last update 30/10/2015

Come to the fourth DCEXS Symposium on November the 17th: "Innovative in silico strategies in biomedical research"

The symposium, organized by the Department of Experimental and Health Sciences (DCEXS) and the GRIB (IMIM-UPF) will be held on Tuesday, November 17th 2015, at the Barcelona Biomedical Research Park (PRBB) auditorium and will bring together leading researchers in the vibrant field of biomedical research, to explore new advances in in silico strategies.

Confirmed Speakers: Alfonso Valencia, Mihaela Zavolan, Caroline Gubser Keller, Marta Filizola, Gerhard Ecker,  Bart Vannieuwenhuyse, Joaquín Dopazo

The symposium is open to everybody interested in biomedical research, and there are no registration fees. However, the number of places available are limited so you are kindly asked to register here.

Do you have a poster? Present it at the symposium reception, you can win an iPad! Send an email with your abstract to by the 8th of November.

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EU-ToxRisk: an integrated european ‘Flagship’ program driving mechanism-based toxicity testing and risk assessment for the 21st century

In a large (30 Million €) H2020-supported collaborative project, academia joins forces with small and medium-sized enterprises (SMEs), large industry, contract research organisations (CROs) and regulatory bodies to achieve a paradigm shift in toxicology towards a more efficient and animal-free chemical safety assessment.

The Research Programme on Biomedical Informatics, GRIB (UPF-IMIM) will have a major role in this project bringing its expertise in Bioinformatics and Chemoinformatics. In particular, members of GRIB will be responsible of compiling and making available to the rest of the consortium the enabling computational technologies that will play a central role in the project. These include read-across and quantitative structure-activity methods, in silico pharmacokinetics, platforms for the analysis of omics information, and statistical methods for data analysis and visualization. This contributions will be aligned to the role that GRIB is playing in IMI projects focused on the safety assessment of drugs: the eTOX project focused on the in silico prediction of in vivo toxicity, and the iPiE one aiming to assess the ecotoxicological risks of pharmaceuticals.

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El GRIB premiat al I Concurs d'Innovació del PSMAR

El projecte guanyador “Sistema de suport a la decisió. Petició intel·ligent de proves radiològiques en patologia mamàriava ser presentat per Manuel Pastor, Oriol López i Ferran Sanz, membres dels grups de FarmacoInformàtica i Biomedicina Computacional del GRIB juntament amb Maria del Mar Vernet, coordinadora de la Unitat Funcional de Patologia Mamària de l'Hospital del Mar.

Durant el mes de setembre, al passadís central de l'Hospital del Mar, es pot veure l'exposició dels 10 projectes finalistes. El I Concurs d'Innovació és una iniciativa que vol fomentar la cultura de la innovació a l'entorn del PSMAR, en el marc de l'Institut Hospital del Mar d'Investigacions Mèdiques IMIM, i donar visibilitat als projectes d'innovació en salut, no només dels professionals de la institució sinó també dels pacients i les seves famílies.

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DisGeNET Platform presented at the BioHackathon 2015 in Nagasaki.

Núria Queralt, postdoctoral researcher of the Integrative Bioinformatics group of GRIB (IMIM-UPF), has been invited to present DisGeNET: A discovery platform for the dynamical exploration of human diseases and their genes at the BioHackathon 2015.

DisGeNET is a discovery platform on human diseases and their genes, developed by the Integrative Biomedical Informatics group, led by Laura I. Furlong and F. Sanz. DisGeNET covers the full spectrum of human diseases, and currently contains more than 400,000 associations between approx. 17,000 genes and 14,000 diseases. 

 The BioHackathon conference focus on standardization and interoperability of bioinformatics information and web services for improving integration, preservation and utilization of databases in life sciences and it has been organized by the National Bioscience Database Center (NBDC) and Database Center for Life Science (DBCLS) since 2008. 

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Open PHACTS wins European Linked Open Data award

We are delighted to announce that project Open PHACTS has been awarded first place in the Linked Open Data Award of the inaugural European Linked Data Contest (ELDC). An international jury of ambassadors from over 15 European countries elected Open PHACTS as the winner.

The Open PHACTS project has built a platform for drug discovery that integrates data over diverse sets of public chemistry and biological data.  It currently connects linked open data from 12 different data sources, including chemical compounds, protein targets, biological pathways and tissues, and diseases. The diversity and size and of the Open PHACTS data are growing rapidly, and it contains currently more than 3 billion triples. The Open PHACTS project is a unique collaboration between European academic groups, small businesses and large pharmaceutical companies, partially funded by the EU.

GRIB participates in the Open PHACTS project as coordinator of one of the workpackages.

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De novo genes: starting to solve the mystery of their origins

A new collaboration amongst scientists at different centres at the PRBB, with Mar Albà from the Evolutionary Genomics Group of GRIB (IMIM-UPF) as leading author, has come up with a new mechanism for explaining the formation of de novo genes. Although commonly new genes arise by gene duplication and diversification of the copy, some genes appear in genomic regions which did not previously contain any gene, as compared with other species. How do these genes originate from nothing?

On this publication the authors propose – based on transcriptomic comparisons between humans and three other mammals – that first new regulatory motifs/promoters appeared in those regions, which lead to an activation of transcription and the origin of new potentially functional genes. Alba’s group have actually identified hundreds of putative de novo genes in the human genome.

You can read more about this in the Evolutionary Genomics’ group blog in this and this post, where they also point out to an interesting overview on the history of de novo genes, by Emily Singer.

Pub reference (Dec 2015): Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R, Marqués-Bonet T, Alba MM. Origins of De Novo Genes in Human and Chimpanzee. PLoS Genet, 2015;  11(12)

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Mutations in the dark region of the genome cause leukaemia

A study published in Nature on 22 July have decoded the genome of more than five hundred patients with leukaemia and have identified recurrent mutations in non-coding regions of the genome, which provides new clues to the development of cancer. This study is the first to complete the analysis of five hundred genomes within the International Cancer Genome Consortium (ICGC) and it most important finding is the identification of mutations in areas of the genome that do not code for proteins whose functional significance is still very little known. These regions represent 98% of our genome, but they are so little known that they are not usually analysed in patients. This study has enabled defining sixty genes whose mutations cause tumour development.

The study has been conducted by researchers Carlos López-Otín, of the University of Oviedo, and Elías Campo, from the IDIBAPS and the University of Barcelona. They coordinated a team of over sixty researchers working at centres belonging to the Spanish Chronic Lymphatic Leukaemia Genome Consortium, including Núria López Bigas, ICREA researcher and Head of the Biomedical Genomics Group of GRIB (IMIM-UPF), Carlota Rubio and David Tamborero, researchers of her team.

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Constitució de l'Associació Bioinformatics Barcelona - BIB

(Nota de Premsa)

L'associació BIB compta amb 25 entitats membres entre universitats, centres de recerca, instituts de recerca hospitalària, grans infraestructures científiques, empreses i altres institucions, a més de 23 entitats en procés d'incorporació.
La primera junta directiva està formada per la presidenta Dra. Ana Ripoll (UAB), el secretari Dr. Arcadi Navarro (UPF) i el tresorer Dr. Alfons Nonell (Mind the Byte).
Neix amb la voluntat d'involucrar a totes les entitats per generar iniciatives i dinàmiques col·laboratives en recerca avançada, transferència de coneixement i formació, que projectin Barcelona i Catalunya com un pol de referència internacional en l’àmbit de la bioinformàtica.
Donarà resposta als reptes plantejats pel creixement de macrodades (big data) en els àmbits de salut i agroalimentari, com per exemple la medicina personalitzada i l'agricultura de precisió.

La primera iniciativa sorgida del BIB ha estat el disseny d'estudis pioners en tot l'Estat: la formació professional de tècnics informàtics amb orientació bioinformàtica que es posarà en marxa en el curs 2015-16, i el primer grau interuniversitari en bioinformàtica en el Sistema Universitari Català previst pel curs 2016-17.

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The Master in Bioinformatics for Health Sciences of the UPF classified as one of the best in Spain

The Master in Bioinformatics for Health Sciences of the Pompeu Fabra University has been classified as one of the best in Spain acording the ranking published by "El Mundo"

The master in Bioinformatics aims to provide professionals and researchers with expertise and skills geared towards developing new computational strategies and IT systems that are useful in biomedical research. The master has a faculty staff with both a long experience in teaching and research careers widely recognized. To implement this master, expert researchers on each field have been selected at Universitat Pompeu Fabra and Universitat de Barcelona on each of the subjects taught: Molecular Biology, Genetics, Mathematics, Pharmacology, Biochemistry, Drug Design and others. An important part of the faculty staff, including the coordination of the master are members of the Research Programme on Biomedical Informatics (GRIB).

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GRIB organise the "Cancer genomics and personalised medicine workshop: focus on pancreas cancer"

The workshop is addressed to researchers and students interested in cancer genomics and the main objective is to provide a view of top research projects in cancer genomics research, with a special focus on Pancreas Cancer. Speakers include Prof Ben Raphael, from Brown University (USA), who will talk about The Cancer Genome Atlas Project on Pancreatic Adenocarcinoma. Prof. David Chang, from the Institute of Cancer Sciences at the University of Glasgow, who will discuss molecular stratification approaches on pancreatic cancer. Dr. Stepha Ossowski (from the Centre for Genomic Regulation), who will address the challenge of identifying driver mutations in heterogenous or low purity tumour samples. Finally Prof. Kristen Van Steen (University of Liege, Belgium), will talk about integrative approaches in cancer.

The Biomedical Genomics group of GRIB, led by Núria López-Bigas, as members of the EUPancreas COST Action organize this event hosted by the Barcelona Biomedical Research Park the 1st of July. The EUPancreas COST Action is an integrated european platform for pancreas cancer research: from basic science to clinical and public health interventions.

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