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Seminars, events & talks

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

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, 23th February, 2017, 12:00

Integrative Biomedical Informatics

Identifying temporal patterns in patient disease trajectories: a population-based study

The widespread use of electronic health record (EHR) datasets has facilitated the massive collection of patient health information, thereby enabling researchers to conduct large-scale studies of comorbidities. The term comorbidity can be defined as the co-occurrence of two or more diseases within the same individual. The factor of time has, typically, not been taken into account in most of the relevant works. However, by incorporating the time dimension into a comorbidity study more complex disease patterns and their temporal characteristics can be revealed. In this work, a large-scale temporal comorbidity study is performed on a local (Catalonian) health database. The disease-history vectors of individual patients are compared between each other in order to extract common disease trajectories (i.e. shared by at least 2 patients). By using statistical-significance tests on the common disease trajectories of length=2, significant pairwise disease associations are identified and their temporal directionality is assessed. Subsequently, a novel unsupervised clustering algorithm, based on the Dynamic Time Warping (DTW) technique, is applied on all extracted common disease trajectories (length>=2), in order to group them according to the temporal patterns that they share. It will be shown that DTW can successfully cluster the disease-trajectory signals under investigation, which consist of various time scales and durations, although they do not exhibit any obvious temporal alignment. In this manner, important key clusters can be identified with trajectories that share the same time-dependent characteristics. A time-dependent comorbidity analysis is expected to facilitate the early diagnosis of a disease and prevent any adverse outcomes, by permitting the prediction of the disease progression along time.

Speaker: Alexia Giannoula

Room Aula room 473.10 (4th floor)

Sunday, 4th September, 2016, 13:30 - 17:00 (half day tutorial)

Integrative Biomedical Informatics

Tutorial at ECCB 2016 - DisGeNET: a discovery platform to support translational research on human diseases

Recent technological breakthroughs have produced an unprecedented increase in the amount of data on the genetic determinants of diseases. To unveil the molecular mechanisms that underlie diseases and to support drug discovery projects, it is necessary to place these data in the context of the current biomedical knowledge. Despite the large volume of information available, its analysis and interpretation are hindered because it is annotated using different criteria and vocabularies and fragmented across different resources. Furthermore, a large fraction of data on diseases is only available as free text in biomedical publications. To overcome these difficulties we have developed DisGeNET (Piñero et al, 2015), a discovery platform that contains information on human diseases and their genes. In this tutorial we will provide an overview of the main features of DisGeNET, and then introduce the suite of tools that the platform offers to support translational research.  The tutorial includes a hands-on session organized around case studies that will illustrate how to use these tools. Materials will be made available via the DisGeNET website. Target audience: the tutorial is aimed at a variety of audiences: bioinformaticians, systems biology users, biologists, and healthcare practitioners.

Speaker: Laura I. Furlong and Janet Piñero - IBI group of GRIB (IMIM-UPF)

Room 15th European Conference on Computational Biology - The Hague, Netherlands - World Forum Convention Center

Monday, 30th May, 2016, 12:00

Integrative Biomedical Informatics

Making big sense from big data in toxicology

Scientific Sessions PRBB Organizer: PRBB_CRG Conferences. Hosts: Esther Barreiro & Ferran Sanz 

Speaker: Prof. Thomas Hartung, Center for Alternatives to Animal Testing, Doerenkamp-Zbinden Foundation. Evidence-based Toxicology, Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health. Baltimore, USA.

Room Marie Curie Room (Charles Darwin Sq.) PRBB.

Thursday, 17th March, 2016, 12:00

Integrative Biomedical Informatics

"Extracting biological data from the Science Literature"

Abstract: The scientific literature constitutes a rich and diverse source of information essential for any research line in life sciences. The volume of scientific publications is growing year by year generating a large accumulation of literature, due to the constant developments and advances in the biomedical domain. Text Mining (TM) emerges to address the need generated by the continuous growth of scientific literature in the biomedical domain. In this talk I will give an overview of TM and how it can help us to find relevant information from a large set of documents. I will present the BeFree System, a text mining tool developed as part of my PhD thesis and its application to different projects related to investigating the genetic basis of diseases, the therapeutic and undesired effects of drugs, and the effect of drugs in the environment.

Speaker: Alex Bravo - Integrative Bioinformatics group of GRIB (IMIM-UPF)

Room Aula room 473.10 (4th floor)

Monday, 7th December, 2015

Integrative Biomedical Informatics

DisGeNET: a discovery platform for translational bioinformatics

SWAT4LS International Conference 2015 in Cambridge, UK:

Speaker: Nuria Queral Rosinach, IBI Group, GRIB

Tuesday, 1st December, 2015

Integrative Biomedical Informatics

DisGenet RDF&SPARQL: how to use + modeling challenges

Upcoming PhD course on Semantic Web technologies offered by SIB in Geneva. We are pleased to announce that a lecture on DisGeNET-RDF developed in the IBI group is included in the course "Using the Semantic Web for faster (Bio-)Research", Geneva 30 November till 3 December 2015. Accessing and using existing public data is a hassle, yet it is crucial for designing good experiments. This 4 day course, co-organized by SIB and CUSO/Staromics, will teach PhD students on how to use semantic web technologies for their own research. It includes an in-depth exploration of Semantic Web concepts such as RDF (data modelling), SPARQL (asking questions on your data), OWL (reasoning for deducing new facts about your data) The course will teach you how to use these technologies in your day to day research, as well as how you can share your data with the rest of the world.

Speaker: Núria Queralt Rosinach, IBI Group (GRIB)

Thursday, 12th November, 2015, 12:00

Integrative Biomedical Informatics

"Uncovering disease mechanisms through network biology in the era of next generation sequencing"

Characterizing the behavior of disease genes in the context of biological networks has the potential to shed light on disease mechanisms, and produce new candidate disease genes and therapeutic targets. Previous studies addressing the network properties of disease genes have produced seemingly contradictory results. We have explored the causes of these seeming discrepancies and assessed the relationship between disease genes' network roles and their tolerance to deleterious germline variants in human populations leveraging on: different interactome resources, a comprehensive catalog of disease genes and exome variation data. We found that the most salient network features of disease genes are driven by cancer genes and that genes related to different types of diseases play network roles whose centrality is inversely correlated to their tolerance to likely deleterious germline mutations. This proved to be a network multiscale signature, including global, mesoscopic and local network centrality features. Cancer driver genes, the most sensitive to deleterious variants, occupy the most central positions, followed by dominant disease genes and then by recessive disease genes, which are tolerant to variants and isolated within their network modules.

Speaker: JANET PIÑERO Biomedical Informatics, GRIB

Room Aula room 473.10 (4th floor)

Thursday, 5th November, 2015, 12:00

Integrative Biomedical Informatics

DisGeNET: a discovery platform for translational bioinformatics (PRBB Computational Genomic Seminars)

In this talk I will present the DisGeNET Discovery Platform for the dynamical exploration and analysis of human diseases and their genes. The platform consists of a comprehensive knowledge base of over 400,000 gene-disease associations arising from both expert-curated databases and information extracted from the scientific literature using text mining, with special attention paid to the explicit provenance of the association. The DisGeNET platform provides a set of analysis tools designed to facilitate and foster the study of the molecular underpinning of human diseases. The talk will also illustrate the semantic knowledge representation of DisGeNET, and how to explore and analyze the data using different tools with special emphasis on harnessing the data using Semantic Web technologies.

Speaker: Núria Queralt Rosinach, IBI Group (GRIB)

Room Aula room 473.10 (4th floor)



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