AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production
PI: Dr Andrew Davie
Funded by: Biotechnology and Biological Sciences Research Council
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Dr Michaël Bekaert
Senior Lecturer
Institute of Aquaculture Pathfoot Building, University of Stirling, Stirling, FK9 4LA
Contact details
- Email michael.bekaert@stir.ac.uk
- Telephone+44 (0)1786 467870
ORCID 
0000-0002-1206-7654
About me
My current research projects rely on the most up to date next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases.
Research
I have a number of research interests including:
Evolution and conservation of sex chromosomes Drug resistance mechanisms High Density SNP Linkage Map and QTL analysis Genome Sequencing and characterisation of highly virulent bacterial strain Genetic diversity and connectivity marine organsisms Gene and genome duplications Genomics & transcriptomics in non-model organisms
Projects
Optimsation and implementation of sterile triploid salmon in Scotland
PI: Professor Herve Migaud
Funded by: Biotechnology and Biological Sciences Research Council
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Identifying molecular determinants of drug susceptibility in salmon lice (Lepeophtheirus salmonis)
PI:
Funded by: Biotechnology and Biological Sciences Research Council
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ParaFishControl - Advanced Tools and Research Strategies for Parasite Control in European farmed fish
PI: Professor James Bron
Funded by: European Commission
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Efficacy testing of immersion and oral vaccines for Aeromonas hydrophila in Tilapia an Vietnamese catfish
PI: Professor Sandra Adams
Funded by: International Veterinary Vaccinology Network
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AquaExcel2020
PI: Mr John Bostock
Funded by: European Commission
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Genomic breeding for gill health and lice resistance in salmon: Towards a step improvement in accuracy and affordability
PI: Professor James Bron
Funded by: Scottish Aquaculture Innovation Centre
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Identifying molecular determinants of drug susceptibility in salmon lice (Lepeophtheirus salmonis)
PI: Dr Armin Sturm
Funded by: Scottish Salmon Producers Organisation
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Outputs
Article
Li R, Bekaert M, Wu L, Mu C, Song W, Migaud H & Wang C (2019) Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes. Marine Drugs, 17 (8). https://doi.org/10.3390/md17080466; https://doi.org/10.3390/md17080466
Article
Sindbis virus polyarthritis outbreak signalled by virus prevalence in the mosquito vectors
Lundström JO, Hesson JC, Schäfer ML, Östman Ö, Semmler T, Bekaert M, Weidmann M, Lundkvist Å & Pfeffer M (2019) Sindbis virus polyarthritis outbreak signalled by virus prevalence in the mosquito vectors. PLoS Neglected Tropical Diseases, 13 (8), Art. No.: e0007702. https://doi.org/10.1371/journal.pntd.0007702
Article
Razgour O, Forester B, Taggart JB, Bekaert M, Juste J, Ibáñez C, Puechmaille SJ, Novella-Fernandez R, Alberdi A & Manel S (2019) Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections. Proceedings of the National Academy of Sciences of the United States of America, 116 (21), pp. 10418-10423. https://doi.org/10.1073/pnas.1820663116
Article
Carmona-Antoñanzas G, Helgesen KO, Humble JL, Tschesche C, Bakke MJ, Gamble L, Bekaert M, Bassett DI, Horsberg TE, Bron JE & Sturm A (2019) Mutations in voltage-gated sodium channels from pyrethroid resistant salmon lice (Lepeophtheirus salmonis). Pest Management Science, 75 (2), pp. 527-536. https://doi.org/10.1002/ps.5151
Article
Ulrich K, Wehner S, Bekaert M, Paola ND, Dilcher M, Muir KF, Taggart JB, Matejusova I & Weidmann M (2018) Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades. Journal of General Virology, 99 (12), pp. 1567-1581. https://doi.org/10.1099/jgv.0.001155
Article
Hansen S, Faye O, Sanabani SS, Faye M, Böhlken-Fascher S, Faye O, Sall AA, Bekaert M, Weidmann M, Czerny C & Abd El Wahed A (2018) Combination Random Isothermal Amplification and Nanopore Sequencing For Rapid Identification of the Causative Agent of an Outbreak. Journal of Clinical Virology, 106, pp. 23-27. https://doi.org/10.1016/j.jcv.2018.07.001
Article
New diagnostic SNP molecular markers for the Mytilus species complex
Wilson J, Matejusova I, McIntosh RE, Carboni S & Bekaert M (2018) New diagnostic SNP molecular markers for the Mytilus species complex. PLOS ONE, 13 (7), Art. No.: e0200654. https://doi.org/10.1371/journal.pone.0200654
Article
Development of a single-tube one-step RT-LAMP assay to detect the Chikungunya virus genome
Lopez Jimena B, Wehner S, Harold G, Bakheit M, Frischmann S, Bekaert M, Faye O, Sall AA & Weidmann M (2018) Development of a single-tube one-step RT-LAMP assay to detect the Chikungunya virus genome [Detection of Chikunguny a virus by RT-LAMP]. PLoS Neglected Tropical Diseases, 12 (5), Art. No.: e0006448. https://doi.org/10.1371/journal.pntd.0006448; https://doi.org/10.1371/journal.pntd.0006448
Article
Lopez-Jimena B, Bekaert M, Bakheit M, Frischmann S, Patel P, Simon-Loriere E, Lambrechts L, Duong V, Dussart P, Harold G, Fall C, Faye O, Sall AA & Weidmann M (2018) Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype [Detection of each DENV serotype by RT-LAMP]. PLOS Neglected Tropical Diseases, 12 (5), Art. No.: e0006381. https://doi.org/10.1371/journal.pntd.0006381
Article
Evolution and conservation of Characidium sex chromosomes
Utsunomia R, Scacchetti PC, Hermida M, Fernandez-Cebrian R, Taboada X, Fernandez C, Bekaert M, Mendes NJ, Robledo D, Mank JE, Taggart J, Oliveira C, Foresti F & Martinez P (2017) Evolution and conservation of Characidium sex chromosomes. Heredity, 119 (4), pp. 237-244. https://doi.org/10.1038/hdy.2017.43
Article
Subcellular localization and function study of a secreted phospholipase C from Nocardia seriolae
Xia L, Liang H, Xu L, Chen J, Bekaert M, Zhang H & Yu L (2017) Subcellular localization and function study of a secreted phospholipase C from Nocardia seriolae. FEMS Microbiology Letters, 364 (17), Art. No.: fnx143. https://doi.org/10.1093/femsle/fnx143
Article
Carmona-Antoñanzas G, Bekaert M, Humble JL, Boyd S, Roy W, Bassett DI, Houston RD, Gharbi K, Bron JE & Sturm A (2017) Maternal inheritance of deltamethrin resistance in the salmon louse Lepeophtheirus salmonis (Krøyer) is associated with unique mtDNA haplotypes. PLoS ONE, 12 (7), Art. No.: e0180625. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180625; https://doi.org/10.1371/journal.pone.0180625
Article
Mac Aogain M, Fennelly N, Walsh A, Lynagh Y, Bekaert M, Lawlor B, Walsh P, Kelly B, Rogers TR & Crowley B (2017) Fourteen Draft Genome Sequences for the First Reported Cases of Azithromycin-Resistant Neisseria gonorrhoeae in Ireland. Genome Announcements, 5 (23), Art. No.: e00403-17. https://doi.org/10.1128/genomeA.00403-17
Article
Gene-centromere mapping in meiotic gynogenetic European seabass
Oral M, Colléter J, Bekaert M, Taggart JB, Palaiokostas C, McAndrew BJ, Vandeputte M, Chatain B, Kuhl H, Reinhardt R, Peruzzi S & Penman DJ (2017) Gene-centromere mapping in meiotic gynogenetic European seabass. BMC Genomics, 18 (1), Art. No.: 449. https://doi.org/10.1186/s12864-017-3826-z
Article
Ramirez-Paredes J, Larsson P, Wehner S, Bekaert M, Ohrman C, Metselaar M, Thompson KD, Richards R, Penman D & Adams A (2017) Draft Genome Sequence of Francisella noatunensis subsp. orientalis STIR-GUS-F2f7, a Highly Virulent Strain Recovered from Diseased Red Nile Tilapia Farmed in Europe. Genome Announcements, 5 (11), Art. No.: e01555-16. https://doi.org/10.1128/genomeA.01555-16
Article
Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic
Mathiesen SS, Thyrring J, Hemmer-Hansen J, Berge J, Sukhotin A, Leopold P, Bekaert M, Sejr MK & Nielsen EE (2017) Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic. Evolutionary Applications, 10 (1), pp. 39-55. https://doi.org/10.1111/eva.12415
Book Chapter
McAndrew B, Penman D, Bekaert M & Wehner S (2016) Tilapia genomic studies. In: MacKenzie S & Jentoft S (eds.) Genomics in Aquaculture. London: Elsevier, pp. 105-130. http://store.elsevier.com/Genomics-in-Aquaculture/isbn-9780128014189/
Article
Tsai HY, Robledo D, Lowe NR, Bekaert M, Taggart JB, Bron J & Houston RD (2016) Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome. G3: Genes Genomes Genetics, 6 (7), pp. 2173-2179. https://doi.org/10.1534/g3.116.029009
Article
Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing
Brown J, Taggart J, Bekaert M, Wehner S, Palaiokostas C, Setiawan AN, Symonds JE & Penman D (2016) Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing. BMC Genomics, 17 (1), Art. No.: 448. https://doi.org/10.1186/s12864-016-2773-4
Article
Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, Bekaert M & Teeling EC (2016) A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals. Molecular Ecology Resources, 16 (1), pp. 150-162. https://doi.org/10.1111/1755-0998.12447
Article
Sirimanapong W, Thompson KD, Ooi EL, Bekaert M, Collet B, Taggart J, Bron J, Green D, Shinn A, Adams A & Leaver M (2015) The effects of feeding β-glucan to Pangasianodon hypophthalmus on immune gene expression and resistance to Edwardsiella ictaluri. Fish and Shellfish Immunology, 47 (1), pp. 595-605. https://doi.org/10.1016/j.fsi.2015.09.042
Article
Trumbic Z, Bekaert M, Taggart J, Bron J, Gharbi K & Mladineo I (2015) Development and validation of a mixed tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758). BMC Genomics, 16, Art. No.: 1007. https://doi.org/10.1186/s12864-015-2208-7
Article
Carmona-Antonanzas G, Carmichael SN, Heumann J, Taggart J, Bron J, Bekaert M, Sturm A & Gharbi K (2015) A survey of the ATP-binding cassette (ABC) gene superfamily in the salmon louse (Lepeophtheirus salmonis). PLoS ONE, 10 (9), Art. No.: e0137394. https://doi.org/10.1371/journal.pone.0137394
Article
Palaiokostas C, Bekaert M, Taggart J, Gharbi K, McAndrew B, Chatain B, Penman D & Vandeputte M (2015) A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax). Genetics Selection Evolution, 47, Art. No.: 68. https://doi.org/10.1186/s12711-015-0148-y
Article
The butterfly plant arms-race escalated by gene and genome duplications
Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glockner G, Platts AE, Pires JC, Heckel DG, Der JP, Wafula EK, Tang M, Hofberger JA, Smithson A, Hall JC & Blanchette M (2015) The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences, 112 (27), pp. 8362-8366. https://doi.org/10.1073/pnas.1503926112
Article
Walsh P, Bekaert M, Carroll J, Manning T, Kelly B, O'Driscoll A, Lu X, Smith C, Dickinson P, Templeton K, Ghazal P & Sleator RD (2015) Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary. Genome Announcements, 3 (3), Art. No.: e00471-15. https://doi.org/10.1128/genomeA.00471-15
Article
A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus)
Palaiokostas C, Bekaert M, Khan MGQ, Taggart J, Gharbi K, McAndrew B & Penman D (2015) A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus). BMC Genomics, 16 (1), Art. No.: 171. https://doi.org/10.1186/s12864-015-1383-x
Article
A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats
Hayden S, Bekaert M, Goodbla A, Murphy WJ, Davalos LM & Teeling EC (2014) A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats. Molecular Biology and Evolution, 31 (4), pp. 917-927. https://doi.org/10.1093/molbev/msu043
Article
Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)
Houston RD, Taggart J, Cezard T, Bekaert M, Lowe NR, Downing A, Talbot RT, Bishop SC, Archibald AL, Bron J, Penman D, Davassi A, Brew F, Tinch AE, Gharbi K & Hamilton A (2014) Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar). BMC Genomics, 15 (1), Art. No.: 90. https://doi.org/10.1186/1471-2164-15-90
Article
Gene duplication and phenotypic changes in the evolution of Mammalian metabolic networks
Bekaert M & Conant GC (2014) Gene duplication and phenotypic changes in the evolution of Mammalian metabolic networks. PLoS ONE, 9 (1), Art. No.: e87115. https://doi.org/10.1371/journal.pone.0087115
Article
Carmichael SN, Bekaert M, Taggart J, Christie HRL, Bassett DI, Bron J, Skuce P, Gharbi K, Skern-Mauritzen R & Sturm A (2013) Identification of a sex-linked SNP marker in the salmon louse (Lepeophtheirus salmonis) using RAD sequencing. PLoS ONE, 8 (10), Art. No.: e77832. https://doi.org/10.1371/journal.pone.0077832
Article
Palaiokostas C, Bekaert M, Davie A, Cowan M, Oral M, Taggart J, Gharbi K, McAndrew B, Penman D & Migaud H (2013) Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing. BMC Genomics, 14 (1), Art. No.: 566. https://doi.org/10.1186/1471-2164-14-566
Article
Palaiokostas C, Bekaert M, Khan MGQ, Taggart J, Gharbi K, McAndrew B & Penman D (2013) Mapping and Validation of the Major Sex-Determining Region in Nile Tilapia (Oreochromis niloticus L.) Using RAD Sequencing. PLoS ONE, 8 (7), Art. No.: e68389. http://dx.doi.org/10.1371/journal.pone.0068389; https://doi.org/10.1371/journal.pone.0068389
Article
Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire
Bekaert M, Lowe NR, Bishop SC, Bron J, Taggart J & Houston RD (2013) Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire. PLoS ONE, 8 (7), Art. No.: e70136. https://doi.org/10.1371/journal.pone.0070136
Article
Carmichael SN, Bron J, Taggart J, Ireland J, Bekaert M, Burgess S, Skuce P, Nisbet A, Gharbi K & Sturm A (2013) Salmon lice (Lepeophtheirus salmonis) showing varying emamectin benzoate susceptibilities differ in neuronal acetylcholine receptor and GABA-gated chloride channel mRNA expression. BMC Genomics, 14, Art. No.: 408. https://doi.org/10.1186/1471-2164-14-408
Article
Kirwan JD, Bekaert M, Commins JM, Davies KT, Rossiter SJ & Teeling EC (2013) A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals. Evolutionary Applications, 6 (3), pp. 412-422. https://doi.org/10.1111/eva.12047
Article
Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
Bekaert M (2012) Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation. PLoS ONE, 7 (11), p. e49903. https://doi.org/10.1371/journal.pone.0049903
Article
Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis
Bekaert M, Edger PP, Hudson CM, Pires JC & Conant GC (2012) Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytologist, 196 (2), pp. 596-605. https://doi.org/10.1111/j.1469-8137.2012.04302.x
Article
Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications
Hudson CM, Puckett EE, Bekaert M, Pires JC & Conant GC (2011) Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications. Genome Biology and Evolution, 3, pp. 1369-1380. https://doi.org/10.1093/gbe/evr115
Article
Bekaert M, Edger PP, Pires JC & Conant GC (2011) Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints. Plant Cell, 23 (5), pp. 1719-1728. https://doi.org/10.1105/tpc.110.081281
Article
Transcriptional robustness and protein interactions are associated in yeast
Bekaert M & Conant GC (2011) Transcriptional robustness and protein interactions are associated in yeast. BMC Systems Biology, 5, p. Article 62. http://www.biomedcentral.com/1752-0509/5/62; https://doi.org/10.1186/1752-0509-5-62
Article
Copy Number Alterations among Mammalian Enzymes Cluster in the Metabolic Network
Bekaert M & Conant GC (2011) Copy Number Alterations among Mammalian Enzymes Cluster in the Metabolic Network. Molecular Biology and Evolution, 28 (2), pp. 1111-1121. https://doi.org/10.1093/molbev/msq296
Article
The status of the cryptic bat species, Myotis mystacinus and Myotis brandtii in Ireland
Boston ESM, Buckley DJ, Bekaert M, Gager Y, Lundy MG, Scott DD, Prodohl PA, Montgomery WI, Marnell F & Teeling EC (2010) The status of the cryptic bat species, Myotis mystacinus and Myotis brandtii in Ireland. Acta Chiropterologica, 12 (2), pp. 457-461. https://doi.org/10.3161/150811010X538025
Book Chapter
Computational resources for studying recoding
Bekaert M (2010) Computational resources for studying recoding. In: Atkins, JF, Gesteland & RF (eds.) Recoding: expansion of decoding rules enriches gene expression. Nucleic acids and molecular biology, 24. Berlin: Springer, pp. 435-461. http://dx.doi.org/10.1007/978-0-387-89382-2_20
Article
White-Nose Syndrome Fungus (Geomyces destructans) in Bat, France
Puechmaille SJ, Verdeyroux P, Fuller H, Gouilh MA, Bekaert M & Teeling EC (2010) White-Nose Syndrome Fungus (Geomyces destructans) in Bat, France. Emerging Infectious Diseases, 16 (2), pp. 290-293. https://doi.org/10.3201/eid1602.091391
Article
Recode-2: new design, new search tools, and many more genes
Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF & Baranov PV (2010) Recode-2: new design, new search tools, and many more genes. Nucleic Acids Research, 38 (Supplement 1), pp. D69-D74. https://doi.org/10.1093/nar/gkp788
Article
Ecological adaptation determines functional mammalian olfactory subgenomes
Hayden S, Bekaert M, Crider TA, Mariani S, Murphy WJ & Teeling EC (2010) Ecological adaptation determines functional mammalian olfactory subgenomes [Sara Hayden1,3, Michaël Bekaert1,3, Tess A. Crider2, Stefano Mariani1, William J. Murphy2,4 and Emma C. Teeling1,4]. Genome Research, 20 (1), pp. 1-9. https://doi.org/10.1101/gr.099416.109
Article
UniPrime2: a web service providing easier Universal Primer design
Boutros R, Stokes N, Bekaert M & Teeling EC (2009) UniPrime2: a web service providing easier Universal Primer design. Nucleic Acids Research, 37 (Supplement 2), pp. W209-W213. https://doi.org/10.1093/nar/gkp269
Article
UniPrime: a workflow-based platform for improved universal primer design
Bekaert M & Teeling EC (2008) UniPrime: a workflow-based platform for improved universal primer design. Nucleic Acids Research, 36 (10), p. e56. https://doi.org/10.1093/nar/gkn191
Article
Bekaert M, Ivanov IP, Atkins JF & Baranov PV (2008) Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs. BMC Bioinformatics, 9 (178). https://doi.org/10.1186/1471-2105-9-178
Article
Bekaert M, Atkins JF & Baranov PV (2006) ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting. Bioinformatics, 22 (20), pp. 2463-2465. https://doi.org/10.1093/bioinformatics/btl430
Article
Bekaert M & Rousset J (2005) An extended signal involved in eukaryotic - 1 frameshifting operates through modification of the E site tRNA. Molecular Cell, 17 (1), pp. 61-68. https://doi.org/10.1016/j.molcel.2004.12.009
Article
Towards a computational model for-1 eukaryotic frameshifting sites
Bekaert M, Bidou L, Denise A, Duchateau-Nguyen G, Forest J, Froidevaux C, Hatin I, Rousset J & Termier M (2003) Towards a computational model for-1 eukaryotic frameshifting sites. Bioinformatics, 19 (3), pp. 327-335. https://doi.org/10.1093/bioinformatics/btf868