Research Topics
Genomes and GenesSpecies | Li Yeh ChuangSummaryAffiliation: I-Shou University Country: Taiwan Publications
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Detail Information
Publications
Antioxidant activity of various parts of Cinnamomum cassia extracted with different extraction methodsCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 807, Taiwan
Molecules 17:7294-304. 2012..Based on the results, the ethanol extracts of Cinnamon barks have potential value as an antioxidant substitute and this study also provide a better technique to extract the natural antioxidant substances from C. cassia...
SNP-RFLPing: restriction enzyme mining for SNPs in genomesHsueh Wei Chang
Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Taiwan
BMC Genomics 7:30. 2006..Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes...
Improved binary PSO for feature selection using gene expression dataLi Yeh Chuang
Department of Chemical Engineering, I Shou University, Kaohsiung 840, Taiwan
Comput Biol Chem 32:29-37. 2008....- LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPsHsueh Wei Chang
Department of Chemical Engineering, I Shou University, Kaohsiung, Taiwan
BMC Genet 10:26. 2009..Linkage disequilibrium (LD) mapping is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting services for genotyping... - V-MitoSNP: visualization of human mitochondrial SNPsLi Yeh Chuang
Department of Chemical Engineering, I Shou University, 840, Taiwan
BMC Bioinformatics 7:379. 2006..The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved... - SNP ID-info: SNP ID searching and visualization platformCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Taiwan, ROC
OMICS 12:217-26. 2008..In conclusion, the SNP ID-info provides a visualized SNP ID environment for multiple inputs and assists systematic SNP association studies. The server and user manual are available at http://bio.kuas.edu.tw/snpid-info... - Odds ratio-based genetic algorithms for generating SNP barcodes of genotypes to predict disease susceptibilityHsueh Wei Chang
Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
OMICS 12:71-81. 2008..Therefore, this paper introduces a powerful procedure for analysis of disease-associated SNP barcode in genome-wide genes... - SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotypingHsueh Wei Chang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
BMC Bioinformatics 11:173. 2010.... - A combined bisulfite restriction analysis bioinformatics tool: methyl-typingCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
Methods Mol Biol 791:73-88. 2011..It is a fast and efficient tool for providing all possible methylation sites of restriction enzymes... - Restriction enzyme mining for SNPs in genomesLi Yeh Chuang
Department of Chemical Engineering, I Shou University, Kaohsiung, Taiwan, ROC
Anticancer Res 28:2001-7. 2008.... - Features for computational operon prediction in prokaryotesLi Yeh Chuang
Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I Shou University, Taiwan
Brief Funct Genomics 11:291-9. 2012.... - Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotypingHsueh Wei Chang
Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
OMICS 13:253-60. 2009..The software is fully compatible with Microsoft Windows. The program and user manual are available at http://bio.kuas.edu.tw/Seq-SNPing for download... - Dynamic programming for single nucleotide polymorphism ID identification in systematic association studiesCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
Kaohsiung J Med Sci 25:165-76. 2009..It is freely available at http://bio.kuas.edu.tw/SNPosition/... - Chaotic particle swarm optimization for detecting SNP-SNP interactions for CXCL12-related genes in breast cancer preventionLi Yeh Chuang
Institute of Biotechnology and Chemical Engineering, I Shou University, Taiwan
Eur J Cancer Prev 21:336-42. 2012..The CPSO method can effectively identify SNP-SNP interactions in complex biological relationships underlying the progression of breast cancer... - A hybrid BPSO-CGA approach for gene selection and classification of microarray dataLi Yeh Chuang
Department of Chemical Engineering, and Institute of Biotechnology and Chemical Engineering, I Shou University Kaohsiung, Taiwan
J Comput Biol 19:68-82. 2012..The experimental results indicate that the proposed method not only effectively reduce the number of genes expression level, but also achieves a low classification error rate... - Methyl-Typing: an improved and visualized COBRA software for epigenomic studiesCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
FEBS Lett 584:739-44. 2010..Therefore, the Methyl-Typing tool provides a comprehensive COBRA-restriction enzyme mining. It is freely available at http://bio.kuas.edu.tw/methyl-typing... - Chaotic genetic algorithm for gene selection and classification problemsLi Yeh Chuang
Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan, P R China
OMICS 13:407-20. 2009..The experimental results show that the proposed method not only effectively reduced the number of gene expression levels, but also achieved lower classification error rates than other methods... - Combinational polymorphisms of seven CXCL12-related genes are protective against breast cancer in TaiwanGau Tyan Lin
Department of Orthopedic Surgery, Kaohsiung Medical University, Chung Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
OMICS 13:165-72. 2009.... - Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimizationHsueh Wei Chang
Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
Comput Biol Chem 33:114-9. 2009..Therefore, this paper introduces a powerful procedure to analyze disease-associated SNP-SNP interaction in genome-wide genes... - Fuzzy support vector machines for adaptive Morse code recognitionCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 807, Taiwan
Med Eng Phys 28:925-31. 2006..Statistical analyses demonstrated that the proposed method elicited a higher recognition rate than other algorithms in the literature... - hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressorsCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, and Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
PLoS ONE 5:e14369. 2010..There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers... - Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithmsCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
Kaohsiung J Med Sci 28:362-8. 2012..In conclusion, the proposed OR-GA method successfully generates SNP barcodes, which allow oral cancer risk to be evaluated and in the process the OR-GA method identifies possible SNP-SNP interactions... - An improved PSO algorithm for generating protective SNP barcodes in breast cancerLi Yeh Chuang
Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan
PLoS ONE 7:e37018. 2012..However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions... - CpGPAP: CpG island predictor analysis platformLi Yeh Chuang
Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan
BMC Genet 13:13. 2012..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)... - Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithmCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
BMC Bioinformatics 11:509. 2010..It is a time- and cost-effective SNP genotyping method that has the advantage of simplicity. However, computation of feasible CTPP primers is still challenging... - Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithmCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
PLoS ONE 6:e17729. 2011..However, current algorithms and tools are mostly focused on the primer design for a local region in the genomic sequence. Accordingly, it is still challenging to provide the primer sets for the entire mtDNA... - Computational analysis of simulated SNP interactions between 26 growth factor-related genes in a breast cancer association studyCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan, Republic of China
OMICS 15:399-407. 2011..01) for specific SNP barcodes with two to five SNPs. Therefore, we were able to identify potential combined growth factor-related genes together with their SNP barcodes that were protective against breast cancer by in silico analysis... - Tag SNP selection using particle swarm optimizationLi Yeh Chuang
Dept of Chemical Engineering, I Shou University, Kaohsiung, Taiwan
Biotechnol Prog 26:580-8. 2010..For STAMPA and SVM/STSA, BPSO effective improved prediction accuracy for smaller and larger scale data sets. These results demonstrate that the BPSO method selects tag SNP with higher accuracy no matter the scale of data sets is used... - An improved PCR method for gender identification of eaglesHsueh Wei Chang
Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
Mol Cell Probes 22:184-8. 2008..When used with 28 samples of S. cheela hoya, our improved universal primers provided a fast and precise gender identification assay... - Chemical composition and antibacterial activities of Illicium verum against antibiotic-resistant pathogensJyh Ferng Yang
Department of Chemical Engineering, I Shou University, Kaohsiung, Taiwan
J Med Food 13:1254-62. 2010..These extracts from I. verum can be further developed into antibiotic medicines due to their proven antibacterial activity... - An introduction to mitochondrial informaticsHsueh Wei Chang
Department of Biomedical Science and Environmental Biology, Center of Excellence for Environmental Medicine, Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
Methods Mol Biol 628:259-74. 2010..Some databases with similar function are integrated and compared... - Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimizationCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
Cancer Epidemiol 33:147-54. 2009..Simultaneous analyses for multiple SNP interactions associated with many diseases and cancers are essential; however, these analyses are still computationally challenging... - A hybrid feature selection method for DNA microarray dataLi Yeh Chuang
Department of Chemical Engineering, I Shou University, Kaohsiung 80041, Taiwan
Comput Biol Med 41:228-37. 2011..The classification accuracy obtained by the proposed method was higher in ten out of the eleven gene expression data set test problems when compared to other classification methods from the literature... - Tabu search and binary particle swarm optimization for feature selection using microarray dataLi Yeh Chuang
Department of Chemical Engineering, I Shou University, Kaohsiung, Taiwan
J Comput Biol 16:1689-703. 2009..Experimental results show that our method simplifies features effectively and either obtains higher classification accuracy or uses fewer features compared to other feature selection methods... - Particle swarm optimization with reinforcement learning for the prediction of CpG islands in the human genomeLi Yeh Chuang
Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan
PLoS ONE 6:e21036. 2011..These islands are usually located in the 5' end of genes. Recently, several algorithms for the prediction of CpG islands have been proposed... - A two-stage feature selection method for gene expression dataLi Yeh Chuang
Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan, Republic of China
OMICS 13:127-37. 2009..The experimental results show that the proposed method can effectively select relevant gene subsets, and achieves higher classification accuracy than previous studies... - Binary particle swarm optimization for operon predictionLi Yeh Chuang
Department of Chemical Engineering, I Shou University, Kaohsiung, Taiwan
Nucleic Acids Res 38:e128. 2010..This method has enabled us to predict operons with high accuracy for these three genomes, for which only limited data on the properties of the operon structure exists... - PPO: predictor for prokaryotic operonsLi Yeh Chuang
Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan
Bioinformatics 26:3127-8. 2010..Availability and implementation: PPO is freely available at http://bio.kuas.edu.tw/PPO/... - SNP combinations in chromosome-wide genes are associated with bone mineral density in Taiwanese womenGau Tyan Lin
Department of Orthopaedic Surgery, Chung Ho Memorial Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
Chin J Physiol 51:32-41. 2008..54- to 4.68-fold increased risk for low BMD, comparing to other SNP combinations. In conclusion, our data suggest that several gene polymorphisms may be cooperatively involved in the development of osteoporosis... - Genotype and antibiotic susceptibility patterns of drug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii isolates in TaiwanCheng Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan, Republic of China
Microb Drug Resist 14:281-8. 2008..The results obtained from this study reveal that the majority of these isolates displayed multiple drug resistance phenotypes that were associated with their mutational gene profiles... - Specific PCR product primer design using memetic algorithmCheng Hong Yang
Dept of Electronic Engineering, National Kaohsiung University of Applied Sciences, Taiwan
Biotechnol Prog 25:745-53. 2009..The results further indicate that the proposed method finds optimal or near-optimal primer sets and effective PCR products in a dry dock experiment. Related materials are available online at http://bio.kuas.edu.tw/ma-pd/... - URPD: a specific product primer design toolLi Yeh Chuang
Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I Shou University, Kaohsiung, Taiwan
BMC Res Notes 5:306. 2012..Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users... - Sequence-based polymorphisms in the mitochondrial D-loop and potential SNP predictors for chronic dialysisJin Bor Chen
Division of Nephrology, Department of Internal Medicine, Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
PLoS ONE 7:e41125. 2012..The aim of this study was to investigate the prevalence of single nucleotide polymorphisms (SNPs) within the D-loop among chronic dialysis patients and healthy controls... - Anti-proliferative effect of methanolic extract of Gracilaria tenuistipitata on oral cancer cells involves apoptosis, DNA damage, and oxidative stressChi Chen Yeh
Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
BMC Complement Altern Med 12:142. 2012..Previously, we found that water extract of G. tenuistipitata was able to modulate oxidative stress-induced DNA damage and its related cellular responses... - Counter-propagation network with variable degree variable step size LMS for single switch typing recognitionCheng-Huei Yang
Department of Electronics Communication Engineering, National Kaohsiung Institute of Marine Technology, Taiwan
Biomed Mater Eng 14:23-32. 2004..Statistical analyses demonstrated that the proposed method elicited a better recognition rate in comparison to alternative methods in the literature... - Combinational polymorphisms of four DNA repair genes XRCC1, XRCC2, XRCC3, and XRCC4 and their association with oral cancer in TaiwanChing Yu Yen
Department of Oral and Maxillofacial Surgery, Chi Mei Medical Center, Tainan, and School of Dentistry, Taipei Medical University, Taipei, Taiwan
J Oral Pathol Med 37:271-7. 2008..In this study, we focused on the joint effect for SNP combinations of four DNA repair genes, X-ray repair cross-complementing groups (XRCCs) 1-4, involved in major cancer-related pathways... - Morse code application for wireless environmental control systems for severely disabled individualsCheng-Hong Yang
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 807, Taiwan, ROC
IEEE Trans Neural Syst Rehabil Eng 11:463-9. 2003..Experimental results revealed that three participants with physical handicaps were able to gain access to electronic facilities after two months' practice with the new system...