MedBioinformatics project celebrates the 8th General Assembly Meeting

The eighth General Assembly meeting of the MedBioinformatics project took place in Hinxton (UK) on June 14th 2017 at the Wellcome Genome Campus. This one-day meeting was focused on presenting updates from research activities of all project partners and to define a workplan to accomplish the goals of the project, with special attention to the various use cases being developed in collaboration with clinicians and translational researchers. 

The project coordinator made announcement of the 3rd European Conference on Translational Bioinformatics (ECTB2018) which is planned for April 16-17th 2018, organized by the GRIB (IMIM-UPF) at the Barcelona Biomedical Research Park (PRBB), Barcelona.

The project MedBioinformatics "Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities" aims to develop useful bioinformatics tools and applications, and autonomously usable for analysing the huge amount of data and knowledge generated in healthcare and biomedical research in order to facilitate translational research and precision medicine. European project funded by H2020 for the period 2015-2018 and coordinated by the GRIB.

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Supporting public-private partnerships in genomics and health

Over 80 participants from industry and academia gathered in Barcelona on 6-7 June for the ELIXIR Innovation and SME forum. Hosted by ELIXIR Spain, the two-day event showcased successful companies making use of public bioinformatics resources, and presented free bioinformatics resources available through ELIXIR and ELIXIR Spain.

The programme included presentations of ELIXIR and ELIXIR Spain resources as well as companies and SMEs active in bioinformatics, genomics and health research. Three keynotes each presented different aspects of working with open data in life science research: Roderic Guigo from the CRG gave a general overview of the Open data in genomics including the European Genome-phenome ArchiveFerran Sanz, director of GRIB (IMIMUPF) and participant of ELIXIR Spain, showed several examples of how bioinformatics can support pharmaceutical research; and David Henderson from Bayer AG  talked about reuse of biomedical data in pharmaceutical research. Colm Carroll from the Innovative Medicines Initiative (IMI) presented some of the future funding opportunities in this area

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Image provided by the authors, GRIB-UPF


Scientists reveal for the first time the details of protein association at the atomic level

The groups of Frank Noé at Freie Universität Berlin, and Gianni de Fabritiis, ICREA research professor and head of the Computational Biophysics group of GRIB ( IMIM- UPF), have now collaborated to produce what is the first atomic-detail computer simulation of the process of protein-protein association and dissociation. The results were published in the scientific journal Nature Chemistry and were validated with experimental data.

The main challenge was that atomic-detail molecular dynamics are incredible expensive to simulate. Key to the success of the Berlin-Barcelona team was the combination of several new technologies that enabled a "divide and conquer" approach to the problem. GPUGRID, a distributed network developed by De Fabritiis' group was employed to collect compute time on graphic processing units (GPUs) from Nvidia by volunteers around the globe. Thousands of short simulations were conducted that way, coordinated by a novel machine learning algorithm in such way that the overall protein association process could be simulated within one year instead of having to wait 10,000 years. Markov modeling, a method pioneered by Noé and colleagues, was used to combine the many short simulations to an overall dynamical model that describes protein association and dissociation in full detail. "This was clearly a risky but important proof of principle and we are happy that we managed to show that the simulations are able to capture associations between proteins", says De Fabritiis.

This achievement opens the door to understanding the details of viral infections, the inner workings of the immune system, and many other problems with biomedical or biotechnological relevance.

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Formation of a GPCR signaling complex with arrestin


How proteins find each other to form signaling complexes

A study led by Jana Selent, head of the GPCR drug discovery group of GRIB (IMIM-UPF) and Martha Sommer (Institute of Medical Physics and Biophysics at the Faculty of Medicine in Charité Hospital, Berlin) published in the journal Nature Communications, focused on how G-protein-coupled receptors (GPCRs) and arrestin form complexes. The human GPCR family is an important class of targets for nearly half of all medicines prescribed today with the majority being involved in sensory and neuronal processes. Complex formation with intracellular signaling proteins such as arrestin is critical for many bodily processes. In this context, the published study identifies a previously unknown binding element critical to GPCR-arrestin interaction. Using a combination of computer simulations and site-directed fluorescence spectroscopy, the researchers were able to show that loops within the C-edge of arrestin are anchored to the membrane while forming pre- and high affinity complexes with GPCRs.  This discovery opens up a whole new field of research regarding how the membrane influences formation of GPCR signaling complexes with arrestin. Ultimately, these insights can be exploited for proposing new strategies to modulate this important class of drug targets.

Pub Reference: Ciara C.M. Lally, Brian Bauer, Jana Selent & Martha E. Sommer. C-edge loops of arrestin function as a membrane anchor. Nature Communications, 2017. doi: 10.1038/ncomms14258.

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From Tue 6 June 2017, 13:30 to Wed 7 June 2017, 14:00

ELIXIR Innovation and SME Forum next 6th & 7th of June 2017 at PRBB. Don't miss it!

Public-private partnerships in open data.

Registration ends in an hour!!!!

Come to the ELIXIR Innovation and SME forum which aim is to showcase to companies the free data resources and services that are available through ELIXIR Spain and ELIXIR Europe more generally. It will feature talks from ELIXIR partners on some of the key databases and resources and present examples of innovative companies that are already using public data in their businesses.

The event is free and open to all companies large and small, in the Barcelona region and further afield. It is organised by ELIXIR Spain and the ELIXIR Hub in collaboration with Innovative Medicines Initiative (IMI), biocatBioInformatics Barcelona (BIB) and Barcelona Biomedical Research Park (PRBB) and is particularly relevant for large and small companies active in the genomics and health domains.

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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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Celebrada la X Conferencia Anual de Plataformas Tecnológicas de Investigación Biomédica

La Conferencia se celebró en Madrid los días 7 y 8 de marzo y contó con la asistencia de casi 300 personas entre investigadores, autoridades y representantes de las administraciones y de compañías farmacéuticas, entre otros. Durante estos días, se abordaron cuestiones sobre investigación clínica, proyectos concretos de reutilización de datos para investigación biomédica, investigación en enfermedades raras, nuevas redes de investigación para la cooperación público-privada, innovación en centros públicos y colaboración con la industria biofarmacéutica. Todas las presentaciones y videos de esta Conferencia están disponibles en

Ferran Sanz, director del GRIB y copresidente, junto con Javier Urzay, subdirector general de Farmaindustria, de la Plataforma Tecnológica Española de Medicamentos Innovadores (PTEMI), presentó la sesión sobre "Análisis masivos de datos y reutilización de datos para la investigación biomédica".

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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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Chemotargets, one of the five top Biotechs at BIO Europe Spring 2017

From 20th to 22nd March, Barcelona will host the BIO Europe Spring 2017, the most important european partnering conference in the biotech and pharma sectors. The aim of this international conference is to bring together pharmaceutical, biotechnology and financial firms to form alliances and partnerships for achieving common goals. More than 1,400 companies from 45 countries are expected to participate, with more than 2,400 people attending.

Chemotargets, the spin-off  of GRIB (IMIM-UPF) dedicated to developing software for predicting the mechanism of action and safety of new drugs, directed by Jordi Mestres, head of the Systems Pharmacology research group, is one of the 5 biotech companies from Barcelona invited to take part.

At labiotech website, one of the leading digital media channels covering European Biotech news, presented this handful of local companies in its article "Meet these 5 Awesome Biotechs from Barcelona at BIO Europe Spring 2017", highlighting some of them for their innovative diagnostic and therapy-related technology. 

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New role of cholesterol in regulating brain proteins discovered

May be key in central nervous system diseases such as Alzheimer's

A study led by researchers of GRIB (IMIM-UPF) and the Institute of Medical Physics and Biophysics at the Faculty of Medicine in Charité Hospital, Berlin, published in the journal Nature Communications, demonstrates that the cholesterol present in cell membranes can interfere with the function of an important brain membrane protein, through a previously unknown mode of interaction. Specifically, cholesterol is capable of regulating the activity of the adenosine receptor, by invading it and accessing the active site. This will allow new ways of interacting with these proteins to be devised that in the future could lead to drugs for treating diseases like Alzheimer's.

The adenosine receptor belongs to the GPCR family (G Protein-Coupled Receptors), a large group of proteins located in cell membranes, which are key in the transmission of signals and communication between cells. GPCRs are therefore involved in the majority of important physiological processes, including the interpretation of sensory stimuli such as vision, smell, and taste, the regulation of the immune and inflammatory system, and behaviour modulation.

Explanatory video in which you can see how cholesterol leaves the neuronal membrane and get within the adenosine receptor:

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