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03/12/2018

Judith Pérez, winner of the collaborative poster session at the 2nd DCEXS PhD students' symposium

Congratulations to Judith Pérez, predoctoral researcher of the Integrative Biomedical Informatics Group of GRIB, awarded for the poster entitled "ResMarkerDB: a database of biomarkers of response to antibody therapy for breast and colorectal cancer". ResMarkerDB aims to promote the identification of existing and new actionable biomarkers of drug response in cancer and acts as a centralized repository that gathers information of biomarkers of response to therapeutic monoclonal antibodies for breast and colorectal cancer. Indeed, it integrates information from available public repositories and new data extracted and curated from the literature. Furthermore, ResMarkerDB allows exploration, visualization and prioritization of biomarker data and its response to therapy in a specific cancer type according to the evidence supporting their association and potential clinical usefulness. More information of this resource at http://resmarkerdb.org.

The poster session was part of the 2nd PhD students' symposium of the Department of Experimental and Health Sciences (DCEXS) held last 22&23rd of November in the PRBB. The DCEXS holds every year this symposium featuring leading topics in biomedical research, such as quantitative biology, genetics or neuroscience. Last year it was focused on doctoral students and this year it has been organized by a committee with representatives from all collectives.

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28/11/2018

Optimizing collaboration between academia and the pharmaceutical industry to improve the toxicological evaluation of drugs

A new article by Manuel Pastor, Jordi Quintana and Ferran Sanz shares their experience in the eTOX project to improve the transfer of models from academia to industry.

Researchers Manuel Pastor, Jordi Quintana and Ferran Sanz have published an article in the journal Frontiers in Pharmacology in which they share their experience gained in the transfer of computational predictive models from academic to industrial environments. This experience was acquired in the already concluded eTOX project, funded by the Innovative Medicines Initiative (IMI). The main results of this project pave the way for a new model of collaboration by the pharmaceutical industries among themselves and also between them and the world of academia, by sharing data and knowledge in order to improve the toxicological evaluation of compounds for potential use in drugs.

"In this article we have shared our experience in the adaptation of computational tools for drug discovery generated in academia for use in the pharmaceutical industry. It is an aspect that is often overlooked in this type of projects", says Manuel Pastor, head of the GRIB's Pharmacoinformatics group. "We have described some of the problems identified and the solutions we apply to solve or mitigate them", he adds.

In the project, the pharmaceutical companies contributed data generated and stored internally to train predictive models. One of the problems encountered was the need to share confidential information, such as the structure of compounds under development. Given that such data are highly sensitive, the companies were opposed to letting this information out of their internal repositories.

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21/11/2018

GRIB participated in the iPiE Forum Meeting held in Brussels from the 13th to the 15th of November

The iPiE consortium members met in Brussels, hosted by Janssen in its Diegem offices. The first day, the meeting was structured in workshops and general sessions on updates discussions. The second day counted with the attendance of the Scientific Advisory Board members of the project, to whom the last achievements and progress was presented. The last day was aimed to discuss on the prioritisation guidelines which are being developed in the final months of the project.

iPiE aims to develop predictive frameworks that use information from existing datasets on environmental fate and effects of Active Pharmaceutical Ingredients (APIs), toxicological studies, pharmacological mode of action and in silico models to support more intelligent environmental testing of pharmaceuticals. The iPiE project has delivered models to estimate concentrations of pharmaceuticals in surface waters, sediments and soils across Europe as well as the models for predicting effects of pharmaceuticals on aquatic organisms. One of the major iPiE achievements was the development and the release of the iPiEsys software which allows the database to be searched and predictive models to be run. The guidance on how the software system and associated predictive tools can be used is under development and it is expected to be delivered early next year.

More about the project at http://i-pie.org/

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16/11/2018

Conocer la toxicidad para mejorar la seguridad

El éxito del proyecto eTOX, nacido en 2010 en el marco de la iniciativa europea IMI (Innovative Medicines Initiative) dio paso en 2017 a un nuevo proyecto, herencia del anterior, pero bastante más ambicioso: eTRANSAFE. En ambos casos, se trata de compartir datos de investigación relacionados con la toxicidad para mejorar la seguridad de nuevos compuestos en desarrollo aprovechando la información que las compañías farmacéuticas extraen de sus procesos.

Ferran Sanz, coordinador académico de ambos proyectos y director del GRIB, manifiesta que "estamos orgullosos de haber conseguido que las compañías accedieran a compartir sus datos preclínicos en el eTOX", aunque reconoce que "los dos primeros años costó un poco". Ahora, la segunda etapa va un paso más allá porque requiere poner en común datos de ensayos clínicos. No obstante, recuerda que sólo se comparten datos de toxicidad y seguridad; nunca de eficacia, que serían los más sensibles. La previsión es que la nueva base de datos sea mucho mayor, porque se hará con más agilidad gracias al SEND y porque amplía el espectro de datos a reunir: tanto preclínicos como clínicos.

Lee la entrevista completa publicada por Diario Médico en su último newsletter.

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05/11/18

eTRANSAFE project at the IMI’s 10th Anniversary Celebration

eTRANSAFE was present at the IMI 10th Anniversary Scientific Symposium and the IMI Stakeholder Forum, both events were jointly held in Brussels in the framework of the IMI's 10th anniversary celebration. The IMI Stakeholder Forum held on the 24th of October had as theme 'The value of cross-sectoral health research and innovation'. eTRANSAFE Project Coordinator, Ferran Sanz , Director of GRIB (IMIM-UPF), participated in this event and took part in a session entitled "Case study: how to apply Technology convergence in safety", together with other members from Novartis, Mimetas, Sanofi and GIRP. During this session Prof. Sanz had the chance to introduce eTRANSAFE and to discuss on the benefits of data sharing contributing to the improvement of safety assessment.

IMI is funded jointly by the European Union (represented by the European Commission) and the European pharmaceutical industry (represented by EFPIA, the European Federation of Pharmaceutical Industries and Associations). The EU funding comes from Horizon 2020 and the EU's Seventh Framework Programme for Research (FP7). More info about IMI 10th Anniversary: here

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05/11/2018

University and social networks: adapt or be left behind

With just over fifteen years social networks have become indispensable for society, with billions of users. They have become the main sources of information and sharing of content for many of them, especially the youngest. Communication has changed in a profound and disruptive way. 

Social platforms have multiplied since then and each passing year there is an exponential increase in their infiltration among internauts. In fact, they have practically become the main sources of information and content sharing for a large number of users, especially for young people.


Read this article published on the digital magazine 365UPF with the opinions of teachers and researchers on the subject and the contributions of Angela Leis and Miquel Angel Mayer, members of the Integrative Biomedical Informatics group of GRIB stressing the potential of social networks to detect and predict health issues and their role in the classroom.

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Imatge de microscopia que mostra les cèl·lules piramidals de l'hipocamp del ratolí Thy1-EGFP

5/10/2018

A mechanism whereby cannabis would affect the plasticity of neural circuits is identified

A team led by Andrés Ozaita shows how the main psychoactive component of cannabis affects the machinery required to maintain the protein balance in the hippocampus.

A study led by Andrés Ozaita, a researcher at the Neuropharmacology Laboratory at UPF, shows how the main psychoactive component of cannabis affects the machinery required to maintain the protein balance in the hippocampus. They have discovered a mechanism whereby the cannabis would affect synaptic plasticity, i.e., the neurons' ability to respond to stimuli, modifying their connections, which are essential for learning and memory. The study, conducted in rodents, has been published in the journal Biochemical Pharmacology. The study also involved Joaquim Aguirre-Plans, Baldo Oliva and Emre Guney, researchers of the Structural Bioinformatics and Integrative Bioinformatics groups of GRIB.

Reference article: Salgado-Mendialdúa V, Aguirre-Plans J, Guney E, Reig-Viader R, Maldonado R, Bayés A, Oliva B, Ozaita A. Delta9-tetrahydrocannabinol modulates the proteasome system in the Brain. Biochemical Pharmacology (2018), https://doi.org/10.1016/j.bcp.2018.08.026.

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Participants in the think tank meeting in Ranco, Italy

05/10/2018

GRIB participates in the think tank meeting co-organized by the Center for Animal Alternatives to Testing-Europe and the project EU-ToxRisk.

The meeting took place in Ranco, Italy from 16th to 18th of July 2018 and was focused on "Internationalisation of read across as validated non-animal method (NAM) for regulatory toxicology". More than 20 read-across international experts from regulatory agencies, industry, and academia met to discuss about the necessary steps which would be necessary to boost the standardization of the read-across method and to expand its use and acceptance among international regulatory organizations. Manuel Pastor, head of the  PharmacoInformatics group of GRIB and leader of the workpackage applying read across methods within the EU-ToxRisk project, participated on this meeting.

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18/08/2018

Jorge Ruiz Orera receives one of the Doctoral School PhD Special Awards from the PhD Programme in Biomedicine of the Pompeu Fabra University

During the 2016-2017 academic year, 106 PhD theses were read and eight of them have been awarded

Congratulations to Jorge Ruiz Orera, doctoral student at the Evolutionary Genomics group of GRIB  (IMIM-UPF) for his thesis "Understanding the mechanisms of de novo gene evolution using transcriptomics data", supervised by Dr. Mar Albà. In his research, he investigated the mechanisms for de novo gene origination and evolution using highthroughput sequencing of complete transcripts and ribosome-protected fragments. The thesis identifies thousands of new de novo genes in human, chimpanzee, and mouse and presents evidence that these genes are mostly expressed from recently arisen promoters. It also shows that a large number of poorly conserved genes, including genes previously believed to be non-coding, are translated and finds a link between the capacity of a sequence to be translated and its nucleotide sequence composition. This doctoral research shows that there is abundant raw material for de novo birth of new functional proteins, and hence, its results contribute to a better understanding of the mechanisms of gene evolution. This thesis has been awarded with the International PhD Mention.

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10/08/2018

"We found a way to share the unsharable", an interview with the eTOX project coordinators F. Pognan and F. Sanz

The eTOX project partners developed innovative strategies and novel software tools to better predict the safety and side effects of new candidate medicines for patients. In an interview with the Innovative Medicine Iniciative (IMI) Programme Office, project coordinator Francois Pognan of Novartis, and academic coordinator Ferran Sanz, Director of GRIB (IMIM-UPF), explain how the tools developed by the project are already helping pharmaceutical companies make better-informed decisions in their pursuit of developing safer drugs for patients.

"For the academic world", Ferran Sanz says, "the way in which we have learned how to collaborate with the pharmaceutical industry is potentiating our capabilities to create spin offs and to establish research contracts with the pharmaceutical industry, beyond this particular project".

Read the interview at 'We found a way to share the unsharable' - an interview with the eTOX...

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