GRIB. Research Unit on Biomedical Informatics





News & activities

3rd Workshop on High-Throughput Molecular Dynamics (HTMD) in Barcelona

The event will take place on 10th & 11th of November at the Barcelona Biomedical Research Park (PRBB) in Barcelona. Registration closes the 30th of September.

The aim of this workshop is to learn the latest developments of high-throughput molecular dynamics simulations with practical lectures and real data and to give scientists the opportunity to exchange their experiences. Hands-on session and training will be given using HTMD a powerful programmable environment to prepare, handle, simulate and analyze molecular simulations, and efficient GPU-based MD simulations, and standard protocols to execute numerical experiments. There will be at the end of the workshop a session on applying what you have learned on your data/proteins.

This workshop is a great opportunity for industrial partners to get an overview of the state-of-the-art in molecular simulations for medicinal chemistry and drug design.

Acellera is a technology spin off of the GRIB, focused on delivering services and solutions to companies and academic institutions on computing intensive, mission-critical applications. By exploiting heavily optimized molecular simulations and the outstanding computational capabilities of new accelerator processors, we help to achieve otherwise unreachable results using current standard technology.

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visual summary of the research

Cellular stress activates an important anti-cancer protein

Researchers at UPF have discovered that the RB protein, responsible for stopping cell proliferation and therefore preventing tumor formation, is activated under cellular stress. The Structural Bioinformatics group of GRIB led by Baldo Oliva has participated on this work led by Eulàlia de Nadal and Francesc Posas, leaders of the research group on Cell Signaling of the UPF.

The study has been published in the journal Molecular Cell and shows that RB is also important to stop cell progression in response to cellular stress. Under these conditions, the brake is essential for cell survival. A very remarkable fact is that this new mechanism predominates over others that normally regulate the activity of RB. Therefore, the external activation of this mechanism could be used to block cell division.

As Francesc Posas, co-leader of the study says, "this discovery may be relevant in cancer biology because RB is a key protein in cell proliferation and many types of tumor coincide on the inactivation of this protein. If we get to reverse this inhibition, we could stop proliferation."

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Last project

NONCODRIVERS

The project NONCODRIVERS "Finding noncoding cancer drivers", aims to characterize the role of mutations in non-coding regions in the most prevalent tumours of the population. The work will count with the collaboration of the International Cancer Genome Consortium, an organization created for the classification of the molecular profile of 50 different types of cancer. The project aims to identify those non-coding alterations that are more relevant for tumour biology through computational methods and will explore new therapeutic strategies that can revert its effects by means of the creation of the corresponding cellular models. The project​ is funded for the period 2016-2021 by the European Research Council (ERC) with an ERC Consolidator grants given to Nuria López-Bigas, head of the Biomedical Genomics group of GRIB.

http://bg.upf.edu/blog/2016/02/erc-consolidator-granted-to-our-lab-to-find-noncoding-cancer-drivers/

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Last publications

  • Gubern A, Joaquin M, Marquès M, Maseres P, Garcia-Garcia J, Amat R, González-Nuñez D, Oliva B, Real FX, de Nadal E, Posas F. The N-terminal phosphorylation of RB by p38 bypasses its inactivation by CDKs and prevents proliferation in cancer cells. Molecular Cell, 2016 DOI: 10.1016/j.molcel.2016.08.015.
  • Martin S, Bellora N, González-Vallinas J, Irimia M, Chebli K, DeToledo M, Raabe M, Eyras E, Urlaub H, Blencowe BJ, Tazi J. Preferential Binding of a stable G3BP Ribonucleoprotein Complex to Intron-retaining Transcripts in Mouse Brain and Modulation of their Expression in the Cerebellum. J Neurochem, 2016;. PMID: 27513819 . DOI: 10.1111/jnc.13768.
  • Roberto G, Leal I, Sattar N, Loomis AK, Avillach P, Egger P, van Wijngaarden R, Ansell D, Reisberg S, Tammesoo ML, Alavere H, Pasqua A, Pedersen L, Cunningham J, Tramontan L, Mayer MA, Herings R, Coloma P, Lapi F, Sturkenboom M, van der Lei J, Schuemie MJ, Rijnbeek P, Gini R. Identifying Cases of Type 2 Diabetes in Heterogeneous Data Sources: Strategy from the EMIF Project. PLoS ONE 2016; 11(8): e0160648. PMID: 27580049 . DOI: 10.1371/journal.pone.0160648.
  • Trincado JL, Sebestyen E, Pages A, Eyras E. The prognostic potential of alternative transcript isoforms across human tumors. Genome Med, 2016; 8 (1): 85. PMID: 27535130 . DOI: 10.1186/s13073-016-0339-3 AUG 17 2016.

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