Journal club - ANGEN

2025.

JC13. 15.07.2025.

GAbridge

Rosengren, E, Rossi, C, Heino, M T & Sinding, M-H. (2024). New finds of European bison identified through the systematic DNA-based species identification of archaeological remains of large bovines from Scandinavia. Journal of Archaeological Science: Reports, 57, 104668. https://doi.org/10.1016/j.jasrep.2024.104668

Niemi, M., Sajantila, A. and Vilkki, J. (2016), Temporal variation in coat colour (genotypes) supports major changes in the Nordic cattle population after Iron Age. Anim Genet, 47: 495-498. https://doi.org/10.1111/age.12445

JC12. 08.07.2025.

PhenoGeno

Lewerentz, F., Vanhala, T. K., Johansen, L. B., Paulsson, M., Glantz, M., & de Koning, D. J. (2024). Re-sequencing of the casein genes in Swedish Red cattle giving milk with diverse protein profiles and extreme rennet coagulation properties. JDS communications, 5(4), 299–304. https://doi.org/10.3168/jdsc.2023-0412

JC11. 16.05.2025.

PhenoGeno

Bisutti, V., Mota, L. F. M., Giannuzzi, D., Toscano, A., Amalfitano, N., Schiavon, S., Pegolo, S., & Cecchinato, A. (2024). Infrared spectroscopy coupled with machine learning algorithms for predicting the detailed milk mineral profile in dairy cattle. Food chemistry, 461, 140800. https://doi.org/10.1016/j.foodchem.2024.140800

Yengo, L., Yang, J., Keller, M. C., Goddard, M. E., Wray, N. R., & Visscher, P. M. (2021). Genomic partitioning of inbreeding depression in humans. American journal of human genetics, 108(8), 1488–1501. https://doi.org/10.1016/j.ajhg.2021.06.005

JC10. 13.05.2025.

GAbridge

Urciuoli, A., Martínez, I., Quam, R. et al. Semicircular canals shed light on bottleneck events in the evolution of the Neanderthal clade. Nat Commun 16, 972 (2025). https://doi.org/10.1038/s41467-025-56155-8

Chacón-Duque, J. C., Thomas Thorpe, J. A., Li, W., Dehasque, M., Pečnerová, P., Barlow, A., Díez-Del-Molino, D., Henneberger, K., Jin, C., Moreland, K. N., Paijmans, J. L. A., van der Valk, T., Westbury, M. V., Wijnands, F., Barnes, I., Germonpré, M., Hall, E., Hewitson, S., Mol, D., Nikolskiy, P., … Dalén, L. (2025). A Million Years of Mammoth Mitogenome Evolution. Molecular biology and evolution, 42(4), msaf065. https://doi.org/10.1093/molbev/msaf065

JC9. 24.03.2025.

PhenoGeno

Castellani, C. A., Longchamps, R. J., Sun, J., Guallar, E., & Arking, D. E. (2020). Thinking outside the nucleus: Mitochondrial DNA copy number in health and disease. Mitochondrion, Volume 53, 214-223. https://doi.org/10.1016/j.mito.2020.06.004.

JC8. 14.03.2025.

GAbridge

Daly, K. G., Mullin, V. E., Hare, A. J., Halpin, Á., Mattiangeli, V., Teasdale, M. D., Rossi, C., Geiger, S., Krebs, S., Medugorac, I., Sandoval-Castellanos, E., Özbaşaran, M., Duru, G., Gülcür, S., Pöllath, N., Collins, M., Frantz, L., Vila, E., Zidarov, P., Stoddart, S., … Bradley, D. G. (2025). Ancient genomics and the origin, dispersal, and development of domestic sheep. Science (New York, N.Y.), 387(6733), 492–497. https://doi.org/10.1126/science.adn2094

JC7. 20.02.2025.

PhenoGeno

Manuskript Shihabi et al. Convergent genomic signatures of adaptation in Livestock Guardian Dogs and Gray Wolves.

JC6. 11.02.2025. 

GAbridge

Speidel, L., Silva, M., Booth, T. et al. High-resolution genomic history of early medieval Europe. Nature 637, 118–126 (2025). https://doi.org/10.1038/s41586-024-08275-2

JC5. 14.01.2025.

GAbridge

Utsunomiya, Y. T., Milanesi, M., Utsunomiya, A. T. H., Torrecilha, R. B. P., Kim, E. S., Costa, M. S., Aguiar, T. S., Schroeder, S., do Carmo, A. S., Carvalheiro, R., Neves, H. H. R., Padula, R. C. M., Sussai, T. S., Zavarez, L. B., Cipriano, R. S., Caminhas, M. M. T., Hambrecht, G., Colli, L., Eufemi, E., Ajmone-Marsan, P., … Garcia, J. F. (2017). A PLAG1 mutation contributed to stature recovery in modern cattle. Scientific reports, 7(1), 17140. doi:10.1038/s41598-017-17127-1

PhenoGeno

Laubenthal, L., Hoelker, M., Frahm, J., Dänicke, S., Gerlach, K., Südekum, K. H., Sauerwein, H., & Häussler, S. (2016). Mitochondrial DNA copy number and biogenesis in different tissues of early- and late-lactating dairy cows. Journal of dairy science, 99(2), 1571–1583. https://doi.org/10.3168/jds.2015-9847

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2024.

JC4. 6.12.2024.

GAbridge

Rossi, C., Sinding, M. S., Mullin, V. E., Scheu, A., Erven, J. A. M., Verdugo, M. P., Daly, K. G., Ciucani, M. M., Mattiangeli, V., Teasdale, M. D., Diquelou, D., Manin, A., Bangsgaard, P., Collins, M., Lord, T. C., Zeibert, V., Zorzin, R., Vinter, M., Timmons, Z., Kitchener, A. C., … Bradley, D. G. (2024). The genomic natural history of the aurochs. Nature, 635(8037), 136–141. https://doi.org/10.1038/s41586-024-08112-6

PhenoGeno

Gupta, R., Kanai, M., Durham, T. J., Tsuo, K., McCoy, J. G., Kotrys, A. V., Zhou, W., Chinnery, P. F., Karczewski, K. J., Calvo, S. E., Neale, B. M., & Mootha, V. K. (2023). Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature, 620(7975), 839–848. https://doi.org/10.1038/s41586-023-06426-5

JC3. 21.11.2024.

GAbridge

Ren, Y., Khatkar, M. S., MacPhillamy, C., Wang, H., McEwin, R. A., Chen, T., Pitchford, W. S., & Low, W. Y. (2024). Evaluating the Efficacy of Target Capture Sequencing for Genotyping in Cattle. Genes, 15(9), 1218. https://doi.org/10.3390/genes15091218

PhenoGeno

Brajkovic, V., Pocrnic, I., Kaps, M., Špehar, M., Cubric-Curik, V., Ristov, S., Novosel, D., Gorjanc, G., & Curik, I. (2024). Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: empirical results and modelling challenges. Journal of dairy science, S0022-0302(24)01221-9. Advance online publication. https://doi.org/10.3168/jds.2024-25203

JC2. PhenoGeno - 31.10.2024.

Sanglard L.P., Kuehn L.A., Snelling W.M., Spangler M.L. (2022) Influence of environmental factors and genetic variation on mitochondrial DNA copy number. J Anim Sci http://doi: 10.1093/jas/skac059

JC1. GAbridge - 24.10.2024.

Günther, T., Chisausky, J., Galindo-Pellicena, M. Á., Iriarte, E., Cortes Gardyn, O., ... & Valdiosera, C. (2024.) The Genomic Legacy of Human Management and sex-biased Aurochs hybridization in Iberian Cattle. eLife https://elifesciences.org/reviewed-preprints/93076

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2023.

JC14. - 02.02.2023.

Daly, K. G., Mattiangeli, V., Hare, A. J., Davoudi, H., Fathi, H., Doost, S. B., ... & Bradley, D. G. (2021). Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains. Proceedings of the National Academy of Sciences, 118(25), e2100901118. https://doi.org/10.1073/pnas.2100901118

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2022.

JC13. - 24.02.2022.

Gaynor, R. C., Gorjanc, G., & Hickey, J. M. (2021). AlphaSimR: an R package for breeding program simulations. G3, 11(2), jkaa017. https://doi.org/10.1093/g3journal/jkaa017

JC12. - 17.02.2022.

Santiago, E., Novo, I., Pardiñas, A. F., Saura, M., Wang, J., & Caballero, A. (2020). Recent demographic history inferred by high-resolution analysis of linkage disequilibrium. Molecular Biology and Evolution, 37(12), 3642-3653. https://doi.org/10.1093/molbev/msaa169

JC11. - 03.02.2022.

Bittante, G., Penasa, M., & Cecchinato, A. (2012). Invited review: Genetics and modeling of milk coagulation properties. Journal of dairy science, 95(12), 6843-6870. https://doi.org/10.3168/jds.2012-5507

Frizzarin, M., Gormley, I. C., Berry, D. P., Murphy, T. B., Casa, A., Lynch, A., & McParland, S. (2021). Predicting cow milk quality traits from routinely available milk spectra using statistical machine learning methods. Journal of Dairy Science, 104(7), 7438-7447. https://doi.org/10.3168/jds.2020-19576

JC10. - 27.01.2022.

Dadousis, C., Biffani, S., Cipolat-Gotet, C., Nicolazzi, E. L., Rossoni, A., Santus, E., Bittante A., Cecchinato, A. (2016). Genome-wide association of coagulation properties, curd firmness modeling, protein percentage, and acidity in milk from Brown Swiss cows. Journal of dairy science, 99(5), 3654-3666. https://doi.org/10.3168/jds.2015-10078

JC9. - 20.01.2022.

Izlaganje znanstvenih radova predanih za WCGALP kongres.

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2021.

JC8. - 16.12.2021.

Serranito, B., Cavalazzi, M., Vidal, P., Taurisson-Mouret, D., Ciani, E., Bal, M., ... & Da Silva, A. (2021). Local adaptations of Mediterranean sheep and goats through an integrative approach. bioRxiv. https://doi.org/10.1101/2021.01.22.427461

JC7. - 09.12.2021.

Yurtman, E., Özer, O., Yüncü, E., Dağtaş, N. D., Koptekin, D., Çakan, Y. G., ... & Özer, F. (2021). Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication. Communications Biology, 4(1), 1-11. https://doi.org/10.1038/s42003-021-02794-8

JC6. - 25.11.2021.

Ristov, S., Brajkovic, V., Cubric-Curik, V., Michieli, I., & Curik, I. (2016). MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information. Genetics Selection Evolution, 48(1), 1-10. https://doi.org/10.1186/s12711-016-0242-9 

JC5. - 12.11.2021.

Furholt, M. (2021). Mobility and social change: Understanding the European Neolithic period after the archaeogenetic revolution. Journal of Archaeological Research, 1-55. https://doi.org/10.1007/s10814-020-09153-x

JC4. - 04.11.2021.

Kammeraad, D. - Tečaj o manipuliranju/radu sa sekvencama (WGS podaci) u SVS programu (Golden Helix)

JC3. - 28.10.2021.

Chen, Z. H., Zhang, M., Lv, F. H., Ren, X., Li, W. R., Liu, M. J., ... & Li, M. H. (2018). Contrasting patterns of genomic diversity reveal accelerated genetic drift but reduced directional selection on X-chromosome in wild and domestic sheep species. Genome biology and evolution, 10(5), 1282-1297. https://doi.org/10.1093/gbe/evy085

JC2. - 21.10.2021.

Ciani, E., Mastrangelo, S., Da Silva, A., Marroni, F., Ferenčaković, M., Ajmone-Marsan, P., ... & Lenstra, J. A. (2020). On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools. Genetics Selection Evolution, 52, 1-14. https://doi.org/10.1186/s12711-020-00545-7

JC1. - 07.10.2021.

Gernigon, K. (2016). Villages before houses? The neolithization of Europe reconsidered through the concept of the household. Palethnologie. Archéologie et sciences humaines, (8).  https://journals.openedition.org/palethnologie/527

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2019.

JC1. - 25.10.2019

Martin S H, Davey J W,Jiggins C D (2015) Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci. Mol.Biol.Evol. 32(1):244–257 DOI: 10.1093/molbev/msu269

JC2. - 8.11.2019

Park S D E et al. (2015) Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biology 16:234 DOI: 10.1186/s13059-015-0790-2

JC3. - 15.11.2019

Verdugo M P et al. (2019) Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science 365, 173–176

JC4. – 29.11.2019

Chen N et al. (2018) Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nature Communications 9:2337 DOI: 10.1038/s41467-018-04737-0