The promiscuity of chemical probes discovered

A new computer tool developed by researchers of the Systems Pharmacology group of GRIB (IMIM-UPF) led by Jordi Mestres, lets the interaction between small molecules and thousands of proteins be predicted to study their relationship to different diseases. The study, published in the prestigious journal ACS Chemical Biology and chosen to be on the cover has proven that many of these small molecules or chemical probes are not as selective as believed, but instead interact with multiple proteins, which could lead to confusion in experimental results. Understanding these interactions is key to developing more efficient and safer pharmaceuticals. 

Art. Reference: Antolín A, Mestres J. Distant Polypharmacology among MLP Chemical ProbesACS Chem Biol. DOI: 10.1021/cb500393m

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A new and efficient method discovers switches predictive of cancer

A new publication of the Computational Genomics group of GRIB (IMIM-UPF) led by Eduardo Eyras, has been published in the journal Nucleic Acids Research and explains the results of applying a new computational method to project data from the Cancer Genome Atlas (TCGA) branch funded by the National Institutes of Health (NIH) US project ICGC (International Cancer Genome Consortium). This work represents the first large-scale analysis published, describing alterations in splicing of new cancers using RNA sequencing data from more than 4000 samples.

In this work, they discovered that there exist many splicing switches in patients with the same cancer type and showed that these switches separate with high accuracy tumor and normal samples, and different types of cancer from each other, providing a predictive signature for the disease.

click here to read the full article

Ref. publ.: Sebestyen E, Zawisza M, Eyras E. Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer", Nucleic Acids Research, 2015; doi: 10.1093 / NAR / gku1392.

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Thesis defence of María Martí: “Ligand selectivity at GPCRS: from multi-target binding profiles to biased agonism”

On 10rd of February, María Martí, member of the PharmacoInformatics group of GRIB (IMIM-UPF) will defend her thesis at 11:00 at Josep Marull Room (QMAR building). You are all invited to this event.

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Thesis defence of Jaume Bonet: "Exploiting protein fragments in protein modelling and function prediction"

On 30rd of January, Jaume Bonet, member of the Structural Bioinformatics group of GRIB (IMIM-UPF) will defend his thesis at 11:00 at Josep Marull Room (QMAR building). You are all invited to this event.

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Algorithm identifies networks of genetic changes across cancers

The application of a novel computational algorithm called HotNet2 to a pan-cancer cohort comprising somatic alterations from 12 tumor types has resulted in the detection of combinations of rare somatic mutations that contribute to tumorigenesis. The novelty of the algorithm consists in the analysis of somatic alterations across genes taking into account the interactions of their products in the development of biological functions, rather than individual genes. By pooling together alterations affecting interacting genes, the statistical power to detect driver element modules increases. Furthermore, it is possible to gain new insights into the biological processes involved in tumorigenesis. This is an essential step to develop therapeutic strategies to fight tumors.

Researchers of the Biomedical Informatics group of GRIB (IMIM-UPF) led by Nuria Lopez-Bigas has participated on this work published in Nature Genetics. The study was a team effort from an array of research groups, led by Benjamin Raphael (Director of the Center for Computational Molecular Biology at Brown University, USA).

More details of this work and interview to Dr. Raphael at science daily website.

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Thesis defence of Javier García: "Protein-protein interaction network: management of databases and its applications on the computational study of protein-protein interactions”

Today 23rd of January, Javier García, member of the Structural Bioinformatics group of GRIB (IMIM-UPF) will defend his thesis at 11:00 at Sala Ramon y Cajal – Campus Mar (PRBB). You are all invited to this event.

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Javier García, SBI group (on the left) receives the prize from Stephen Friend, President of Sage Bionetworks

Congratulations to the Structural Bioinformatics group of GRIB awarded in the Rheumatoid Arthritis Responder Challenge

The researchers of the Structural Bioinformatics group of GRIB, led by Baldo Oliva, recently participated in Subchallenge 2 of the RA Responder challenge in which participants had to identify individuals most likely to fail response to antiTNF therapy as defined by EULAR category.  The prediction of SBI group was done by using Gaussian processes for regression based on specific SNP dosages.The description of the SBI group method, as well as code, can be found here. The results of this work has been presentad at the Seventh Annual RECOMB/ISCB Conference.

The RA Responder Challege is one of the DREAM Challenges that pose fundamental questions about systems biology and translational medicine. Designed and run by a community of researchers from a variety of organizations, the challenges invite participants to propose solutions — fostering collaboration and building communities in the process.

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El proyecto EMIF permitirá la reutilización eficiente de las fuentes de información biomédica

El proyecto "tiene como objetivo la creación de un espacio que permita la reutilizacion eficiente de las fuentes de información biomédica", explica Ferran Sanz, director del GRIB. Actualmente, "la gran cantidad de información relacionada con la salud de las personas abre posibilidades de avanzar en la investigación médica y en el desarrollo de nuevos tratamientos", indica; pero "estos datos se encuentran almacenados en repositorios dispersos, situados habitualmente de forma aislada en distintos sistemas, utilizando diferentes lenguajes de codificación e idiomas", añade. A través de EMIF se quiere promover la Plataforma Común de Información "que posibilite el acceso, la conexión y el análisis de fuentes de información clínica y de investigación biomédica, y la gestión de aspectos relativos al uso de estándares de datos, interoperabilidad semántica o aspectos legales, de ética y privacidad, para mejorar la práctica clínica en beneficio de los pacientes y de la población en general".

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El GRIB participa en el II Simposi en Bioinformàtica i Biologia Computacional

El GRIB participa en el II Simposi en Bioinformàtica i Biologia Computacional que es celebra avui 12 de desembre, de 9.00 a 18.30 hores, a la seu de l'Institut d'Estudis Catalans (C/ Carme, 47. Barcelona).

La jornada ha estat oberta per Roderic Guigó, catedràtic de genètica del Departament de Ciències Experimentals i de la Salut (CEXS) de la UPF i coordinador de la secció la Secció de Biologia Computacional de la Societat Catalana de Biologia de l'IEC, conjuntament amb Anna Ripoll, presidenta de Bioinformatics Barcelona (BiB).

El programa del simposi s'articula al voltant de quatre sessions,  a càrrec de rellevants ponents en els àmbits de la Jornada: John Overington, EBI-EMBL Cambridge (Regne Unit); David Posada, Universitat de Vigo, Alfonso Valencia, CNIO (Madrid) i Ramon Maspons, AQuAS (Barcelona), cadascun dels quals presentarà dos treballs seleccionats.

Aquesta és la segona trobada de bioinformàtics de Catalunya, i compta amb la col·laboració de Bioinformatics Barcelona (BiB), una nova plataforma de la qual  Ferran Sanz, director del GRIB (UPF-IMIM), n'és el director científic.

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Come to the II Bioinformatics and Computational Biology Symposium on December the 12th

The II Bioinformatics and Computational Biology Symposium, jointly organized by the Societat Catalana de Biologia (SCB) and Bioinformatics Barcelona (BIB) will take place at the Institut d'Estudis Catalans on the 12th of December, 2014 with the participation of four great Keynote speakers and will select 8 abstracts for oral presentations.
The keynote speakers will be
John Overington (EBI-EMBL, Cambridge), David Posada (U de Vigo), Alfonso Valencia (CNIO, Madrid) and Ramon Maspons (AQuAS, Barcelona).

Please register before 10th of December 2014 

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