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

AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production
PI: Dr Andrew Davie
Funded by: Biotechnology and Biological Sciences Research Council
01/01/2019–31/12/2021

AquaExcel2020
PI: Mr John Bostock
Funded by: European Commission
01/10/2015–30/09/2020

ParaFishControl - Advanced Tools and Research Strategies for Parasite Control in European farmed fish
PI: Professor James Bron
Funded by: European Commission
01/04/2015–31/03/2020

Optimsation and implementation of sterile triploid salmon in Scotland
PI: Professor Herve Migaud
Funded by: Biotechnology and Biological Sciences Research Council
01/10/2014–31/12/2018

Identifying molecular determinants of drug susceptibility in salmon lice (Lepeophtheirus salmonis)
PI:
Funded by: Biotechnology and Biological Sciences Research Council
02/12/2014–31/05/2018

Identifying molecular determinants of drug susceptibility in salmon lice (Lepeophtheirus salmonis)
PI: Dr Armin Sturm
Funded by: Scottish Salmon Producers Organisation
02/12/2014–01/12/2017

Outputs

Article

Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

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

Mutations in voltage-gated sodium channels from pyrethroid resistant salmon lice (Lepeophtheirus salmonis) (Forthcoming/Available Online)

Carmona-Antoñanzas G, Helgesen KO, Humble JL, Tschesche C, Bakke MJ, Gamble L, Bekaert M, Bassett DI, Horsberg TE, Bron JE & Sturm A (2018) Mutations in voltage-gated sodium channels from pyrethroid resistant salmon lice (Lepeophtheirus salmonis) (Forthcoming/Available Online). Pest Management Science. https://doi.org/10.1002/ps.5151.

Article

Combination Random Isothermal Amplification and Nanopore Sequencing For Rapid Identification of the Causative Agent of an Outbreak

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 and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype

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

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

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)
FEMS Microbiology Letters, 364 (17), Art. No.: fnx143.

Article

Maternal inheritance of deltamethrin resistance in the salmon louse Lepeophtheirus salmonis (Krøyer) is associated with unique mtDNA haplotypes

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

Fourteen Draft Genome Sequences for the First Reported Cases of Azithromycin-Resistant Neisseria gonorrhoeae in Ireland

Mac Aogain M, Fennelly N, Walsh A, Lynagh Y, Bekaert M, Lawlor B, Walsh P, Kelly B, Rogers TR & Crowley B (2017)
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, Colleter J, Bekaert M, Taggart J, Palaiokostas C, McAndrew B, Vandeputte M, Chatain B, Kuhl H, Reinhardt R, Peruzzi S & Penman DJ (2017)
BMC Genomics, 18 (1), Art. No.: 449. https://doi.org/10.1186/s12864-017-3826-z.

Article

Draft Genome Sequence of Francisella noatunensis subsp. orientalis STIR-GUS-F2f7, a Highly Virulent Strain Recovered from Diseased Red Nile Tilapia Farmed in Europe

Ramirez-Paredes J, Larsson P, Wehner S, Bekaert M, Ohrman C, Metselaar M, Thompson KD, Richards R, Penman D & Adams A (2017)
Genome Announcements, 5 (11), Art. No.: e01555-16.

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.

Article

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome

Tsai HY, Robledo D, Lowe NR, Bekaert M, Taggart JB, Bron J & Houston RD (2016)
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)
BMC Genomics, 17 (1), Art. No.: 448.

Book Chapter

Tilapia genomic studies

McAndrew B, Penman D, Bekaert M & Wehner S (2016) Tilapia genomic studies. In: MacKenzie S, Jentoft S (ed.). Genomics in Aquaculture, London: Elsevier, pp. 105-130.

Article

A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals

Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, Bekaert M & Teeling EC (2016)
Molecular Ecology Resources, 16 (1), pp. 150-162.

Article

Development and validation of a mixed tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

Trumbic Z, Bekaert M, Taggart J, Bron J, Gharbi K & Mladineo I (2015)
BMC Genomics, 16, Art. No.: 1007.

Article

The effects of feeding β-glucan to Pangasianodon hypophthalmus on immune gene expression and resistance to Edwardsiella ictaluri

Sirimanapong W, Thompson KD, Ooi EL, Bekaert M, Collet B, Taggart J, Bron J, Green D, Shinn A, Adams A & Leaver M (2015)
Fish and Shellfish Immunology, 47 (1), pp. 595-605.

Article

A survey of the ATP-binding cassette (ABC) gene superfamily in the salmon louse (Lepeophtheirus salmonis)

Carmona-Antonanzas G, Carmichael SN, Heumann J, Taggart J, Bron J, Bekaert M, Sturm A & Gharbi K (2015)
PLoS ONE, 10 (9), Art. No.: e0137394.

Article

A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax)

Palaiokostas C, Bekaert M, Taggart J, Gharbi K, McAndrew B, Chatain B, Penman D & Vandeputte M (2015)
Genetics Selection Evolution, 47, Art. No.: 68.

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)
Proceedings of the National Academy of Sciences, 112 (27), pp. 8362-8366.

Article

Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary

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)
BMC Genomics, 16 (1), Art. No.: 171.

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)
Molecular Biology and Evolution, 31 (4), pp. 917-927.

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)
BMC Genomics, 15 (1), Art. No.: 90.

Article

Gene duplication and phenotypic changes in the evolution of Mammalian metabolic networks

Bekaert M & Conant GC (2014)
PLoS ONE, 9 (1), Art. No.: e87115.

Article

Identification of a sex-linked SNP marker in the salmon louse (Lepeophtheirus salmonis) using RAD sequencing

Carmichael SN, Bekaert M, Taggart J, Christie HRL, Bassett DI, Bron J, Skuce P, Gharbi K, Skern-Mauritzen R & Sturm A (2013)
PLoS ONE, 8 (10), Art. No.: e77832.

Article

Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing

Palaiokostas C, Bekaert M, Davie A, Cowan M, Oral M, Taggart J, Gharbi K, McAndrew B, Penman D & Migaud H (2013)
BMC Genomics, 14 (1), Art. No.: 566.

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)
PLoS ONE, 8 (7), Art. No.: e70136.

Article

Mapping and Validation of the Major Sex-Determining Region in Nile Tilapia (Oreochromis niloticus L.) Using RAD Sequencing

Palaiokostas C, Bekaert M, Khan MGQ, Taggart J, Gharbi K, McAndrew B & Penman D (2013)
PLoS ONE, 8 (7), Art. No.: e68389.

Article

Salmon lice (Lepeophtheirus salmonis) showing varying emamectin benzoate susceptibilities differ in neuronal acetylcholine receptor and GABA-gated chloride channel mRNA expression

Carmichael SN, Bron J, Taggart J, Ireland J, Bekaert M, Burgess S, Skuce P, Nisbet A, Gharbi K & Sturm A (2013)
BMC Genomics, 14, Art. No.: 408.

Article

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals

Kirwan JD, Bekaert M, Commins JM, Davies KT, Rossiter SJ & Teeling EC (2013)
Evolutionary Applications, 6 (3), pp. 412-422.

Article

Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation

Bekaert M (2012)
PLoS ONE, 7 (11), p. e49903.

Article

Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

Bekaert M, Edger PP, Hudson CM, Pires JC & Conant GC (2012)
New Phytologist, 196 (2), pp. 596-605.

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)
Genome Biology and Evolution, 3, pp. 1369-1380. https://doi.org/10.1093/gbe/evr115.

Article

Transcriptional robustness and protein interactions are associated in yeast

Bekaert M & Conant GC (2011)
BMC Systems Biology, 5, p. Article 62.

Article

Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints

Bekaert M, Edger PP, Pires JC & Conant GC (2011)
Plant Cell, 23 (5), pp. 1719-1728.

Article

Copy Number Alterations among Mammalian Enzymes Cluster in the Metabolic Network

Bekaert M & Conant GC (2011)
Molecular Biology and Evolution, 28 (2), pp. 1111-1121.

Article

White-Nose Syndrome Fungus (Geomyces destructans) in Bat, France

Puechmaille SJ, Verdeyroux P, Fuller H, Gouilh MA, Bekaert M & Teeling EC (2010)
Emerging Infectious Diseases, 16 (2), pp. 290-293.

Book Chapter

Computational resources for studying recoding

Bekaert M (2010) Computational resources for studying recoding. In: Atkins, JF, Gesteland, RF (ed.). Recoding: expansion of decoding rules enriches gene expression. Nucleic acids and molecular biology, 24, Berlin: Springer, pp. 435-461.

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)
Acta Chiropterologica, 12 (2), pp. 457-461.

Article

Ecological adaptation determines functional mammalian olfactory subgenomes

Hayden S, Bekaert M, Crider TA, Mariani S, Murphy WJ & Teeling EC (2010)
Genome Research, 20 (1), pp. 1-9.

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)
Nucleic Acids Research, 38 (Supplement 1), pp. D69-D74.

Article

UniPrime2: a web service providing easier Universal Primer design

Boutros R, Stokes N, Bekaert M & Teeling EC (2009)
Nucleic Acids Research, 37 (Supplement 2), pp. W209-W213.

Article

UniPrime: a workflow-based platform for improved universal primer design

Bekaert M & Teeling EC (2008)
Nucleic Acids Research, 36 (10), p. e56.

Article

Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs

Bekaert M, Ivanov IP, Atkins JF & Baranov PV (2008)
BMC Bioinformatics, 9 (178).

Article

ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting

Bekaert M, Atkins JF & Baranov PV (2006)
Bioinformatics, 22 (20), pp. 2463-2465. https://doi.org/10.1093/bioinformatics/btl430.

Article

An extended signal involved in eukaryotic - 1 frameshifting operates through modification of the E site tRNA

Bekaert M & Rousset J (2005)
Molecular Cell, 17 (1), pp. 61-68.

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)
Bioinformatics, 19 (3), pp. 327-335.

University of Stirling

Dr Michaël Bekaert

About me

Research centres/groups