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Seminars, events & talks

Thursday, 9th November, 2017, 12:00

Integrative Biomedical Informatics

PsyGeNET: a knowledge resource on psychiatric diseases and their genes

Psychiatric disorders constitute one of the main causes of disability worldwide. During the past years, considerable research on the genetic architecture of such diseases has been conducted, although little understanding of their etiology has been achieved. The difficulty to access up-to-date, relevant genotype-phenotype information has hampered the application of this wealth of knowledge to translational research and clinical practice in order to improve diagnosis and treatment of psychiatric patients. PsyGeNET has been developed with the aim of supporting research on the genetic architecture of psychiatric diseases, by providing integrated and structured accessibility to their genotype-phenotype association data, together with a set of analysis and visualization tools. PsyGeNET contains up-to-date information on genes associated with mood disorders (depression, bipolar disorder), psychosis (schizophrenia) and substance use disorders (alcohol, cannabis and cocaine use disorders, substance-induced depressive disorder and psychoses). The current version of PsyGeNET (version 2.0) contains 3,771 associations between 1,549 genes and 117 psychiatric disease concepts. PsyGeNET offers several metrics for the prioritization of the information, including the Evidence Index that takes into account the negative evidence found in publications for a particular gene-disease association. The PsyGeNET database has been developed by extracting gene-disease associations from the literature with the text mining tool BeFree (https://bitbucket.org/ibi_group/befree), followed by a process of curation by a team of 22 domain experts. A web-based annotation tool supported the curation process. The data is accessible through a web interface (http://www.psygenet.org/) and the psygenet2r Bioconductor package (https://bioconductor.org/packages/release/bioc/html/psygenet2r.html). Moreover, the psygenet2r package implements several functions to visualize and analyze the PsyGeNET data in a clear and meaningful way and allows performing comorbidity analysis based on shared genes. Due to its special focus on psychiatric diseases and comprehensiveness, PsyGeNET represents a valuable resource for the analysis of the molecular underpinning of psychiatric disorders and their comorbidities.

Speaker: Alba Gutiérrez-Sacristán

Room Aula room 473.10 (4th floor)

Wednesday, 18th October, 2017, 12:00

Structural Bioinformatics

How to analyze the structure of proteins without using Cryo-EM

Sesiones científicas, CRG Group Leader Seminars; Organizador: PRBB Group Leader Seminar

Speaker: Miguel Beato / Baldo Oliva / Eduard Sabidó / Roni Wright

Room Sala Ramón y Cajal, PRBB

Friday, 22th September, 2017, 11:00 - 12:00

Computational Biophysics

Molecular simulation methods for ensemble-based drug design

Speaker: Julien Michel, Royal Society University Research Fellow, School of Chemistry Joseph Black Building, University of Edinburgh

Room Xipre (173.06-183.01), PRBB Building

Thursday, 22th June, 2017, 12:00 - 13:00

Integrative Biomedical Informatics

DisGeNET discovery platform 5.0: Illuminating the study of human diseases

In the last few decades, our knowledge about the genetic underpinnings of human diseases has grown at an unprecedented pace. Data resulting from GWAS studies, experiments in animal models, and from exome sequencing pipelines are freely available, but scattered across several repositories. To enable translation of this wealth of knowledge into better disease biomarkers and drug therapies, this information should be made readily available to translational researchers and clinicians. DisGeNET (http://www.disgenet.org/) is a platform that fulfills this need. It contains one of the largest available collections of genes and variants associated to human diseases. This is achieved by the integration of data from several specialized resources on gene and variant-disease associations with information extracted from automatically mining Medline abstracts. Here, we present DisGeNET 5.0, containing more than 500,000 gene-disease associations, and over 135,000 variant-disease associations. The associations are annotated using community-based standards, including a variety of disease vocabularies and are enriched and expanded by linking them to other key resources covering the chemical and omics spaces. DisGeNET 5.0 also includes several new improvements, besides more disease associations: a) a new curated source: the PsyGeNET database, b) an improvement of the text-mining pipeline to extract gene-disease and variant-disease associations from publications, c) non-coding variants associated to disease, d) disease-phenotype associations, and e) gene-phenotype associations from the Human Phenotype Ontology. With its fifth release, DisGeNET is an established and mature resource, which is increasingly used in the investigation of the genetic basis of human diseases and to support drug discovery projects.

Speaker: Janet Piñero, GRIB (IMIM/UPF)

Room Aula room 473.10 (4th floor) , PRBB

Wednesday, 7th June, 2017, 14:00-15.30

Computational RNA Biology

Integrative analysis of cancer transcriptomes

Speaker: Eduardo Eyras, Head of Computational RNA Biology lab, GRIB.

Room Charles Darwin Room, PRBB Building.

Tuesday, 6th June, 2017

Integrative Biomedical Informatics

ELIXIR Innovation and SME Forum

The ELIXIR Innovation and SME Forum: Genomics, bioinformatics and health - Public-private partnerships in open data" is organized by ELIXIR Spain and the ELIXIR Hub in collaboration with Innovative Medicines Initiative (IMI), BIOCATBioinformatics Barcelona (BIB), Barcelona Biomedical Research Park (PRBB) and the GRIB (IMIM-UPF). It will be held on 6-7 June 2017 at PRBB Auditorium and  is particularly relevant for large and small companies active in the genomics and health domains.. The aim of this Innovation and SME forum is to showcase to companies the free data resources and services that are available through ELIXIR Spain and ELIXIR Europe more generally. It will feature talks from ELIXIR partners on some of the key databases and resources and present examples of innovative companies that are already using public data in their businesses. The event is free and open to all companies large and small, in the Barcelona region and further afield. 

Thursday, 1st June, 2017, 12:00 - 13:00

Computational RNA Biology

Measuring ribosome profiling at isoform level: a step towards unveiling alternative splicing funcional impact

 The alternative processing of transcribed genomic loci through alternative transcript initiation, splicing and polyadenylation, is an intermediate step in mRNA maturation, between transcription and translation. These mechanisms produce different mature mRNA transcripts and determine the transcript repertoire of cells. There is evidence showing that the differential production of transcript isoforms, especially through the mechanism of alternative splicing, is crucial in multiple biological processes such as cell differentiation, acquisition of tissue-specific functions, DNA repair, as well as in multiple pathologies, including cancer. This has been exhaustively shown at RNA level but it remains elusive at protein level. Sequencing of ribosome-protected RNA fragments, or ribosome profiling, provides detailed information on the transcripts being translated in the cell. In this work, we have analysed the quantification of individual transcript coding sequences (CDSs) from ribosome profiling using both RNA-seq and Ribo-seq data from human and murine gliomas. Moreover, we investigated to what extend differential transcript usage and differential splicing impacts protein production. We describe for the first time evidence for differential translation of coding regions associated to differential transcript usage and alternative splicing, and in particular for the differential translation of microexons, which have a crucial role in neural tissue.

Speaker: Marina Reixachs

Room Aula room 473.10 (4th floor)

Friday, 21th April, 2017, 13:00

PharmacoInformatics

Big data in chemical safety assessment, challenges and opportunities

BIGCHEM BCN 2017: school about Computational Chemistry and Pharmacology.  Traditional methods for chemical safety assessment based in animal testing are being replaced by alternatives approaches, more acceptable from an ethical point of view. This situation gives the opportunity to exploit the vast amount of data already obtained from in vivo studies and other sources, even if the application of this concept in practice is being more difficult than expected.

Speaker: Manuel Pastor - Head of of the PharmacoInformatics group of GRIB

Room Charles Darwin Room - PRBB

Thursday, 20th April, 2017, 13:00

Systems Pharmacology

Large-Scale Predictive Drug Safety

BIGCHEM BCN 2017: school about Computational Chemistry and Pharmacology. The recent explosion of data linking drugs, proteins, and pathways with safety events has promoted the development of integrative systems approaches to large-scale predictive drug safety that pave the way towards gaining a better understanding of the mechanisms leading to adverse outcomes.

Speaker: Jordi Mestres - Head of the Systems Pharmacology group of GRIB

Room Charles Darwin Room - PRBB

Friday, 10th March, 2017, 11:00-12:00

Computational Biophysics

Structural prediction of protein-protein interactions for the upcoming challenges in biomedicine

Speaker: Juan Fernández Recio, Research Director, BSC.

Room Ramón y Cajal Room, PRBB Building



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