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Article
Open AccessApplication of deep learning to predict the low serum albumin in new hemodialysis patients
Serum albumin level is a crucial nutritional indicator for patients on dialysis. Approximately one-third of patients on hemodialysis (HD) have protein malnutrition. Therefore, the serum albumin level of patien...
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Chapter and Conference Paper
Improved Classification Method for Detecting Potential Interactions Between Genes
Multifactor dimensionality reduction (MDR) constitutes a highly accurate classification algorithm for gene–gene interaction (GGI) identification. GGI detection quality is commonly assessed using the correct cl...
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Chapter and Conference Paper
An Improved Multi-factor Dimensionality Reduction Approach to Identify Gene-Gene Interactions
Genetic component of disease risk can be determined by gene–gene interactions. Multifactor dimensionality reduction (MDR) has widely used to identify gene–gene interactions based on the binary classification i...
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Article
Open AccessProtein folding prediction in the HP model using ions motion optimization with a greedy algorithm
The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction ...
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Article
Open AccessCumulative receiver operating characteristics for analyzing interaction between tissue visfatin and clinicopathologic factors in breast cancer progression
Visfatin has been reported to be associated with breast cancer progression, but the interaction between the visfatin and clinicopathologic factors in breast cancer progression status requires further investiga...
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Article
Open AccessPublisher Correction: Multiobjective differential evolution-based multifactor dimensionality reduction for detecting gene–gene interactions
A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
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Article
Open AccessMultiobjective differential evolution-based multifactor dimensionality reduction for detecting gene–gene interactions
Epistasis within disease-related genes (gene–gene interactions) was determined through contingency table measures based on multifactor dimensionality reduction (MDR) using single-nucleotide polymorphisms (SNPs...
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Article
Open AccessAn efficiency analysis of high-order combinations of gene–gene interactions using multifactor-dimensionality reduction
Multifactor dimensionality reduction (MDR) is widely used to analyze interactions of genes to determine the complex relationship between diseases and polymorphisms in humans. However, the astronomical number o...
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Article
Open AccessIdentification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm
Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP perform...
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Article
Open AccessIdentifying association model for single-nucleotide polymorphisms of ORAI1 gene for breast cancer
ORAI1 channels play an important role for breast cancer progression and metastasis. Previous studies indicated the strong correlation between breast cancer and individual single nucleotide polymorphisms (SNPs) of...
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Article
Specific primer design for the polymerase chain reaction
The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and charac...
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Article
Particle swarm optimization algorithm for analyzing SNP–SNP interaction of renin-angiotensin system genes against hypertension
Most non-significant individual single nucleotide polymorphisms (SNPs) were undiscovered in hypertension association studies. Their possible SNP–SNP interactions were usually ignored and leaded to missing heri...
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Article
Open AccessImproved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer
Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case–control studies is an impo...
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Article
Open AccessAnti-proliferative effect of methanolic extract of Gracilaria tenuistipitata on oral cancer cells involves apoptosis, DNA damage, and oxidative stress
Methanolic extracts of Gracilaria tenuistipitata (MEGT) were obtained from the edible red algae. Previously, we found that water extract of G. tenuistipitata was able to modulate oxidative stress-induced DNA dama...
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Article
Open AccessURPD: a specific product primer design tool
Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzin...
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Article
Open AccessCpGPAP: CpG island predictor analysis platform
Genomic islands play an important role in medical, methylation and biological studies. To explore the region, we propose a CpG islands prediction analysis platform for genome sequence exploration (CpGPAP).
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Protocol
A Combined Bisulfite Restriction Analysis Bioinformatics Tool: Methyl-Ty**
In this chapter, we introduce our developed freeware tool Methyl-Ty**. It provides methylation-related bioinformatics with a special focus on combined bisulfite restriction analysis (COBRA). We give an overv...
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Article
Open AccessConfronting two-pair primer design for enzyme-free SNP genoty** based on a genetic algorithm
Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method produces allele-specific DNA bands of different lengths by adding four designed primers and it achieves the single nucleotide polym...
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Article
Open AccessSNP-RFL** 2: an updated and integrated PCR-RFLP tool for SNP genoty**
PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genoty** and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome....
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Chapter and Conference Paper
Confronting Two-Pair Primer Design Using Particle Swarm Optimization
Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is a novel PCR technique had been applied to many SNPs (Single Nucleotide Polymorphisms) genoty** experiments successfully in the recent...
