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Article
Sequence and analysis of rice chromosome 4
Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research1. Here we re...
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Article
Open AccessExistence and global stability of positive periodic solutions of a discrete predator-prey system with delays
We study the existence and global stability of positive periodic solutions of a periodic discrete predator-prey system with delay and Holling type III functional response. By using the continuation theorem of ...
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Article
Open AccessIn silico discovery of human natural antisense transcripts
Several high-throughput searches for ppotential natural antisense transcripts (NATs) have been performed recently, but most of the reports were focused on cis type. A thorough in silico analysis of human transcri...
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Article
Comparative analysis of whole-genome sequences of Streptococcus suis
The outbreak of Streptococcus suis recently in some districts of Sichuan Province in China has caused over 30 deaths and over 200 infections in human beings. In order to study the pathogenicity mechanism and to p...
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Article
Open AccessDiscovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS)
The liver is the largest human internal organ – it is composed of multiple cell types and plays a vital role in fulfilling the body's metabolic needs and maintaining homeostasis. Of these cell types the hepato...
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Article
Siting analyses for water quality sampling in a catchment
Pollution loads discharged from upstream development or human activities significantly degrade the water quality of a reservoir. The design of an appropriate water quality sampling network is therefore importa...
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Article
The contribution of cis-regulatory elements to head-to-head gene pairs’ co-expression pattern
Transcription regulation is one of the most critical pipelines in biological process, in which cis-elements play the role as gene expression regulators. We attempt to deduce the principles underlying the co-expre...
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Article
Open AccessHuman gene expression sensitivity according to large scale meta-analysis
Genes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc....
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Article
Open AccessGEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and a...
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Article
Open AccessRevealing parasite influence in metabolic pathways in Apicomplexa infected patients
As an obligate intracellular parasite, Apicomplexa interacts with the host in the special living environment, competing for energy and nutrients from the host cells by manipulating the host metabolism. Previou...
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Article
Open AccessAssociation of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues
Embryogenesis is the process by which the embryo is formed, develops, and establishes developmental hierarchies of tissues. The recent advance in microarray technology made it possible to investigate the tissu...
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Article
A knowledge-based engineering system for assembly sequence planning
In this study, we developed a knowledge-based engineering (KBE) system to assist engineers in promptly predicting a near-optimal assembly sequence. A three-stage assembly optimization approach with some heuris...
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Article
Development of genetically engineered CD4+ and CD8+ T cells expressing TCRs specific for a M. tuberculosis 38-kDa antigen
Cell-mediated immunity is critical to the clearance of Mycobacterium tuberculosis due to the primarily intracellular niche of this pathogen. Adoptive transfer of M. tuberculosis-specific effector T cells has been...
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Article
The role of ABC efflux pump, Rv1456c-Rv1457c-Rv1458c, from Mycobacterium tuberculosis clinical isolates in China
Recently the ATP-binding cassette (ABC) efflux pumps have been proved to be a major component of drug resistance in Mycobacterium tuberculosis. The objective of this study was to investigate the expression profil...
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Article
Open AccessOptimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an import...
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Article
Optimization models for siting water quality monitoring stations in a catchment
A water quality monitoring network (WQMN) must be designed so as to adequately protect the water quality in a catchment. Although a simulated annealing (SA) method was previously applied to design a WQMN, the ...
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Article
Open AccessAn efficient cluster-based power saving scheme for wireless sensor networks
In this article, efficient power saving scheme and corresponding algorithm must be developed and designed in order to provide reasonable energy consumption and to improve the network lifetime for wireless sens...
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Article
Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations
Human coagulation Factor X (FX), a member of the vitamin K-dependent serine protease family, is a crucial component of the human coagulation cascade. Activated FX (FXa) participates in forming the prothrombina...
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Article
In silico analysis of amino acid biosynthesis and proteolysis in Lactobacillus delbrueckii subsp. bulgaricus 2038 and the implications for bovine milk fermentation
The amino acid biosynthesis pathway and proteolytic system of Lactobacillus delbrueckii subsp. bulgaricus 2038 (L. bulgaricus 2038), a mainstay of large-scale yogurt production, were modeled based on its genomic ...
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Article
Open AccessA comparative analysis of tissue gene expression data from high-throughput studies
High-throughput technologies were employed over the past decade to study the expression profiles of cells and tissues. There are large collections of accumulated data from public databases and numerous researc...
