SVGMapping: an R package to map omic data sets onto pathways templates

SVGMapping: an R package to map omic data sets onto pathways template

Genome-wide transcriptome analysis of hydrogen production in the cyanobacterium Synechocystis: Towards the identification of new players

International audienceWe report the development of new tools and methods for facile integration and meaningful representation of high throughput data generated by genome-wide analyses of the model cyanobacterium Synechocystis PCC6803, for future genetic engineering aiming at increasing its level of hydrogen photoproduction. These robust tools comprise new oligonucleotide DNA microarrays to monitor the transcriptomic responses of all 3725 genes of Synechocystis, and the SVGMapping method and custom-made templates to represent the metabolic reprogramming for improved hydrogen production. We show, for the first time, that the AbrB2 repressor of the hydrogenase-encoding operon, also regulates metal transport and protection against oxidative stress, as well as numerous plasmid genes, which have been overlooked so far. This report will stimulate the construction and global analysis of hydrogen production mutants with the prospect of developing powerful cell factories for the sustainable production of hydrogen, as well as investigations of the probable role of plasmids in this process

BIS2Analyzer: a server for co-evolution analysis of conserved protein families

International audienceAlong protein sequences, co-evolution analysis identifies residue pairs demonstrating either a specific co-adaptation, where changes in one of the residues are compensated by changes in the other during evolution or a less specific external force that affects the evolutionary rates of both residues in a similar magnitude. In both cases, independently of the underlying cause, co-evolutionary signatures within or between proteins serve as markers of physical interactions and/or functional relationships. Depending on the type of protein under study, the set of available homologous sequences may greatly differ in size and amino acid variability. BIS2Analyzer, openly accessible at http://www.lcqb.upmc.fr/BIS2Analyzer/, is a web server providing the online analysis of co-evolving amino-acid pairs in protein alignments, especially designed for vertebrate and viral protein families, which typically display a small number of highly similar sequences. It is based on BIS2, a re-implemented fast version of the co-evolution analysis tool Blocks in Sequences (BIS). BIS2Analyzer provides a rich and interactive graphical interface to ease biological interpretation of the results

Analysing Institutions Interdisciplinarity by Extensive Use of Rao-Stirling Diversity Index

<div><p>This paper shows how the Rao-Stirling diversity index may be extensively used for positioning and comparing institutions interdisciplinary practices. Two decompositions of this index make it possible to explore different components of the diversity of the cited references in a corpus of publications. The paper aims at demonstrating how these bibliometric tools can be used for comparing institutions in a research field by highlighting collaboration orientations and institutions strategies. To make the method available and easy to use for indicator users, this paper first recalls a previous result on the decomposition of the Rao-Stirling index into multidisciplinarity and interdisciplinarity components, then proposes a new decomposition to further explore the profile of research collaborations and finally presents an application to Neuroscience research in French universities.</p></div

Number of publications with identified research units for Aix-Marseille, Strasbourg and Paris 7 Universities.

<p>Number of publications with identified research units for Aix-Marseille, Strasbourg and Paris 7 Universities.</p

Contributions of categories to the overall interdisciplinarity indicator for Aix-Marseille, Strasbourg and Paris 7 universities.

<p>Contributions of categories to the overall interdisciplinarity indicator for Aix-Marseille, Strasbourg and Paris 7 universities.</p

Article interdisciplinarity index <i>STa</i> and number of citations in a 3 year window for Aix-Marseille, Strasbourg and Paris 7 Universities.

<p>Displayed articles are in the top 20% percentile of the most cited publications. A polynomial curve with degree 3 is fitted for each university.</p

Statistics for the comparison of universities interdisciplinarity indicators.

<p>Statistics for the comparison of universities interdisciplinarity indicators.</p