Congratulations to Babita Singh, for the Best Science Poster prize at the IV Bioinformatics and Genomics Symposium held in Barcelona last December.
Babita is a predoctoral researcher at the Computational RNA Biology group of GRIB (UPF-IMIM) led by Eduardo Eyras. The poster, entitled "Landscape of Somatic Mutations in RNA Splicing Regulatory Elements in Cancer" was selected through participants voting and presents the second chapter of the Babita´s thesis about cis component of alternative splicing in cancer i.e. mutations on regulatory regions that could potentially result to differential splicing. For this purpose it is used the whole genome sequencing data obtained from The Cancer Genome Atlas (TCGA) for 13 different cancer types using ~17million mutations.
The IV Bioinformatics and Genomics Symposium took place at the Parc de Recerca Biomèdica de Barcelona (PRBB) on the 20th of December of 2016. This symposium was organized together by the Section of Computational Biology and Bioinformatics and the Section of Genomics and Proteomics of the Societat Catalana de Biologia (SCB) and the Bioinformatics Barcelona Association (BIB) and nearly 300 participants attended the symposium.
For more information and Poster link click here
El GRIB va participar en aquesta quarta edició en la que els organitzadors de la jornada han rebut més de setanta estudis, dels quals una vintena es van presentar oralment. Alguns investigadors catalans vénen des de llurs centres de treball actuals a Suècia, els Estats Units o la Gran Bretanya, i tornen per un dia al seu lloc d'origen per bescanviar coneixements i promoure col·laboracions. L'acte d'inauguració va comptar amb l'actual secretari d'Universitats i Recerca de la Generalitat de Catalunya, el Sr. Arcadi Navarro, científic de formació i especialitzat en bioinformàtica. A més, entre els ponents hi ha hagut dos investigadors dels dos centres de bioinformàtica més punters de la Gran Bretanya i d'Europa: l'European Bioinformatics Institute (EMBL-EBI) i el Wellcome Trust Sanger Institute. L'empresa europea de serveis digitals ATOS va ser el patrocinador tecnològic aportant una xerrada sobre computació d'altes prestacions o High-Performance Computing (HPC), i la DAMM va patrocinar l'espai de treball en xarxa (networking).
Genetic erosion following extreme population declines can become an added burden for the recovery of endangered species. A study just published in Genome Biology based on whole genome sequences of the Iberian lynx reports extremely low levels of genetic diversity and an excess of deleterious variants as major consequences of serial population contractions. Genomic studies of endangered species like this are providing insights into patterns of genomic erosion and how they can affect species viability. Hopefully, genomics will also contribute to saving species from extinction, adding a new tool to the species conservation toolbox.
Reference: Abascal et al. (including Alba MM, Villanueva-Cañas JL, Ruiz-Orera, J). Genome Biology. 14th Dec 2016. DOI: 10.1186/s13059-016-1090-1. https://goo.gl/dobxiW
You're still in time to sign up for the third visit of the "Get BIB", focused on this occasion on the Research Program on Biomedical Informatics (GRIB), joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of UPF.
The presentation will take place on Monday 12 December from 10:00 to 12:00h at Ramón y Cajal room of Barcelona Biomedical Research Park (Doctor Aiguader, 88, Barcelona), and since seating is limited, it needs your attendance confirmation by sending an email to email@example.com
Identified a new factor essential for the development of these aggressive tumours. This protein helps to define aspects that distinguish melanoma from other types of cancer
A recent publication at Nature Communications identified a new factor essential for the development of these aggressive tumours: the CPEB4, a protein that is crucial for melanoma cell survival. This protein helps to define aspects that distinguish melanoma from other types of cancer.
The Computational RNA Biology group of GRIB led by Eduardo Eyras has participated on this study headed by Marisol Soengas from the Spanish National Cancer Research Centre (CNIO), senior author of this paper, an expert in researching the "identity" of melanomas.
Reference article: Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of oncogenic drivers in melanoma. Eva Pérez-Guijarro, Panagiotis Karras, Metehan Cifdaloz, Raúl Martínez-Herranz, Estela Cañón, Osvaldo Graña, Celia Horcajada, Direna Alonso-Curbelo, Tonantzin G. Calvo, Gonzalo Gomez, Nicolas Bellora, Erica Riveiro-Falkenbach, Pablo Otiz-Romero, José Luis Rodríguez-Peralto, Lorena Maestre, Giovanna Roncador, Juan C de Agustín Asensio, Colin R. Goding, Eduardo Eyras, Diego Megías, Raúl Méndez and María S. Soengas. Nature Communications (2016). DOI: http://dx.doi.org/10.1038/NCOMMS13418
Next Monday, 28th of November at 11:00, Àlex Bravo Serrano, member of the Integrative Biomedical Informatics group of GRIB will defense his thesis "BeFree: a text mining system for the extraction of biomedical information from the literature" at Josep Marull room of the Universitat Pompeu Fabra.
Next Friday, 25th of November at 11:30, José Carlos Gómez Tamayo, member of the PharmacoInformatics group of GRIB will defense his thesis "Development and application of computational techniques to drug discovery and structure-function relationships" at PRBB Auditorium.
The EU-ToxRisk project and the Toxicology in the 21st Century (Tox21) initiative in the US have agreed to collaborate on efforts to reduce the use of animals and achieve more efficient chemical safety assesments. A total of 28 representatives from both projects gathered in a workshop held in Mainz (Germany) on the 12th-14th September 2016 to initiate collaboration across areas of mutual interest within the field of risk assessment.
Two groups of GRIB participate in the EU-ToxRisk project coordinating the application of computational methods: the PharmacoInformatics group led by Manuel Pastor and the Integrative Bioinformatics group led by Ferran Sanz, and therefore will play a major role in this collaboration. In particular, the GRIB will participate in the joint development and validation of core methodologies for hazard and risk assessment, as read-across, quantitative AOP and similarity metrics.
The aim of this workshop is to learn the latest developments of high-throughput molecular dynamics simulations with practical lectures and real data and to give scientists the opportunity to exchange their experiences. Hands-on session and training will be given using HTMD a powerful programmable environment to prepare, handle, simulate and analyze molecular simulations, and efficient GPU-based MD simulations, and standard protocols to execute numerical experiments. There will be at the end of the workshop a session on applying what you have learned on your data/proteins.
This workshop is a great opportunity for industrial partners to get an overview of the state-of-the-art in molecular simulations for medicinal chemistry and drug design.
Acellera is a technology spin off of the GRIB, focused on delivering services and solutions to companies and academic institutions on computing intensive, mission-critical applications. By exploiting heavily optimized molecular simulations and the outstanding computational capabilities of new accelerator processors, we help to achieve otherwise unreachable results using current standard technology.
In its 10th anniversary, the GRIB group led by Eduardo Eyras changes its name to "Computational RNA Biology group" to reflect the contributions by the group during these past years and its well-recognized expertise in the study of different aspects of RNA using computational methods, including RNA structure, RNA splicing regulation, chromatin and RNA, alternative splicing, non-coding RNAs, as well as the relevance of RNA biology in cancer. You can read more about the activities of the group in this web and also at the new group website: http://comprna.upf.edu/