Publications and communications of Carole Charlier

Jayaraman, S., Zhao, R., Krishna Chitneedi, P., Kumar Kadri, N., Costa-Monteiro-Moreira, G., Salavati, M., Charlier, C., Boichard, D., Sanchez, M.-P., Pausch, H., Kühn, C., Prendergast, J. G. D., & Clark, E. L. (2026). A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits. Genomics, 111284. doi:10.1016/j.ygeno.2026.111284

Li, S., Myster, F., Darimont, C., Tang, L., Javaux, J., Sandor, R., Costa Monteiro Moreira, G., Gualdron Duarte, J. L., Crepin, P., Dive, M., Mayeres, P., Druet, T., Netea, M. G., Georges, M., Charlier, C., & Gillet, L. (2026). Genetic and non-genetic factors distinctly shape the variation of the immune response in cattle. Nature Communications. doi:10.1038/s41467-025-68234-x

Jivanji, S., Wilkinson, E., Tang, L., Tiplady, K. M., Yeates, A., Harland, C., Gray, C., Couldrey, C., Worth, G., Gamache, I., Desjardins, J., Tabares, J. A. A., Yamanaka, N., McNaughton, L., Brennan, L., Cloutier, M.-P., Cowan, M., Ellison, R., Fransen, T., ... Littlejohn, M. D. (14 November 2025). Structural and epistatic regulatory variants cause hallmark white spotting in cattle. Science Advances, 11 (46), 5913. doi:10.1126/sciadv.adt5913

Weikard, R., Bhushan, R., Becker, D., Hadlich, F., Charlier, C., Costa Monteiro Moreira, G., & Kuehn, C. (06 October 2025). Elucidating the landscape of genome-wide chromatin interaction sites of the lncRNA TUG1 in bovine cell lines and liver tissue. Genomics, 117 (6), 111135. doi:10.1016/j.ygeno.2025.111135

Darimont, C., Li, S., Myster, F., Javaux, J., Pathammavong, M., Tang, L., Gualdron Duarte, J. L., Crepin, P., Druet, T., Georges, M., Mayeres, P., Charlier, C., & Gillet, L. (05 September 2024). Development of a Systems Immunology Approach to Explore Factors Influencing Vaccination Response in Belgian Blue Cattle [Poster presentation]. The 8th European Veterinary Immunology Workshop in Dublin, Dublin, Ireland.

Chitneedi, P. K., Hadlich, F., Moreira, G. C. M., Espinosa-Carrasco, J., Li, C., Plastow, G., Fischer, D., Charlier, C., Rocha, D., Chamberlain, A. J., & Kuehn, C. (September 2024). EQTL-Detect: Nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts. NAR Genomics and Bioinformatics, 6 (3). doi:10.1093/nargab/lqae122

Yuan, C., Gualdron Duarte, J. L., Charlier, C., Takeda, H., Georges, M., & Druet, T. (26 July 2024). Unravelling the genetic architecture of height and muscular development traits in Belgian Blue cattle and using it for genomic prediction [Paper presentation]. 7th International Conference of Quantitative Genetics (ICQG), Vienne, Austria.

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

Meyermans, R., Janssens, S., Coussé, A., Tinel, S., Gorssen, W., Lepot, F., Hubin, X., Mayeres, P., Veulemans, W., De Wilde, N., Druet, T., Georges, M., Charlier, C., Claerebout, E., & Buys, N. (2024). Genetic and genomic analysis of Belgian Blue's susceptibility for psoroptic mange. Genetics, Selection, Evolution, 56 (1), 52. doi:10.1186/s12711-024-00921-7

Robic, A., Hadlich, F., Costa Monteiro Moreira, G., Louise Clark, E., Plastow, G., Charlier, C., & Kühn, C. (January 2024). Innovative construction of the first reliable catalogue of bovine circular RNAs. RNA Biology, 21 (1), 52 - 74. doi:10.1080/15476286.2024.2375090

Salavati, M., Clark, R., Becker, D., Kühn, C., Plastow, G., Dupont, S., Costa Monteiro Moreira, G., Charlier, C., & Clark, E. L. (2023). Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing. G3: Genes, Genomes, Genetics. doi:10.1093/g3journal/jkad108

Gualdrón Duarte, J. L., Yuan, C., Gori, A.-S., Moreira, G. C. M., Takeda, H., Coppieters, W., Charlier, C., Georges, M., & Druet, T. (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

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. (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

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.*. (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

Gualdron Duarte, J. L., Gori, A.-S., Costa Monteiro Moreira, G., Georges, M., Charlier, C., & Druet, T. (2022). Sequence-based multi-trait genome-wide association study for linear classification traits in Belgian Blue beef cattle. In Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen Academic Publishers.

Lee, Y. L., Bosse, M., Coppieters, W., Veerkamp, R., Karim, L., Oget, C., Druet, T., Groenen, M., Georges, M., Bouwman, A., & Charlier, C. (2022). Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs. In Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen Academic Publishers.

Oget, C., Costa Monteiro Moreira, G., Karim, L., Coppieters, W., Charlier, C., Georges, M., & Druet, T. (2022). Fine-Scale Study of Meiotic Recombination in Cattle. In Veerkamp Roel & de Haas Yevette, Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen Academic Publishers.

Rombouts, T., Druet, T., Gualdron Duarte, J. L., Ahariz, N., Karim, L., Coppieters, W., De Smet, S., Georges, M., & Charlier, C. (2022). A hypomorphic mutation in the ATP2A1 gene increases muscle mass yet compromises meat quality of Belgian Blue cattle. In Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen Academic Publishers.

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. (2022). Enrichment of causative variants in tissue-specific and shared ATAC-Seq peaks in cattle. In Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen Academic Publishers.

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

Meyermans, R., Janssens, S., Coussé, A., Gorssen, W., Hubin, X., Mayeres, P., Veulemans, W., Claerebout, E., Charlier, C., & Buys, N. (15 February 2022). Myostatin mutation causing double muscling could affect increased psoroptic mange sensitivity in dual purpose Belgian Blue cattle. Animal, 16 (3), 100460. doi:10.1016/j.animal.2022.100460

Kadri, N. K., Zhang, J., Oget-Ebrad, C., Wang, Y., Couldrey, C., Spelman, R., Charlier, C., Georges, M., & Druet, T. (2022). High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle. BMC Genomics, 23 (1), 114. doi:10.1186/s12864-022-08328-8

Alemu, S. W., Kadri, N. K., Harland, C., Faux, P., Charlier, C., Caballero, A., & Druet, T. (2021). An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree. Heredity, 126, 410-423. doi:10.1038/s41437-020-00383-9

Artesi, M.* , Hahaut, V.* , Cole, B.* , Lambrechts, L., Ashrafi, F., Marçais, A., Hermine, O., Griebel, P., Arsic, N., van der Meer, F., Burny, A., Bron, D., BIANCHI, E., DELVENNE, P., BOURS, V., Charlier, C., Georges, M., Vandekerckhove, L.* , Van den Broeke, A.* , & Durkin, K.*. (2021). PCIP-seq: simultaneous sequencing of integrated viral genomes and their integration sites with long reads. Genome Biology, 22, 97. doi:10.1186/s13059-021-02307-0

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

Gualdron Duarte, J. L., Gori, A.-S., Hubin, X., Lourenco, D., Charlier, C., Misztal, I., & Druet, T. (2020). Performances of Adaptive MultiBLUP, Bayesian regressions, and weighted-GBLUP approaches for genomic predictions in Belgian Blue beef cattle. BMC Genomics, 21 (1), 545. doi:10.1186/s12864-020-06921-3

Zhang, J., Kadri, N. K., Mullaart, E., Spelman, R., Fritz, S., Boichard, D., Charlier, C., Georges, M., & Druet, T. (2020). Genetic architecture of individual variation in recombination rate on the X chromosome in cattle. Heredity, 125 (5), 304-316. doi:10.1038/s41437-020-0341-9

Artesi, M., Hahaut, V., Ashrafi, F., Marcais, A., Hermine, O., Griebel, P., Arsic, N., van der Meer, F., Burny, A., Bron, D., Charlier, C., Georges, M., Van den Broeke, A., & Durkin, K. (2019). Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads 558130. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/237583. doi:10.1101/558130

Georges, M., Charlier, C., & Hayes, B. (2019). Harnessing genomic information for livestock improvement. Nature Reviews. Genetics. doi:10.1038/s41576-018-0082-2

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.

Rosewick, N.* , Durkin, K.* , Artesi, M.* , Marçais, A., Hahaut, V., Griebel, P., Avettand-Fenoel, V., Burny, A., Charlier, C., Hermine, O., Georges, M., & Van den Broeke, A. (23 May 2017). Cis-perturbation of cancer drivers by the HTLV-1/BLV proviruses is an early determinant of leukemogenesis. Nature Communications, 8. doi:10.1038/ncomms15264

Agerholm, J. S., McEvoy, F. J., Heegaard, S., Charlier, C., Jagannathan, V., & Drogemuller, C. (2017). A de novo missense mutation of FGFR2 causes facial dysplasia syndrome in Holstein cattle. BMC Genetics, 18 (1), 74. doi:10.1186/s12863-017-0541-3

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

Xu, X., Ectors, F., Davis, E. E., Pirottin, D., Cheng, H., Farnir, F., Hadfield, T., Cockett, N., Charlier, C., Georges, M., & Takeda, H. (16 October 2015). Ectopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy. PLoS ONE, 10 (10), 0140594. doi:10.1371/journal.pone.0140594

Rosewick, N., Durkin, K., Marçais, A., Artesi, M., Hermine, O., Charlier, C., Georges, M., & Van den Broeke, A. (28 August 2015). HTLV-1/BLV antisense-RNA dependent host gene perturbation in pre-leukemic and leukemic clones. Retrovirology, 12 (1).

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

Cheng, H., Xu, X., Hadfield, T., Cockett, N., Charlier, C., Georges, M., & Takeda, H. (30 October 2014). Experimental evaluation does not reveal a direct effect of microRNA from the callipyge locus on DLK1 expression. BMC Genomics, 15, 944. doi:10.1186/1471-2164-15-944

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

Kumar Kadri, N., Sahana, G., Charlier, C., Iso-Touru, T., Guldbrandtsen, B., Karim, L., Sander Nielsen, U., Panitz, F., Pedersen Aamand, G., Schulman, N., Georges, M., Vilkki, J., Sandø Lund, M., & Druet, T. (January 2014). A 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock. PLoS Genetics, 10 (1), 1004049. doi:10.1371/journal.pgen.1004049

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

Druet, T., Perez-Pardal, L., Charlier, C., & Gautier, M. (2013). Identification of large selective sweeps associated with major genes in cattle. Animal Genetics, 44 (6), 758-62. doi:10.1111/age.12073

Zhang, Z., Guillaume, F., Sartelet, A., Charlier, C., Georges, M., Farnir, F., & Druet, T. (June 2012). Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification. Bioinformatics, 28 (19), 2467-2473. doi:10.1093/bioinformatics/bts348

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

Hiard, S., Charlier, C., Coppieters, W., Georges, M., & Baurain, D. (2010). Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Research, 38 (Database), 640-D651. doi:10.1093/nar/gkp926

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.

Pirottin, D., Takeda, H., Tamma, N., Delcombel, R., Georges, M., & Charlier, C. (2008). A mouse model for polar overdominance ? In XX International Congress of Genetics.

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.

Pirottin, D., Caiment, F., Takeda, H., Tamma, N., Georges, M., & Charlier, C. (2007). A mouse model for polar overdominance ? In Workshop RiboReg, Carry le Rouet, France, 2007.

Davis, E., Caiment, F., Tordoir, X., Cavaille, J., Ferguson-Smith, A., Cockett, N., Georges, M., & Charlier, C. (10 May 2005). Erratum to : RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus (vol 15, pg 746, 2005). Current Biology, 15 (9), 884. doi:10.1016/j.cub.2005.02.060

Cockett, N. E., Smit, M. A., Bidwell, C. A., SEGERS, K., Hadfield, T. L., Snowder, G. D., Georges, M., & Charlier, C. (2005). The callipyge mutation and other genes that affect muscle hypertrophy in sheep. Genetics, Selection, Evolution, 37 Suppl 1, 65-81. doi:10.1051/gse:2004032

Berghmans, S., SEGERS, K., Shay, T., Cockett, N., Georges, M., & Charlier, C. (2001). Breakpoint mapping positions the callipyge gene within a 450-kilobase chromosome segment containing the DLK1 and GTL2 genes. Mammalian Genome, 12 (2), 183-5. doi:10.1007/s003350010246