BiMine+: An efficient algorithm for discovering relevant biclusters of DNA microarray data

Biclustering is a very useful tool for analyzing microarray data. It aims to identify maximal groups of genes which are coherent with maximal groups of conditions. In this paper, we propose a biclustering algorithm, called BiMine+, which is able to detect significant biclusters from gene expression data. The proposed algorithm is based on two original features. First, BiMine+ is based on the use of a new tree structure, called Modified Bicluster Enumeration Tree (MBET), on which biclusters are represented by the profile shapes of genes. Second, BiMine+ uses a pruning rule to avoid both trivial biclusters and combinatorial explosion of the search tree. The performance of BiMine+ is assessed on both synthetic and real DNA microarray datasets. Experimental results show that BiMine+ competes favorably with several state-of-the-art biclustering algorithms and is able to extract functionally enriched and biologically relevant biclusters

Pattern-driven neighborhood search for biclustering of microarray data

Biclustering aims at finding subgroups of genes that show highly correlated behaviors across a subgroup of conditions. Biclustering is a very useful tool for mining microarray data and has various practical applications. From a computational point of view, biclustering is a highly combinatorial search problem and can be solved with optimization methods

BicFinder: a biclustering algorithm for microarray data analysis

In the context of microarray data analysis, biclustering allows the simultaneous identification of a maximum group of genes that show highly correlated expression patterns through a maximum group of experimental conditions (samples). This paper introduces a heuristic algorithm called BicFinder (The BicFinder software is available at: http://www.info.univ-angers.fr/pub/hao/BicFinder.html) for extracting biclusters from microarray data. BicFinder relies on a new evaluation function called Average Correspondence Similarity Index (ACSI) to assess the coherence of a given bicluster and utilizes a directed acyclic graph to construct its biclusters. The performance of BicFinder is evaluated on synthetic and three DNA microarray datasets. We test the biological significance using a gene annotation web-tool to show that our proposed algorithm is able to produce biologically relevant biclusters. Experimental results show that BicFinder is able to identify coherent and overlapping biclusters

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.This work was supported by the projects CGL2012-39627-C03-01 and 02 of the Spanish Ministry of Economy and Competitiveness, which were also co-financed with FEDER support from the European Union. TG group research is funded in part by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161), a grant from the Qatar National Research Fund grant (NPRP 5-298-3-086) and a grant from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC (grant agreement no. ERC-2012-StG-310325)

FEA-Assisted steady-state modelling of a spoke type IPM machine with enhanced flux weakening capability

Interior permanent magnet (IPM) machines with spoke-type design are possible candidates for various applications, including vehicle traction. One of their drawback is the high demagnetizing current required in the flux weakening region to let the motor achieve high speeds. This problem can be mitigated by equipping the motor with a mechanical devices consisting of mobile rotor yokes. These move radially by centrifugal force so as to reduce the air-gap flux at high speed with no need for demagnetizing current injection. This paper addresses the problem of modeling such IPM motor to study its steady-state behavior under different operating conditions, both in the full-flux and in the flux-weakening region of the speed range. The approach uses a limited set of non-linear finite element analysis to characterize the dependency of motor flux linkages on the stator currents and rotor position. Interpolating functions are then obtained to mathematically capture this dependency and plug it into the steady-state electromechanical equations of the motor. The effectiveness and accuracy of the method are assessed through on-load measurements taken on the modelled motor both in low and high speed operation

Recovery, assessment, and molecular characterization of minor olive genotypes in Tunisia

Olive is one of the oldest cultivated species in the Mediterranean Basin, including Tunisia, where it has a wide diversity, with more than 200 cultivars, of both wild and feral forms. Many minor cultivars are still present in marginal areas of Tunisia, where they are maintained by farmers in small local groves, but they are poorly characterized and evaluated. In order to recover this neglected germplasm, surveys were conducted in different areas, and 31 genotypes were collected, molecularly characterized with 12 nuclear microsatellite (simple sequence repeat (SSR)) markers, and compared with 26 reference cultivars present in the Tunisian National Olive collection. The analysis revealed an overall high genetic diversity of this olive’s germplasm, but also discovered the presence of synonymies and homonymies among the commercialized varieties. The structure analysis showed the presence of different gene pools in the analyzed germplasm. In particular, the marginal germplasm from Ras Jbal and Azmour is characterized by gene pools not present in commercial (Nurseries) varieties, pointing out the very narrow genetic base of the commercialized olive material in Tunisia, and the need to broaden it to avoid the risk of genetic erosion of this species in this country