Tools




Seminars, events & talks

Wednesday, 9th June, 2010, Thu, Jun 10, 2010 11:00 AM

"Structure-Based Discovery of Small Molecule Correctors of F508 CFTR"

Speaker: Ori Kalid - Director, Computational Drug Discovery, EPIX Pharmaceuticals Host lab: Ferran Sanz, Biophysic ad Biochemistry Computation, UPF

Room Room 473.10 AULA - 4th floor

Sunday, 6th June, 2010, 12:00

“Stochastic Epigenetic variation as a driving force of development, evolutionary adaptation and disease”

Neo-Darwinian evolutionary theory is based on exquisite selection of phenotypes caused by small genetic variations, which is the basis of quantitative trait contribution to phenotype and disease. Epigenetics is the study of nonsequence-based changes, such as DNA methylation, heritable during cell division. Previous attempts to incorporate epigenetics into evolutionary thinking have focused on Lamarckian inheritance, that is, environmentally directed epigenetic changes. Here, we propose a new non-Lamarckian theory for a role of epigenetics in evolution. We suggest that genetic variants that do not change the mean phenotype could change the variability of phenotype; and this could be mediated epigenetically. This inherited stochastic variation model would provide a mechanism to explain an epigenetic role of developmental biology in selectable phenotypic variation, as well as the largely unexplained heritable genetic variation underlying common complex disease. We provide two experimental results as proof of principle. The first result is direct evidence for stochastic epigenetic variation, identifying highly variably DNA-methylated regions in mouse and human liver and mouse brain, associated with development and morphogenesis.
The second is a heritable genetic mechanism for variable methylation, namely the loss or gain of CpG dinucleotides over evolutionary time.
Finally, we model genetically inherited stochastic variation in evolution, showing that it provides a powerful mechanism for evolutionary adaptation in changing environments that can be mediated epigenetically. These data suggest that genetically inherited propensity to phenotypic variability, even with no change in the mean phenotype, substantially increases fitness while increasing the disease susceptibility of a population with a changing environment.

Speaker: Rafael Irizarry, Johns Hopkins University, Baltimore (USA)

Room 473.10 (Aula)

Wednesday, 2nd June, 2010, Thu, Jun 3, 2010 11:00 AM

"Evaluating protein sequence alignments using residue contact information".

Speaker: Jena François Taly Host lab: Cedric Notredame, Bioinformatics and Genomics, CRG

Room Room 473.10 AULA - 4th floor

Wednesday, 19th May, 2010, Thu, May 20, 2010 11:00 AM

"Predicting Alternative Splicing in Yeast"

Speaker: Mireya Plass Host lab: Eduardo Eyras, Computational Genomics, UPF

Room Room 473.10 AULA - 4th floor

Wednesday, 12th May, 2010, Thu, May 13, 2010 11:00 AM

"Constitutive CTCF binding sites define mandatory boundaries in vertebrate genomes"

Speaker: David Martin - Roderic Guigo, Bioinformatics and Genomics, CRG

Room Room 473.10 AULA - 4th floor

Tuesday, 4th May, 2010, Wed, May 5, 2010 3:00 PM - 5:00 PM

Biana: a software framework for compiling biological interactions and analyzing networks

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Speaker: Javier García-García, GRIB (UPF- IMIM)

Monday, 5th April, 2010, Tue, Apr 6, 2010 3:00 PM

Integration of biological annotations and networks using Cytoscape (hands on tutorial)

Cytoscape is a widely used open-source software for visualization and analysis of networks. There is a wide range of plugins available facilitating the analysis of biological networks (protein-protein interaction networks, biological pathways etc). This hands on tutorial will give a short introduction to Cytoscape and will focus on the integration of biological annotations with networks. Requirements: People should bring their laptops with Cytoscape verision 2.6.3 installed. Cytoscape can be downloaded here: http://www.cytoscape.org/download.php?file=cyto263 The slides will be available after the talk. Material needed for the tutorial will be available shortly before the tutorial on http://ibi.imim.es/.

Speaker: Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB)

Room seminar room 2 (470-PRBB)

Tuesday, 2nd March, 2010, Wed, Mar 3, 2010 3:00 PM

A brief introduction to latex for curious non users

Latex is an open source text document markup language broadly used among scientists. We propose a hands on two hours tutorial to show the basics features of this language. Everything you need is just your notebook! If your laptop is mounting linux check that you have the latex compiler and one of the most used editors (kile, texmaker, lyx) If your laptop is a mac you can get everything you need to follow the tutorial here .http://guides.macrumors.com/InstallingLaTeXonaMac. If you are a window user, please send a mail to aledda@imim.es and we will provide you with a live cd.

Speaker: Alice Ledda, Evolutionary Genomics, GRIB

Room PRBB 470

Monday, 1st February, 2010, Tue, Feb 2, 2010 11:00 AM

GEM Hands on

We will continue the GEM tutorial with more practical cases.

Speaker: Paolo Ribeca, CRG

Room Room 473.10 AULA - 4th floor

Wednesday, 27th January, 2010, 11:00

"Using Nasonia and Haploid Genetics to Reveal Evolutionary Genomic Processes of Adaptation and Speciation?"

Speaker: Jack Werren - University of Rochester, NY, US

Room 473.10 - PRBB



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