GRIB. Research Unit on Biomedical Informatics





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European project iPiE celebrates a workshop at the PRBB

On the 8th and 9th of February 2017 took place at PRBB (Barcelona) the iPiE WP6 workshop on ""Interfacing prediction models to iPiEsys" jointly organized by the project partners Molecular Networks and the GRIB (IMIM-UPF), addressing the prediction model developers within the consortium. 

During the workshop, a first prototype of the project prediction system (iPiEsys) was demonstrated using an acute fish toxicity model. The list of models that will be contributed by each partners was discussed as well as the technical details of their integration into iPiEsys. Also in this direction, a hands-on exercise showed the model developers the functionalities of eTOXlab, which was proposed as a framework for the development of iPiE predictive models.

The project iPiE: "Intelligence Led Assessment of Pharmaceuticals in the Environment", aims to develop a predictive framework that utilise existing information and in silico models to support more intelligent environmental testing of pharmaceuticals in development and to prioritise legacy pharmaceuticals for full environmental risk assessment and/or environmental (bio) monitoring.  iPiE is an european project funded by IMI for the period 2015-2017.

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Alba receiving the prize from Professor Isaac Kohane

Alba Gutiérrez-Sacristán, winner of the first prize at the Datathon on Autism SSC data

Congratulations to Alba Gutiérrez-Sacristán for the first prize won at the Datathon on Autism SSC data celebrated during the last month of February at the Department of Biomedical Informatics (DBMI), Harvard Medical School​ (USA).​ Alba is a predoctoral researcher at the Integrative Bioinformatics group of GRIB (IMIM-UPF) and she is doing a six months stage at DBMI of  Harvard Medical School, working on analyzing Autism data sets, integrating genetic and clinical data to model disease expression using the R statistical tool connected to a i2b2/tranSMART database.

The Datathon on Autism SSC data was addressed to all labs at DBMI or working on PI-SURE. Participants were required to create in a month the coolest use case on Autism Simons Simplex Data combining clinical and Exome variant data using the BD2K PIC-SURE API and jupyter notebooks.  

Alba created an R package in order to help researchers to analyse both clinical and molecular data included in the Simons Simple Collection, a permanent repository of genetic samples from 2,600 simplex families, each of which has one child affected with an autism spectrum disorder, and unaffected parents and siblings, winning the first price!

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Last project

TransQST

The european project TransQSTTranslational Quantitative Systems Toxicology aims to develop novel computational approaches using the best available data from the public and private domains to address the problems of drug safety. Funded by IMI2 for the period 2017-2021.

http://transqst.org/

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Last publications

  • Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ, Bomane A, Cosson B, Eyras E, Rasko JE, Ritchie W. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol, 2017; 18(1):51. PMID: 28298237 . DOI: 10.1186/s13059-017-1184-4.
  • Mularoni L, Ramos-Rodríguez M, Pasquali L. The Pancreatic Islet Regulome Browser. Front Genet 2017; 8: 13. PMID: 28261261 .
  • Oddi S, Stepniewski TM, Totaro A, Selent J, Scipioni L, Dufrusine B, Fezza F, Dainese E, Maccarrone M. Palmitoylation of cysteine 415 of CB1 receptor affects ligand-stimulated internalization and selective interaction with membrane cholesterol and caveolin 1. Biochim Biophys Acta, 2017. PMID: 28215712 . DOI: 10.1016/j.bbalip.2017.02.004.
  • Lally CCM, Bauer B, Selent J, Sommer ME. C-edge loops of arrestin function as a membrane anchor. Nature Communications, 2017. PMID: 28220785 . DOI: 10.1038/ncomms14258.

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