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Octavio Martinez de la Vega (CV)

Principal Investigator

Octavio Martinez de la Vega (CV)

Principal Investigator




See my page in Google Scholar
See my Researcher Profile at Thompson Reuters
See also the page of our Computational Biology Lab.

Research

We are interested in the design of methods for gaining biological knowledge from the analysis of high-throughput data, mainly from genomics, transcriptomics and molecular markers.

The philosophy of the group is that biological discovery is preceded, or at least run in parallel, to the design of proper methods of data analysis. This is particularly true now that Biology is flooded with quantitative data arising from the new sequencing technologies, microarrays, and other high-throughput technologies. We have worked on methods for the estimation of quantitative trait loci (QTLs), as well as the estimation of genetic diversity using molecular markers, automatic pipelines for processing and analyzing ESTs and more recently RNA-Seq data, algorithms for the assembling and annotation of genomes and the application of Shannon’s information theory to estimate transcriptome and gene properties.

Papers related with current research

  • Nathalia M.V. Flórez-Zapata, M. Humberto Reyes-Valdés, Fernando Hernandez- Godínez and Octavio Martínez (2014). Transcriptomic landscape of prophase I sunflower male meiocytes. Front. Plant Sci. - Plant Genetics and Genomics Front Plant Sci.; 5: 277. Published online 2014 Jun 16. doi: 10.3389/fpls.2014.00277

  • Luis A Martínez-López, Neftalí Ochoa-Alejo and Octavio Martínez (2014). Dynamics of the chili pepper transcriptome during fruit development. BMC Genomics 15:143 doi:10.1186/1471-2164-15-143

  • Luis Fernando García-Ortega and Octavio Martínez (2015). How many genes are expressed in a transcriptome? Estimation and results for RNA-seq. PLoS One Accepted, May 2015.


Other relevant publications


2010

Martínez O., H. Reyes-Valdés, L. Herrera-Estrella. (2010) “Cancer reduces transcriptome specialization”. PloS One, 5(5), e10398. Public Library of Science. doi:10.1371/journal.pone.0010398.g001.

2009

The Palomero genome suggests metal effects on domestication.

Vielle-Calzada JP, Martínez de la Vega O, Hernández-Guzmán G, Ibarra-Laclette E, Alvarez-Mejía C, Vega-Arreguín JC, Jiménez-Moraila B, Fernández-Cortés A, Corona-Armenta G, Herrera-Estrella L, Herrera-Estrella A.

Science. 2009 Nov 20;326(5956):1078.

2009

Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing.

Vega-Arreguín JC, Ibarra-Laclette E, Jiménez-Moraila B, Martínez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A.

BMC Genomics. 2009 Jul 6;10:299.

2008

Defining diversity, specialization, and gene specificity in transcriptomes through information theory.

Martínez O, Reyes-Valdés MH.

Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9709-14. Epub 2008 Jul 7.

2008

The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.

Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E, Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, Caballero J, Siefert J, Eguiarte L, Vielle JP, Martínez O, Souza V, Herrera-Estrella A, Herrera-Estrella L.

Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5803-8. Epub 2008 Apr 11.

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