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Dr. Mar Albà

09/05/2022

The GRIB receives an ERC grant of 2.5 million euros to expand knowledge of the human genome

Dr. Mar Albà, ICREA professor and coordinator of the Evolutionary Genomics Group, director of the GRIB and associate professor at UPF, has received a grant of 2.5 million euros from the European Research Council (ERC), to develop the NovoGenePop project. This study seeks to expand our current knowledge of the human genome by searching for genes that are specific to certain individuals or populations.

Over the next five years, the group led by Dr. Albà will work on "opening up new horizons in research, studying the diversity of genes in populations". Their field of study focuses on de novo genes, those that have been created recently due to mutations that accumulate constantly and which have no negative consequences for the organism. Having bioinformatics tools for identifying these genes can be very useful in a number of fields. "The aim is to take a step forward in our understanding of how new genes are formed from the genome, not on long evolutionary scales, but at the population level", explains Dr. Albà. The goal of the project is to identify the diversity of these novel genes, based on data from yeast populations and human cell lines, for which genomic sequences are already available. Using massive RNA and protein sequencing tools, it will be possible to detect novel genes and identify the mutations associated with their formation. To refine the research, the data will be compared with information from other related species.

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Author: María José Falaguera; Title: Systems pharmacology network

20/04/2022

​Thesis defense of María José Falaguera on Tuesday 26th of April at 12pm

​Next Tuesday 26th of April at 12pm, María José Falaguera, member of the the Systems Pharmacology Group of GRIB will read her thesis: "Illuminating the chemical space of therapeutical relevance: from pharmaceutical patents to untargeted proteins". It will take place in room 61.206 of the UPF Campus Mar building (2nd floor). You are invited to attend this event.

Abstract:

Systems pharmacology is the discipline that studies the so-called 'pharmacological space' with a holistic and network-based perspective. Its​ challenge is to shed light on the astonishingly sophisticated biological processes that characterize living cells, and the effect that exogenous​ chemical entities with therapeutic purposes have when entering them. From this perspective, a series of novel computationally-developed​ methodologies are presented in this Thesis. They aim from the exploration of the pharmacologically-relevant chemical space claimed in patents, to the unveiling of pharmacological opportunities to drug yet untargeted proteins.

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CompBioMed project Logo

16/05/2022

Registration open at the workshop: METHODS IN MOLECULAR SIMULATIONS AND MACHINE LEARNING (MMSML)

The MMSML Workshop will be held at the Barcelona Biomedical Research Park (PRBB) from 14th to 16th of July 2022 and is organized by the Computational Science group of GRIB led by Gianni de Fabritiis as part of the training activities of CompBioMed2, a European Commission H2020 funded Centre of Excellence focused on the use and development of computational methods for biomedical applications. Comprising members from academia, industry and the healthcare sector, CompBioMed2 has established itself as a hub for practitioners in the field, successfully nucleating a substantial body of research, education, training, innovation and outreach within the nascent field of Computational Biomedicine.

Registration at the web of the event 

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22/03/2022

The European Research Network on Signal Transduction (ERNEST) has established an Emergency Fund for Ukrainian researchers.

Researchers affiliated to any legal entity in Ukraine (for example, schools and universities, research centers, governmental institutions, or private companies) are eligible to apply for this funding.

For more information you can contact Jana Selent (vice-chair of the ERNEST - Cost Action 18133) or visit this website.

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19/01/2021

Lilian Boll obtains one of the grants of the INPhINIT PhD program of La Caixa Foundation

We welcome the predoctoral researcher Lilian Boll who has obtained one of the 65 grants of the INPhINIT PhD Program of La Caixa Foundation for her project "Identification of neo-epitopes in cancer derived from non-canonical proteins and their potential use in immunotherapy" to study neoantigens at the Evolutionary Genomics group of the GRIB.

Neoantigens are tumor-specific antigens generated by mutations in tumor cells, which are only expressed in tumor cells. "One of the approaches in immunotherapy is to block cellular checkpoints so that the immune system recognizes tumor cells by their neoantigens," explains Lilian Boll. "With data from oncology patients, I want to characterize neoantigens genomically and structurally to better understand how we can use them to predict treatment response in patients" adds the researcher.

This grant, aimed at researchers of all nationalities who are interested in carrying out doctoral studies in Spain or Portugal, will allow Boll to carry out the project over 3 years and with a total financial endowment of 122,592 euros for the entire period. In addition, the grant includes a comprehensive complementary training program in soft skills, researcher welfare and preparation for the future.

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GPCRmd, one of the platforms developed in this thesis, uncovers the dynamics of most G protein-coupled receptors (GPCRs) with known three-dimensional structure

Thesis defence of Mariona Torrens Fontanals: "Making protein dynamics FAIR: Research platforms for the collection, dissemination, and analysis of molecular dynamics simulations"

Next Friday, 11th of February at 11:00, Mariona Torrens Fontanals, member of the  the GPCR Drug Discovery Group of GRIB will read her thesis: "​Making protein dynamics FAIR: Research platforms for the collection, dissemination, and analysis of molecular dynamics simulations​".

You can attend to this event online ​shorturl.at/exPTZ

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Author: Adrià Pérez; KIX-cMyb binding pathway

20/01/2022

Thesis defence of Adrià Pérez: "Learning How to Simulate: applying machine learning methods to improve molecular dynamics simulations"

Next ​Thursday 27th of January at 10:00 am, Adrià Pérez, member of the Computational Science group of GRIB will read his thesis: "Learning How to Simulate: applying machine learning methods to improve molecular dynamics simulations".

The event will be online. Free access at https://upf-edu.zoom.us/j/89823439190

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From left to right: Jana Selent and Mariona Torrens-Fontanals.

15/12/2021

New online tool for predicting the impact of SARS-CoV-2 mutations on its protein components

Press Release IMIM 14/12/2021

Researchers now have a new tool available for tackling SARS-CoV-2, analysing this virus, and finding new ways to fight COVID-19, namely the SCoV2-MD database (available at www.scov2-md.org). The resource houses detailed atomic, dynamic and 3D information on all known 3D-structured proteins in this coronavirus. In total, it contains 360 gigabits of data covering the majority of the 29 proteins: four structural, sixteen non-structural, and nine accessory proteins. Nucleic Acids Research has published a paper on how it works, which it considers to be one of the most prominent articles ever published in the journal.

"What is really novel is that we use dynamic data combined with the evolution of the virus to predict its impact on protein function", explains Jana Selent, lead author of the paper on this new tool. To do this, "In addition to protein behaviour simulations, the information available on the genetics of the virus has been taken into account to calculate and predict the impact of mutations", adds Toni Giorgino, co-lead author of the article. This makes SCoV2-MD a useful tool for visualising how these SARS-CoV-2 mutations will affect its ability to transmit and infect human cells through the changes produced in their constituent proteins.

Meanwhile, this new tool can also help researchers develop new treatments and vaccines against COVID-19. "Watching the simulations allows us to see and understand how it behaves, how it works, and which parts of the protein's structure are important and possible targets for new treatments", says Mariona Torrens-Fontanals, also a researcher at GPCR Drug Discovery Group of IMIM and first author of the study. It even makes it possible to predict whether coronavirus mutations could affect the ability of the antibodies generated by COVID-19 vaccines to recognise the virus and activate the immune system against it.

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Artificial intelligence and computational methods will save a lot of time in drug development. Photo by the National Cancer Institute on Unsplash.

15/12/2021

A strategic agreement of Chemotargets with CRG to accelerate the development of new drugs

The CRG and the drug identification company Chemotargets, a spin-off of the GRIB, have joined forces to promote the development of new therapies for different diseases, such as cancer or fibrosis.

The Centre for Genomic Regulation (CRG) and the biotechnology company Chemotargets have reached a collaboration agreement to facilitate and accelerate the process of searching for therapeutic targets and the subsequent drug development.

This initiative combines, on the one hand, the experience of the CRG in the identification of new therapeutic targets for diseases such as cancer, fibrosis, eye diseases, blood diseases or diseases that cause inflammation; and on the other, the cutting-edge technology, computational methods and data analysis offered by Chemotargets, a spin off of the Systems Phamacology group of GRIB led by Jordi Mestres.

Read more at El·lipse magazine https://ellipse.prbb.org/a-strategic-agreement-to-accelerate-the-development-of-new-drugs/

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12/1/2022

Join this seminar "Bioinformatics for Neuroscience Research: omics, statistics and data analysis" by Dr. Júlia Perera, on Wednesday 12nd of January at 12:00 h.

We invite you to the next IMIM Seminar on Hottopics in Neuroscience that will take place on Wednesday 12/1/2022 at 12:00 h. Dr. Júlia Perera (Bioinformatics Unit, MARGenomics & GRIB) will talk about "Bioinformatics for Neuroscience Research: omics, statistics and data analysis".

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