Article

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

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

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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

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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

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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

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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 [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

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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

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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

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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

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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

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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) 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

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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

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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) 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

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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

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Book Chapter

Tilapia genomic studies

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

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) 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

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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

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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) 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

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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) 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

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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) 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

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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) 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

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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) 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

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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

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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

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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

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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

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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

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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

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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) 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

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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) 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

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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) 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

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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

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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) 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

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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) 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

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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

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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

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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

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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

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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) 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

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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

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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

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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

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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

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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

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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

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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

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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) 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

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Article

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

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

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Article

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

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

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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

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