Tools




Seminars, events & talks

Thursday, 2nd June, 2011, 11:00-12:00

Unravelling the complexity of molecular kinetics: states, pathways and experimental evidence

Simulations of the conformational equilibrium of macromolecules typically reveal a complex network of conformational states and transition rates between the states. In contrast, experimental results, such as dynamical fingerprints of macromolecules, often seem to indicate two- or three state kinetics. Markov state models, which are an efficient method to capture and summarize the information obtained from molecular simulation, can be used to predict these dynamical fingerprints and to reconcile experiment with simulation. In the first part of the lecture, I will given an overview of how to extract metastable states and dominant pathways from a given Markov model. Then, I will use a four-state model of a protein folding equilibrium to illustrate how dynamical fingerprints can be predicted from a given Markov model. From the equations of this method it becomes evident that (i) there might be no process which corresponds to the common notion of folding; (ii) often the experiment will be insensitive to some of the processes present in the system. These effects cause the difference in complexity between experimental and simulation results. Lastly, it is not only possible to predict dynamical fingerprints, but one can also use Markov models to design experiments to selectively measure specific processes. This will be demonstrated for a fluorescence quenching experiment of the MR121-G9-W peptide.

Speaker: Dr. Bettina Keller (Computational Molecular Biology, Freie Universität Berlin, Germany)

Room Seminar Room “Xipre” 173.06 (PRBB – 1st Floor)

Wednesday, 25th May, 2011, 11:00

An integrative approach for epigenetic data analysis

"High-Throughput sequencing (HTS) has revolutionized the study of gene regulation and expression.
However, there is a strong need for methods that facilitate the integration of multiple datasets to build predictive models. We present a computational framework to analyze and integrate epigenetic data, which allows the development of predictive models of gene regulation. Within this framework, we provide tools to carry out analysis of HTS data from DNA-protein binding, RNA-protein binding and RNA expression assays.
In particular, we have developed a method that can effectively characterize significant changes in epigenetic patterns genome-wide, including promoters, enhancers and genic regions. Furthermore, we provide a tool for building predictive models based on Machine Learning (ML) from multiple datasets. Using the published datasets, we show that our ML methodology allows us to predict the expression change from chromatin properties with 95% accuracy. Additionally, our tools allow the integration of a variety of input datasets and the application of many different ML methods. We finally discuss how this computational framework can be applied to the study of the epigenetic changes in cancer."

Speaker: Eduardo Eyras - Computational Genomics, UPF

Room 473.10 PRBB

Monday, 23th May, 2011, 15:30

Improvements in computer simulations in biomedicine and how they are going on-line

Molecular simulations and biochemical kinetics modelling are among the most computing demanding problems in biomedicine. In this talk I will introduce several improvements our group has been developing in the last years, and how they have been applied to a variety of questions proposed by our fellow experimentalists. However, an increasing demand for simple and multiplatform bioinformatics and simulations methods to tackle a variety of problems in biomedicine exists. Thus, the natural move of a research group to make its software widely spread is to create web portals and web services that habilitate others to use its tools in an easy way. We will show the concept of Activ8 as an extremely simple to use and absolutely expandable platform for building computational protocols on-line. Examples of its use will range from research to training.

Speaker: Dr. Jordi Villà i Freixa

Room Sala d’actes, planta baixa, Àrea General HUVH

Monday, 23th May, 2011, 10:00 - 14:00

Jornada sobre patents en l'àmbit de la Biomedicina

En el marc de la Plataforma Tecnológica Española de Medicamentos Innovadores, copresidida per Ferran Sanz, director del Programa de Recerca en Informàtica Biomèdica de l'IMIM (Institut de Recerca Hospital del Mar), s'organitza el proper 24 de maig a l'Auditori del Parc de Recerca Biomèdica de Barcelona (PRBB), una Jornada sobre patents en l'àmbit de la biomedicina. Aquesta jornada està dirigida pel professor Pascual Segura, agent de la propietat industrial de la Universitat de Barcelona i director del seu centre de patents. L'objectiu de la Jornada és explicar la importància dels drets de propietat industrial, què es pot patentar i sota quines condicions, entre molts altres temes. La inscripció que és gratuïta podeu realitzar-la clicant aquí.

Speaker: Pascual Segura - Universitat de Barcelona

Room Auditori del PRBB

Thursday, 5th May, 2011, 11:00

Thesis of Alice Ledda: “Distribution and evolution of short sequence tandem repeats in eukaryotic genomes”

We investigated the use of next generation sequencing data, from the 1000 Genomes Pilot Projects, to quantify microsatellite variability in the human population and discover putative new loci involved in trinucleotide repeat expansion diseases.

We analysed microsatellites phylogenetic conservation to learn about the role of selection in shaping microsatellite evolution. The first study concluded that in vertebrate lineages amino acid tandem repeats were more conserved than similar sequences located in non-coding regions. This lead us to the conclusion that evolution was preserving repeats in protein-coding regions. In a second stage we analzed the conservation of microsatellites in different genomic regions, comparing them with the conservation of microsatellite in intergenic region. We concluded that selection was not preserving microsatellites only in exons but also in other genomic regions.

Room room Josep Marull, Dr. Aiguader 80.

Wednesday, 4th May, 2011, 11:00 AM

Pyicos: a versatile toolbox for regulatory genomics"

A revolution is taking place in the study of gene regulation: High-throughput sequencing has become the basis of various techniques, like ChIP-Seq, RNA-Seq, CLIP-Seq, and new techniques evolve constantly. But do we need a new specialized tool to analyze each data type? Not necessarily! We propose Pyicos (http://sourceforge.net/projects/pyicos/), a generic tool that can adapt to various data types, by providing operations that are typically required for their manipulation and analysis. Pyicos is open-source and its input are genomic positions obtained from the mapper of choice. We show the high accuracy of Pyicos by comparing it to methods, specifically designed for the analysis of ChIP-Seq, RNA-Seq or CLIP-Seq data. With its flexibility and suitability for integration, Pyicos provides a convenient basis for the study of gene regulation.

Speaker: Sonja Althammer - Biomedical Informatics, UPF

Room 473.10_Aula

Thursday, 28th April, 2011, 11:00-12:00

A combined experimental and theoretical approach to study protein aggregation

Protein misfolding and aggregation into amyloid structures are associated with dozens of human diseases. Recent studies have provided compelling evidence for the formation of aggregates conformationally related to those underlying such disorders in yeast and bacterial cytosols. Thus, myloid-like aggregation seems to be an omnipresent process in both eukaryotic and prokaryotic organisms. The ease with which yeast and bacteria can be genetically and biochemically manipulated suggest that they might become useful systems for studying how and why proteins aggregate inside the cell and could provide a tractable environment to rationally model such phenomenon. This “in the cell” studies, combined with the computational analysis of the common as well as the differential structural and sequential properties of the proteins involved in human amyloid diseases might be of much help in deciphering the molecular mechanisms behind protein aggregation.

Speaker: Prof. Salvador Ventura - Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona

Room Room Xipre 173.06 (PRBB – 1st Floor)

Thursday, 14th April, 2011, 11:00-12:00

Linking function to dynamics in globular, multidomain and unstructured proteins using NMR

A detailed understanding of the biological function of macromolecules requires knowledge of both, their three dimensional structure and their time-dependent fluctuations. Methods to determine the structure of proteins are now well established and the static representations that they provide have contributed much to our understanding of the stability and biological function of proteins (structure-function relationship). In contrast, the characterization of structural fluctuations at atomic resolution is still in its infancy, particularly for motions taking place at biologically relevant time scales (dynamics-function relationship). Such information can be derived from residual dipolar couplings (RDCs) measured by nuclear magnetic resonance (NMR). In this communication we present the determination of native ensembles for globular, multi-domain and disordered proteins that explicitly represent their structural heterogeneity in the sub-millisecond time scale. The detailed descriptions of macromolecular dynamics achieved have allowed us to characterize: i) the transfer of structural information across a surface patch in ubiquitin involved in molecular recognition by the proteins that regulate protein degradation [1], ii) the role of inter-domain motions of T4 Lysozyme in enzymatic catalysis [2], and iii) the native (residual) contacts in chemically denatured ubiquitin that initiate the folding of this protein [3].

Speaker: XAVIER SALVATELLA - Laboratory of Molecular Biophysics, Institute for Research in Biomedicine.

Room Room 473.10 (PRBB - 4th Floor)

Wednesday, 13th April, 2011, Thu, Apr 14, 2011 11:00 AM - Thu, Apr 14, 2011 12:00 PM

TBD

Speaker: Larry Stanton - Deputy director of GIS Singapore

Room 473.10 PRBB

Wednesday, 6th April, 2011, Thu, Apr 7, 2011 11:00 AM - Thu, Apr 7, 2011 12:00 PM

GSVA: Gene Set Variation Analysis

Speaker: Sonja Hänzelmann - Functional Genomics. Biomedical Informatics, UPF

Room 473.10 PRBB



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