Results overview: Found 9 records in 0.03 seconds.
Articles, 9 records found
Articles 9 records found  
1.
12 p, 12.8 MB Gut eukaryotic communities in pigs : diversity, composition and host genetics contribution / Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries) ; Prenafeta-Boldú, Francesc (Institut de Recerca i Tecnologia Agroalimentàries) ; Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Gonzalez-Rodriguez, Olga (Institut de Recerca i Tecnologia Agroalimentàries) ; Dalmau Bueno, Antoni (Institut de Recerca i Tecnologia Agroalimentàries) ; Quintanilla, Raquel (Institut de Recerca i Tecnologia Agroalimentàries) ; Ballester Devis, Maria (Institut de Recerca i Tecnologia Agroalimentàries)
Background. The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. [...]
2020 - 10.1186/s42523-020-00038-4
Animal Microbiome, Vol. 2 (May 2020) , art. 18  
2.
A pilot RNA-seq study in 40 Pietrain ejaculates to characterize the porcine sperm microbiome / Gòdia, Marta (Centre de Recerca en Agrigenòmica) ; Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries) ; Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Darwich Soliva, Laila (Universitat Autònoma de Barcelona. Centre de Recerca en Sanitat Animal) ; López, Samantha (Universitat de Barcelona. Departament de Física de la Matèria Condensada) ; Rodríguez-Gil, Joan E. (Universitat Autònoma de Barcelona. Departament de Medicina i Cirurgia Animals) ; Yeste Oliveras, Marc (Universitat de Girona. Institut de Tecnologia Agroalimentària) ; Sánchez Bonastre, Armando (Centre de Recerca en Agrigenòmica) ; Clop, Alex (Centre de Recerca en Agrigenòmica)
The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput characterization of the swine sperm microbiome remains scarce. [...]
2020 - 10.1016/j.theriogenology.2020.08.001
Theriogenology, Vol. 157 (November 2020) , p. 525-533
2 documents
3.
14 p, 1.9 MB Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species / Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Gezan, Salvador Alejandro (University of Florida. School of Forest Resources and Conservation (USA)) ; Ferrão, Luis Felipe V. (University of Florida. Horticultural Sciences Department (USA)) ; Osorio, Luis F. (University of Florida. IFAS Gulf Coast Research and Education Center (USA)) ; Monfort Vives, Amparo (Centre de Recerca en Agrigenòmica) ; Muñoz, Patricio R. (University of Florida. Horticultural Sciences Department (USA)) ; Whitaker, Vance M. (University of Florida. IFAS Gulf Coast Research and Education Center (USA)) ; Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, applications to polyploid organisms are still scarce, partly due to limited genome resources and the complexity of this system. [...]
2020 - 10.3389/fpls.2020.00025
Frontiers in plant science, Vol. 11 (February 2020) , art. 25  
4.
9 p, 1.0 MB Estimating conformational traits in dairy cattle with deepAPS : A two-step deep learning automated phenotyping and segmentation approach / Nye, Jessica (Centre de Recerca en Agrigenòmica) ; Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Assessing conformation features in an accurate and rapid manner remains a challenge in the dairy industry. While recent developments in computer vision has greatly improved automated background removal, these methods have not been fully translated to biological studies. [...]
2020 - 10.3389/fgene.2020.00513
Frontiers in genetics, Vol. 11 (May 2020) , art. 513  
5.
2 p, 462.8 KB Link-HD : a versatile framework to explore and integrate heterogeneous microbial communities / Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Renand, Gilles (Université Paris-Saclay. Institut National de la Recherche Agronomique. Génétique Animale et Biologie Intégrative (France)) ; Morgavi, Diego P. (Institut National de la Recherche Agronomique (França)) ; Ramayo-Caldas, Yuliaxis (Université Paris-Saclay. Institut National de la Recherche Agronomique. Génétique Animale et Biologie Intégrative (France))
Motivation: We present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of 'Structuration des Tableaux A Trois Indices de la Statistique-Analyse Conjointe de Tableaux', a family of methods designed to integrate information from heterogeneous data. [...]
2020 - 10.1093/bioinformatics/btz862
Bioinformatics, Vol. 36, Issue 7 (April 2020) , p. 2298-2299  
6.
11 p, 594.5 KB Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows / Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries. Torre Marimon) ; Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Popova, Milka (Université Clermont Auvergne. Institut National de la Recherche Agronomique. VetAgro Sup (France)) ; Estellé Fabrellas, Jordi (Université Paris-Saclay. Institut National de la Recherche Agronomique. Génétique Animale et Biologie Intégrative (France)) ; Bernard, Aurelien (Université Clermont Auvergne. Institut National de la Recherche Agronomique. VetAgro Sup (France)) ; Pons, Nicolas (Institut National de la Recherche Agronomique. Metagenopolis Unit (France)) ; Bellot, Pau (Centre de Recerca en Agrigenòmica) ; Mach, Núria (Université Paris-Saclay. Institut National de la Recherche Agronomique. AgroParisTech (France)) ; Rau, Andrea (Université Paris-Saclay. Institut National de la Recherche Agronomique. AgroParisTech (France)) ; Roume, Hugo (Institut National de la Recherche Agronomique. Metagenopolis Unit (France)) ; Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica) ; Faverdin, Philippe (Institut National de la Recherche Agronomique (França)) ; Edouard, Nadège (Institut National de la Recherche Agronomique (França)) ; Ehrlich, Dusko (Institut National de la Recherche Agronomique. Metagenopolis Unit (France)) ; Morgavi, Diego P. (Université Clermont Auvergne. Institut National de la Recherche Agronomique (France)) ; Renand, Gilles (Université Paris-Saclay. Institut National de la Recherche Agronomique. AgroParisTech (France))
Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. [...]
2020 - 10.1111/jbg.12427
Journal of Animal Breeding and Genetics, Vol. 137, Issue 1 (January 2020) , p. 49-59  
7.
9 p, 1.4 MB SeqBreed : a python tool to evaluate genomic prediction in complex scenarios / Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica) ; Ramírez-Ayala, Lino C. (Centre de Recerca en Agrigenòmica) ; Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica)
Background: Genomic prediction (GP) is a method whereby DNA polymorphism information is used to predict breeding values for complex traits. Although GP can significantly enhance predictive accuracy, it can be expensive and difficult to implement. [...]
2020 - 10.1186/s12711-020-0530-2
Genetics Selection Evolution, Vol. 52 (February 2020) , art. 7  
8.
19 p, 2.0 MB A guide for using deep learning for complex trait genomic prediction / Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica) ; Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica)
Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. [...]
2019 - 10.3390/genes10070553
Genes, Vol. 10, Issue 7 (July 2019) , art. 553  
9.
8 p, 1.0 MB pSBVB : A versatile simulation tool to evaluate genomic selection in polyploid species / Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Monfort Vives, Amparo (Centre de Recerca en Agrigenòmica) ; Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Genomic Selection (GS) is the procedure whereby molecular information is used to predict complex phenotypes and it is standard in many animal and plant breeding schemes. However, only a small number of studies have been reported in horticultural crops, and in polyploid species in particular. [...]
2019 - 10.1534/g3.118.200942
G3, Vol. 9, Issue 2 (February 2019) , p. 327-334  

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