Pompeu Fabra University is a university in Barcelona, Catalonia, Spain. Founded in 1990, it is named after the Catalan philologist Pompeu Fabra. Currently , the University offers 22 undergraduate degrees, 25 official masters, and 9 PhD programs, as well as around 100 UPF masters. It is currently the only Spanish university to figure in the Times Higher Education top 200 ranking at position 164. Wikipedia.
Di Croce L.,University Pompeu Fabra |
Di Croce L.,Catalan Institution for Research and Advanced Studies |
Helin K.,Copenhagen University
Nature Structural and Molecular Biology | Year: 2013
Polycomb group (PcG) proteins are epigenetic regulators of transcription that have key roles in stem-cell identity, differentiation and disease. Mechanistically, they function within multiprotein complexes, called Polycomb repressive complexes (PRCs), which modify histones (and other proteins) and silence target genes. The dynamics of PRC1 and PRC2 components has been the focus of recent research. Here we discuss our current knowledge of the PRC complexes, how they are targeted to chromatin and how the high diversity of the PcG proteins allows these complexes to influence cell identity. © 2013 Nature America, Inc. All rights reserved.
Lehner B.,University Pompeu Fabra
Trends in Genetics | Year: 2011
'Disease-causing' mutations do not cause disease in all individuals. One possible important reason for this is that the outcome of a mutation can depend upon other genetic variants in a genome. These epistatic interactions between mutations occur both within and between molecules, and studies in model organisms show that they are extremely prevalent. However, epistatic interactions are still poorly understood at the molecular level, and consequently difficult to predict de novo. Here I provide an overview of our current understanding of the molecular mechanisms that can cause epistasis, and areas where more research is needed. A more complete understanding of epistasis will be vital for making accurate predictions about the phenotypes of individuals. © 2011 Elsevier Ltd.
Furlong L.I.,University Pompeu Fabra
Trends in Genetics | Year: 2013
One of the challenges raised by next generation sequencing (NGS) is the identification of clinically relevant mutations among all the genetic variation found in an individual. Network biology has emerged as an integrative and systems-level approach for the interpretation of genome data in the context of health and disease. Network biology can provide insightful models for genetic phenomena such as penetrance, epistasis, and modes of inheritance, all of which are integral aspects of Mendelian and complex diseases. Moreover, it can shed light on disease mechanisms via the identification of modules perturbed in those diseases. Current challenges include understanding disease as a result of the interplay between environmental and genetic perturbations and assessing the impact of personal sequence variations in the context of networks. Full realization of the potential of personal genomics will benefit from network biology approaches that aim to uncover the mechanisms underlying disease pathogenesis, identify new biomarkers, and guide personalized therapeutic interventions. © 2012 Elsevier Ltd.
Gabaldon T.,University Pompeu Fabra |
Koonin E.V.,U.S. National Center for Biotechnology Information
Nature Reviews Genetics | Year: 2013
Orthologues and paralogues are types of homologous genes that are related by speciation or duplication, respectively. Orthologous genes are generally assumed to retain equivalent functions in different organisms and to share other key properties. Several recent comparative genomic studies have focused on testing these expectations. Here we discuss the complexity of the evolution of gene-phenotype relationships and assess the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles. © 2013 Macmillan Publishers Limited. All rights reserved.
Pazo D.,University of Cantabria |
Montbrio E.,University Pompeu Fabra
Physical Review X | Year: 2014
Large communities of biological oscillators show a prevalent tendency to self-organize in time. This cooperative phenomenon inspired Winfree to formulate a mathematical model that originated the theory of macroscopic synchronization. Despite its fundamental importance, a complete mathematical analysis of the model proposed by Winfree-consisting of a large population of all-to-all pulse-coupled oscillators-is still missing. Here, we show that the dynamics of the Winfree model evolves into the so-called Ott- Antonsen manifold. This important property allows for an exact description of this high-dimensional system in terms of a few macroscopic variables, and also allows for the full investigation of its dynamics. We find that brief pulses are capable of synchronizing heterogeneous ensembles that fail to synchronize with broad pulses, especially for certain phase-response curves. Finally, to further illustrate the potential of our results, we investigate the possibility of "chimera" states in populations of identical pulse-coupled oscillators. Chimeras are self-organized states in which the symmetry of a population is broken into a synchronous and an asynchronous part. Here, we derive three ordinary differential equations describing two coupled populations and uncover a variety of chimera states, including a new class with chaotic dynamics.