Tools
15/03/2021
Thesis defence of Angela Leis: "Studying Depression through Big Data Analytics on Twitter"
Next Thursday, 18th of March at 10:30, Angela Leis, member of the Integrative Biomedical Informatics group of GRIB will read her thesis "Studying Depression through Big Data Analytics on Twitter".
The event will be online. Free access at: https://eu.bbcollab.com/guest/6142d06f38ad4724bcae539b8479d90a
8/3/2021
The virtual 11th CM of the EU project eTRANSAFE was held on 16&17 of February 2021
The eTRANSAFE consortium gathered for the 11th time to assess and discuss recent project developments as well as short-term plans until the next assembly scheduled in June. During this 2-day event consisting of 6 sessions, the project partners presented the latest results aimed towards achieving the project objectives of building a translational system for toxicology assessment.
The Enhancing TRANslational SAFEty Assessment through Integrative Knowledge Management (eTRANSAFE) project develops an integrative data infrastructure and innovative computational methods and tools that aim to drastically improve the feasibility and reliability of translational safety assessment during the drug development process. This infrastructure will be underpinned by development of open standards and robust policies widely accepted by stakeholders, including regulatory agencies and international organisations.
18/09/2020
Decryption of a molecular code that regulates the behavior of the cells
The research group of GPCR Drug Discovery, in collaboration with the Indian Institute of Technology in Kanpur, has deciphered how nature adjusts the response of the human cell to abundant extracellular stimuli (e.g., smell, taste, light, hormones, etc.).
When a cell receives an extracellular stimulus, it initiates a signaling process that can result in major physiological changes. This process is mediated by cell membrane proteins such as G protein coupled receptors (GPCRs). Depending on the stimulus, those receptors regulate cell activity through different molecular mechanisms.
The researchers have been able to interpret one of the main molecular mechanisms of cell regulation. "Using biophysical and biochemical assays combined with state-of-the-art computer simulations, we have been able to decipher a phosphorylation code that fine-tunes the cell behaviour" explains Dr. Jana Selent, head of the GPCR Drug Discovery group and one of the co-coordinators of this study.
18/09/2020
The Computational Science group of GRIB participates in the AIDD Project, an innovative training network of the European Commission
The project is funded by the European Union within the framework of the Marie-Skłodowska-Curie actions with 3.93 million Euro. and is coordinated by the Helmholtz Zentrum München
The Advanced Machine Learning for Innovative Drug Discovery (AIDD) project will bring together fifteen institutions from ten European countries and the University of British Columbia (Canada) to train sixteen PhD students in close collaboration with associated partners from the USA, Australia, China, Israel and other countries. The project is funded by the European Union within the framework of the Marie-Skłodowska-Curie actions with 3.93 million Euro. and is coordinated by the Helmholtz Zentrum München.
Artificial intelligence (AI) and machine learning are becoming an increasingly important working basis for the chemical industry. However, the application of AI in this field is not easy and requires extensive knowledge of chemistry. The aim of the new AIDD network is to prepare a future generation of scientists with outstanding skills in both machine learning and chemistry to innovate drug research.
"The project combines theoretical expertise with access to valuable proprietary data and the expertise of the industrial partners in medicinal and synthetic chemistry and will thus contribute innovative AI methods. Another main focus of AIDD is to train the next generation of researchers in interdisciplinary drug discovery and thus make a valuable contribution to future research in Europe", said AIDD project coordinator Igor Tetko.
24/08/2020
Nature Methods selects Jana Selent as the featured author of the month for August
Jana Selent, coordinator of the GPCR drug discovery group of GRIB, has been selected as the featured author of the month for the August edition in the journal Nature Methods.
Recently, the Group of Jana Selent published his latest article GPCRmd uncovers the dynamics of the 3D-GPCRome in this journal, where she presents a new tool to study one of the key elements in cell signaling, G protein-coupled receptors (GPCRs) which are the target of almost 40% of current drugs.
This tool, the GPCRmd platform, will help improve our understanding of the function of these receptors, which are critical for transmitting signals to the interior of cells. The design of this tool has been made possible thanks to a consortium of researchers from 23 different institutions of 10 different European countries and the United States, led by the group of Dr. Jana Selent and with important contributions from researchers of the Paul Scherrer Institute (PSI) in Switzerland and the Autonomous University of Barcelona.
El Hospital del Mar y el GRIB participan en los proyectos EHDEN Pilot y EHDEN COVID-19 Rapid Collaboration
El objetivo principal del proyecto europeo EHDEN: European Health Data & Evidence Network, es la realización de análisis de datos clínicos a gran escala en Europa (Real-World Clinical Data), mediante la utilización de herramientas bioinformáticas y estándares basados en la iniciativa internacional OHDSI y OMOP common data model (CDM). EHDEN permitirá acelerar la realización de los estudios y la investigación relativos a la caracterización de los pacientes con COVID-19 y otras patologías, así como evaluar los mejores tratamientos y gestión clínica de estos pacientes, con la utilización de millones de historias clínicas en Europa. Los dos proyectos en que participa el Hospital del Mar y el GRIB están liderados por el Dr. Robert Güerri, coordinador de la Unidad COVID-19 del Servicio de Infeccionas del Hospital del Mar e investigador del Grupo de investigación en patología infecciosa y antimicrobianos del Instituto Hospital del Mar de Investigaciones Médicas (IMIM) y por el Dr. Miguel-Angel Mayer del GRIB Integrative Biomedical Informatics Group (IMIM-UPF). "EHDEN nos ofrece la posibilidad de trabajar de forma colaborativa, con herramientas bioinformáticas muy potentes para el análisis y la integración masiva de datos de fuentes muy diversas, algo que es esencial y que puede ayudar a combatir esta pandemia y salvar vidas" explica Mayer.
Nou projecte VEIS: Valorització de EGA per la Indústria i la Societat
El GRIB participa en aquest projecte el qual uneix els principals grups de bioinformàtica catalans que estan impulsant i liderant projectes dirigits a dissenyar, avaluar i, en última instància, implantar la infraestructura necessària en entorns clínics amb un clar component de la medicina personalitzada. Per aconseguir aquest objectiu, el consorci compta amb 3 de les principals institucions hospitalàries de l'entorn.
L'objectiu principal és crear un ecosistema obert de tecnologies (Barcelona Computational Biomedical Ecosystem, BCBE) que cobreixi i s'adapti a les necessitats d'anàlisi i interpretació de dades òmiques i clíniques en entorns d'investigació i aplicació en biomedicina, a través de la base de dades EGA i el seu model federal Local EGA.
23/07/2020
Two GRIB innovations developed in the framework of the eTRANSAFE project, acknowledged by the European Commission’s Innovation Radar
The Innovation Radar, a European Commission initiative to identify high potential innovations and innovators in EU-funded research and innovation framework programmes, has selected two innovations developed by the GRIB in the project eTRANSAFE, to be included on the Innovation Radar platform: the preclinical text mining solution for treatment response and the Advanced in silico modelling to predict toxicity.
These innovations, developed by the Integrative Bioinformatics group and the PharmacoInformatics group of GRIB (IMIM - UPF) stemming from the project work, have been classified by the Innovation Radar as Exploring innovations in the early phases of technological readiness and have been published on the EU-funded innovations website on July 20th 2020, thus joining the 3600+ EU-funded innovations already showcased on the platform.
16/07/2020
New tool for studying key drug targets
The results from this study, published in Nature Methods, can support the development of new drugs fighting Alzheimer’s disease or cancer
G protein-coupled receptors (GPCRS) are one of the key elements mediating basic stimuli like our response to mosquito bites or to this last-minute goal scored by our favorite football team. In fact, these proteins are the target of almost 40% of the currently approved drugs. However, until now, researchers did not have access to a tool employing molecular simulations to achieve a better understanding of GPCR function.
Therefore, a consortium of researchers from 23 different institutions of 10 different European countries and the United States have joined forces to design and build a tool that will help improve our understanding of the function of these receptors, which are responsible of transmitting signals to the interior of cells. The GPCRmd platform is the result of this work, lead and coordinated by the GPCR Drug Discovery group of GRIB (IMIM - UPF), and the Paul Scherrer Institute (PSI) in Switzerland, with support from the Autonomous University of Barcelona.
Dr. Jana Selent, head of the GPCR group at GRIB and main corresponding author of this study explains: "we have used state-of-the-art technology that requires highly specific knowledge, like molecular simulations, to build an online resource where scientists from different disciplines can easily inspect and analyze a comprehensive set of molecular simulations of GPCRs". This will allow, according to Dr. Ramon Guixà-González, postdoctoral researcher at PSI in Switzerland and co-corresponding author of this study, "to extract information that will be helpful in the study and development of new drugs targeting diseases as relevant as cancer or Alzheimer's disease". Other relevant authors of this study are Ismael Rodríguez Espigares and Mariona Torrens Fontanals, postdoctoral and predoctoral researchers at the GRIB.
25/06/2020
GRIB participates in the Disc4All Project, an innovative training network of the European Commission
It is one of the ten projects selected in Catalonia as Innovative Training Network (ITN) Marie Sklodowska-Curie
Ferran Sanz, Laura I. Furlong and Baldo Oliva will participate in the Disc4All project: Training network to advance integrated computational simulations in translational medicine, applied to intervertebral disc degeneration, coordinated by Jérôme Noailly, principal investigator in the Biomechanics and Mechanobiology research area at BCN MedTech of UPF. It is one of the ten selected projects in Catalonia as an Innovative Training Network (ITN) Marie Sklodowska-Curie, in the European Commission's ITN MSC Actions call.
The European innovative training networks (ITN) aim to train a new generation of researchers in their early stages who are creative, enterprising and innovative, capable of dealing with the challenges of the future and turn knowledge and ideas into products and services with an economic and a social benefit. ITN programmes within the framework of the European Commission's Marie Sklodowska-Curie Actions support joint competitive programmes for training in research or joint doctorates. These programmes will be implemented by partnerships of universities, research centres, businesses, SMEs and other stakeholders in Europe and the rest of the world.
As part of this project, the GRIB will train young researchers in the tools available to analyze genomic data (DisGeNET) and comorbidities (comoRbidity). DisGeNET is a public knowledge management platform that offers information on genes and genomic variants associated with human diseases, which is obtained by integrating data from more than a dozen public resources and the scientific literature It contains one of the most comprehensive collections of genes and variants associated with human diseases that is currently available. On the other hand comoRbidity, is a program designed to provide a systematic and complete analysis of the comorbidities of the disease from both a clinical and molecular perspective.
