Vélez, J. L., Pérez-Rodrı́guez, P., Nilforooshan, M. A., & Ruı́z Flores, A. (2025). Comparison of mmachine learning methods for predicting genomic breeding values for growth traits in Braunvieh cattle. Revista Mexicana de Ciencias Pecuarias, 16(1), 179–193. https://doi.org/10.22319/rmcp.v16i1.6616
Nilforooshan, M. A., Ruı́z-Flores, A., Pérez-Rodrı́guez, P., Pabiou, T., Saavedra-Jiménez, L. A., & Valerio-Hernández, J. E. (2025). Multitrait analysis of growth traits for the optimization of breeding value prediction in Braunvieh cattle. Revista Mexicana de Ciencias Pecuarias, 16(1), 55–68. https://doi.org/10.22319/rmcp.v16i1.6648
Nilforooshan, M. A. (2024a). FnR: R package for computing inbreeding and numerator relationship coefficients. BMC Ecology and Evolution, 24(1), 99. https://doi.org/10.1186/s12862-024-02285-4
Nilforooshan, M. A. (2024b). Short Communication: Reduced GBLUP equations to core animals in the algorithm for proven and young (APY). Veterinary and Animal Science, 23, 100334. https://doi.org/10.1016/j.vas.2024.100334
Valerio-Hernández, J. E., Ruı́z-Flores, A., Nilforooshan, M. A., & Pérez-Rodrı́guez, P. (2023). Single-step genomic evaluation for growth traits in a Mexican Braunvieh cattle population. Animal Bioscience, 36(7), 1003–1009. https://doi.org/10.5713/ab.22.0158
Nilforooshan, M. A. (2023a). Extension of the reduced animal model to single-step methods. Journal of Animal Science, 101, skac272. https://doi.org/10.1093/jas/skac272
Nilforooshan, M. A. (2023b). The algorithm for proven and young (APY) from a different perspective. bioRxiv, 2022.11.23.517757. https://doi.org/10.1101/2022.11.23.517757
Nilforooshan, M. A. (2022a). A note on the conditioning of the H–1 matrix used in single-step GBLUP. Animals 12(22), 3208. https://doi.org/10.3390/ani12223208
Nilforooshan, M. A. & Ruı́z-Flores, A. (2022). Understanding factors influencing the estimated genetic variance and the distribution of breeding values. Frontiers in Genetics, 13, 1000228. https://doi.org/10.3389/fgene.2022.1000228
Nilforooshan, M. A. (2022b). pedSimulate – An R package for simulating pedigree, genetic merit, phenotype, and genotype data. Revista Brasileira de Zootecnia, 51, e20210131. https://doi.org/10.37496/rbz5120210131
Nilforooshan, M. A. (2022c). Compensating for the increase in the sum of eigenvalues and monitoring the bending performance for conditioning covariance matrices in multi-trait livestock evaluations. Animal - Open Space, 1(1), 100005. https://doi.org/10.1016/j.anopes.2022.100005
Nilforooshan, M. A. (2022d). A new computational approach to Henderson’s method of computing the inverse of a numerator relationship matrix. Livestock Science, 257, 104848. https://doi.org/10.1016/j.livsci.2022.104848
Nilforooshan, M. A. & Jorjani, H. (2022). Invited review: A quarter of a century—International genetic evaluation of dairy sires using MACE methodology. Journal of Dairy Science, 105(1), 3–21. https://doi.org/10.3168/jds.2021-20927
Lee, M. A., Newman, S.-A., Dodds, K. G., Nilforooshan, M. A., Auvray, B., McIntyre, S., & Campbell, D. (2021). Genomic evaluations of sheep in New Zealand. New Zealand Journal of Animal Science and Production, 81, 106–111. http://www.nzsap.org/proceedings/genomic-evaluations-sheep-new-zealand
Saavedra-Jiménez, L. A., Ramı́rez-Valverde, R., Núñez-Domı́nguez, R., Ruı́z-Flores, A., Garcı́a-Muñiz, J. G., & Nilforooshan, M. A. (2021). Effect of two phantom parent grouping strategies on the genetic evaluation of growth traits in Mexican Braunvieh cattle. Revista Mexicana De Ciencias Pecuarias, 12(3), 878–892. https://doi.org/10.22319/rmcp.v12i3.5562
Nilforooshan, M. A., Garrick, D., & Harris, B. (2021a). Alternative ways of computing the numerator relationship matrix. Frontiers in Genetics, 12, 1236. https://doi.org/10.3389/fgene.2021.655638
Nilforooshan, M. A. & Garrick, D. (2021a). Reduced animal models fitting only equations for phenotyped animals. Frontiers in Genetics, 12, 372. https://doi.org/10.3389/fgene.2021.637626
Nilforooshan, M. A. (2020a). mbend: An R package for bending non-positive-definite symmetric matrices to positive-definite. BMC Genetics, 21, 97. https://doi.org/10.1186/s12863-020-00881-z
Nilforooshan, M. A. & Saavedra-Jiménez, L. A. (2020). ggroups: An R package for pedigree and genetic groups data. Hereditas, 157, 17. https://doi.org/10.1186/s41065-020-00124-2
Nilforooshan, M. A. (2020b). Memory-efficient self-cross-product for large matrices using R and Python. Journal of Mathematical and Computational Science, 10(3), 497–506. https://doi.org/10.28919/jmcs/4457
Nilforooshan, M. A. (2020c). Updating genetic relationship matrices and their inverses: A methodology note. Canadian Journal of Animal Science, 100(2), 292–298. https://doi.org/10.1139/CJAS-2019-0106
Nilforooshan, M. A. (2020d). Application of single-step GBLUP in New Zealand Romney sheep. Animal Production Science, 60(9), 1136–1144. https://doi.org/10.1071/AN19315
Nilforooshan, M. A. & Lee, M. (2019). The quality of the algorithm for proven and young with various sets of core animals in a multi-breed sheep population. Journal of Animal Science, 97(3), 1090–1100. https://doi.org/10.1093/jas/skz010
Nilforooshan, M. A., Jakobsen, J. H., Fikse, W. F., Berglund, B., & Jorjani, H. (2014). Multiple-trait multiple-country genetic evaluation of Holstein bulls for female fertility and milk production traits. Animal, 8(6), 887–894. https://doi.org/10.1017/S1751731114000895
Behdad, S., Edriss, M. A., Nilforooshan, M. A., & Movassagh, A. H. (2013). Wool characteristics of Bakhtiari sheep and the correlated responses to selection for pre-weaning daily gain. Indian Journal of Animal Sciences, 83(1), 82–85. http://epubs.icar.org.in/ejournal/index.php/IJAnS/article/view/26453
Nilforooshan, M. A. (2011). Multiple-trait multiple country genetic evaluation of fertility traits in dairy cattle (Publication No. 2011:31) [Doctoral dissertation, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala]. https://res.slu.se/id/publ/33755
Nilforooshan, M. A., Fikse, W. F., Berglund, B., Jakobsen, J. H., & Jorjani, H. (2011). Short communication: Quantifying bias in a single-trait international model ignoring covariances from multiple-trait national models. Journal of Dairy Science, 94(5), 2631–2636. https://doi.org/10.3168/jds.2010-3863
Nilforooshan, M. A., Jakobsen, J. H., Fikse, W. F., Berglund, B., & Jorjani, H. (2010). Application of a multiple-trait, multiple-country genetic evaluation model for female fertility traits. Journal of Dairy Science, 93(12), 5977–5986. https://doi.org/10.3168/jds.2010-3437
Nilforooshan, M. A. (2010). Contemporary grouping in mixed-size dairy herds experiencing four seasons. Turkish Journal of Veterinary and Animal Sciences, 34(2), 129–135. https://doi.org/10.3906/vet-0710-18
Nilforooshan, M. A., Khazaeli, A., & Edriss, M. A. (2008). Effects of missing pedigree information on dairy cattle genetic evaluations (short communication). Archives Animal Breeding, 51(2), 99–110. https://doi.org/10.5194/aab-51-99-2008
Edriss, M. A., Hosseinnia, P., Edrisi, M., Rahmani, H. R., & Nilforooshan, M. A. (2008). Prediction of second parity milk performance of dairy cows from first parity information using artificial neural network and multiple linear regression methods. Asian Journal of Animal and Veterinary Advances, 3(4), 222–229. https://doi.org/10.3923/ajava.2008.222.229
Hosseinia, P., Edrisi, M., Edriss, M. A., & Nilforooshan, M. A. (2007). Prediction of second parity milk yield and fat percentage of dairy cows based on first parity information using neural network system. Journal of Applied Sciences, 7(21), 3274–3279. https://doi.org/10.3923/jas.2007.3274.3279
Edriss, M. A., Dashab, G., Ghareh Aghaji, A. A., Nilforooshan, M. A., & Movassagh, H. (2007). A study on some physical attributes of Naeini sheep wool for textile industry. Pakistan Journal of Biological Sciences, 10(3), 415–420. https://doi.org/10.3923/pjbs.2007.415.420
Nilforooshan, M. A. & Edriss, M. A. (2007). Comparison of Holstein bull semen sources on milk traits in Isfahan province in Iran. Archives Animal Breeding, 50(1), 71–83. https://doi.org/10.5194/aab-50-71-2007
Edriss, M. A., Nilforooshan, M. A., & Sadeghi, J. M. (2006). Estimation of direct genetic and maternal effects for production traits of Iranian Holstein cows using different animal models. Pakistan Journal of Biological Sciences, 9(4), 636–640. https://doi.org/10.3923/pjbs.2006.636.640
Dashab, G., Edriss, M. A., Ghare Aghaji, A. A., Movasagh, H., & Nilforooshan, M. A. (2006). Wool fiber quality of Naeini sheep. Pakistan Journal of Biological Sciences, 9(2), 270–276. https://doi.org/10.3923/pjbs.2006.270.276
Nilforooshan, M. A. & Edriss, M. A. (2004). Effect of age at first calving on some productive and longevity traits in Iranian Holsteins of the Isfahan province. Journal of Dairy Science, 87(7), 2130–2135. https://doi.org/10.3168/jds.S0022-0302(04)70032-6
Nilforooshan, M. A. (2003). Genetic evaluation and comparison between domestic and imported (Canada, USA, Europe) sperms for milk yield, fat yield, and fat percentage in some dairy farms of Isfahan province [Master’s thesis, Isfahan (Khorasgan) Azad University, Isfahan]. https://doi.org/10.5281/zenodo.4297235
Nilforooshan, M. A. (2023c). Code & Data — Genomic evaluations reduced to equations for core animals in the algorithm for proven and young (APY). figshare. https://doi.org/10.6084/m9.figshare.20539650.v3
Nilforooshan, M. A. (2022e). Code & Data — A note on the conditioning of the H-1 matrix used in single-step GBLUP. Mendeley Data. https://doi.org/10.17632/cn9jzpj7fg.1
Nilforooshan, M. A. (2022f). Code & Data — Understanding factors influencing the estimated genetic variance and the distribution of breeding values. Mendeley Data. https://doi.org/10.17632/zd3xx54j62.3
Nilforooshan, M. A. (2022h). Code & Data — Further improvement of bending performance for conditioning covariance matrices. Mendeley Data. https://doi.org/10.17632/gnyrym4mv4.3
Nilforooshan, M. A. (2022i). Twenty simulated pedigrees with different combinations of three parameters using R package pedSimulate. Mendeley Data. https://doi.org/10.17632/c4pv8w8pmp.2
Nilforooshan, M. A. (2021). Code – A new computational approach to Henderson’s method for computing the inverse of a numerator relationship matrix. Mendeley Data. https://doi.org/10.17632/db9pd7ns6d.2
Nilforooshan, M. A., Garrick, D., & Harris, B. (2021b). Code & Data – Alternative ways of computing the numerator relationship matrix. figshare. https://doi.org/10.6084/m9.figshare.13497939.v1
Nilforooshan, M. A. (2019). Benchmarking matrix self-cross-products, using R and Python functions. Mendeley Data. https://doi.org/10.17632/vk8vy7ghnf.1
Wang, Y., Tiplady, K. M., Reynolds, E. G. M., Nilforooshan, M. A., Couldrey, C., & Harris, B. L. (2023, August 26–September 1). Genomic prediction with selected sequence variants in gestation length of New Zealand dairy cattle [Slides file, Abstract file]. In Proceedings of the 74th Annual meeting of the European Association for Animal Production, Lyon, France (p. 164, Vol. 29).
Harris, B. L., Sherlock, R. G., & Nilforooshan, M. A. (2022, July 3–8). Large-scale multiple-trait single-step marker model implementation. In Proceeding of the 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, The Netherlands (pp. 1360–1363). https://doi.org/10.3920/978-90-8686-940-4_324
Nilforooshan, M. A., Auvray, B., & Lee, M. (2018, February 11–16). Animal-specific combining of the GRM and the NRM in single-step GBLUP [Poster file, Paper file]. In Proceeding of the 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand (pp. 1360–1363).
Pabiou, T., Nilforooshan, M. A., Venot, E., & Moore, K. (2015, January 19–21). Interbeef presents new opportunities for beef farmers [Paper file]. In British Cattle Conference, Telford, England (pp. 15–18).
Pabiou, T., Nilforooshan, M. A., Laloe, D., Hjerpe, E., & Venot, E. (2014, August 17–22). Across-country genetic parameters in beef cattle for Interbeef weaning weight genetic evaluation [Poster file, Paper file]. In Proceeding of the 10th World Congress on Genetics Applied to Livestock Production, Vancouver, Canada.
Venot, E., Pabiou, T., Hjerpe, E., Nilforooshan, M. A., Launay, A., & Wickham, B. (2014, August 17–22). Benefits of Interbeef international genetic evaluations for weaning weight [Paper file]. In Proceeding of the 10th World Congress on Genetics Applied to Livestock Production, Vancouver, Canada.
Mäntysaari, E., & Nilforooshan, M. A. (2014, May 20–21). Effect of the size of the reference population on the validation reliability of national genomic evaluations [Slides file]. In Interbull Meeting, Berlin, Germany.
Nilforooshan, M. A. (2014, May 20–21). A review of the validation of national genomic evaluations[Slides file, Paper file]. In Interbull Bulletin, Berlin, Germany (pp. 111–117, Vol. 48).
Nilforooshan, M. A. & Hjerpe, E. (2014, March 10). Interbeef report on weaning genetic evaluation performed in March 2014 for Charolais and Limousin. In Interbeef Technical Meeting, Uppsala, Sweden.
Braillon, L., & Nilforooshan, M. A. (2013, August 27). Review of the Interbeef proof publication proposal [Slides file]. In Interbeef Technical Meeting, Nantes, France.
Nilforooshan, M. A., Hjerpe, E., Palucci, V., & Dürr, J. (2013, March 27–28). Interbeef report on weaning genetic evaluation for Charolais and Limousin [Slides file]. In Interbeef Technical Meeting, Aarhus, Denmark.
Nilforooshan, M. A. (2012, December 6–7). Report on the weaning weight phenotypic data editing for Charolais and Limousin [Slides file]. In Interbeef Technical Meeting, Uppsala, Sweden.
Jorjani, H., Jakobsen, J., Nilforooshan, M. A., Hjerpe, E., Zumbach, B., Palucci, V., & Dürr, J. (2011, February 27–28). Genomic evaluation of BSW populations. InterGenomics: Results and deliverables [Slides file, Paper file]. In Interbull Bulletin, Guelph, Ontario, Canada (pp. 5–8, Vol. 43).
Nilforooshan, M. A., Rönnegård, L., & Jorjani, H. (2010, August 1–6). Various statistical models for prediction of SNP effects from a multi-national/breed reference population [Poster file, Paper file]. In Proceeding of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany.
Nilforooshan, M. A., Zumbach, B., Jakobsen, J., Loberg, A., Jorjani, H., & Dürr, J. (2010, May 31–June 4). Validation of national genomic evaluations [Slides file, Paper file]. In Interbull Bulletin, Riga, Latvia (pp. 56–61, Vol. 42).
Nilforooshan, M. A., Jakobsen, J., Fikse, F., Berglund, B., & Jorjani, H. (2009, August 21–24). MT-MACE for female fertility and milk yield [Slides file, Paper file]. In Interbull Bulletin, Barcelona, Spain (pp. 68–71, Vol. 40).
Nilforooshan, M. A. (2009a, December 7). International genetic evaluations of fertility traits using MT-MACE [Poster file]. In Faculty research day, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Nilforooshan, M. A. (2009b, June 4). International genetic evaluations of fertility traits using MT-MACE [Poster file]. In The 80th Anniversary of the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Nilforooshan, M. A., Jakobsen, J., Fikse, F. W., Berglund, B., & Jorjani, H. (2009, January 26–29). International genetic evaluations for female fertility traits using multi-trait MACE [Slides file, Paper file]. In Interbull Bulletin, Uppsala, Sweden (pp. 99–102, Vol. 39).
Nilforooshan, M. A., Fikse, F. W., & Jorjani, H. (2008, August 24–27). International genetic evaluations of fertility traits considering more than one trait per country [Slides file, Abstract file]. In Proceeding of the 59th Annual meeting of the European Association for Animal Production, Vilnius, Lithuania (p. 268, Vol. 14).