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Seminars, events & talks

Thursday, 12th November, 2015, 12:00

Integrative Biomedical Informatics

"Uncovering disease mechanisms through network biology in the era of next generation sequencing"

Characterizing the behavior of disease genes in the context of biological networks has the potential to shed light on disease mechanisms, and produce new candidate disease genes and therapeutic targets. Previous studies addressing the network properties of disease genes have produced seemingly contradictory results. We have explored the causes of these seeming discrepancies and assessed the relationship between disease genes' network roles and their tolerance to deleterious germline variants in human populations leveraging on: different interactome resources, a comprehensive catalog of disease genes and exome variation data. We found that the most salient network features of disease genes are driven by cancer genes and that genes related to different types of diseases play network roles whose centrality is inversely correlated to their tolerance to likely deleterious germline mutations. This proved to be a network multiscale signature, including global, mesoscopic and local network centrality features. Cancer driver genes, the most sensitive to deleterious variants, occupy the most central positions, followed by dominant disease genes and then by recessive disease genes, which are tolerant to variants and isolated within their network modules.

Speaker: JANET PIÑERO Biomedical Informatics, GRIB

Room Aula room 473.10 (4th floor)

Thursday, 5th November, 2015, 12:00

Integrative Biomedical Informatics

DisGeNET: a discovery platform for translational bioinformatics (PRBB Computational Genomic Seminars)

In this talk I will present the DisGeNET Discovery Platform for the dynamical exploration and analysis of human diseases and their genes. The platform consists of a comprehensive knowledge base of over 400,000 gene-disease associations arising from both expert-curated databases and information extracted from the scientific literature using text mining, with special attention paid to the explicit provenance of the association. The DisGeNET platform provides a set of analysis tools designed to facilitate and foster the study of the molecular underpinning of human diseases. The talk will also illustrate the semantic knowledge representation of DisGeNET, and how to explore and analyze the data using different tools with special emphasis on harnessing the data using Semantic Web technologies.

Speaker: Núria Queralt Rosinach, IBI Group (GRIB)

Room Aula room 473.10 (4th floor)

Thursday, 5th November, 2015, 12.00-13.00

Computational Biophysics

The Virtual Human: In Silico Methods for Personalised Medicine

The era of personalised medicine offers at once a huge opportunity and a major challenge to computational science. The potential impact centres around our ability to marshall substantial quantities of patient data and to use them to perform predictive, mechanistic modelling and simulation in order to deliver therapies and to enhance clinical decision making, on time scales which are far shorter than those usually considered in the context of academic research and development activities. Secure access to personal data, as well as to powerful computational resources, is essential. I shall provide a couple of examples which illustrate the current state of the art. One addresses clinical decision support in the context of blood flow within neurovascular pathologies; the other is concerned with patient specific drug discovery and treatment. We shall discuss the underlying e-infrastructure requirements, including data, compute and networks, and reflect on the potential for cloud and other forms of e-infrastructure provision to meet the anticipated future demand for resources.

Speaker: Peter V. Coveney, Department of Chemistry, UCL.

Room Charles Darwin Room

Wednesday, 4th November, 2015, 12.00-13.00

Integrative Biomedical Informatics

New generation biomarkers based on mechanistic insight into disease

The impact of the genomic revolution in the field of medicine has been enormous. The concept of personalized medicine has evolved to precision medicine, which aims to find better ways of defining diseases by relating conventional clinical-pathological diagnostic criteria with state-of-the-art molecular profiling methodologies. Besides, a more precise diagnostic of the disease, based on the description of their molecular mechanisms would allow creating innovative diagnostic, prognostic, and therapeutic strategies precisely tailored to each patient's requirements. To achieve this, a deeper, systems-based understanding of these disease drivers is required. Here I will discuss how primary gene expression and gene variation data can be integrated and transformed into mechanism-based biomarkers containing higher-level information on disease mechanisms by means of relatively simple models of functional pathways. 

Speaker: Joaquín Dopazo, Head of Computational Genomics Dept., CIPF, Valencia, Spain

Room Ramón y Cajal Room

Thursday, 29th October, 2015, 12:00

GPCR drug discovery

Nucleotide excision repair is impaired by binding of transcription factors to DNA

Somatic mutations are one of the major genetic alterations that contribute to the transformation of normal cell into cancer cell. The rate of somatic mutations appear in great variability across the genome due to chromatin organization, DNA accessibility and replication timing. However, other variables that may influence the mutation rate locally, such as DNA-binding proteins, are unknown. Here we demonstrate that the rate of somatic mutations in melanoma tumors is highly increased at active transcription factor binding sites and nucleosome embedded DNA compared to their flanking regions due to impaired nucleotide excision repair activity.

Speaker: SABARINATHAN RADHAKRISHNAN Biomedical Genomics, GRIB (IMIM-UPF)

Room Aula room (4th floor)

Thursday, 8th October, 2015, 12:00

Computational RNA Biology

Exploiting processing patterns to study small non-coding RNAs

Small non-coding RNAs play a vital role in several cellular processes. Their pattern of processing and its traces in short RNA-Seq reads data is a powerful and unbiased resource that can be used to study those important molecules. Here we present a collection of software tools based on the analysis of processing patterns for the discovery, annotation and characterization of small non-coding RNAs.

Speaker: AMADIS PAGÉS - Computational Genomics, GRIB

Room Marie Curie Room (Ground floor)

Tuesday, 7th July, 2015, Wednesday, July 8 at 12:00h

GPCR drug discovery

Long non-coding RNAs as a source of new peptides.

High throughput sequencing of the eukaryotic transcriptome has resulted in the identification of many transcripts that lack long conserved open reading frames and which have been classified as long non-coding RNAs (lncRNAs). The majority of them are expressed at low levels and do not have a known function. Despite having been annotated as non-coding RNAs, the sequencing of ribosome-protected RNA fragments (ribosome profiling) has revealed that many of them are scanned by ribosomes and are likely to translate short peptides. We have examined single nucleotide polymorphism (SNP) data and have found evidence of purifying selection on the corresponding coding regions. We propose that lncRNAs provide the necessary raw material for the evolution of new functional proteins during evolution.


Group Leader Seminars are always on Wednesdays at 12:00h at the Auditorium, Sala Marie Curie or, exceptionally, at the Aula 473.

Speaker: Mar Albà

Room PRBB Auditorium

Thursday, 21th May, 2015, 11:00h

Functional Genomics

Mapping eQTL networks with mixed graphical Markov models and the genetic control of gene expression in yeast network hub genes

Speaker: Robert Castelo - Functional Genomics Group - GRIB

Room 473.10

Friday, 15th May, 2015, 12:00

GPCR drug discovery

Targeted DNA- and RNA sequencing of cancer predisposition genes and B-cell repertoire

Speaker: Marton Munz, PhD. Wellcome Trust Centre for Human Genetics, University of Oxford

Room Sala Xipre

Thursday, 16th April, 2015, 11:00h

Computational RNA Biology

RNA processing alterations as drivers and prognostic markers of cancer

Abstract:

Alterations in RNA processing are emerging as important signatures to understand tumor formation and to develop new therapeutic strategies. However, it is not yet known the extent to which these alterations can be considered drivers or whether specific patterns of RNA processing can be predictive of prognosis. We describe our efforts to determine the functional impact and relevance in cancer of RNA processing alterations measured in 11 cancer types. We describe multiple alterations in RNA regulatory proteins and their target genes, and investigate RNA alterations that are predictive of tumor stage and survival. These novel signatures expand the catalogue of candidate actionable alterations in tumors and potentially complement current strategies in precision cancer medicine.

Speaker: EDUARDO EYRAS Computational Genomics Group - GRIB

Room Aula room (4th floor)



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