Another success for CRS4 Bioinformatica in the international DREAM 2011 competition

Printer-friendly version

DreamThe DREAM project is an international initiative which aims at unbiased evaluation of the algorithms for systems biology data analysis. Annually, the DREAM organizes a set of challenges in which teams from all over the world can enter to try out their algorithms. The participants receive experimental data from which they need to make prediction. The challenge organizers then evaluate each algorithm by checking how well its predictions match with an actual 'gold standard truth'.

This year one of the challenges involved Next Generation Sequencing data analysis. Participants were invited to predict transcripts and their splicing variants from short-read RNA-seq data from mandril, rhinoceros and human.

Massimiliano Orsini and Alberto de la Fuente from CRS4 Bioinformatica participated in this challenge using a pipeline they developed for de-novo transcriptome assembly and several transcript verification steps. They were one of the best performing teams in this challenge, among participants from renowned places such as MIT and the Broad institute (MIT/Harvard).

Massimiliano Orsini was invited to orally present on his RNA-seq data analysis pipeline at the 4th RECOMB Conference on Regulatory Genomics, Systems Biology, and DREAM Challenges held in Barcelona from 13th-19th October.

“Data such as considered in this challenge is currently massively obtained by the Sequencing and Genotyping Platform at CRS4”, explains de la Fuente, “and by having compared our methods to the state-of-the-art worldwide, we now know that we can analyze these data with high confidence.”

“Of course there is room for improvement”, says Orsini, “and now we will use the DREAM benchmark to further optimize our pipeline.”

“This is part of our current development of cutting-edge technologies for high-throughput data analysis”, adds Giorgio Fotia, the director of CRS4 Bioinformatica, “good analysis methods is of utmost importance for the development of models for personalized-medicine and to support the studies on the genetic bases of human diseases that are currently on going here in Sardinia.”

DREAM project: http://www.the-dream-project.org/

The challenge: http://www.the-dream-project.org/challanges/dream6-alternative-splicing-challenge

The RECOM/DREAM conference: http://recomb-dream2011.org/index.php/recomb2011/recombdream2011