Yuliaxis Ramayo Caldas
AgreenSkills session, year: 1st session, 2013
Receiving laboratory: GABI Animal Genetics and Integrative Biology Jouy-en-Josas, France
Country of origin : Spain
Computational biology tools for de novo and quantitative metagenomics characterisation in livestock – application to porcine and bovine gastrointestinal tract datasets
Microbiomes and their effects on hosts are emerging as outstanding ecosystems to study in various scientific fields. Due to their unprecedented throughput and precision, next-generation sequencing techniques have revolutionized the study of these complex gastrointestinal microbial communities and their interactions with the host. However, the exponential increase in sequencing power has allowed for the generation of increasingly large metagenomic datasets that are becoming difficult to analyze. This challenging task demands state-of-the-art computational biology tools able to manage the massive amounts of next generation sequencing data being generated and, also, to perform the challenging biostatistical analysis once the metagenomics quantitative data are ready. The global aim of this project is to implement such tools in generic data analysis pipelines and to use them to contribute to the production and exploitation of the microbiota catalogues for the porcine and bovine gastrointestinal datasets. Such approaches will be used within two active international consortia in targeting the characterization of metagenome catalogues for the porcine intestinal tract and the bovine rumen. The results will contribute to generate and analyze the highly expected metagenome reference catalogues for the pig intestinal tract and the bovine rumen as well as state-of-the-art computational tools for metagenomics data analysis. At the mid-long term, these achievements will represent a relevant step towards the characterization of livestock microbiota as a relevant new factor to include in animal science technologies.
I have finished my PhD at the Universitat Autònoma de Barcelona (Spain) in July 2013. My PhD project was supervised by Doctors Josep M. Folch and Miguel Perez-Enciso, and was focused on the use of computational biology and statistical genetics methods for the identification of genes related with meat quality in pigs. Earlier, in 2007 I obtained an MSc in Quantitative and Molecular Genetics applied to livestock granted by Mediterranean Agronomic Institute of Zaragoza and the International Centre for Advanced Mediterranean Agronomic Studies (IAMZ-CIHEAM, Zaragoza, Spain). Previously, I obtained a degree in Veterinary Sciences at the Universidad de Granma (Cuba) in 2006.
Today’s high-throughput technologies facilitate, like never before, the access to genomic information. However, the real challenge lies in providing functional links that bridge the gap between these vast amounts of genomic data and complex phenotypes. My research interests are related to develop statistical and computational tools that help us to understand the genetic basis of socio-economic relevant traits in the fields of agriculture genomics and livestock production.
- 1. J. Corominas, Y. Ramayo-Caldas, A. Puig-Oliveras, D. Pérez-Montarelo, J.L. Noguera, J.M. Folch, M. Ballester. Polymorphism in the ELOVL6 Gene Is Associated with a Major QTL Effect on Fatty Acid Composition in Pigs. PLoS ONE 01/2013; 8(1):e53687.
- W. Burgos-Paz, C.A. Souza, H.J. Megens, Y. Ramayo-Caldas, M. Melo, C. Lemús-Flores, E. Caal, HW. Soto, R. Martínez, L A. Álvarez, L. Aguirre, V. Iñiguez, MA. Revidatti, O R Martínez-López, S Llambi, A Esteve-Codina, M C Rodríguez, R P M A Crooijmans, SR. Paiva, LB. Schook, MAM. Groenen & M. Pérez-Enciso. Porcine colonization of the Americas: a 60k SNP story. Heredity 12/2012. doi: 10.1038/hdy.2012.109.
- Y. Ramayo-Caldas, N. Mach, A. Esteve-Codina, J. Corominas, A. Castelló, M. Ballester, J. Estellé, N. Ibáñez-Escriche, A. I Fernández, M. Pérez-Enciso, J. M Folch. Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition. BMC Genomics 10/2012; 13:547.
- M. Ballester, Anna Castelló, Y. Ramayo-Caldas, J. M Folch. A Quantitative Real-Time PCR Method Using an X-Linked Gene for Sex Typing in Pigs. Molecular Biotechnology 07/2012.
- Y. Ramayo-Caldas, A. Mercadé, A. Castelló, B. Yang, C. Rodríguez, E. Alves, I. Díaz, N. Ibáñez-Escriche, J.L. Noguera, M. Pérez-Enciso, A.I. Fernández, J.M. Folch. Genome-wide association study for intramuscular fatty acid composition in an Iberian x Landrace cross. Journal of Animal Science 07/2012; 90(9):2883-93.
- D. Pérez-Montarelo, N. J Hudson, A. I Fernández, Y. Ramayo-Caldas, B. P Dalrymple, A. Reverter. Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome. PLoS ONE 01/2012; 7(9):e46159.
- A. I Fernández, D. Pérez-Montarelo, C. Barragán, Y. Ramayo-Caldas, N. Ibáñez-Escriche, A. Castelló, J. L. Noguera, L. Silió, J. M. Folch, M C. Rodríguez. Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip. BMC Genetics 05/2012; 13:41.
- J. Corominas, Y. Ramayo-Caldas, A. Castelló, M. Muñoz, N. Ibáñez-Escriche, J.M. Folch, M. Ballester. Evaluation of the porcine ACSL4 gene as a candidate gene for meat quality traits in pigs. Animal Genetics 03/2012; 43(6):714-20.
- M. Muñoz, E. Alves, Y. Ramayo-Caldas, J. Casellas, C. Rodríguez, J.M. Folch, L. Silió, A.I. Fernández. Recombination rates across porcine autosomes inferred from high-density linkage maps. Animal Genetics 12/2011; 43(5):620-3.
- Y. Ramayo-Caldas, A. Castelló, R. Pena, E. Alves, A. Mercadé, C. Souza, A.I. Fernández, M. Perez-Enciso, J.M. Folch. Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC Genomics. 01/2010. doi: 10.1186/1471-2164-11-593.
- 11. Y. Ramayo, I.N. Shemeret’eva, M. Pérez-Enciso. Mitochondrial DNA diversity in wild boar from the Primorsky Krai Region (East Russia). Animal Genetics 02/2011; 42(1):96-9.
– 2009 – 2013. PhD Scholarship from the Spanish Ministerio de Educación (AP2008-01450)
– 2007 – 2009. MsC Scholarship from the Mediterranean Agronomic Institute of Zaragoza
– 2007. National Award for Researching Students of Agricultural and Livestock Sciences. Cuba. [http://resultados.redciencia.cu/premios/n_acc/contenido_jovenesm_en.php?idpremio=20&year=2007]
– 2006. National Award at the XVI National Computer Science Competition for Students of Higher Education. Cuba
– 2005. National Award at the XV National Computer Science Competition for Students of Higher Education. Cuba
– 2004. Patent (1542-2004) granted by the Centro Nacional de Derecho de Autor (CENDA. La Habana. Cuba) corresponding to the software DosisCalculator.