Publications and communications of Haruko Takeda

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
* These authors have contributed equally to this work.

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

Georges, A., Lavergne, A., Mandai, M., Lepiemme, F., Karim, L., Demeulenaere, L., Aguilar Ortmans, D., Schyns, M., Nguyen, L., Rakic, J.-M., Takahashi, M., Georges, M., & Takeda, H. (21 January 2023). Comparing the transcriptome of developing native and iPSC-derived mouse retinae by single cell RNA sequencing. Scientific Reports, 13 (1), 1223. doi:10.1038/s41598-023-28429-y

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.

Perée, H., Mayer, A., Takeda, H., Karim, L., Deckers, M., Jacques, S., Mni, M., Wéry, M., Azarzar, S., Tokunaga, Y., Coppieters, W., Georges, M., & Rahmouni, S. (May 2021). Comparative analysis of ultra low input RNA sequencing methods for the study of rare immune cell populations [Poster presentation]. 33rd meeting on The Biology of Genomes.

Cheng, Z., Buggiotti, L., Salavati, M., Marchitelli, C., Palma-Vera, S., Wylie, A., Takeda, H., Tang, L., Crowe, M. A., & Wathes, D. C. (2021). Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis. Molecular Biology Reports. doi:10.1007/s11033-021-06494-8

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

Wathes, D. C., Cheng, Z., Salavati, M., Buggiotti, L., Takeda, H., Tang, L., Becker, F., Ingvartsen, K. I., Ferris, C., Hostens, M., & Crowe, M. A. (2021). Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation. Journal of Dairy Science, 104 (3), 3596-3616. doi:10.3168/jds.2020-19165

Lee, Y.-L., Takeda, H., Costa Monteiro Moreira, G., Karim, L., Bosse, M., Bouwan, A., Mullaart, E., Coppieters, W., Georges, M., Druet, T., & Charlier, C. (02 December 2020). Fine resolution CNV catalogue from deeply sequenced cattle genomes [Paper presentation]. EAAP annual meeting.

GEORGES, A., Lavergne, A., Mandai, M., Lepiemme, F., Karim, L., Demeulenaere, L., Aguilar Ortmans, D., Schyns, M., Nguyen, L., RAKIC, J.-M., Takahashi, M., Georges, M., & Takeda, H. (2020). Combined analysis of single cell RNA-Seq and ATAC-Seq data reveals putative regulatory toggles operating in native and iPS-derived retina. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/292544. doi:10.1101/2020.03.02.972497

De Koster, J., Salavati, M., Grelet, C., Crowe, M. A., Matthews, E., O'Flaherty, R., Opsomer, G., Foldager, L., Hostens, M., McLoughlin, N., Fahey, A., Santoro, A., Byrne, C., Rudd, P., Hallinan, S., Wathes, C., Cheng, Z., Fouladi, A., Pollott, G., ... GplusE. (April 2019). Corrigendum to “Prediction of metabolic clusters in early-lactation dairy cows using models based on milk biomarkers”. Journal of Dairy Science, 102 (4), 3778. doi:10.3168/jds.2019-102-4-3778

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

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

Rosewick, N., Momont, M., Durkin, K., Takeda, H., Caiment, F., Cleuter, Y., Vernin, C., Mortreux, F., Wattel, E., Burny, A., Georges, M., & Van den Broeke, A. (2013). Deep sequencing reveals abundant non-canonical retroviral microRNAs in B-cell leukemia/lymphoma. Proceedings of the National Academy of Sciences of the United States of America.

Karim, L.* , Takeda, H.* , Lin, L.* , Druet, T.* , Arias, J. A. C., Baurain, D., Cambisano, N., Davis, S. R., Farnir, F., Grisart, B., Harris, B. L., Keehan, M. D., Littlejohn, M. D., Spelman, R. J., Georges, M.* , & Coppieters, W.*. (2011). Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics, 43 (5), 405-13. doi:10.1038/ng.814
* These authors have contributed equally to this work.

Takeda, H., Charlier, C., Farnir, F., & Georges, M. (2010). Demonstrating polymorphic miRNA-mediated gene regulation in vivo: application to the g+6223G->A mutation of Texel sheep. RNA, 16 (9), 1854-63. doi:10.1261/rna.2131110

Katrincsakova, B., Takeda, H., Urbankova, H., Michaux, L., Jarosova, M., Vandenberghe, P., Georges, M., Charlier, C., & Wlodarska, I. (2009). Methylation analysis of the imprinted DLK1-GTL2 domain supports the random parental origin of the IGH-involving del(14q) in B-cell malignancies. Epigenetics, 4 (7), 469-75. doi:10.4161/epi.4.7.9924

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.

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.

Georges, M., Clop, A., Marcq, F., Takeda, H., Pirottin, D., Tordoir, X., Hiard, S., Bibé, B., Bouix, J., Caiment, F., Eychenne, F., Larzul, C., Laville, E., Meish, F., Milenkovic, D., Tobin, J., & Charlier, C. (June 2006). Polymorphic miRNA-target interactions : A Novel Source of Phenotypic Variation. Cold Spring Harbor Symposia on Quantitative Biology, 71, 343-350. doi:10.1101/sqb.2006.71.056

Takeda, H., Caiment, F., Smit, M., Hiard, S., Tordoir, X., Cockett, N., Georges, M.* , & Charlier, C.*. (23 May 2006). The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis. Proceedings of the National Academy of Sciences of the United States of America, 103 (21), 8119-8124. doi:10.1073/pnas.0602844103
* These authors have contributed equally to this work.

Clop, A.* , Marcq, F.* , Takeda, H.* , Pirottin, D.* , Tordoir, X., Bibe, B., Bouix, J., Caiment, F., Elsen, J.-M., Eychenne, F., Larzul, C., Laville, E., Meish, F., Milenkovic, D., Tobin, J., Charlier, C., & Georges, M. (2006). A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genetics, 38 (7), 813-8. doi:10.1038/ng1810
* These authors have contributed equally to this work.

Pirottin, D., Takeda, H., Georges, M., & Charlier, C. (2006). A mouse model for polar overdominance ? In Conférences Monod : Epigenetic Perspectives from Multiple Organisms.

Georges, M., Charlier, C., Smit, M., Davis, E., Shay, T., Tordoir, X., Takeda, H., Caiman, F., & Cockett, N. (2004). Toward molecular understanding of polar overdominance at the ovine callipyge locus. In B. Stillman & D. Stewart (Eds.), "Epigenetics” Cold Spring Harbor Symposium on Quantitative Biology (pp. 477-483). Cold Spring Harbor Laboratory Press. doi:10.1101/sqb.2004.69.477

Pirottin, D., Poncelet, D., Grobet, L., Royo, L. J., Brouwers, B., Masabanda, J., Takeda, H., Fries, R., Sugimoto, Y., Womack, J. E., Dunner, S., & Georges, M. (1999). High-Resolution, Human-Bovine Comparative Mapping Based on a Closed Yac Contig Spanning the Bovine Mh Locus. Mammalian Genome, 10 (3), 289-93. doi:10.1007/s003359900988