Study of meta-analysis strategies for network inference using information-theoretic approaches

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Reverse engineering of gene regulatory networks (GRNs) from gene expression data is a classical challenge in systems biology. Thanks to high-throughput technologies, a massive amount of gene-expression data has been accumulated in the public repositories. Modelling GRNs from multiple experiments (also called integrative analysis) has; therefore, naturally become a standard procedure in modern computational biology. Indeed, such analysis is usually more robust than the traditional approaches focused on individual datasets, which typically suffer from some experimental bias and a small number of samples. To date, there are mainly two strategies for the problem of interest: the first one (”data merging”) merges all datasets together and then infers a GRN whereas the other (”networks ensemble”) infers GRNs from every dataset separately and then aggregates them using some ensemble rules (such as ranksum or weightsum). Unfortunately, a thorough comparison of these two approaches is lacking. In this paper, we evaluate the performances of various metaanalysis approaches mentioned above with a systematic set of experiments based on in silico benchmarks. Furthermore, we present a new meta-analysis approach for inferring GRNs from multiple studies. Our proposed approach, adapted to methods based on pairwise measures such as correlation or mutual information, consists of two steps: aggregating matrices of the pairwise measures from every dataset followed by extracting the network from the meta-matrix.Peer ReviewedPostprint (author's final draft

A Lightweight IoT Security Protocol

International audienceThe IoT is a technology that enables the inter-connection of smart physical and virtual objects and provides advanced services. Objects or things are generally constrained devices which are limited by their energy, computing and storage capacity. A Wireless Sensor Networks (WSN) is a network composed of devices managed by a CPAN (Personal Area Network Coordinator). The network is used in order to gather and process data of a given environment. It is characterized by their low bit rate and low power consumption, and it uses small size packet in their transmissions. In order to protect the WSN, a mutual authentication between devices is required during the association of a new device. The exchanged data should be authenticated and encrypted. In this work we propose a robust, lightweight and energy-efficient security protocol for the WSN systems. The real tests we made and a performance evaluation of our security protocol are provided

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference

Background: In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. Results: Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. Conclusions: The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.Peer ReviewedPostprint (published version

Rifaximin Reduces Markers of Inflammation and Bacterial 16S rRNA in Zambian Adults with Hepatosplenic Schistosomiasis: A Randomized Control Trial

We thank the Wellcome Trust through the Southern Africa Consortium for Research Excellence for funding this study (WT087537MA)

Achievements of Hinode in the first eleven years

Hinode is Japan’s third solar mission following Hinotori (1981–1982) and Yohkoh (1991–2001): it was launched on 2006 September 22 and is in operation currently. Hinode carries three instruments: the Solar Optical Telescope, the X-Ray Telescope, and the EUV Imaging Spectrometer. These instruments were built under international collaboration with the National Aeronautics and Space Administration and the UK Science and Technology Facilities Council, and its operation has been contributed to by the European Space Agency and the Norwegian Space Center. After describing the satellite operations and giving a performance evaluation of the three instruments, reviews are presented on major scientific discoveries by Hinode in the first eleven years (one solar cycle long) of its operation. This review article concludes with future prospects for solar physics research based on the achievements of Hinode

Achievements of Hinode in the first eleven years

Hinode is Japan’s third solar mission following Hinotori (1981–1982) and Yohkoh (1991–2001): it was launched on 2006 September 22 and is in operation currently. Hinode carries three instruments: the Solar Optical Telescope, the X-Ray Telescope, and the EUV Imaging Spectrometer. These instruments were built under international collaboration with the National Aeronautics and Space Administration and the UK Science and Technology Facilities Council, and its operation has been contributed to by the European Space Agency and the Norwegian Space Center. After describing the satellite operations and giving a performance evaluation of the three instruments, reviews are presented on major scientific discoveries by Hinode in the first eleven years (one solar cycle long) of its operation. This review article concludes with future prospects for solar physics research based on the achievements of Hinode