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Publications

Peer-reviewed publications at QGG

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Xiang, R., Fang, L., Liu, S., Macleod, I. M., Liu, Z., Breen, E. J., Gao, Y., Liu, G. E., Tenesa, A., CattleGTEx Consortium, Mason, B. A., Chamberlain, A. J., Wray, N. R. & Goddard, M. E. (2023). Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle. Cell Genomics, 3(10), Article 100385. https://doi.org/10.1016/j.xgen.2023.100385
Skovbjerg, C. K., Angra, D., Robertson-Shersby-Harvie, T., Kreplak, J., Keeble-Gagnère, G., Kaur, S., Ecke, W., Windhorst, A., Nielsen, L. K., Schiemann, A., Knudsen, J., Gutierrez, N., Tagkouli, V., Fechete, L. I., Janss, L., Stougaard, J., Warsame, A., Alves, S., Khazaei, H. ... Andersen, S. U. (2023). Genetic analysis of global faba bean diversity, agronomic traits and selection signatures. Theoretical and Applied Genetics, 136(5), Article 114. https://doi.org/10.1007/s00122-023-04360-8
Adlam, D., Berrandou, T. E., Georges, A., Nelson, C. P., Giannoulatou, E., Henry, J., Ma, L., Blencowe, M., Turley, T. N., Yang, M. L., Chopade, S., Finan, C., Braund, P. S., Sadeg-Sayoud, I., Iismaa, S. E., Kosel, M. L., Zhou, X., Hamby, S. E., Cheng, J. ... DISCO register (2023). Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation. Nature Genetics, 55(6), 964-972. https://doi.org/10.1038/s41588-023-01410-1
Mei, Q., Liu, H., Zhao, S., Xiang, T. & Christensen, O. F. (2023). Genomic evaluation for two-way crossbred performance in cattle. Genetics Selection Evolution, 55(1), Article 17. https://doi.org/10.1186/s12711-023-00792-4
Raffo, M. A., Cuyabano, B. C. D., Rincent, R., Sarup, P., Moreau, L., Mary-Huard, T. & Jensen, J. (2023). Genomic prediction for grain yield and micro-environmental sensitivity in winter wheat. Frontiers in Plant Science, 13, Article 1075077. https://doi.org/10.3389/fpls.2022.1075077
Tenhunen, S. R., Thomasen, J. R., Sørensen, L. P., Berg, P. & Kargo, M. (2023). Genomic selection has aided Nordic Jersey to decrease risks of inbreeding. 393. Abstract from
74th Annual Meeting of European Federation of Animal Science, Lyon, France.
Wang, X., Li, W., Feng, X., Li, J., Liu, G. E., Fang, L. & Yu, Y. (2023). Harnessing male germline epigenomics for the genetic improvement in cattle. Journal of Animal Science and Biotechnology, 14(1), Article 76. https://doi.org/10.1186/s40104-023-00874-9
Manzanilla Pech, C. I. V., Stephansen, R. B. & Lassen, J. (2023). Heterogeneity of 3D cameras feed intake heritabilities in first parity Holstein, Jersey and Nordic Red cows. In Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science : EAAP Book of Abstracts, Volume 29 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-936-7
Liu, C., Huang, R., Su, G., Hou, L., Zhou, W., Liu, Q., Qiu, Z., Zhao, Q. & Li, P. (2023). Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs. BMC Genomics, 24(1), Article 733. https://doi.org/10.1186/s12864-023-09860-x
Li, J., Zhao, T., Guan, D., Pan, Z., Bai, Z., Teng, J., Zhang, Z., Zheng, Z., Zeng, J., Zhou, H., Fang, L. & Cheng, H. (2023). Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits. Cell Genomics, 3(10), Article 100390. https://doi.org/10.1016/j.xgen.2023.100390
Sahana, J., Cortés-Sánchez, J. L., Sandt, V., Melnik, D., Corydon, T. J., Schulz, H., Cai, Z., Evert, K., Grimm, D. & Wehland, M. (2023). Long-Term Simulation of Microgravity Induces Changes in Gene Expression in Breast Cancer Cells. International Journal of Molecular Sciences , 24(2), Article 1181. https://doi.org/10.3390/ijms24021181
Hellwing, A. L. F., Vestergaard, M. & Kargo, M. (2023). Methane emission from purebred Holstein, Nordic Red and F1 crossbred cows of the two breeds. In Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science (pp. 937-937). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-936-7
Boggio, G. M., Christensen, O. F., Legarra, A., Meynadier, A. & Marie-Etancelin, C. (2023). Microbiability of milk composition and genetic control of microbiota effects in sheep. Journal of Dairy Science, 106(9), 6288-6298. https://doi.org/10.3168/jds.2022-22948
Stephansen, R. B., Martin, P., Manzanilla-Pech, C. I. V., Gredler-Grandl, B., Sahana, G., Madsen, P., Weigel, K., Tempelman, R. J., Peñagaricano, F., Gaddis, K. L. P., White, H. M., Santos, J. E. P., Koltes, J. E., Schenkel, F., Hailemariam, D., Plastow, G., Abdalla, E., VandeHaar, M., Veerkamp, R. F. ... Lassen, J. (2023). Novel genetic parameters for genetic residual feed intake in dairy cattle using time series data from multiple parities and countries in North America and Europe. Journal of Dairy Science, 106(12), 9078-9094. https://doi.org/10.3168/jds.2023-23330, https://doi.org/10.3168/jds.2023-23330
Friggens, N. C., Ithurbide, M. & Bouquet, A. E. R. (2023). Novel traits related to productive life. Abstract from 45th ADSA Discover Conference, Itasca, Illinois, United States.
Bouquet, A. E. R., Nielsen, H. M., Milkevych, V., Kargo, M., Thomasen, J. R. & Slagboom, M. (2023). Optimizing dairy cattle breeding goals to improve production and udder health of crossbred cows. In Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science Wageningen Academic Publishers.
Jiang, Y. F., Wang, S., Wang, C. L., Xu, R. H., Wang, W. W., Jiang, Y., Wang, M. S., Jiang, L., Dai, L. H., Wang, J. R., Chu, X. H., Zeng, Y. Q., Fang, L. Z., Wu, D. D., Zhang, Q. & Ding, X. D. (2023). Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience, 26(3), Article 106119. https://doi.org/10.1016/j.isci.2023.106119
Schoeler, T., Speed, D., Porcu, E., Pirastu, N., Pingault, J. B. & Kutalik, Z. (2023). Participation bias in the UK Biobank distorts genetic associations and downstream analyses. Nature Human Behaviour, 7(7), 1216-1227. https://doi.org/10.1038/s41562-023-01579-9
Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G., Zhou, S., Zhang, X., Bao, Z., Zhang, Y., Song, B., Zhou, Y., Zhou, Y., Gagnon, E., Särkinen, T., Knapp, S., Zhang, C., Städler, T., Buckler, E. S. & Huang, S. (2023). Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell, 186(11), 2313-2328.e15. https://doi.org/10.1016/j.cell.2023.04.008
Salunke, S., Shrivastava, A. K., Hashmi, M. F., Ahuja, B. & Bokde, N. D. (2023). Quad Key-Secured 3D Gauss Encryption Compression System with Lyapunov Exponent Validation for Digital Images. Applied Sciences (Switzerland), 13(3), Article 1616. https://doi.org/10.3390/app13031616
Slagboom, M., Nielsen, H. M., Kargo, M., Henryon, M. & Hansen, L. S. (2023). Simulating breeding programs based on mass selection in black soldier fly (Hermetia illucens). Abstract from
74th Annual Meeting of European Federation of Animal Science, Lyon, France.
Persichilli, C., Karaman, E., Finocchiaro, R., Pilla, F., Fabris, A., Visentin, G. & Cassandro, M. (2023). Study of fertility traits in Italian Jersey Cattle. Italian Journal of Animal Science, 22(sup1), 41. Article 0563. https://aspacongress2023.com/wp-content/uploads/2023/06/ASPA-25th-Congress-Book-of-Abstract_compressed.pdf
Zhao, P., Peng, C., Fang, L., Wang, Z. & Liu, G. E. (2023). Taming transposable elements in livestock and poultry: a review of their roles and applications. Genetics Selection Evolution, 55(1), Article 50. https://doi.org/10.1186/s12711-023-00821-2
Jayakodi, M., Golicz, A. A., Kreplak, J., Fechete, L. I., Angra, D., Bednář, P., Bornhofen, E., Zhang, H., Boussageon, R., Kaur, S., Cheung, K., Čížková, J., Gundlach, H., Hallab, A., Imbert, B., Keeble-Gagnère, G., Koblížková, A., Kobrlová, L., Krejčí, P. ... Andersen, S. U. (2023). The giant diploid faba genome unlocks variation in a global protein crop. Nature, 615(7953), 652-659. https://doi.org/10.1038/s41586-023-05791-5
Wang, X., Gao, Y., Li, C. J., Fang, L., Liu, G. E., Zhao, X., Zhang, Y., Cai, G., Xue, G., Liu, Y., Wang, L., Zhang, F., Wang, K., Zhang, M., Li, R., Gao, Y. & Li, J. (2023). The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle. BMC genomic data, 24(1), Article 39. https://doi.org/10.1186/s12863-023-01139-0
Bolormaa, S., Haile-Mariam, M., Marett, L., Miglior, F., Baes, C. F., Schenkel, F. S., Connor, E. E., Manzanilla Pech, C. I. V., Wall, E., Coffey, M., Goddard, M., MacLeod, I. & Pryce, J. E. (2023). Use of dry-matter intake recorded at multiple time periods during lactation increases the accuracy of genomic prediction for dry-matter intake and residual feed intake in dairy cattle. Animal Production Science, 63(11), 1113-1125. Article AN23022. https://doi.org/10.1071/AN23022
Hsu, Y. H. H., Pintacuda, G., Liu, R., Nacu, E., Kim, A., Tsafou, K., Petrossian, N., Crotty, W., Suh, J. M., Riseman, J., Martin, J. M., Biagini, J. C., Mena, D., Ching, J. K. T., Malolepsza, E., Li, T., Singh, T., Ge, T., Egri, S. B. ... Wellcome Trust Case Control Consortium (2023). Using brain cell-type-specific protein interactomes to interpret neurodevelopmental genetic signals in schizophrenia. iScience, 26(5), Article 106701. https://doi.org/10.1016/j.isci.2023.106701
Saedi, N., Lund, M. S. & Karaman, E. (2023). Using genomic markers and microbiome data to predict methane emissions from Holstein cows. In Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-936-7
Long, E. M., Romay, M. C., Ramstein, G., Buckler, E. S. & Robbins, K. R. (2023). Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava. Frontiers in Plant Science, 13, Article 1041925. https://doi.org/10.3389/fpls.2022.1041925
Jain, S. K., Bhatia, R., Shrivastava, N., Salunke, S., Hashmi, M. F. & Bokde, N. D. (2023). Virtual Grid-Based Routing for Query-Driven Wireless Sensor Networks. Future Internet, 15(8), Article 259. https://doi.org/10.3390/fi15080259
Zhao, P., Gu, L., Gao, Y., Pan, Z., Liu, L., Li, X., Zhou, H., Yu, D., Han, X., Qian, L., Liu, G. E., Fang, L. & Wang, Z. (2023). Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Communications Biology, 6(1), Article 894. https://doi.org/10.1038/s42003-023-05234-x
Salunke, S., Ahuja, B., Hashmi, M. F., Marriboyina, V. & Bokde, N. D. (2022). 5D Gauss Map Perspective to Image Encryption with Transfer Learning Validation. Applied Sciences, 12(11), Article 5321. https://doi.org/10.3390/app12115321
Gredler-Grandl, B., Raymond, B., Schopen, G. C. B., Chitneedi, P. K., Cai, Z., Manzanilla Pech, C. I. V., Iso-Touru, T., Fischer, D., Bolormaa, S., Chud, T. C. S., Schenkel, F. S., Wang, Y., Li, C., Hailemariam, D., Villanueva, B., Fernandez, A., Kuehn, C., Sahana, G., Lidauer, M. ... Bouwman, A. C. (2022). Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses. In WCGALP 2022 Programme book Wageningen Academic Publishers. https://www.wageningenacademic.com/pb-assets/wagen/WCGALP2022/02_010.pdf
Croiseau, P., Saintilan, R., Baur, A., Croue, I., Ducrocq, V., Thomasen, J. R., Karaman, E., Boichard, D., Leclerc, H. & Cuyabano, B. C. D. (2022). Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde x Holstein x Red Danish). In WCGALP 2022 Programme book Wageningen Academic Publishers. https://www.wageningenacademic.com/pb-assets/wagen/WCGALP2022/02_001.pdf
Saintilan, R., Croiseau, P., Baur, A., Croue, I., Ducrocq, V., Thomasen, J. R., Karaman, E., Boichard, D., Leclerc, H. & Cuyabano, B. C. D. (2022). Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde x Holstein x Red Danish). In Proceedings of the 2022 Interbull Meeting (pp. 18-22) https://journal.interbull.org/index.php/ib
Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Xiang, R., Chamberlain, A. J., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Navarro, P., Rocha, D., Li, X., Yan, Z., Li, C. ... Fang, L. (2022). A multi-tissue atlas of regulatory variants in cattle. Nature Genetics, 54(9), 1438-1447. https://doi.org/10.1038/s41588-022-01153-5
Sammad, A., Zhang, H., Shi, R., Dong, Y., Luo, H., Chen, Z., Liu, L., Guo, G., Liu, A. & Wang, Y. (2022). A Post-GWAS Functional Analysis Confirming Effects of Three BTA13 Genes CACNB2, SLC39A12, and ZEB1 on Dairy Cattle Reproduction. Frontiers in Genetics, 13, Article 882951. https://doi.org/10.3389/fgene.2022.882951
Marašinskienė, Š., Šveistienė, R., Kosińska-Selbi, B., Schmidtmann, C., Ettema, J. F., Juškienė, V. & Kargo, M. (2022). Application of a Bio-Economic Model to Demonstrate the Importance of Health Traits in Herd Management of Lithuanian Dairy Breeds. Animals, 12(15), Article 1926. https://doi.org/10.3390/ani12151926
Sawant, M., Patil, R., Shikhare, T., Nagle, S., Chavan, S., Negi, S. & Bokde, N. D. (2022). A Selective Review on Recent Advancements in Long, Short and Ultra-Short-Term Wind Power Prediction. Energies, 15(21), Article 8107. https://doi.org/10.3390/en15218107
Manzanilla Pech, C. I. V., Stephansen, R. B. & Lassen, J. (2022). Breeding for feed efficient and low methane-emitting dairy cows is feasible. Abstract from 73 Annual Meeting of the European Federation of Animal Science, Porto, Portugal.
Nagy, I., Veeckman, E., Liu, C., Bel, M. V., Vandepoele, K., Jensen, C. S., Ruttink, T. & Asp, T. (2022). Chromosome-scale assembly and annotation of the perennial ryegrass genome. BMC Genomics, 23(1), Article 505. https://doi.org/10.1186/s12864-022-08697-0
Chen, S., Liu, S., Shi, S., Jiang, Y., Cao, M., Tang, Y., Li, W., Liu, J., Fang, L., Yu, Y. & Zhang, S. (2022). Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits. BMC Biology, 20(1), 273. Article 273. https://doi.org/10.1186/s12915-022-01459-0
Yang, W., Yu, J., Yao, Y., Chen, S., Zhao, B., Liu, S., Zhou, L., Fang, L. & Liu, J. (2022). Comparative immune-relevant transcriptome reveals the evolutionary basis of complex traits. iScience, 25(12), Article 105572. https://doi.org/10.1016/j.isci.2022.105572
Yao, Y., Liu, S., Xia, C., Gao, Y., Pan, Z., Canela-Xandri, O., Khamseh, A., Rawlik, K., Wang, S., Li, B., Zhang, Y., Pairo-Castineira, E., D’Mellow, K., Li, X., Yan, Z., Li, C. J., Yu, Y., Zhang, S., Ma, L. ... Tenesa, A. (2022). Comparative transcriptome in large-scale human and cattle populations. Genome Biology, 23(1), Article 176. https://doi.org/10.1186/s13059-022-02745-4
Alemu, S. W., Bijma, P., Calus, M. P. L., Liu, H., Fernando, R. L. & Dekkers, J. C. M. (2022). Comparison of linkage disequilibrium estimated from genotypes versus haplotypes for crossbred populations. Genetics Selection Evolution, 54(1), Article 12. https://doi.org/10.1186/s12711-022-00703-z