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MOTIVATION Inferring a gene regulatory network exclusively from microarray expression profiles is a difficult but important task. The aim of this work is to compare the predictive power of some of the most popular algorithms in different conditions (like data taken at equilibrium or time courses) and on both synthetic and real microarray data. We are in(More)
BACKGROUND Reverse-engineering gene networks from expression profiles is a difficult problem for which a multitude of techniques have been developed over the last decade. The yearly organized DREAM challenges allow for a fair evaluation and unbiased comparison of these methods. RESULTS We propose an inference algorithm that combines confidence matrices,(More)
UNLABELLED End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of(More)
BACKGROUND In the past years devising methods for discovering gene regulatory mechanisms at a genome-wide level has become a fundamental topic in the field of systems biology. The aim is to infer gene-gene interactions in an increasingly sophisticated and reliable way through the continuous improvement of reverse engineering algorithms exploiting microarray(More)
SUMMARY SysGenSIM is a software package to simulate Systems Genetics (SG) experiments in model organisms, for the purpose of evaluating and comparing statistical and computational methods and their implementations for analyses of SG data [e.g. methods for expression quantitative trait loci (eQTL) mapping and network inference]. SysGenSIM allows the user to(More)
SUMMARY BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets(More)
BACKGROUND In yeast, genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short (approx. 40 min) and long (approx. 300 min) periods. RESULTS The dynamical regulation due to mRNA stability is found to be an important aspect of the genome-wide coordination of the long-period yeast metabolic cycle. It(More)
BACKGROUND The concept of reverse engineering a gene network, i.e., of inferring a genome-wide graph of putative gene-gene interactions from compendia of high throughput microarray data has been extensively used in the last few years to deduce/integrate/validate various types of "physical" networks of interactions among genes or gene products. RESULTS(More)
In this work we present a strategy to integrate Hadoop-based applications into the Galaxy platform along with an extensible implementation of this adapter and related utilities. The strategy is based on the idea of introducing a new Galaxy datatype that provides a layer of indirection, thus relaxing the requirement to place data on a Galaxy-accessible file(More)