Publications

Peer-reviewed publications at QGG

Liu, H., Christensen, O. F., Eiríksson, J. H., Boichard, D., Milkevych, V., Thomasen, J. R. & Karaman, E. (2026). Accuracy of local ancestry inference and its impact on genomic prediction in admixed dairy cattle populations. Journal of Dairy Science, 109(3), 2743-2758. https://doi.org/10.3168/jds.2025-27019, https://doi.org/10.3168/jds.2025-27019

Svenning, A., Mougeot, G., Alison, J., Chevalier, D., Molina, N. C., Ong, S. Q., Bjerge, K., Carrillo, J., Høye, T. T. & Geissmann, Q. (2026). A general method for detection and segmentation of terrestrial arthropods in images. Methods in Ecology and Evolution, 17(3), 727-739. https://doi.org/10.1111/2041-210x.70249

Muchina, P., Kinyua, J., Khamis, F., Tanga, C. M., Satti, M. A., Gebreyesus, G., Sahana, G. & Cai, Z. (2026). A haplotype reference panel and genotype imputation framework for the black soldier fly (Hermetia illucens). Genomics, 118(2), Article 111206. https://doi.org/10.1016/j.ygeno.2026.111206

Zhang, H., Windhorst, A., Bornhofen, E., Tulpova, Z., Novak, P., Macas, J., Simkova, H., Nadzieja, M., Kim, J. M., Cram, D., Cao, Y., Konkin, D. J. F., Sass, O., Welna, G., Himmelbach, A., Mascher, M., Link, W., Kwon, S.-J., Yang, T.-J. ... Jayakodi, M. (2026). Allelic variation at a single locus distinguishes spring and winter faba beans. Nature Genetics, 58(3), 655-663. https://doi.org/10.1038/s41588-026-02524-y

Bouquet, A. E. R. & Cai, Z. (2026). Assessment of opportunities to switch to polled bulls in organic cattle production in relation to genetic issues. DCA - Nationalt Center for Fødevarer og Jordbrug. Advisory report from DCA – National Center for Food and Agriculture

Hof, J., Vermeulen, S. & Richters, A. (2026). Biased associations between number of BCG instillations and outcome in non-muscle-invasive bladder cancer. BJU International, 137(1), 226. https://doi.org/10.1111/bju.16866

Hansen, M., Nielsen, H. M., Zaalberg, R. M., Thomasen, J. R. & Kargo, M. (2026). Breeding programmes in organic livestock: principles, challenges and opportunities: case study of organic dairy cattle in Denmark. In ANIMAL : Science Proceedings (pp. 43-45). Elsevier. https://doi.org/10.1016/j.anscip.2026.03.034

Verweij, J. W., Nielsen, H. M. & Buitenhuis, A. J. (2026). Comparative analysis of genetic diversity in rainbow trout (Oncorhynchus mykiss) populations from Denmark and Finland using SNP data. Aquaculture, 616, Article 743706. https://doi.org/10.1016/j.aquaculture.2026.743706

Chen, L., Li, H., Teng, J., Wang, Z., Qu, X., Chen, Z., Cai, X., Zeng, H., Bai, Z., Li, J., Pan, X., Yan, L., Wang, F., Lin, L., Luo, Y., Sahana, G., Lund, M. S., Ballester, M., Crespo-Piazuelo, D. ... Yi, G. (2026). Construction of a Multitissue Cell Atlas Reveals Cell-Type-Specific Regulation of Molecular and Complex Phenotypes in Pigs. Advanced Science, 13(8), Article e04961. https://doi.org/10.1002/advs.202504961

Vahedi Torghabeh, B., Moslemi, C., Asp, T., Yu, X. & Ramstein, G. (2026). Detection of deleterious variants by protein language models is improved by nucleotide conservation at three evolutionary timescales in rice. Earth and Space Science Open Archive. https://doi.org/10.22541/essoar.177046418.89192569/v1

Aalborg, T., Christiansen, M. T., Romé, H., Chawade, A., Bagge, M. & Nielsen, K. L. (2026). Drone-imaging assisted genome-wide association studies reveal key quantitative trait loci for emergence and late blight resistance in tetraploid potato. Crop Science, 66(2), Article e70261. https://doi.org/10.1002/csc2.70261

Clark, EL., Amaral, A., Baranasic, D., Barta, E., Cartick, G., Chua, P., Espinosa-Carrasco, J., Fang, L., Fischer, D., Foissac, S., Gillard, G., Giuffra, E., Hartwig, T., Heil, KF., Henkel, C., Kadarmideen, HN., Klingström, T., MacHugh, DE., Murdoch, BM. ... Larzul, C. (2026). Establishing the ELIXIR Domestic Animals Genome and Phenome Community. F1000Research, 15(ELIXIR)(339), Article 339. https://doi.org/10.12688/f1000research.177500.1

Madsen, C. K., Hama, J., Nielsen, B., Janss, L., Ottosen, C.-O., Ramstein, G. & Brinch-Pedersen, H., (2026). Forædling af planter med forbedrede klimaeffekter, No. 2025-0896873, 24 p., Jan 09, 2026. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Stephansen, R. B., Poulsen, B. G., Lassen, J. & Jensen, J. (2026). Genetic associations between feed efficiency traits and breeding goal traits in Nordic Holsteins. JDS Communications , 7(2), 198-203. https://doi.org/10.3168/jdsc.2025-0898

Sun, J., Ibragimov, E., Morsing, M. K., Rydal, M. P., Nielsen, L. N., Cai, Z., Nielsen, J. P., Fredholm, M. & Karlskov-Mortensen, P. (2026). Genome-Wide Association Studies for 24 Hematological Traits in Production Pigs Before and After Weaning. Animal Genetics, 57(2), Article e70091. https://doi.org/10.1002/age.70091

Bordbar, F., Jensen, J., Wadood, A. A., Jebessa, E., Cai, B. & Nie, Q. (2026). Genomic insights into egg production in Mahuang chickens: identification of key loci and candidate genes through whole genome sequencing and validation. Animal, 20(3), Article 101762. https://doi.org/10.1016/j.animal.2026.101762

Vahedi Torghabeh, B., Moslemi, C., Jensen, J. D., Hentrup, S., Li, T., Yu, X., Wang, H., Asp, T. & Ramstein, G. (2026). Genomic language models improve cross-species gene expression prediction and accurately capture regulatory variant effects in Brachypodium mutant lines. bioRxiv. https://doi.org/10.64898/2026.02.27.708524

Foldager, L., Lindgren, S. D., Gebreyesus, G. & Thodberg, K. (2026). Halevækst for ukuperede og kuperede svin fra fødsel til slagt: var den kuperet kortere end lovgivningen tillader? In P. Linde (Ed.), Symposium i Anvendt Statistik 2026 (pp. 184-193). Fødevare- og Ressourceøkonomisk Institut, Københavns Universitet & Symposium i Anvendt Statistik.

Ahmad, A., Gebreyesus, G., Wold, J. P., Sonesson, A. K., Berg, P. & Difford, G. F. (2026). High-throughput NIR-based phenotyping for genomic prediction of feed intake and production traits in Atlantic Salmon. Aquaculture, 611, Article 743006. https://doi.org/10.1016/j.aquaculture.2025.743006

Bak, N. K., Østergaard, S. K., Schacksen, P. S., Nielsen, J. L., Rohde, P. D. & Kristensen, T. N. (2026). Host genetics and diet jointly shape the microbiome of Drosophila melanogaster but do not predict lifespan or age-related traits. Biogerontology, 27(3), Article 99. https://doi.org/10.1007/s10522-026-10431-2

Muchina, P., Kinyua, J., Khamis, F., Tanga, C. M., Bett, R., Ssepuuya, G., Nakimbugwe, D., Sinding, M.-H. S., Gebreyesus, G., Sahana, G. & Cai, Z. (2026). Human-mediated dispersal and breeding reshape global genomic patterns in black soldier flies. Genomics, 118(2), Article 111208. https://doi.org/10.1016/j.ygeno.2026.111208

Hao, D., Han, H., Li, D., Sun, Y., Wang, Y., Yan, H., Li, G., Liu, H., Li, B., Li, F. & Liu, W. (2026). Lactobacillus salivarius SNK-6 improves egg quality, yolk nutrient composition, and yolk flavor profile in laying hens via modulation of tissue metabolites and Cecal microbiomes. Poultry Science, 105(5), Article 106649. https://doi.org/10.1016/j.psj.2026.106649

Baghooee, M. & Geissmann, Q. (2026). Insect size matters: Using image and dimensions together improves image classification. Ecological Informatics, 94, Article 103664. https://doi.org/10.1016/j.ecoinf.2026.103664

Teng, J., Zhao, X., Yan, Q., Yang, J., Pei, F., Zhang, X., Duan, C., Chen, Z., Xu, Q., Liu, Y., Xue, G., Xia, S., Wang, H., Gu, Y., Fang, L., Liu, H., Gao, H., An, J., Jiang, L. ... Zhang, Q. (2026). Integrative analysis of GWAS, Bayesian fine-mapping, Mendelian randomization and colocalization reveals genetic determinants underlying milk-related traits in dairy cattle. Genetics Selection Evolution, 58(1), Article 4. https://doi.org/10.1186/s12711-025-01028-3

An, B., Luo, N., Liu, P., Wei, L., Fang, L., Wen, J. & Zhao, G. (2026). Integrative meta-GWAS and lipidomics reveal genetic regulators of nutritional fatty acids and lipid metabolites in chicken liver lipid accumulation. Journal of Agriculture and Food Research, 27, Article 102673. https://doi.org/10.1016/j.jafr.2026.102673

Liu, P., An, B., Zheng, J., Wang, Q., Yang, Z., Li, Z., Liu, D., Ying, F., Wen, J., Fang, L. & Zhao, G. (2026). Integrative Omics Defines Metabolic Biomarkers and Genetic Regulatory Mechanisms of Mortality Risk. Advanced Science, 13(3), Article e14464. https://doi.org/10.1002/advs.202514464

Gao, Y., Yang, L., Kuhn, K., Li, W., Zanton, G., Bowman, M., Zhao, P., Zhou, Y., Fang, L., Cole, J. B., Rosen, B. D., Ma, L., Li, C., Baldwin, R. L., Van Tassell, C. P., Zhang, Z., Smith, T. P. L. & Liu, G. E. (2026). Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle. Journal of Advanced Research, 79, 137-150. https://doi.org/10.1016/j.jare.2025.04.014

Thodberg, K., Gebreyesus, G. & Foldager, L. (2026). Måling af halelængde hos grise med kuperede haler i deres vækstperiode. DCA - Nationalt Center for Fødevarer og Jordbrug. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Buitenhuis, A. J., Guo, X., Sørensen, A. C., Ostersen, T. & Christensen, O. F. (2026). Meat quality traits in a commercial Duroc pig population are affected by genetics but not by Nuclear Magnetic Resonance-based metabolite profile measured in blood. Journal of Animal Science, 104, Article skag105. https://doi.org/10.1093/jas/skag105, https://doi.org/10.1093/jas/skag105

Lin, Q., Cai, X., Zhong, Z., Li, T., Chen, X., Ayalew, W., Xu, Z., Wei, C., Zhang, X., Cheng, H., Zhang, Z., Li, X., Tang, Y., Chen, S., Zhou, J., Si, J., Wu, X., Ning, C., Wang, Q. ... Zhang, Z. (2026). Meta-GWAS of Pig Semen Quality Traits Reveals Conserved Genes Regulating Mammalian Fertility. Advanced Science, 13(16), Article e15203. https://doi.org/10.1002/advs.202515203

Russello, H., Alison, J., He, Z. & Geissmann, Q. (2026). miniMon: A low-cost, low-tech mini timelapse camera trap for monitoring arthropods. Abstract from Environmental and Behavioral Monitoring with Open Source, Low Cost Tools' Symposium (SICB 2026).

BeLOVE Study Group (2026). Multi-cohort proteogenomic analyses reveal genetic effects across the proteome and diseasome. Cell. Advance online publication. https://doi.org/10.1016/j.cell.2026.03.049

Pan, X., Gong, W., Cai, X., Teng, J., Cai, J., Zeng, H., Ayalew, W., Shen, Q., Zhong, Z., Wang, Y., Zhang, W., Tian, Y., Xu, D., Gao, Y., Yin, H., Zhang, Y., Hou, J., Zhou, T., Li, J. ... Zhang, Z. (2026). Multi-Tissue Genetic Regulation of RNA Editing in Pigs. Advanced Science, 13(17), Article e18238. https://doi.org/10.1002/advs.202518238

Wang, C., Zhang, Y., Chen, C., Xu, X., Qin, S., Qi, J., Bao, Y., Li, H., Chen, R., Zheng, W., Chen, Z., Fang, L., Zhao, Y. & Liu, Y. (2026). Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs. Advanced Science, 13(20), Article e74200. https://doi.org/10.1002/advs.74200

Asp, T., (2026). Notat vedrørende ansøgning om brug af cisgene kartofler i sædskifteforsøg, No. 2026-0932063, 6 p., Feb 24, 2026. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Asp, T., (2026). Notat vedrørende ansøgning om brug af genomredigeret byg i sædskifteforsøg, No. 2026-0932063, 10 p., Feb 24, 2026. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Teng, J., Zhang, W., Gong, W., Chen, J., Gao, Y., Fang, L. & Zhang, Z. (2026). OmiGA for ultra-efficient molecular quantitative trait loci mapping. Nature Communications, 17(1), Article 2680. https://doi.org/10.1038/s41467-026-68978-0

Kragh-Schwarz, M. V., Birkedal, H., Birk, J. O., Trtik, P., Strobl, M., Nielsen, L. P. & Bentien, A. (2026). Operando neutron imaging of an alkaline electrolysis cell for mapping gas distributions. Journal of Power Sources, 662, Article 238525. https://doi.org/10.1016/j.jpowsour.2025.238525

Bouquet, A. E. R., Meinert, C. Æ. & Kargo, M. (2026). Optimizing selection decisions in the Danish Dairy Shorthorn conservation program. DCA - Nationalt Center for Fødevarer og Jordbrug. Advisory report from DCA – National Center for Food and Agriculture

Ollivier, R., Robin, S., Galland, M., Paulmann, M. K., Shih, P. Y., Morlière, S., Gershenzon, J., Kunert, G., Pilet-Nayel, M. L., Simon, J. C. & Sugio, A. (2026). Pea transcriptional and phytohormonal responses to adapted and non-adapted aphid biotypes at early stages of infestation. Scientific Reports, 16(1), Article 8456. https://doi.org/10.1038/s41598-026-38098-2

Yang, L., Gao, Y., Kuhn, K. L., Bhowmik, N., Li, W., Zanton, G., Fang, L., Cole, J. B., Li, C., Baldwin, VI, R. L., Van Tassell, C. P., Rosen, B. D., Ma, L., Smith, T. P. L. & Liu, G. E. (2026). Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle. Nature Communications, 17(1), Article 2186. https://doi.org/10.1038/s41467-026-68807-4

Wang, S., Khaipho-Burch, M., Johnson, L. C., Miller, Z. R., Bradbury, P. J., Speed, D., Allen, W. J., Romay, M. C., Xue, J., Buckler, E. S., Ramstein, G. P. & Song, B. (2026). Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize. Genome Research, 36(1), 214-225. https://doi.org/10.1101/gr.280514.125

Şen, A., Karaman, E., Heegaard, C. W., Poulsen, N. A. & Buitenhuis, A. J. (2026). Predicting riboflavin (vitamin B₂) and cobalamin (vitamin B₁₂) concentrations in Danish cow milk using Fourier transform mid infrared spectra. International Dairy Journal, 179, Article 106656. https://doi.org/10.1016/j.idairyj.2026.106656

Zaalberg, R. M., Andersen, L. B., Noel, S. J., Buitenhuis, A. J., Jensen, K. & Gebreyesus, G. (Accepted/In press). Prediction of amino acid content in live black soldier fly larvae using near infrared spectroscopy. Journal of Insects as Food and Feed. https://doi.org/10.1163/23524588-bja10381

Ithurbide, M., Bouquet, A., Rupp, R., Puillet, L. & Friggens, N. C. (2026). Resilience and Robustness in the Service of Longevity and Sustainable Efficiency in Dairy Production. Annual Review of Animal Biosciences, 14(1), 229-250. https://doi.org/10.1146/annurev-animal-041125-111332

Shi, T., Shan, H., Wang, H., Guo, X., Li, H., Han, B., Zhu, S., Wang, F., Tan, G., Niyazbekova, Z., Ren, J., Zhou, Y., Zhang, Q., Zheng, W., Jia, M., Zhang, A., Cao, X., Sun, H., Sun, D. ... Jiang, Y. (2026). Single-Cell Transcriptomic Atlases of Camels and Cattle Unravel Molecular Evolution of Digestive and Metabolic Systems. Advanced Science, 13(20), Article e19346. https://doi.org/10.1002/advs.202519346

Liu, J., Li, Y., Yu, X., Ren, B., Chen, H., Ding, F., Jiang, F., Ottosen, C. O., Song, X., Mittler, R., Wu, Z. & Zhou, R. (2026). Specific redox homeostasis, ion accumulation and gas exchange responses in tomato plants subjected to combined drought and salinity stresses. Scientia Horticulturae, 355, Article 114543. https://doi.org/10.1016/j.scienta.2025.114543

Chevalier, D., Geissmann, Q. & Carrillo, J. (2026). Taxonomic effects of white and amber LED artificial light at night on arthropods. Biological Conservation, 317, Article 111798. https://doi.org/10.1016/j.biocon.2026.111798

Hou, Y., Zou, D., Chu, Q., Zhan, B., Wang, R., Guan, D., Wang, W., Feng, X., Li, X., Zhu, X., Bai, Z., Gao, Y., Yin, H., Xu, T., Yuan, Z., Hu, X., Yang, N., Zhou, H., Fang, L. & Zhang, Z. (2026). The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity. Nucleic Acids Research, 54(D1), D982-D993. https://doi.org/10.1093/nar/gkaf731

Romé, H. J. S., Bagge, M. & Jensen, J. (2026). The Genetic Basis of Resistance to Late Blight in Tetraploid Potatoes. Crop Breeding, Genetics and Genomics, 8(1). https://doi.org/10.20900/cbgg20260001

Lund, P., Maigaard, M., Jensen, M. B., Brask, M. J., Thorsteinsson, M., Stephansen, R. B., Nielsen, H. M., Villumsen, T. M., Nørgaard, J. V., Jensen, S. K., Stødkilde-Jørgensen, L., Hansen, N. P. & Weisbjerg, M. R., (2026). TRL for nye teknologier og tiltag, som potentielt kan reducere udledningen af metan eller andre klimagasser indenfor Fødevarestyrelsens ressort, No. 2025-0917878, 25 p., Jan 23, 2026. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Kurta, K., Sallam, M., Elmersson, L., Enrich-Essvein, T., Vias-Valera, S., Gunnarsson, S., Wall, H., Dunn, I. C., de Koning, D. J., Johnsson, M. & Rodriguez-Navarro, A. B. (2026). Variation in cranial and caudal keel bone composition and its association with keel damage severity in laying hens. Poultry Science, 105(6), Article 106859. https://doi.org/10.1016/j.psj.2026.106859

Liu, X., Wang, T., Zheng, Z., Dong, C., Liu, W., Niu, Z., Yang, Y., Wu, X., Qiu, Q., Yang, Y., Li, K., Lenstra, J. A., Yan, P., Kang, M., Li, B., Fang, L. & Liu, J. (2025). A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans. BMC Biology, 23(1), Article 208. https://doi.org/10.1186/s12915-025-02311-x

Kratschmer, A. K., Blicher-Mathiesen, G., Frederiksen, R. R., Thorsen, M., Janss, L. & Giannini-Kurina, F. (2025). Abstract 153 Satelite imaging insights on autumn cover, catch crop establishment, and nitrogen load in Danish catchments. Abstract from LuWQ2025. Land Use and Water Quality: Agriculture and the Environment , Aarhus, Denmark.

Lissner, E. S., Janns, L., Giannini-Kurina, F., Blicher-Mathiesen, G. & Thorsen, M. (2025). Abstract 154 Field-level nitrogen leadching and crop yield under extreme climate events. Abstract from LuWQ2025. Land Use and Water Quality: Agriculture and the Environment , Aarhus, Denmark.

Liu, H., Zhang, J., Cui, T., Zhang, X., Li, K., Wang, F., Luo, Q., Fei, S., Chen, B., Zhu, C., Chen, K., Zhu, X., Li, B., Zhao, J., Fang, L. & Ou, M. (2025). A chromosome-level genome assembly of the male darkbarbel catfish (Pelteobagrus vachelli) using PacBio HiFi and Hi-C data. Scientific Data, 12(1), Article 351. https://doi.org/10.1038/s41597-025-04662-0

White, E. L. F., Kjetså, M., Peippo, J., Morgan, L., Kantanen, J., Comizzoli, P., Steffensen, L. L., Kargo, M., Matson, T., Mayer, I. & Honkatukia, M. (2025). Across borders – the status and future opportunities for long-term conservation of Nordic animal genetic resources. Genetic Resources, 6(11), 57-70. https://doi.org/10.46265/genresj.baiq2696

Chu, T. T. & Jensen, J. (2025). ADAM-multi: software to simulate complex breeding programs for animals and plants with different ploidy levels and generalized genotypic effect models to account for multiple alleles. Frontiers in Genetics, 16, Article 1513615. https://doi.org/10.3389/fgene.2025.1513615

Yin, H., Zhao, Q., Yang, L., Yi, G., Yao, W., Fang, L. & Bai, L. (2025). A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs. BMC Genomics, 26(1), Article 484. https://doi.org/10.1186/s12864-025-11490-4

Han, B., Li, H., Zheng, W., Zhang, Q., Chen, A., Zhu, S., Shi, T., Wang, F., Zou, D., Song, Y., Ye, W., Du, A., Fu, Y., Jia, M., Bai, Z., Yuan, Z., Liu, W., Tuo, W., Hope, J. C. ... Sun, D. (2025). A multi-tissue single-cell expression atlas in cattle. Nature Genetics, 57(10), 2546-2561. https://doi.org/10.1038/s41588-025-02329-5

Zhu, S. L., Yan, Y. N., Jia, M. H., Li, H. C., Han, B., Shi, T., Xu, L. B., Wang, X. W., Zhang, Q., Zheng, W. J., Xu, J. H., Chen, L., Qi, W., Cai, S. J., Chen, X. P., Gu, F. F., Liu, J. X., Liu, G. E., Jiang, Y. ... Sun, H. Z. (2025). Antioxidants promote metabolic remodeling in cattle rumen epithelium revealed by single-cell resolution. iMeta, 4(6), Article e70100. https://doi.org/10.1002/imt2.70100

Thorsteinsson, M. M., Schönherz, A. A., Noel, S. J., Cai, Z., Niu, Z., Hellwing, A. L. F., Lund, P., Weisbjerg, M. R. & Nielsen, M. O. (2025). A preliminary study on the effects of red Bonnemaisonia hamifera seaweed on methane emissions from dairy cows. JDS Communications , 6(2), 217-222. https://doi.org/10.3168/jdsc.2024-0670

Stephansen, R. B., van Breukelen, A. E., Almasi, F., González-Recio, O., Teran, E., Milkevych, V., Miglior, F., Baes, C. F., Bakke, K. A., Benzoni, L., Finocchiaro, R., Frizzarin, M., Krattenmacher, N., Lassen, J., Pryce, J. E., Richardson, C. & Gredler-Grandl, B. (2025). Are methane sniffer phenotypes useful for genetic ranking of dairy cattle? In Book of Abstracts - ADSA 2025 Annual Meeting (pp. 143-144). Article 1513 https://www.adsa.org/Portals/0/SiteContent/Docs/Meetings/2025ADSA/Abstracts_BOOK_2025_20250624-1249.pdf

Hanini, A. & Beljadid, A. (2025). A semi-implicit method for modeling salinity and temperature in variable-density flow. Mathematics and Computers in Simulation, 238, 222-239. https://doi.org/10.1016/j.matcom.2025.04.032

Shi, R., van der Linden, A., Ducro, B., Puillet, L. & Bouquet, A. (2025). Assessing future economic and environmental impacts of selecting resilient dairy cows using integrated mechanistic and genetic modelling. Animal, 19(12), Article 101716. https://doi.org/10.1016/j.animal.2025.101716

Markant, A., Tabrizi, F., Grönvall, H., Speed, D. & Åhs, F. (2025). Association Between Polygenic Risk Scores and Treatment Response to Antidepressants, Benzodiazepines, and Antihistamines in Anxiety and Depression. Biological Psychiatry: Global Open Science, 5(3), Article 100470. https://doi.org/10.1016/j.bpsgos.2025.100470

Nielsen, H. M., Kargo, M. & Jørgensen, L. (2025). Avl tilpasset økologiske produktionssystemer og forbrugerpræferencer. In Program Økologikongres 2025

Morales Moreira, Z. P., Kak, K., Wei, Z. W., Yanez-Ortuno, D., Wang, N. R., Hedges, J. B., Chen, M. Y., Geissmann, Q., Zhang, W., Chatterton, S., Ryan, K. S. & Haney, C. H. (2025). Azomycin produced by Pseudomonas has both phytotoxic and anti-oomycete activity. Journal of Bacteriology, 207(12). https://doi.org/10.1128/jb.00292-25

Teng, J., Duan, C., Zhang, X., Chen, Z., Ning, C., Li, R., Gao, Y., Gao, H., Liu, H., Li, J., Wang, X. & Zhang, Q. (2025). Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle. Journal of Dairy Science, 108(8), 8637-8647. https://doi.org/10.3168/jds.2025-26361

Drachmann, F. F., Johansen, K., Kargo, M., Buitenhuis, A. J. & Therkildsen, M. (2025). Beef-on-dairy: current and potential meat quality of dairy-based beef production with culled Holstein cows and Danish Blue × Holstein crossbred calves. Acta Agriculturae Scandinavica A: Animal Sciences, 74(1), 72-82. https://doi.org/10.1080/09064702.2024.2403656, https://doi.org/10.1080/09064702.2024.2403656

Henry, J., Berrandou, T., Brewster, L. M. & Bouatia-Naji, N. (2025). Blood Pressure, Cardiometabolic Traits, and Cardiovascular Events in Women With Uterine Fibroids: A Genetic Correlation and Mendelian Randomization Study. Journal of the American Heart Association, 14(8), Article e036697. https://doi.org/10.1161/JAHA.124.036697

Sandrock, C., Generalovic, T. N., Paul, K., Petersen, G. E. L., Sellem, E., Smith, M. B., Tapio, M., Yakti, W., Beukeboom, L. W., Deruytter, D., Jiggins, C. D., Lefebvre, T., Librado, P., Pannebakker, B. A., Picard, C. J., Rhode, C., Sørensen, J. G., Bouwman, A. C., Hansen, L. S. & Obšteter, J. (2025). BugBook: Genetics of insects as food and feed. Journal of Insects as Food and Feed, 11(18), S397-S455. https://doi.org/10.1163/23524588-bja10260

Cantet, R. J. C. & Jensen, J. (2025). Causal inference and GWAS: Rubin, Pearl, and Mendelian randomization. Journal of Animal Breeding and Genetics, 142(2), 200-213. https://doi.org/10.1111/jbg.12898

Hansen, L. S., Bouwman, A. C., Sahana, G., Slagboom, M., Nielsen, H. M. & Ellen, E. D. (2025). Comparative evaluation of phenotypic, pedigree, and family-based selection in insect breeding using stochastic simulation. Animal, 19(4), Article 101475. https://doi.org/10.1016/j.animal.2025.101475

Zhou, H., Clark, E., Guan, D., Lagarrigue, S., Fang, L., Cheng, H., Tuggle, C. K., Kapoor, M., Wang, Y., Giuffra, E. & Egidy, G. (2025). Comparative Genomics and Epigenomics of Transcriptional Regulation. Annual Review of Animal Biosciences, 13(1), 73-98. https://doi.org/10.1146/annurev-animal-111523-102217

Dai, D., Si, J., Jiang, L., Han, B., Wang, K., Wang, X., Yan, S., Yin, Y., Chen, W., Mao, H., Pauciullo, A., Li, S. T., Fang, L. & Zhang, Y. (2025). Comparative Single-Cell Transcriptomic Landscape Reveals the Regulatory Mechanisms of Lactation during Selective Breeding in Asian Water Buffalo. Advanced Science, 12(37), Article e08847. https://doi.org/10.1002/advs.202508847

Adeniyi, O. O., Grochowska, E., Cai, Z. & Lühken, G. (2025). Comparative transcriptome analysis reveals genes associated with variation in liver copper concentration in Polish Merino sheep. Scientific Reports, 15(1), Article 19576. https://doi.org/10.1038/s41598-025-04330-8

Ali, Z., Tan, Q. W., Lim, P. K., Chen, H., Pfeifer, L., Julca, I., Lee, J. M., Classen, B., de Vries, S., de Vries, J., Vinter, F., Alvarado, C., Layens, A., Mizrachi, E., Motawie, M. S., Joergensen, B., Ulvskov, P., Van de Peer, Y., Ho, B. C. ... Mutwil, M. (2025). Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls. Nature Plants, 11(5), 1028-1048. Article gix116. https://doi.org/10.1038/s41477-025-01978-y

Poulsen, B. G., Lourenco, D., Ostersen, T., Nielsen, B., Leite, N. G., Henryon, M. & Christensen, O. F. (2025). Comparison between repeatability, reproductive stage stratified repeatability, and relative risk models for prediction of breeding values for functional survival in rotationally crossbred sows. Genetics Selection Evolution, 57(1), Article 72. https://doi.org/10.1186/s12711-025-01019-4

Digel, L., Justesen, M. L., Madsen, N. S., Fransaert, N., Wouters, K., Bonné, R., Plum-Jensen, L. E., Marshall, I. P. G., Jensen, P. B., Nicolas-Asselineau, L., Drace, T., Bøggild, A., Hansen, J. L., Schramm, A., Bøjesen, E. D., Nielsen, L. P., Manca, J. V. & Boesen, T. (2025). Comparison of cable bacteria genera reveals details of their conduction machinery. EMBO Reports, 26(7), 1749-1767. Article 13699. https://doi.org/10.1038/s44319-025-00387-8

Si, J., Dai, D., Gorkhali, N. A., Wang, M., Wang, S., Sapkota, S., Kadel, R. C., Sadaula, A., Dhakal, A., Faruque, M. O., Omar, A. I., Sari, E. M., Ashari, H., Dagong, M. I. A., Yindee, M., Rushdi, H. E., Elregalaty, H., Amin, A., Radwan, M. A. ... Zhang, Y. (2025). Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis). Advanced Science, 12(4), e2407615. Article 2407615. https://doi.org/10.1002/advs.202407615

Magnussen, M. G., Bouquet, A. E. R., Nielsen, H. M., Thomasen, J. R., Hjortø, L., Voergaard, J. L. & Kargo, M. (2025). Consequences of including CO2 taxes in the selection index of the Danish Blue line used for beef on dairy crossbreeding. In Book of Abstracts of the 76th Annual Meeting of the European Federation of Animal Science (pp. 583-583). EAAP.

Fang, L. (2025). Context-specific regulatory variants in precision medicine and agriculture. Nature Reviews. Genetics, 26(2), 81. https://doi.org/10.1038/s41576-024-00798-8

Jensen, K., Thormose, S., Noer, N. K., Schou, T. M., Kargo, M., Gligorescu, A., Nørgaard, J. V., Hansen, L. S., Zaalberg, R. M., Nielsen, H. M. & Kristensen, T. N. (2025). Controlled and polygynous mating in the black soldier fly: advancing breeding programs utilizing quantitative genetic designs. Journal of Insects as Food and Feed, 11(13), 2321-2331. Article 20142144. https://doi.org/10.1163/23524588-bja10205

Skovbjerg, C. K., Sarup, P., Wahlström, E., Jensen, J. D., Orabi, J., Olesen, L., Jensen, J., Jahoor, A. & Ramstein, G. (2025). Correction: Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program (Heredity, (2025), 134, 1, (33-48), 10.1038/s41437-024-00733-x). Heredity, 134(3), 248-249. https://doi.org/10.1038/s41437-025-00751-3

Hansen, L. S., Bouwman, A. C., Sahana, G., Slagboom, M., Nielsen, H. M. & Ellen, E. D. (2025). Data for: Comparative evaluation of phenotypic, pedigree, and family-based selection in insect breeding using stochastic simulation. Dataset, Dryad Digital Repository. https://doi.org/10.5061/dryad.h18931zx7

Hendriksen, N. B., Madsen, C. K. & Sahana, G., (2025). DCA response to EFSA public consultation PC-1460 regarding scientific and technical assistance for a regular horizon scanning to assess new scientific data on plants, animals, microorganisms and products thereof obtained by new genomic techniques., No. 2025-0833795, 38 p., Jun 13, 2025. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Chalabi, S., Loonen, L., Boekhorst, J., Li, H., Fang, L., Harrison, P. W., Lakhal, W., Lluch, J., Sokolov, A., Djebali, S., Rau, A., Giuffra, E. & Wells, J. (2025). Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets. Genomics, 117(2), Article 110995. https://doi.org/10.1016/j.ygeno.2025.110995

Christensen, T., Denver, S., Lund, T. B., Olsen, S. B., Nielsen, H. M., Kargo, M. & Sandøe, P. (2025). Do consumers want specialized breeding goals for organic dairy cows – and how much are they willing to pay for individual breeding traits?. Abstract from The International Food Marketing Research Symposium (IFMRS) 2025, Athen, Greece.

Balbuena, L., Åhs, F., Peters, E., Mendes-Silva, A. & Speed, D. (2025). Does the Path From Cigarette Smoking to Suicide Death Go Through the Hospital? A Causal Mediation Analysis in a National Canadian Sample. Tobacco Use Insights, 18. https://doi.org/10.1177/1179173X251349612

Giagnoni, G., Foldager, L., Stephansen, R. B., Liu, H., Lassen, J. & Weisbjerg, M. R. (2025). Do feed conversion efficiency and its inverse, feed conversion ratio, differ in their distributions for dairy cows?. 200. Abstract from 76th Annual Meeting of The European Federation of Animal Science, Innsbruck, Austria.

Zhu, D., Shi, K., Li, C., Yan, Y., Li, H., Bai, Z., Tan, L., Guan, D., Zhao, Y., Wang, Y., Fan, B., Jiang, Z., Xu, Z., Feng, C., Fang, L., Hu, X. & ChickenGTEx Consortium (2026). Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits. Nature Communications, 17(1), Article 553. Advance online publication. https://doi.org/10.1038/s41467-025-67245-y

Holur, P., Enevoldsen, K. C., Rajesh, S., Mboning, L., Georgiou, T., Bouchard, L. S., Pellegrini, M. & Roychowdhury, V. (2025). Embed-Search-Align: DNA sequence alignment using Transformer models. Bioinformatics, 41(3), Article btaf041. https://doi.org/10.1093/bioinformatics/btaf041

Ssemakula, F., Nawoya, S., Kunyanga, C. N., Akol, R., Nakimbugwe, D., Bett, R. C., Karstoft, H., Bjerge, K., Katumba, A., Mwikirize, C. & Gebreyesus, G. (2025). Emerging technologies for fast determination of nutritional quality and safety of insects for food and feed: A review. Computers and Electronics in Agriculture, 239, Article 111126. https://doi.org/10.1016/j.compag.2025.111126

Shrestha, M., Bai, Z., Gholipourshahraki, T., Hjelholt, A. J., Hu, S., Kjolby, M., Rohde, P. D. & Sørensen, P. (2025). Enhanced genetic fine mapping accuracy with Bayesian Linear Regression models in diverse genetic architectures. PLoS Genetics, 21(7), 1-30. Article e1011783. https://doi.org/10.1371/journal.pgen.1011783

van der Heide, M. E. & Janss, L., (2025). Estimated usage of organic and non-organic feed and protein-rich feedstuff for organic pig and poultry in 2024, No. 2025-0830467, 22 p., Sept 10, 2025. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Þórarinsdóttir, Þ., Eiriksson, J., Gautason, E., Thomasen, J. R. & Liu, H. (2025). Evaluating genomic breeding programs for a small dairy cattle population with widespread use of private bulls. Journal of Dairy Science, 108(11), 12450-12462. https://doi.org/10.3168/jds.2025-26592

Ramírez-Díaz, J., Bobbo, T., Guldbrandtsen, B., Schönherz, A. A., Cozzi, P., Kusza, S., Sahana, G., Stella, A. & Manunza, A. (2025). Exploring the complex population structure and admixture of four local Hungarian sheep breeds. Frontiers in Genetics, 16, Article 1507315. https://doi.org/10.3389/fgene.2025.1507315

Mouritzen, T. W., Meurer, K. H. E., Bornhofen, E., Janss, L., Weih, M. & Andersen, S. U. (2025). Faba bean genetics and crop growth models – progress to date and opportunities for integration. Plant and Soil, 514(1), 47-64. https://doi.org/10.1007/s11104-025-07459-7

Tariku, H. G., Nielsen, H. M., Walusimbi, S., Hansen, L. S., Gebreyesus, G., Rugira-Kugonza, D., Bett , R. C., Nakimbugwe, D., Geoffrey, S. & Kassie, G. T. (2025). Farmers’ Preferences for Larval Traits in Small-Scale Black Soldier Fly (Hermetia illucens) Production System [019]. 43-43. Poster session presented at BSFcon 2025, Cambridge, United Kingdom.

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Jette Odgaard Villemoes