Bioinformatics and Genomics

Group leader:  Roderic Guigó Serra

Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, ...). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and annotation in genomic sequences. Some of our current projects are:

There are now -50- geneid (1.4) species-specific parameter files

tree of life showing geneid-trained species

We have recently added three new species-specific parameter files to our ab initio gene predictor (geneid) home page. This has allowed us to reach a new milestone. We now have FIFTY parameter files for geneid with which we can predict genes in a wide range of species spanning all four "classical Kingdoms" (Animal, Plantae, Fungi and Protist). This tree-of-life rectangular cladogram portrays all the species for which we now possess a geneid parameter file.

With the latest addition to our list of geneid parameter files we can now also predict protein-coding genes on the model cereal/grass/monocot Brachypodium distachyon, on the ciliated protozoan Tetrahymena thermophila and on the potential plant pahogen fungus Fusarium oxysporum.

RECOMB 2012 (16th International Conference on Research in Computational Molecular Biology)

Recomb 2012

RECOMB 2012 (the 16th International Conference on Research in Computational Molecular Biology) will take place in vibrant and beautiful Barcelona from the 21 to 24 April 2012. On this year's conference there will be a strong focus on the computational challenges arising from the extraordinary developments in high throughput technologies. Participants will enjoy a full agenda of keynote talks, paper presentations, and poster sessions, with ample opportunities to get a sample some of the city life of Barcelona. The meeting also overlaps with Sant Jordi (Saint George), on April 23, the patron of Catalonia, and one of the most important civic holidays in the country. In order to get more information on RECOMB 2012 and how to register please click here.

---PLEASE NOTE EARLY REGISTRATION HAS BEEN EXTENDED UNTIL 31 JANUARY 2012!!---

New ab initio gene predictor geneid parameter files available

We have recently added four new species-specific parameter files to our ab initio gene predictor (geneid) home page.

These four new parameter files allow for gene predictions in Bombus terrestris, Bombus impatiens (two insects of the order Hymenoptera) , Plasmodium vivax (protozoal parasite which is one of the causative agents of malaria) and Phaseolus vulgaris (common bean).

We currently have forty-four parameter files for our ab initio gene prediction program geneid which allow us to predict genes in a wide range of species spanning all four "classical Kingdoms" (Animal, Plantae, Fungi and Protist).

X CRG Annual Symposium "Computational Biology of Molecular Sequences" (10-11 November 2011)

On the 10-11 of November 2011 our group headed by Roderic Guigo will be organizing a two-day CRG symposium on “Computational Biology of Molecular Sequences” which will bring together renowned Computational Biologists from around the world, including both pioneers in the field, as well as promising young scientists. Presentations, discussions and dialogue during the Symposium will contribute to survey the status of a discipline that, at the intersection of Biology and Computation, will have an enormous impact on the world of the XXIst century.

You may obtain more information on the objectives of the symposium, the current list of confirmed speakers and instructions on how to register by clicking here. The poster of the symposium can be downloaded by clicking here.

Installing programs and modules needed by Selenoprofiles

This page covers the installation of programs and modules used by selenoprofiles (profile-based gene prediction in genomes, you can find it here). Since I encountered some problems installing or running them in some computers, I created this page to help whoever will run in the same problems, this being to install selenoprofiles or not. All installations here refer to Unix systems. I will go through: blastall, exonerate, genewise and the python modules networkx, fpconst and SOAPpy.

Joint CRG-CRM Meeting on Mathematics in Genomics and Systems Biology

The "Centre de Regulació Genòmica" (CRG) and the "Centre de Recerca Matemàtica" (CRM) have co-organized a one-day meeting on “Mathematics in Genomics and Systems Biology” on Oct 22 2010 at the Parc de Recerca Biomèdica of Barcelona (PRBB).

The purpose of this joint meeting was to bring together two scientific communities -biologists and mathematicians- and explore research interfaces between both. Invited researchers from CRG and PRBB presented those aspects of their work more appealing to mathematical approach, while mathematicians linked to CRM will talk about mathematical models of potential interest to experimentalists.

You may access the meeting's agenda and the presentations of many of the symposium speakers by clicking here

IX CRG Annual Symposium (Medical Genome Sequencing: Understanding the genomes of disease)

This symposium was organized by Roderic Guigo and Xavier Estivill and held on the 28-29 Oct 2010. It aimed at establishing a forum for capturing the latest advances in genomic sequencing technologies and its various medical applications. The two-day meeting featured talks by international keynote speakers outlining the current status of medical sequencing, and putting forth the technological challenges ahead. More information on this past event can be obtained by clicking here.

Long Noncoding RNAs with Enhancer-like Function in Human Cells

Roderic Guigo and former post-Doc Thomas Derrien were involved in a study recently published in the journal Cell that looked into the function of the long noncoding RNAs (ncRNAs). This type of RNA molecule constitutes a large portion of the mammalian transcriptome even though their biological functions remained unclear. This study helped shed light on the role of long ncRNAs. For example it was shown 1) that long ncRNAs activate neighboring protein-coding genes, 2) activating long ncRNAs have a similar behavior to that of enhancer elements and 3) more specifically, the depletion of both genes directly involved in hematopoiesis or its adjacent ncRNA both show similar cellular migration defects.

Bibliography

Sequence Mapping and Assembly Assessment Project (SMAAP): RGASP3/dnGASP

SMAAP (RGASP3/dnGASP) is a collaborative effort among researchers to compare and evaluate methods and strategies for de novo genome assembly and RNASeq read alignment using data from 2nd generation sequencing platforms.

Roderic Guigo of the CRG and Ivo Gut of the CNAG will be coordinating the upcoming RGASP3 project.

The rules and all current information concerning RGASP3 and dnGASP can be found on this page.

This project is a collaboration between the CRG, CNAG (Barcelona) and the Sanger Centre (Hixton, UK).

BIOINFORMATICS SYSTEMS ADMINISTRATOR (JOB OFFER)

Reference: 
BIOADM1009

The Institute:

The Centre for Genomic Regulation (CRG) is an innovative centre created in December 2000 and located in the Barcelona Biomedical Research Park (PRBB). The mission of the CRG is to promote excellent basic research in biomedicine, cutting-edge technology development and high quality training of the next generation of scientists.

CRG has a highly international culture and the working language is English.

For more information visit our website http://www.crg.es

Post Description:

Bioinformatics and Genomics group picture 2011
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