UNAL-Purdue develop successful bioinformatics workshops
The ongoing collaboration between Professors Esperanza Torres, from Universidad Nacional de Colombia (UNAL), and Michael Gribskov from Purdue, has been fruitful. It all began when Torres, a molecular biologist, spent her sabbatical at Purdue in 2013-14. She worked closely with Professor Mary Catherine Aime, in the Department of Botany and Plant Pathology on research projects focused on fungi. Torres also took bioinformatics classes taught by Professor Gribskov, with whom she shared an interest in genomics and bioinformatics research.
Upon her return to Colombia, Professors Torres and Gribskov started to put together research proposals and search for funding for these proposals.
In 2015, Torres and Gribskov organized a one-week course funded by UNAL entitled “Differential Gene Expression Analysis Using RNA-SEQ.” The main topic of this course was differential expression analysis of genes, and it was aimed at masters and doctoral students. It included over 50 hours of instruction covering both theoretical and hands-on application of transcriptomic analysis methods. Transcriptomics is the study of transcriptome (the complete set of RNA transcripts produced by the genome under specific circumstances or in a specific cell) using high-throughput methods. The course was a great success and drew the attention of 72 students, from which 30 were chosen to take the course.
Also in 2015, Torres sent an undergraduate student, Daniel Ariza, to Purdue University to work with Gribskov as part of the Undergraduate Research at Purdue-Colombia (UREP-C) program. Torres also sent two more undergraduate student researchers to Purdue, Julian Andrés Velásquez with UREP-C to work with Dr. Ronald Rico, and Liliana Marcela Daza through Nexo Global to work with Dr. Lori Hoagland.
From June 7th to 24th 2016, Prof. Maria Isabel Chacón and Torres organized a course entitled: Principles of Genomic and Metagenomic Data Analysis. This 3-week course was held at UNAL and was offered to postgraduate students and faculty that carry out research in the fields of Genomic and Metagenomics. This course was taught by Gribskov and Dr. Emiliano Barreto (Insituto de Biotecnología), Dr. Aquiles Enrique Darghan (UNAL), Martha Serrano (University of Lausanne), Nicolas Salamín (University of Lausanne), Esperanza Torres (UNAL), Jorge Duitama (CIAT), Maria Isabel Chacón (UNAL). Daniel Ariza, the UREP-C student mentioned above, was the monitor for this course and provided essential assistance in installing software and assisting the faculty and participants.
Future plans for this collaboration include investigating genomics and metagenomics aspects of cacao production in Colombia. This project has been submitted to Colciencias, the primary research and development funding agency in Colombia. If approved, the cacao soil microorganism biodiversity analysis would be done at UNAL and Corpogen, and the metagenomics analysis would be done at Purdue. In terms of current research, there is an on-going transcriptome assembly of avocado project. The samples of this project will be analyzed at the Purdue Genomics Core Facility.
"Differential gene expression analysis using RNA-SEQ" workshop students with Prof. Gribskov and Prof. Torres at Universidad Nacional de Colombia (Bogotá) in the summer of 2015
"Principles of Genomic and Metagenomic Data Analysis" course students with Prof. Gribskov and Prof. Torres at Universidad Nacional de Colombia (Bogotá) in the summer of 2016