A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy.

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names.

PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping.

With the decline in the cost of whole-genome sequencing because of the introduction of next-generation sequencing (NGS) techniques, many public health and clinical laboratories have started to use bacterial whole genomes for epidemiological surveillance and clinical investigation. For epidemiological and clinical purposes in this "NGS era," whole-genome-scale single nucleotide polymorphism (wgSNP) analysis for genotyping is considered suitable. In this paper, we present an online service, PathoBacTyper (http://halst.

Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation.

Background: During the last few years, the knowledge of drug, disease phenotype and protein has been rapidly accumulated and more and more scientists have been drawn the attention to inferring drug-disease associations by computational method. Development of an integrated approach for systematic discovering drug-disease associations by those informational data is an important issue.

Methods: We combine three different networks of drug, genomic and disease phenotype and assign the weights to the edges from available experimental data and knowledge.

An ensemble rank learning approach for gene prioritization.

Several different computational approaches have been developed to solve the gene prioritization problem. We intend to use the ensemble boosting learning techniques to combine variant computational approaches for gene prioritization in order to improve the overall performance. In particular we add a heuristic weighting function to the Rankboost algorithm according to: 1) the absolute ranks generated by the adopted methods for a certain gene, and 2) the ranking relationship between all gene-pairs from each prioritization result.

iADRs: towards online adverse drug reaction analysis.

Adverse Drug Reaction (ADR) is one of the most important issues in the assessment of drug safety. In fact, many adverse drug reactions are not discovered during limited pre-marketing clinical trials; instead, they are only observed after long term post-marketing surveillance of drug usage. In light of this, the detection of adverse drug reactions, as early as possible, is an important topic of research for the pharmaceutical industry.

A brief survey on computational approaches to reveal drug and disease associations.

People worldwide are still threatened by various complex disease phenotypes, especially cancer which is usually caused by the accumulation of multi-factor-driven alterations. Although drugs achieve the therapeutic functions by targeting particular molecular, the therapies used nowadays against diseases are not effective enough due to the limitation of the knowledge about the drug-disease associations. The rapid increasing of the available experimental data and knowledge enable scientists to reveal drug-disease associations by the systematic integration and analysis.

Biomarker identification for prostate cancer and lymph node metastasis from microarray data and protein interaction network using gene prioritization method.

Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF).

Pathway detection from protein interaction networks and gene expression data using color-coding methods and A∗ search algorithms.

With the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topology and applied heuristic search to speed up color-coding method. In the experiments, we tested our methods by applying to two datasets: yeast and human prostate cancer networks and gene expression data set.

Identifying co-targets to fight drug resistance based on a random walk model.

Background: Drug resistance has now posed more severe and emergent threats to human health and infectious disease treatment. However, wet-lab approaches alone to counter drug resistance have so far still achieved limited success due to less knowledge about the underlying mechanisms of drug resistance. Our approach apply a heuristic search algorithm in order to extract active network under drug treatment and use a random walk model to identify potential co-targets for effective antibacterial drugs.

A network flow approach to predict drug targets from microarray data, disease genes and interactome network - case study on prostate cancer.

Background: Systematic approach for drug discovery is an emerging discipline in systems biology research area. It aims at integrating interaction data and experimental data to elucidate diseases and also raises new issues in drug discovery for cancer treatment. However, drug target discovery is still at a trial-and-error experimental stage and it is a challenging task to develop a prediction model that can systematically detect possible drug targets to deal with complex diseases.

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.

Background: Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear.

Analysis of adverse drug reactions using drug and drug target interactions and graph-based methods.

Objective: The purpose of this study was to integrate knowledge about drugs, drug targets, and topological methods. The goals were to build a system facilitating the study of adverse drug events, to make it easier to find possible explanations, and to group similar drug-drug interaction cases in the adverse drug reaction reports from the US Food and Drug Administration (FDA).

Methods: We developed a system that analyses adverse drug reaction (ADR) cases reported by the FDA.