DNA Microarray Data Analysis: A New Survey on Biclustering

There are subsets of genes that have similar behavior under subsets of conditions, so we say that they coexpress, but behave independently under other subsets of conditions. Discovering such coexpressions can be helpful to uncover genomic knowledge such as gene networks or gene interactions. That is why, it is of utmost importance to make a simultaneous clustering of genes and conditions to identify clusters of genes that are coexpressed under clusters of conditions. This type of clustering is called biclustering.Biclustering is an NP-hard problem. Consequently, heuristic algorithms are typically used to approximate this problem by finding suboptimal solutions. In this paper, we make a new survey on biclustering of gene expression data, also called microarray data

Block Mixture Model for the Biclustering of Microarray Data

This publication is a representation of what appears in the IEEE Digital Libraries.International audienceAn attractive way to make biclustering of genes and conditions is to adopt a Block Mixture Model (BMM). Approaches based on a BMM operate thanks to a Block Expectation Maximization (BEM) algorithm and/or a Block Classification Expectation Maximization (BCEM) one. The drawback of these approaches is their difficulty to choose a good strategy of initialization of the BEM and BCEM algorithms. This paper introduces existing biclustering approaches adopting a BMM and suggests a new fuzzy biclustering one. Our approach enables to choose a good strategy of initialization of the BEM and BCEM algorithms

Motif Discovery in Protein Sequences

Biology has become a data‐intensive research field. Coping with the flood of data from the new genome sequencing technologies is a major area of research. The exponential increase in the size of the datasets produced by “next‐generation sequencing” (NGS) poses unique computational challenges. In this context, motif discovery tools are widely used to identify important patterns in the sequences produced. Biological sequence motifs are defined as short, usually fixed length, sequence patterns that may represent important structural or functional features in nucleic acid and protein sequences such as transcription binding sites, splice junctions, active sites, or interaction interfaces. They can occur in an exact or approximate form within a family or a subfamily of sequences. Motif discovery is therefore an important field in bioinformatics, and numerous methods have been developed for the identification of motifs shared by a set of functionally related sequences. This chapter will review the existing motif discovery methods for protein sequences and their ability to discover biologically important features as well as their limitations for the discovery of new motifs. Finally, we will propose new horizons for motif discovery in order to address the short comings of the existent methods

Arabic Handwritten Words Off-line Recognition based on HMMs and DBNs

International audienceIn this work, we investigate the combination of PGM (Propabilistic Graphical Models) classifiers, either independent or coupled, for the recognition of Arabic handwritten words. The independent classifiers are vertical and horizontal HMMs (Hidden Markov Models) whose observable outputs are features extracted from the image columns and the image rows respectively. The coupled classifiers associate the vertical and horizontal observation streams into a single DBN (Dynamic Bayesian Network). A novel method to extract word baseline and a simple and easily extractable features to construct feature vectors for words in the vocabulary are proposed. Some of these features are statistical, based on pixel distributions and local pixel configurations. Others are structural, based on the presence of ascenders, descenders, loops and diacritic points. Experiments on handwritten Arabic words from IFN/ENIT strongly support the feasibility of the proposed approach. The recognition rates achieve 90.42% with vertical and horizontal HMM, 85.03% and 85.21% with respectively a first and a second DBN which outperform results of some works based on PGMs

A biclustering algorithm based on a Bicluster Enumeration Tree: application to DNA microarray data

<p>Abstract</p> <p>Background</p> <p>In a number of domains, like in DNA microarray data analysis, we need to cluster simultaneously rows (genes) and columns (conditions) of a data matrix to identify groups of rows coherent with groups of columns. This kind of clustering is called <it>biclustering</it>. Biclustering algorithms are extensively used in DNA microarray data analysis. More effective biclustering algorithms are highly desirable and needed.</p> <p>Methods</p> <p>We introduce <it>BiMine</it>, a new enumeration algorithm for biclustering of DNA microarray data. The proposed algorithm is based on three original features. First, <it>BiMine </it>relies on a new evaluation function called <it>Average Spearman's rho </it>(ASR). Second, <it>BiMine </it>uses a new tree structure, called <it>Bicluster Enumeration Tree </it>(BET), to represent the different biclusters discovered during the enumeration process. Third, to avoid the combinatorial explosion of the search tree, <it>BiMine </it>introduces a parametric rule that allows the enumeration process to cut tree branches that cannot lead to good biclusters.</p> <p>Results</p> <p>The performance of the proposed algorithm is assessed using both synthetic and real DNA microarray data. The experimental results show that <it>BiMine </it>competes well with several other biclustering methods. Moreover, we test the biological significance using a gene annotation web-tool to show that our proposed method is able to produce biologically relevant biclusters. The software is available upon request from the authors to academic users.</p

Design of Self-Tuning Regulator for Large-Scale Interconnected Hammerstein Systems

This paper deals with the self-tuning regulator for large-scale stochastic nonlinear systems, which are composed of several interconnected nonlinear monovariable subsystems. Each interconnected subsystem is described by discrete Hammerstein model with unknown and time-varying parameters. This self-tuning control is developed on the basis of the minimum variance approach and is combined by a recursive algorithm in the estimation step. The parametric estimation step is performed on the basis of the prediction error method and the least-squares techniques. Simulation results of the proposed self-tuning regulator for two interconnected nonlinear hydraulic systems show the reliability and effectiveness of the developed method

Generations of Sequencing Technologies: From First to Next Generation

DNA sequencing process utilizes biochemical methods in order to determine the correct order of nucleotide bases in a DNA macromolecule using sequencing machines. Ten years ago, sequencing was based on a single type of sequencing that is Sanger sequencing. In 2005, Next Generation Sequencing Technologies emerged and changed the view of the analysis and understanding of living beings. Over the last decade, considerable progress has been made on new sequencing machines. In this paper, we present a non-exhaustive overview of the sequencing technologies by beginning with the first methods history used by the commonly used NGS platforms until today. Our goal is to provide beginners in the field as well as to the amateurs of science a simple and understandable description of NGS technologies in order to provide them with basic knowledge as an initiation into this field in full ardor