Publications (182) View all
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Article: Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithms.
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ABSTRACT: Cancers often involve the synergistic effects of gene-gene interactions, but identifying these interactions remains challenging. Here, we present an odds ratio-based genetic algorithm (OR-GA) that is able to solve the problems associated with the simultaneous analysis of multiple independent single nucleotide polymorphisms (SNPs) that are associated with oral cancer. The SNP interactions between four SNPs-namely rs1799782, rs2040639, rs861539, rs2075685, and belonging to four genes (XRCC1, XRCC2, XRCC3, and XRCC4)-were tested in this study, respectively. The GA decomposes the SNPs sets into different SNP combinations with their corresponding genotypes (called SNP barcodes). The GA can effectively identify a specific SNP barcode that has an optimized fitness value and uses this to calculate the difference between the case and control groups. The SNP barcodes with a low fitness value are naturally removed from the population. Using two to four SNPs, the best SNP barcodes with maximum differences in occurrence between the case and control groups were generated by GA algorithm. Subsequently, the OR provides a quantitative measure of the multiple SNP synergies between the oral cancer and control groups by calculating the risk related to the best SNP barcodes and others. When these were compared to their corresponding non-SNP barcodes, the estimated ORs for oral cancer were found to be great than 1 [approx. 1.72-2.23; confidence intervals (CIs): 0.94-5.30, p < 0.03-0.07] for various specific SNP barcodes with two to four SNPs. 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.The Kaohsiung journal of medical sciences 07/2012; 28(7):362-8. · 0.61 Impact Factor -
Article: URPD: A Specific Product Primer Design Tool.
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ABSTRACT: BACKGROUND: Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software for a rather straight-forward way of visualizing the primer design process for infrequent users. RESULTS: URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. CONCLUSIONS: URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.BMC Research Notes 06/2012; 5(1):306. -
Article: The importance of integrating SNP and cheminformatics resources to pharmacogenomics.
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ABSTRACT: Single nucleotide polymorphisms (SNPs) are the most frequent variants in many genes and are promising markers in relation to drug responses in pharmacogenomics studies. In this review, we emphasized the importance of the cheminformatic-related and SNP-related resources and tools and how they can improve pharmacogenomics studies. Currently, many cheminformatic resources are well developed and provide much information on drug metabolism and targeting. In parallel, there are also many well established SNP-related resources that are able to provide the information related to SNP genotyping, tag SNPs and functional classification. However, cheminformatic and SNP resources have not, as yet, been well-integrated to provide a user-friendly platform for pharmacogenomics studies. This paper presents a brief overview of the many available public resources for cheminformatics (DrugBank, PharmGKB and other drugrelated databases) and SNPs (dbSNP, HapMap, SNP500Cancer, SNP-RFLPing 2 and other SNP tools) and points out the importance of integrating cheminformatic and SNP resources for the future of pharmacogenomics.Current Drug Metabolism 05/2012; 13(7):991-9. · 5.11 Impact Factor -
Article: Antibacterial and antioxidant properties of Ramulus Cinnamomi using supercritical CO2 extraction
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ABSTRACT: In this study, crude extracts of Ramulus Cinnamomi from supercritical carbon dioxide under various extraction conditions were examined for their antioxidant and antibacterial activity. The extractions were conducted in the range of 4,000–6,000psi and 40–50°C, and the solvent to feed ratio of the extraction was 30. The antibacterial activity was tested on the clinical drug-resistant strains, including 27 Acinetobacter baumannii, 20 Pseudomonas aeruginosa and 2 Staphylococcus aureus isolates by the disk diffusion method. The bioassay results indicated that Ramulus Cinnamomi showed obvious antimicrobial activity against the tested strains. This study also found that increasing the temperature and pressure would increase the yield of the supercritical fluid extraction (SFE), even though the best extraction conditions for antibacterial activity were found to be high pressure and low temperature. The minimum inhibitory concentration (MIC) was determined on the crude extract of Ramulus Cinnamomi, indicating that the crude extracts from supercritical extraction showed better antibacterial activity than those obtained by ethanol extraction. Based on the spectrophotometer and bioassay determination, the antimicrobial constituent was identified to be cinnamaldehyde. Time-kill kinetics and scanning electron microscopy (SEM) were employed to monitor the survival characteristics and the changes in morphologies, respectively, of the test microorganisms in the presence of herbal extracts. Moreover, antioxidant activity was evaluated by scavenging of the free radical DPPH. Extracts of Ramulus Cinnamomi provided 50% inhibition at 2mg/ml concentration. This study will provide valuable information for extraction of the natural bioactive component, cinnamaldehyde, from Ramulus Cinnamomi by supercritical extraction.European Food Research and Technology 04/2012; 227(5):1387-1396. · 1.57 Impact Factor -
Article: Mutagenic primer design for mismatch PCR-RFLP SNP genotyping using a genetic algorithm.
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ABSTRACT: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphism (SNP). Designing a feasible primer pair is an important work before performing PCR-RFLP for SNP genotyping. However, in many cases, restriction enzymes to discriminate the target SNP resulting in the primer design is not applicable. A mutagenic primer is introduced to solve this problem. GA-based Mismatch PCR-RFLP Primers Design (GAMPD) provides a method that uses a genetic algorithm to search for optimal mutagenic primers and available restriction enzymes from REBASE. In order to improve the efficiency of the proposed method, a mutagenic matrix is employed to judge whether a hypothetical mutagenic primer can discriminate the target SNP by digestion with available restriction enzymes. The available restriction enzymes for the target SNP are mined by the updated core of SNP-RFLPing. GAMPD has been used to simulate the SNPs in the human SLC6A4 gene under different parameter settings and compared with SNP Cutter for mismatch PCR-RFLP primer design. The in silico simulation of the proposed GAMPD program showed that it designs mismatch PCR-RFLP primers. The GAMPD program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/gampd/.IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 01/2012; 9(3):837-45. · 2.25 Impact Factor
