Computational Biology of RNA Processing

Group leader:  Roderic Guigó

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, etc…). 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. Our group also actively participates in the analysis of many eukaryotic genomes and it in involved in the NIH-funded ENCODE project. Furthermore we are members of two large cancer-studies consortia (chronic lymphocytic leukemia "CLL" and Breast Cancer -Hospital del Mar/CRG/Roche-).  These are some of the other projects we are currently involved in:

    • Gene Prediction/Genome Annotation

    • Genome-Wide Search for Selenoproteins

    • Methods for RNAseq (NGS) data analysis

    • Development of methods to analyze the relationship between chromatin and splicing

    • Long Noncoding RNAs with Enhancer-like Function in Human Cells

NGS'16 Genome Annotation Conference (April 4-6, 2016)

The NGS'16 Genome Annotation Conference was hosted by the International Society for Computational Biology (ISCB) and the Centre for Genomic Regulation (CRG). This year’s edition of ISCB in Barcelona focused on Genome Annotation.
 The NGS is a dedicated conference on cutting-edge approaches relating to the processing and analysis of Genome Annotation methods. It brought together bioinformatics researchers involved in the development of genome annotation methods, along with biologists interested in the establishment and annotation of new reference genomes. For more information on NGS'16 click here.

Several members of the RG group have participated in the conference. Roderic Guigó was one of the hosts of the meeting as well as the chair of one of its sections. Furthermore E. Palumbo, A. Vlasova and J. Lagarde were involved in the teaching of a post-conference workshop/tutorial:

Reproducible genomic data analysis using short and long-read RNAseq data

A. Vlasova, S. Pérez-Lluch, J. Curado, D. Santesmasses and F. Câmara were co-authors in four of the posters presented at the conference:

    •    P30-Active transcription without canonical histone marks   

    •    P43-An integrated gene annotation pipeline for de novo sequenced organisms                          

    •    P55-Computational methods for prediction of selenoprotein genes   

    •    P61-Annotation of selenoprotein genes in vertebrates and their human polymorphisms

We were also colaborators (A. Vlasova, D. Santesmasses and F. Câmara) in a project which was presented by Mateusz Konczal as one of the conference's selected oral presentations: 

Genome of the bulb mite - the model organism  in studies on sexual selection and plants pest.

DECKO: A versatile and scalable new tool for genome editing

The lab recently published a new method called DECKO (Dual Excision CRISPR KnockOut) based on the CRISPR genome editing method. DECKO is a simple and highly-scalable tool for deletion of non-coding genomic elements, including long noncoding RNAs. Read more at: http://www.biomedcentral.com/1471-2164/16/846

"Queen or worker? Flexibility between roles relies on just a few genes"

Two insect species from Latin America, the dinosaur ant and the red paper wasp, have been used to uncover the molecular mechanisms underpinning queen and worker roles in social insects. The research by an international team of scientists brings us closer to understanding how genomes are used to generate castes in social evolution.   Researchers from the University of Bristol, the Babraham Institute (Cambridge, UK) and the Centre for Genomic Regulation - including Anna Vlasova, Francisco Câmara and Roderic Guigó from our "Computational Biology of RNA Processing" group - (Barcelona, Catalunya, Spain) analysed individual wasp and ant brains from queens and workers of both species to see whether caste differences could be explained by variations in how the genome is ‘read’ and regulated. For more information go to:

http://www.babraham.ac.uk/news/2015/10/Queens_workers_insect_societies

(photo and text taken from the Babraham institute web page)

Evolution of SPS proteins on the cover of Genome Research

Our paper on the evolution of selenophosphate synthetases (SPS) has been published on the September issue of Genome Research: http://genome.cshlp.org/content/25/9/1256.full.pdf+htmlThe cover of this issue features an artwork inspired by the paper, and painted by Milena

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

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.

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.

Exon Wrap

By comparing exon-intron position in higher eukaryotes to available large scale nucleosome positioning datasets, we have find that exons tend to have higher nucleosome occupancy than introns (Tilgner et al., NSMB 2009)

Bibliography

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