AL 06 - Bioinformatics

Laboratory Activities with PlantStress Biotech INCT
  • Select vital genes/molecules for gall nematodes (Meloidogyne spp.) by analyzing their genome.

  • Select potential genes involved in resistance from contrasting genotypes (peanuts soybean, rice, cotton and coffee).

  • Integrate legume transcriptome data (beans, soybean and peanuts) submitted to water deficit, generated by mass sequencing (Illumina – HiSeq) in previous projects.

  • Integrate monocotyledonous transcriptome data (rice, corn, wheat, Musa and Sorghum) submitted to water deficit, generated by mass sequencing (Illumina – HiSeq) in previous projects.

  • Integrate transcriptome data from resistant genotypes (beans, soybean, rice, coffee and peanuts) infected by nematodes, generated by mass sequencing (Illumina – HiSeq) in previous projects.

  • Sequence on the Illumina platform a fraction of small RNAs, and their target mRNAs, and circular RNAs of plants (Arachis, Musa, soybean, pitangueira and cashew tree) subjected to biotic and/or abiotic stresses.

  • Analyze sequencing data to check methylation status of gene promoters in the metabolic pathways of interest.

  • Organize an in silico database cured and shared by INCT members.

  • Organize, maintain and share an in vivo bank of the innovation assets obtained in the project shared by INCT members.

Sai

Our time

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Roberto Coiti Togawa

Team Leader

Graduated in Data Processing from the University of Brasília (1984) and doctorate from the University of Bedfordshire (United Kingdom) (2006). He worked for several years in the area of basic software support and systems development. He is currently a research analyst at Embrapa Genetic Resources and Biotechnology. Has experience in Computer Science, with emphasis on Programming Languages, working mainly on the following topics: Development of analysis tools for genomic sequences, Analysis of NGS sequences. Development of analysis tools for protein structures, structural bioinformatics, Development of prediction and analysis tools for Membrane Proteins.

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Priscila Grynberg

She holds a degree in Biological Sciences from the Federal University of Minas Gerais - UFMG (2004), a master's degree in Parasitology from UFMG (2007) and a PhD in Bioinformatics from UFMG (2011). She is currently Researcher A at Embrapa Genetic Resources and Biotechnology - Cenargen. Operates in research projects of functional analysis of gene expression and differential proteomics data, large-scale sequencing of microRNAs and data mining. In 2007, she was awarded the Samuel Pessoa Medal at the 20th Brazilian Congress of Parasitology, when she won first place with a work that associated non-synonymous polymorphisms in the apical membrane protein 1 of Plasmodium vivax (PvAMA-1) with the platelet count in patients infected. She is part of the executive committee of the Brazilian Association of Bioinformatics and Computational Biology (AB3C).

Contact

Roberto Coiti Togawa

EMBRAPA Genetic Resources and Biotechnology

W5 Norte Avenue (end) - P.O. Box 02372 - Postal Code 70770-917 - Brasília, DF - Brazil

E-mail: roberto.togawa@embrapa.br