Publications and communications of Wouter Coppieters

Tang, L., Swedlund, B., Dupont, S., Harland, C., Costa Monteiro Moreira, G., Durkin, K., Artesi, M., Mullaart, E., Sartelet, A., Karim, L., Coppieters, W., Georges, M., & Charlier, C. (09 March 2024). GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle. Nature Communications, 15 (1), 2154. doi:10.1038/s41467-024-46434-1

Gualdrón Duarte, J. L., Yuan, C., Gori, A.-S., Moreira, G. C. M., Takeda, H., Coppieters, W., Charlier, C., Georges, M., & Druet, T. (28 November 2023). Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals. Genetics, Selection, Evolution, 55 (1), 83. doi:10.1186/s12711-023-00857-4

Yuan, C., Tang, L., Lopdell, T., Petrov, V. A., Oget-Ebrad, C., Moreira, G. C. M., Gualdrón Duarte, J. L., Sartelet, A., Cheng, Z., Salavati, M., Wathes, D. C., Crowe, M. A., GplusE Consortium, Coppieters, W., Littlejohn, M., Charlier, C., Druet, T., Georges, M.* , & Takeda, H.*. (October 2023). An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants. Genome Research, 33 (10), 1848 - 1864. doi:10.1101/gr.277947.123

Lee, Y. L., Bosse, M., Takeda, H., Moreira, G. C. M., Karim, L., Druet, T., Oget-Ebrad, C., Coppieters, W., Veerkamp, R. F., Groenen, M. A. M., Georges, M., Bouwman, A. C., & Charlier, C. (01 May 2023). High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data. BMC Genomics, 24 (1), 225. doi:10.1186/s12864-023-09259-8

Hoogstrate, Y., Draaisma, K., Ghisai, S. A., van Hijfte, L., Barin, N., de Heer, I., Coppieters, W., van den Bosch, T. P. P., Bolleboom, A., Gao, Z., Vincent, A. J. P. E., Karim, L., Deckers, M., Taphoorn, M. J. B., Kerkhof, M., Weyerbrock, A., Sanson, M., Hoeben, A., Lukacova, S., ... French, P. J. (10 April 2023). Transcriptome analysis reveals tumor microenvironment changes in glioblastoma. Cancer Cell, 41 (4), 678 - 692.e7. doi:10.1016/j.ccell.2023.02.019

Lee, Y. L., Bosse, M., Coppieters, W., Veerkamp, R., Karim, L., Oget, C., Druet, T., Groenen, M., Georges, M., Bouwman, A., & Charlier, C. (08 July 2022). Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Oget, C., Costa Monteiro Moreira, G., Karim, L., Coppieters, W., Charlier, C., Georges, M., & Druet, T. (08 July 2022). Fine-Scale Study of Meiotic Recombination in Cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Rombouts, T., Druet, T., Gualdron Duarte, J. L., Ahariz, N., Karim, L., Coppieters, W., De Smet, S., Georges, M., & Charlier, C. (08 July 2022). A hypomorphic mutation in the ATP2A1 gene increases muscle mass yet compromises meat quality of Belgian Blue cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Yuan, C., Tang, L., Lopdell, T., Oget, C., Costa Monteiro Moreira, G., Gualdron Duarte, J. L., Cheng, Z., Salavati, M., Wathes, D. C., Crowe, M. A., GplusE consortium, Coppieters, W., Charlier, C., Druet, T., Georges, M., & Takeda, H. (08 July 2022). Enrichment of causative variants in tissue-specific and shared ATAC-Seq peaks in cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Hai, D. M., Yen, D. T., Liem, P. T., Tam, B. M., Huong, D. T. T., Hang, B. T. B., Hieu, D. Q., Garigliany, M.-M., Coppieters, W., Kestemont, P., Phuong, N. T., & Farnir, F. (May 2022). A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data. Genes, 13 (5). doi:10.3390/genes13050923

Yang, H.* , Wu, J.* , Huang, X., Zhou, Y., Zhang, Y., Liu, M., Liu, Q., Ke, S., He, M., Fu, H., Fang, S., Xiong, X., Jiang, H., Chen, Z., Wu, Z., Gong, H., Tong, X., Huang, Y., Ma, J., ... Huang, L.*. (2022). ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature. doi:10.1038/s41586-022-04769-z

Van Vooren, S., Grayson, J., Van Ranst, M., Dequeker, E., Laenen, L., Janssen, R., Gillet, L., Bureau, F., Coppieters, W., Devos, N., Hengchen, B., Wattiau, P., Méhauden, S., Verlinden, Y., Van Baelen, K., Pattery, T., Valentin, J.-P., Janssen, K., Geraerts, M., ... André, E. (21 January 2022). Reliable and Scalable SARS-CoV-2 qPCR Testing at a High Sample Throughput: Lessons Learned from the Belgian Initiative. Life, 12 (2), 159. doi:10.3390/life12020159

Deflandre, B.* , Stulanovic, N.* , Planckaert, S., Anderssen, S., Bonometti, B., Karim, L., Coppieters, W., Devreese, B., & Rigali, S. (2022). The virulome of Streptomyces scabiei in response to cello- oligosaccharide elicitors. Microbial Genomics. doi:10.1099/mgen.0.000760

Oget, C., Kadri, N. K., Moreira, G. C. M., Karim, L., Coppieters, W., Georges, M., & Druet, T. (2022). Benchmarking phasing software with a whole-genome sequenced cattle pedigree. BMC Genomics, 23 (1), 130. doi:10.1186/s12864-022-08354-6

Saegerman, C., Nguyet Diep, A., Renault, V., Donneau, A.-F., Stamatakis, L., Coppieters, W., Michel, F., Breuer, C., Dandoy, M., Ek, O., Gourzonès, C., Schyns, J., Goffin, E., Minner, F., Durkin, K., Artesi, M., Bours, V., Bureau, F., & Gillet, L. (2022). A 2-month field cohort study of SARS-CoV-2 in saliva of BNT162b2 vaccinated nursing home workers. Communications Medicine. doi:10.1038/s43856-021-00067-3

Sacheli, R., Arendrup Maiken, Chowdhary Anuradha, Coppieters, W., Naomé, A., Baurain, D., Hanikenne, M., & Hayette, M.-P. (October 2021). Development of a bioinformatic tool for the treatment of WGS data for dermatophytes typing and characterization: Focus on squalene epoxidase mutations and terbinafine resistance [Poster presentation]. 10th Trends in Medical Mycology (TIMM), Aberdeen, United Kingdom.

Saegerman, C., Donneau, A.-F., Speybroeck, N., Diep, A. N., Williams, A., Stamatakis, L., Coppieters, W., Michel, F., Breuer, C., Dandoy, M., Ek, O., Gourzonès, C., Schyns, J., Goffin, E., Minner, F., Renault, V., Gillet, L.* , & Bureau, F.*. (2021). Repetitive saliva-based mass screening as a tool for controlling SARS-CoV-2 transmission in nursing homes. Transboundary and Emerging Diseases. doi:10.1111/tbed.14280

Muto, V.* , Koshmanova, E.* , Ghaemmaghami Tabrizi, P.* , Jaspar, M., Meyer, C., Elansary, M., Van Egroo, M., Chylinski, D., Berthomier, C., Brandewinder, M., Mouraux, C., Schmidt, C., Hammad, G., Coppieters, W., Ahariz, N., Degueldre, C., Luxen, A., Salmon, E., Phillips, C., ... Vandewalle, G. (16 July 2021). Alzheimer’s disease genetic risk and sleep phenotypes: association with more slow-waves and daytime sleepiness. Sleep, 44 (1), 137. doi:10.1093/sleep/zsaa137

Payen, V. L.* , Lavergne, A.* , Alevra Sarika, N., Colonval, M., Karim, L., Deckers, M., Najimi, M., Coppieters, W., CHARLOTEAUX, B., Sokal, E. M., & El Taghdouini, A. (21 March 2021). Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity. JHEP Reports: Innovation in Hepatology, 3 (3), 100278. doi:10.1016/j.jhepr.2021.100278

Lee, Y.-L., Takeda, H., Costa Monteiro Moreira, G., Karim, L., Mullaart, E., Coppieters, W., Appeltant, R., Veerkamp, R. F., Groenen, M. A. M., Georges, M., Bosse, M., Druet, T., Bouwman, A. C., & Charlier, C. (2021). A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PLoS Genetics, 17 (7), 1009331. doi:10.1371/journal.pgen.1009331

Coppieters, W., Karim, L., & Georges, M. (August 2020). SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk. Genome Research, 30 (8), 1201 - 1207. doi:10.1101/gr.256172.119

Debode, F., Hulin, J., CHARLOTEAUX, B., Coppieters, W., Hanikenne, M., Karim, L., & Berben, G. (2019). Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies. Scientific Reports, 9 (1), 15595. doi:10.1038/s41598-019-51668-x

Naomé, A., Maciejewska, M., Calusinska, M., Martinet, L., Anderssen, S., Adam, D., Tenconi, E., Deflandre, B., Coppieters, W., Karim, L., Hanikenne, M., Baurain, D., Delfosse, P., van Wezel, G., & Rigali, S. (May 2018). Complete Genome Sequence of Streptomyces lunaelactis MM109T, Isolated from Cave Moonmilk Deposits. Genome Announcements, 6 (21), 00435-18. doi:10.1128/genomeA.00435-18

Kadri, N. K., Harland, C., Charlier, C., Karim, L., Cambisano, N., Deckers, M., Mullaart, E., Coppieters, W., Georges, M., & Druet, T. (2018). High resolution mapping of cross-over events in cattle using NGS data. In Proceedings of the World Congress on Genetics Applied to Livestock Production.

Adam, D., Maciejewska, M., Naomé, A., Martinet, L., Coppieters, W., Karim, L., Baurain, D., & Rigali, S. (2018). Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits. Antibiotics, 7(2) (28), 10.3390/antibiotics7020028. doi:10.3390/antibiotics7020028

Ghisdal, L., Baron, C., Lebranchu, Y., Viklicky, O., Konarikova, A., Naesens, A., Kuypers, D., Dinic, M., Alamartine, E., Touchard, G., Antoine, T., Essig, M., Rerolle, J. P., Merville, P., Taupin, J. L., Le Meur, Y., Grall - Jezequel, A., Glowacki, F., Noel, C., ... Abramowicz M. (2017). Genome-wide Association Study of Acute Renal Graft Rejection. American Journal of Transplantation, 17 (1), 201-2019. doi:10.1111/ajt.13912

Li, W.* , Sartelet, A.* , Tamma, N., Coppieters, W., Georges, M., & Charlier, C. (February 2016). Reverse genetic screen for loss-of-function mutations uncovers a frame-shifting deletion in the melanophilin gene accountable for a distinctive coat-color in Belgian Blue Cattle. Animal Genetics, 47 (1), 110-113. doi:10.1111/age.12383

Kadri, N. K., Harland, C., Faux, P., Cambisano, N., Karim, L., Coppieters, W., Fritz, S., Mullaart, E., Baurain, D., Boichard, D., Spelman, R., Charlier, C., Georges, M., & Druet, T. (2016). Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle. Genome Research, 26 (10), 1323-1332. doi:10.1101/gr.204214.116

Sartelet, A.* , Li, W.* , Pailhoux, E., Richard, C., Tamma, N., Karim, L., Fasquelle, C., Druet, T., Coppieters, W., Georges, M., & Charlier, C. (2015). Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. BMC Genomics, 16 (316). doi:10.1186/s12864-015-1528-y

Mariman, R., Coppieters, W., Elansary, M., Karim, L., Crins, F., Mni, M., Gori, A.-S., Aoun, N., Docampo Martínez, E., Dmitrieva, J. B., Fang, M., Theatre, E., Eppe, G., & Georges, M. (24 April 2014). Identification of molecular components of the host-microbiota-connectome by using "Omics Approaches" [Poster presentation]. BeMGI.

Druet, T., Ahariz, N., Cambisano, N., Tamma, N., Michaux, C., Coppieters, W., Charlier, C., & Georges, M. (2014). Selection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle. BMC Genomics, 15 (1), 796. doi:10.1186/1471-2164-15-796

Sartelet, A.* , Stauber, T.* , Coppieters, W., Ludwig, C. F., Fasquelle, C., Druet, T., Zhang, Z., Ahariz, N., Cambisano, N., Jentsch, T. J., & Charlier, C. (January 2014). A missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle. Disease Models and Mechanisms, 7, 119-128. doi:10.1242/dmm.012500

Trivellin, G.* , Daly, A.* , Faucz, F. R., Yuan, B., Rostomyan, L., Larco, D. O., Schernthaner-Reiter, M. H., Szarek, E., Leal, L. F., CABERG, J.-H., CASTERMANS, E., Villa, C., Dimopoulos, A., Chittiboina, P., Xekouki, P., Shah, N. S., Metzger, D., Lysy, P. A., Ferrante, E., ... Stratakis, C. A.*. (2014). Gigantism and Acromegaly Due to Xq26 Microduplications and GPR101 Mutation. New England Journal of Medicine. doi:10.1056/NEJMoa1408028

Berry, S., Coppieters, W., Davis, S., Burrett, A., Thomas, N., Palmer, D., Kelly, V., Obolonkin, V., Sanders, K., Spelman, R., Georges, M., Lehnert, K., & Snell, R. (March 2013). A triad of highly divergent polymeric immunoglobulin receptor (PIGR) haplotypes with major effect on IgA concentration in bovine milk. PLoS ONE, 8 (3), 57219. doi:10.1371/journal.pone.0057219

Sartelet, A., Druet, T., Michaux, C., Fasquelle, C., Geron, S., Tamma, N., Zhang, Z., Coppieters, W., Georges, M., & Charlier, C. (15 March 2012). A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory response. PLoS Genetics, 15 (3), 1002581. doi:10.1371/journal.pgen.1002581

Charlier, C., Agerholm, J. S., Coppieters, W., Karlskov-Mortensen, P., Li, W., de Jong, G., Fasquelle, C., Karim, L., Cirera, S., Cambisano, N., Ahariz, N., Mullaart, E., Georges, M., & Fredholm, M. (2012). A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina. PLoS ONE, 7 (8), 43085. doi:10.1371/journal.pone.0043085

Sandor, C., Li, W., Coppieters, W., Druet, T., Charlier, C., & Georges, M. (2012). Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle. PLoS Genetics, 8 (7), 1002854. doi:10.1371/journal.pgen.1002854

Voz, M., Coppieters, W., Manfroid, I., Baudhuin, A., Von Berg, V., Charlier, C., Meyer, D., Driever, W., Martial, J., & Peers, B. (2012). Fast Homozygosity Mapping and Identification of a Zebrafish ENU-Induced Mutation by Whole-Genome Sequencing. PLoS ONE, 7 (4), 34671. doi:10.1371/journal.pone.0034671

Momozawa, Y., Mni, M., Nakamura, K., Coppieters, W., Almer, S., Amininejad, L., Cleynen, I., Colombel, J.-F., de Rijk, P., Dewit, O., Finkel, Y., Gassull, M. A., Goossens, D., Laukens, D., Lemann, M., LIBIOULLE, C., O'Morain, C., Reenaers, C., Rutgeerts, P., ... Georges, M. (2011). Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nature Genetics, 43 (1), 43-7. doi:10.1038/ng.733

Hiard, S., Charlier, C., Coppieters, W., Georges, M., & Baurain, D. (December 2009). Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates [Poster presentation]. BBC09, the fifth Benelux Bioinformatics Conference, Liège, Belgium.

Baurain, D., Hiard, S., Coppieters, W., Charlier, C., & Georges, M. (29 September 2009). Patrocles: a database of polymorphic miR-mediated gene regulation in vertebrates [Paper presentation]. La face cachée des microRNA, Liège, Belgium.

Fasquelle, C.* , Sartelet, A.* , Li, W., Dive, M., Tamma, N., Michaux, C., Druet, T., Huijbers, I. J., Isacke, C. M., Coppieters, W., Georges, M., & Charlier, C. (2009). Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle. PLoS Genetics, 5 (9), 1000666. doi:10.1371/journal.pgen.1000666

Hiard, S., Baurain, D., Coppieters, W., Tordoir, X., Charlier, C., & Georges, M. (July 2008). Patrocles: a database of polymorphic miRNA-mediated gene regulation [Poster presentation]. XX International Congress of Genetics, Berlin, Germany.

Hiard, S., Baurain, D., Coppieters, W., Tordoir, X., Charlier, C., & Georges, M. (03 March 2008). Patrocles: a database of polymorphic miRNA-mediated gene regulation [Paper presentation]. EADGENE miRNAs workshop and miRNAs in Health and Disease 2 / Satellite Course "A primer in miRNA biology", Liège, Belgium.

Hiard, S., Tordoir, X., Coppieters, W., Charlier, C., & Georges, M. (12 November 2007). Compiling polymorphic miRNA-target interactions: the Patrocles database [Poster presentation]. Benelux Bioinformatics Conference 2007, Leuven, Belgium.

Hiard, S., Tordoir, X., Coppieters, W., Charlier, C., & Georges, M. (15 February 2007). Compiling polymorphic miRNA-target interactions: the Patrocles database [Poster presentation]. Bioinformatics and Modeling : From genomes to network, Liège, Belgium.

Coppieters, W., Kvasz, A., Farnir, F., Arranz, J. J., Grisart, B., Mackinnon, M., & Georges, M. (1998). A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design. Genetics, 149 (3), 1547-55.