicrobiologyOpen, 9 (12) : doi: 10.1002/mbo3.1133

Bollmann-Giolai A, Giolai M, Heavens D, Macaulay I, Malone J, Clark MD (null) A low-cost pipeline for soil microbiome profiling. null, doi: 10.1101/2020.05.07.082305

Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Peel N, Acford-Palmer H, Hoyles L, Clarke P, Hall LJ, Clark MD (null) Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nature Microbiology, 5 (3) : 430 - 442. doi: 10.1038/s41564-019-0626-z

Giolai M, Verweij W, Lister A, Heavens D, Macaulay I, Clark MD (null) Spatially resolved transcriptomics reveals plant host responses to pathogens. null, doi: 10.1101/720086

Peel N, Dicks LV, Heavens D, Percival-Alwyn L, Cooper C, Clark MD, Davies RG, Leggett RM, Yu DW (null) Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet). null, doi: 10.1101/551960

Giolai M, Verweij W, Lister A, Heavens D, Macaulay I, Clark MD (2019) Spatially resolved transcriptomics reveals plant host responses to pathogens. Plant Methods, 15 (1) : doi: 10.1186/s13007-019-0498-5

Ayling M, Clark MD, Leggett RM (null) New approaches for assembly of short-read metagenomic data. null, doi: 10.7287/peerj.preprints.27332v1

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 (null) 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

Armstrong C, Richardson DS, Hipperson H, Horsburgh GJ, Küpper C, Percival-Alwyn L, Clark M, Burke T, Spurgin LG (2018) Genomic associations with bill length and disease reveal drift and selection across island bird populations. Evolution Letters, 2 (1) : 22 - 36. doi: 10.1002/evl3.38

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,

Lu F-H, McKenzie N, Kettleborough G, Heavens D, Clark MD, Bevan MW (null) Independent assessment and improvement of wheat genome assemblies using Fosill jumping libraries. null, doi: 10.1101/219352

Paajanen P, Kettleborough G, López-Girona E, Giolai M, Heavens D, Baker D, Lister A, Wilde G, Hein I, Macaulay I, Bryan GJ, Clark MD (null) A critical comparison of technologies for a plant genome sequencing project. null, doi: 10.1101/201830

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

Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Hoyles L, Clarke P, Hall LJ, Clark MD (null) Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics. null, doi: 10.1101/180406

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

Leggett RM, Clark MD (null) A world of opportunities with nanopore sequencing. null, doi: 10.7287/peerj.preprints.3090v1

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

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X-Q, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature, 544 (7651) : 427 - 433. doi: 10.1038/nature22043

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 (null) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.. Scientific Data, 4 (1) : 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 (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, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X-Q, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N (2017) A chromosome conformation capture ordered sequence of the barley genome.. Nature, 544 (7651) : 427 - 433. doi: 10.1038/nature22043

McMullan M, Rafiqi M, Kaithakottil G, Clavijo B, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, Garcia 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 A, Clark MD (null) The ash dieback invasion of Europe was founded by two individuals from a native population with huge adaptive potential. null, doi: 10.1101/146746

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, López-Girona E, Giolai M, Heavens D, Baker D, Lister A, Cugliandolo F, Wilde G, Hein I, Macaulay I, Bryan GJ, Clark MD (2019) A critical comparison of technologies for a plant genome sequencing project. GigaScience, 8 (3) : doi: 10.1093/gigascience/giy163

Paajanen P, Strauss J, van Oosterhout C, McMullan M, Clark MD, Mock T (null) Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus. Scientific Data, 4 (1) : doi: 10.1038/sdata.2017.149

Zhou J, Reynolds D, Cornu TL, Websdale D, Orford S, Lister C, Gonzalez-Navarro O, Laycock S, Finlayson G, Stitt T, Clark MD, Bevan MW, Griffiths S (null) CropQuant: An automated and scalable field phenotyping platform for crop monitoring and trait measurements to facilitate breeding and digital agriculture. null, doi: 10.1101/161547

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 D, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Di Palma F, Phillips A, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD (null) An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. null, doi: 10.1101/080796

Giolai M, Paajanen P, Verweij W, Percival-Alwyn L, Baker D, Witek K, Jupe F, Bryan G, Hein I, Jones JDG, Clark MD (2016) Targeted capture and sequencing of gene-sized DNA molecules. BioTechniques, 61 (6) : 315 - 322. doi: 10.2144/000114484

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 (null) NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics, btv540 - btv540. doi: 10.1093/bioinformatics/btv540

Rallapalli G, Saunders DGO, Yoshida K, Edwards A, Lugo CA, Collin S, Clavijo B, Corpas M, Swarbreck D, Clark M, Downie JA, Kamoun S, MacLean D (null) 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, 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 (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 DGO (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, Bruijn ED, 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, Elsevier : 219 - 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) null. BMC Bioinformatics, 3 (1) : 29 - 29. doi: 10.1186/1471-2105-3-29

Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson SL, Group TWU-GSCEST (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, 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, Mourrain P, Saint-Etienne L, Fischer N, Aanstad P, Clark M, Strähle U, Rosa F (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, 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 (2001) Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments. Nucleic Acids Research, 29 (23) : 117e - 117. doi: 10.1093/nar/29.23.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, Büssow K, Lehrach H (1999) [13] Construction and analysis of arrayed cDNA libraries. null, 205 - 233. doi: 10.1016/s0076-6879(99)03015-3

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 Y, Clark M, Lehrach H, Gong Z, Korzh V (1999) Zebrafish tbx-c functions during formation of midline structures. Development, 126 (12) : 2703 - 2713. doi: 10.1242/dev.126.12.2703

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 toDrosophila 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>3.0.co;2-6

Holland ND, Zhang S, Clark M, Panopoulou G, Lehrach H, Holland LZ (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>3.3.co;2-q

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, Stein N, Feuillet C, Keller B, Rogers J, Pozniak CJ, Choulet F, Distelfeld A, Poland J, Ronen G, Sharpe AG, Barad O, Baruch K, Keeble-Gagnère G, Mascher M, Ben-Zvi G, Josselin A-A, Himmelbach A, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Koh C, Muehlbauer G, Pasam RK, Paux E, Rigault P, Tibbits J, Tiwari V, Spannagl M, Lang D, Gundlach H, Haberer G, Mayer KFX, Ormanbekova D, Prade V, Šimková H, Wicker T, Swarbreck D, Rimbert H, Felder M, Guilhot N, Kaithakottil G, Keilwagen J, Leroy P, Lux T, Twardziok S, Venturini L, Juhász A, Abrouk M, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Arnaud D, Chalabi S, Chalhoub B, Cory A, Datla R, Davey MW, Jacobs J, Robinson SJ, Steuernagel B, van Ex F, Wulff BBH, Benhamed M, Bendahmane A, Concia L, Latrasse D, Bartoš J, Bellec A, Berges H, Doležel J, Frenkel Z, Gill B, Korol A, Letellier T, Olsen O-A, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S, Fahima T, Glikson V, Raats D, Číhalíková J, Toegelová H, Vrána J, Sourdille P, Darrier B, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Jones JDG, Witek K, Yu G, Small I, Melonek J, Zhou R, Belova T, Kanyuka K, King R, Nilsen K, Walkowiak S, Cuthbert R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Čížková J, Akpinar BA, Biyiklioglu S, Gao L, N’Daiye A, Kubaláková M, Šafář J, Alfama F, Adam-Blondon A-F, Flores R, Guerche C, Loaec M, Quesneville H, Condie J, Ens J, Maclachlan R, Tan Y, Alberti A, Aury J-M, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Kaur G, Luo M, Sehgal S, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana JP, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Holušová K, Plíhal O, Clark MD, Heavens D, Kettleborough G, Wright J, Balcárková B, Hu Y, 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, Cattonaro F, Jiumeng M, Kugler K, Pfeifer M, Sandve S, Xun X, Zhan B, Batley J, Bayer PE, Edwards D, Hayashi S, Tulpová Z, Visendi P, Cui L, Du X, Feng K, Nie X, Tong W, Wang L (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361 (6403) : 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) : 42 - 45. 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.