Guide de lutilisation pédagogique des médias sociaux

Titre de l'écran-titre (visionné le 24 jan. 2013)Cette publication est mise à disposition selon les termes de la licence "Créative Commons". Vous êtes libres de l'utiliser, en tout ou en partie en citant l'auteur, vous ne pouvez pas l'utiliser pour un usage commercial et vous n'êtes pas autorisés à la modifier

Structure determination of mycoplasma pneumoniae genome

Des de l’aparició de les tecnologies de seqüenciació d’alt rendiment, els conjunts de dades biològiques han esdevingut cada cop més grans i complexes, la qual cosa els fa pràcticament impossibles d’interpretar manualment. El paradigma de l’aprenentatge automàtic permet fer una anàlisi sistemàtica de les relacions i patrons existents en els conjuts de dades, tot aprofitant l’enorme volum de dades disponibles. No obstant això, una aplicació poc curosa dels principis bàsics de l’aprenentatge automàtic pot conduir a estimacions massa optimistes, un problema prevalent conegut com a sobreajust. En el camp del plegament de proteïnes, en vam trobar exemples en models publicats que afirmaven tenir un alt poder predictiu, però que es comportaven de forma mediocre devant de dades noves. En el camp de l’epigenètica, problemes com la falta de reproducibilitat, qualitat heterogènia i conflictes entre replicats esdevenen evidents quan es comparen diferents conjunts de dades de ChIP-seq. Per superar aquestes limitacions vam desenvolupar Zerone, un discretitzador de ChIP-seq basat en aprenentatge automàtic que és capaç de combinar informació de diferents replicats experimentals i d’identificar automàticament dades de baixa qualitat o irreproduïbles.Since the appearance of high throughput sequencing technologies, biological data sets have become increasingly large and complex, which renders them practically impossible to interpret directly by a human. The machine learning paradigm allows a systematic analysis of relationships and patterns within data sets, making possible to extract information by leveraging the sheer amount of data available. However, violations of basic machine learning principles may lead to overly optimistic estimates, a prevalent problem known as overfitting. In the field of protein folding, we found examples of this in published models that claimed high predictive power, but that performed poorly on new data. A different problem arises in epigenetics. Issues such as lack of reproducibility, heterogeneous quality and conflicts between replicates become evident when comparing ChIP-seq data sets. To overcome this limitations we developed Zerone, a machine learning-based ChIP-seq discretizer capable of merging information from several experimental replicates and automatically identifying low quality or irreproducible data

Guide de l'utilisation pédagogique des médias sociaux

Ce guide s’adresse aux enseignants, aux conseillers pédagogiques et à toute personne s’intéressant à l’intégration des médias socionumériques dans les activités d’enseignement et d’apprentissage. Il a pour objectif principal de soutenir les enseignants dans l’utilisation pédagogique des médias socionumériques. Il contient quatre sections portant sur différents aspects de l’intégration de ces outils dans la pratique enseignante

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.The research leading to these results was funded by the European Union Seventh Framework Programme (FP7/2007-2013 to L.S.), through the European Research Council, under grant agreement 232913 to L.S. and 609989 to M.A.M-R., the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 634942 to L.S, the Fundación Botín to L.S., the Spanish Ministry of Economy and Competitiveness (BIO2007-61762 to L.S. and BFU2013-47736-P to M.A.M.-R., the National Plan of R+D+i, the ISCIII-Subdirección General de Evaluación y Fomento de la Investigación- (PI10/01702 to L.S.), the Human Frontiers Science Program (RGP0044 to M.A.M.-R.), the ERASynBio/MINECO Grant PCIN-2015-125 to L.S, and the European Regional Development Fund (ERDF) to L.S. We acknowledge support from the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013-2017' (SEV-2012-0208). We acknowledge the support of the CERCA Programme / Generalitat de Catalunya

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

Restraint-based modeling of genomes has been recently explored with the advent of Chromosome Conformation Capture (3C-based) experiments. We previously developed a reconstruction method to resolve the 3D architecture of both prokaryotic and eukaryotic genomes using 3C-based data. These models were congruent with fluorescent imaging validation. However, the limits of such methods have not systematically been assessed. Here we propose the first evaluation of a mean-field restraint-based reconstruction of genomes by considering diverse chromosome architectures and different levels of data noise and structural variability. The results show that: first, current scoring functions for 3D reconstruction correlate with the accuracy of the models; second, reconstructed models are robust to noise but sensitive to structural variability; third, the local structure organization of genomes, such as Topologically Associating Domains, results in more accurate models; fourth, to a certain extent, the models capture the intrinsic structural variability in the input matrices and fifth, the accuracy of the models can be a priori predicted by analyzing the properties of the interaction matrices. In summary, our work provides a systematic analysis of the limitations of a mean-field restrain-based method, which could be taken into consideration in further development of methods as well as their applications.Spanish Ministerio de Economía y Competitividad [BFU2010–19310, BFU2013–47736-P to M.A.M.-R., BIO2007–61762 to L.S.]; European Research Council [609989 to M.A.M.-R., 232913 to L.S.]; Human Frontiers Science Program [RGP0044 to M.A.M.-R.]; Spanish Instituto de Salud Carlos III [PI10/01702 to L.S.]; Fundación Marcelino Botin (to L.S.). Funding for open access charge: ERC Synergy [609989]