Research

Recently, we do our efforts for electric and hybrid vehicles, power electronics, and Renewable energy. Our studying issues include to realize the optimal control strategy for effectively manage hybrid electric vehicles, to reduce vehicle fuel consumption and emissions, as well as guarantee vehicle performance; to develop newly designed dc/dc converters, to develop isolated ac module for photovoltaic energy conversion, to study an active ripple filter (ARF) for eliminating the double-line-frequency (DLF) current ripple of the vehicular energy single-phase DC/AC conversion system, to enhance the conversion efficiency and electrical reliability of the low-voltage fuel-cell (FC) power generation system, the cost and the reliability evaluation for renewable energy systems. The following lists our main researches.

(1) Ching-Ming Lai, Yu-Huei Cheng*, Ming-Hua Hsieh, and Yuan-Chih Lin (2018). Development of a Bidirectional DC/DC Converter with Dual-Battery Energy Storage for Hybrid Electric Vehicle System. IEEE Transactions on Vehicular Technology, December;67(2): 1036-1052; doi:10.1109/TVT.2017.2763157.[SCIE/Scopus/EI] (http://ieeexplore.ieee.org/document/8068246/) (Corresponding Author)

(2) Ching-Ming Lai, Yu-Jen Lin, Yu-Huei Cheng*, and Leehter Yao (2018). Development of a Modular Single-Phase Grid-Tie Inverter System for Fuel-Cell Power Generation. Journal of the Chinese Institute of Engineers, March;41(2), 2018, 112-123; doi:10.1080/02533839.2018.1437365. [SCIE/Scopus/EI] (Corresponding Author)

(3) Jiashen Teh, Ching-Ming Lai, and Yu-Huei Cheng* (2018). Composite Reliability Evaluation for Transmission Network Planning. AIMS Energy, January, 6(1): 170-186; doi: 10.3934/energy.2018.1.170. [Scopus] (http://www.aimspress.com/article/10.3934/energy.2018.1.170) (Corresponding Author)

(4) Ching-Ming Lai, Yun-Hsiu Li, Yu-Huei Cheng, and Jiashen Teh* (2018). A High-Gain Reflex-Based Bidirectional DC Charger with Efficient Energy Recycling for Low-Voltage Battery Charging-Discharging Power Control. Energies, August;11(3), 623; doi:10.3390/en11030623. [SCIE/Scopus/EI] (http://www.mdpi.com/1996-1073/11/3/623)

(5) Jiashen Teh, Chia Ai Ooi, Yu-Huei Cheng, Muhammad Ammirrul AtiqiMohd Zainuri, and Ching-Ming Lai* (2018). Composite Reliability Evaluation of Load Demand Side Management and Dynamic Thermal Rating Systems. Energies, August;11(2), 466; doi:10.3390/en11020466. [SCIE/Scopus/EI] (http://www.mdpi.com/1996-1073/11/2/466)

(6) Yu-Huei Cheng, Ching-Ming Lai, and Jiashen Teh (2017). Genetic Algorithm with Small Population Size for Search Feasible Control Parameters for Parallel Hybrid Electric Vehicles. AIMS Energy, November, 5(6): 930-943; doi:10.3934/energy.2017.6.930. [Scopus] (http://www.aimspress.com/article/10.3934/energy.2017.6.930) (First Author)

(7) Jiashen Teh, Ching-Ming Lai, and Yu-Huei Cheng (2017). Impact of the Real-Time Thermal Loading on the Bulk Electric System Reliability. IEEE Transactions on Reliability, December;66(4): 1110-1119; doi:10.1109/TR.2017.2740158. [SCIE/Scopus/EI] (http://ieeexplore.ieee.org/document/8019838/)

(8) Ching-Ming Lai, Yu-Huei Cheng*, Jiashen Teh, and Yuan-Chih Lin (2017). A New Combined Boost Converter with Improved Voltage Gain as a Battery-Powered Front-End Interface for Automotive Audio Amplifiers. Energies, August;10(8), 1128; doi:10.3390/en10081128. [SCIE/Scopus/EI] (http://www.mdpi.com/1996-1073/10/8/1128) (Corresponding Author)

(9) Yu-Huei Cheng and Ching-Ming Lai (2017). Control Strategy Optimization for Parallel Hybrid Electric Vehicles using Memetic Algorithm. Energies, March;10(3), 305; doi:10.3390/en10030305 [SCIE/Scopus/EI] (http://www.mdpi.com/1996-1073/10/3/305) (First Author)

In the past, we do our efforts for bioinformatics, computational biology, computational intelligence-based methods, and evolutionary computation. Our studying issues include single nucleotide polymorphism genotyping (SNP genotyping), SNP-SNP interaction analysis, SNP sequence alignment and analysis, pharmacogenomics analysis, polymerase chain reaction primer design (PCR primer design), DNA methylation analysis, and mitochondrial visualization and analysis. We have provided many studies for biomedical engineering and biotechnology based on all kinds of algorithms, biological databases, and bioinformatics systems. The following lists our main researches.

1. Single nucleotide polymorphism genotyping (SNP genotyping)

Polymerase Chain Reaction-Restriction Fragment Length Polymorphism, PCR-RFLP is a fast and cheap SNP genotyping method for many small and medium laboratories. In order to assist researchers to perform SNP genotyping using PCR-RFLP, we combined NCBI dbSNP with REBASE, and integrated all kinds of biological databases to develop the available bioinformatic systems. These bioinformatic systems are user-friendly and can effectively perform the work for high-throughput restriction enzymes mining. Furthermore, we also develop computational intelligence-based primer design methods for PCR-RFLP SNP genotyping.

(10) Yu-Huei Cheng* (2015). A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping. IEEE/ACM Transactions on Computational Biology and Bioinformatics. [SCIE/Scopus/EI] (http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7111243) (Single Author)

(11) Li-Yeh Chuang, Yu-Huei Cheng, and Cheng-Hong Yang (2015). PCR-CTPP design for enzyme-free SNP genotyping using memetic algorithm. IEEE Transactions on NanoBioscience, Jan;14(1):12-22. [SCIE/Scopus/EI] (http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7051322)

(12) Yu-Huei Cheng*, Li-Yeh Chuang, and Cheng-Hong Yang (2013). Single Nucleotide Polymorphisms Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Primer Design Using Genetic Algorithm with Fixed and Adaptive Stopping Criteria. Journal of Advanced Mathematics and Applications (JAMA), Dec;2(2):172-181. (http://www.ingentaconnect.com/content/asp/jama/2013/00000002/00000002/art00008) (First Author & Corresponding Author)

(13) Li-Yeh Chuang, Yu-Huei Cheng, Cheng-Huei Yang, and Cheng-Hong Yang (2013). Associate PCR-RFLP assay design with SNPs based on genetic algorithm in appropriate parameters estimation. IEEE Transactions on NanoBioscience, Jun;12(2):119-127. [SCIE/Scopus/EI] [PMID: 23722280] (http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6521454)

(14) Cheng-Hong Yang, Yu-Huei Cheng*, and Li-Yeh Chuang (2012). PCR-CTPP design based on Particle Swarm Optimization with Fuzzy Adaptive Strategy. Engineering Letters, vol. 20(2), pp. 196-202. [Scopus/EI] (http://www.engineeringletters.com/issues_v20/issue_2/index.html) (Corresponding Author)

(15) Cheng-Hong Yang, Yu-Huei Cheng, Cheng-Huei Yang, and Li-Yeh Chuang (2012). Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping using a Genetic Algorithm. IEEE/ACM Transactions on Computational Biology and Bioinformatics, May-Jun;9(3):837-45. [SCIE/Scopus/EI] [PMID: 22331864] (http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6143917)

(16) Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang (2010). Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm. BMC Bioinformatics, Oct 13;11:509. [SCIE/Scopus/EI] [PMID: 20942913] (http://www.biomedcentral.com/1471-2105/11/509)

(17) Hsueh-Wei Chang, Yu-Huei Cheng, Li-Yeh Chuang, and Cheng-Hong Yang. (2010). SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. BMC Bioinformatics, Apr 8;11:173. [SCIE/Scopus/EI] [PMID: 20377871] (http://www.biomedcentral.com/1471-2105/11/173)

(18) Hsueh-Wei Chang, Li-Yeh Chuang, Yan-Jhu Chang, Yu-Huei Cheng, Yu-Chen Hung, Hsiang-Chi Chen, and Cheng-Hong Yang (2009). LD2SNPing: Linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs. BMC Genetics, Jun 6;10:26. [SCIE/Scopus/EI] [PMID: 19500380] (http://www.biomedcentral.com/1471-2156/10/26)

(19) Cheng-Hong Yang, Li-Yeh Chuang, Yu-Huei Cheng, Cheng-Hao Wen, Phei-Lang Chang, and Hsueh-Wei Chang (2008). SNP ID-info: SNP ID searching and visualization platform. OMICS: A Journal of Integrative Biology, Sep;12(3):217-26. [SCIE/Scopus/EI] [PMID: 18582176] (http://online.liebertpub.com/doi/abs/10.1089/omi.2008.0026)

(20) Li-Yeh Chuang, Cheng-Hong Yang, Ke-Hung Tsui, Yu-Huei Cheng, Phei-Lang Chang, Cheng-Hao Wen, and Hsueh-Wei Chang (2008). Restriction enzyme mining for SNPs in genomes. Review. Anticancer Research, Jul-Aug;28(4A):2001-7. [SCIE/Scopus/EI] [PMID: 18649739] (http://ar.iiarjournals.org/content/28/4A/2001.long)

(21) Hsueh-Wei Chang, Cheng-Hong Yang, Phei-Lang Chang, Yu-Huei Cheng, and Li-Yeh Chuang (2006). SNP-RFLPing: restriction enzyme mining for SNP in genomes. BMC Genomics, 7:30. [SCIE/Scopus/EI] [PMID: 16503968] (http://www.biomedcentral.com/1471-2164/7/30)

2. SNP-SNP interaction analysis

Single SNP is possible associating with some diseases and cancers. Interactions among SNPs and SNPs may result in the occurrence or inhibition of some diseases and cancers. In order to study the interactions among SNPs and SNPs if influence diseases and cancers, we used different permutation and combination of SNPs to evaluate the influences. The computational intelligence-based methods were applied to find the relationships by the true samples of diseases and cancers.

(1) Cheng-Hong Yang, Li-Yeh Chuang, Yu-Huei Cheng, Chun-Lin Wang, Cheng-Hao Wen, Hsueh-Wei Chang (2012). Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithms. Kaohsiung Journal of Medical Sciences, Jul;28(7):362-8. [SCIE/Scopus/EI] [PMID: 22726897] (http://www.sciencedirect.com/science/article/pii/S1607551X12000320)

(2) Cheng-Hong Yang, Hsueh-Wei Chang, Yu-Huei Cheng, and Li-Yeh Chuang (2009). Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimization. Cancer Epidemiology, Aug;33(2):147-54. [SCIE/Scopus/EI] [PMID: 19679063] (http://www.sciencedirect.com/science/article/pii/S1877782109000769)

(3) Gau-Tyan Lin, Hung-Fu Tseng, Cheng-Hong Yang, Ming-Feng Hou, Li-Yeh Chuang, Hsiao-Ting Tai, Ming-Hong Tai, Yu-Huei Cheng, Cheng-Hao Wen, Chih-Shan Liu, Chih-Jen Huang, Chun-Lin Wang, and Hsueh-Wei Chang (2009). Combinational Polymorphisms of Seven CXCL12-related Genes Are Protective against Breast Cancer in Taiwan. OMICS: A Journal of Integrative Biology, Apr;13(2):165-72. [SCIE/Scopus/EI] [PMID: 19196101] (http://online.liebertpub.com/doi/abs/10.1089/omi.2008.0050)

3. SNP sequence alignment and analysis

Biological sequence alignment and analysis is fundamental and important tool for bioinformatics and computational biology. Sequence alignment can find the similar structures and functions by comparing their similar degrees between two sequences or among multiple sequences. Many old literatures provided many sequence information, however, no any analysis and discussion for SNPs. We studied the identifying methods for SNPs in an unknown sequence to provide the researchers find out existing SNPs.

(1) Cheng-Hong Yang, Li-Yeh Chuang, Yu-Huei Cheng, Cheng-Hao Wen, and Hsueh-Wei Chang (2009). Dynamic programming for single nucleotide polymorphism ID identification in systematic association studies. Kaohsiung Journal of Medical Sciences, Apr;25(4):165-76. [SCIE/Scopus/EI] [PMID: 19502133] (http://www.sciencedirect.com/science/article/pii/S1607551X09700579)

(2) Hsueh-Wei Chang, Li-Yeh Chuang, Yu-Huei Cheng, Chang-Hsuan Ho, Cheng-Hao Wen, and Cheng-Hong Yang (2009). Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotyping. OMICS: A Journal of Integrative Biology, Jun;13(3):253-60. [SCIE/Scopus/EI] [PMID: 19514837] (http://online.liebertpub.com/doi/abs/10.1089/omi.2008.0058)

(3) Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang (2008). SNP-Flankplus: SNP ID-centric retrieval for SNP flanking sequences. Bioinformation, 3(4):147-9. [SCIE/Scopus/EI] [PMID: 19238236] (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637961/)

(4) Li-Yeh Chuang, Cheng-Hong Yang, Yu-Huei Cheng, and Hsueh-Wei Chang (2007). A Mixed Method for Providing Exact SNP IDs from Sequences, Biomedical Engineering-Applications Basis Communications, vol. 19, no. 4, pp. 251-257. [Scopus/EI] (http://www.worldscientific.com/doi/abs/10.4015/S1016237207000331)

(5) Hsueh-Wei Chang, Yu-Huei Cheng*, Tai-Chen Chen, Cheng-San Yang, Li-Yeh Chuang, and Cheng-Hong Yang (2007). A novel method providing exact SNP IDs from sequences. IAENG International Journal of Computer Science (IJCS), 34:1, IJCS_34_1_17, pp. 127-132. [Scopus/EI] (http://www.iaeng.org/IJCS/issues_v34/issue_1/IJCS_34_1_17.pdf) (Corresponding Author)

4. Pharmacogenomics analysis

Many drugs resources and tools help the SNP-related drug development research work. The integration among these resources and tools is required for leading the researchers effectively utilized. In order to provide drug-related resources and contribute to the integration of pharmacogenomics analysis, we not only combine many important drugs and SNP-related resources and tools to provide a variety of drug information and functions, but also provide SNP genotyping information to assist researchers for drug development.

(1) Yu-Huei Cheng, Li-Yeh Chuang, Hsueh-Wei Chang, and Cheng-Hong Yang (2014). Improved candidate drug mining for Alzheimer’s disease. BioMed Research International (formerly titled Journal of Biomedicine and Biotechnology), vol. 2014, Article ID 897653, 8 pages. [SCIE/Scopus/EI] (http://www.hindawi.com/journals/bmri/2014/897653/) (First Author)

(2) Cheng-Hong Yang, Yu-Huei Cheng*, Li-Yeh Chuang, and Hsueh-Wei Chang (2013). Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping. Bioinformatics, Mar 15;29(6):758-764. [SCIE/Scopus/EI] [PMID: 23418190] (http://bioinformatics.oxfordjournals.org/content/29/6/758.long) (Corresponding Author)

5. Polymerase chain reaction primer design (PCR primer design)

Polymerase chain reaction (PCR) is a very important and common biotechnology for amplify DNA. Before performing PCR, the suitable primers must be designed. However, the primer design is tedious and many primer factors must be considered simultaneously. In order to solve the primer design problem, we used computational intelligence-based methods to design the specific and feasible primers. Furthermore, we also developed several user-friendly primer design systems.

(1) Yu-Huei Cheng, Che-Nan Kuo, and Ching-Ming Lai (2016). Effective Natural PCR-RFLP Primer Design for SNP Genotyping Using Teaching-Learning-Based Optimization with Elite Strategy. IEEE Transactions on NanoBioscience, Oct;15(7):657-665; doi:10.1109/TNB.2016.2597867. [SCIE/Scopus/EI] (http://ieeexplore.ieee.org/document/7530862/) (First Author)

(2) Yu-Huei Cheng, Che-Nan Kuo, and Ching-Ming Lai (2016). An Improved Evolutionary Method with Test in Different Crossover Rates for PCR-RFLP SNP Genotyping Primer Design. International Journal of Mining, Metallurgy & Mechanical Engineering (IJMMME), May;4(1):25-29. ISSN 2320-4052 (Printed Version) ISSN 2320-4060 (Online Version) (http://www.isaet.org/images/extraimages/P0516203.pdf) (First Author)

(3) Yu-Huei Cheng* (2016). A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Jan-Feb;13(1):86-98; doi: 10.1109/TCBB.2015.2430354. [SCIE/Scopus/EI] (http://ieeexplore.ieee.org/document/7111243/) (Single Author)

(4) Yu-Huei Cheng* (2015). Estimation of Teaching-Learning-Based Optimization Primer Design using Regression Analysis for Different Melting Temperature Calculations. IEEE Transactions on NanoBioscience, Jan;14(1):3-12. [SCIE/Scopus/EI] (http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6898025)(Single Author)

(5) Yu-Huei Cheng* (2014). Computational Intelligence-based PCR Primer Selection based on a Novel Teaching-Learning-Based Optimization. IET Nanobiotechnology, Dec;8(4):238-246. [SCIE/Scopus/EI] (http://digital-library.theiet.org/content/journals/10.1049/iet-nbt.2013.0055) (Single Author)

(6) Li-Yeh Chuang, Yu-Huei Cheng*, and Cheng-Hong Yang (2013). Specific primer design for the polymerase chain reaction. Biotechnology Letters, Oct;35(10):1541-9. [SCIE/Scopus/EI] [PMID: 23794048] (http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10529-013-1249-8) (Corresponding Author)

(7) Yu-Huei Cheng* (2013). A Novel Optimization Method for Picking PCR Oligonucleotide Primers. International Journal of Computer Science and Electronics Engineering (IJCSEE), Step;1(4):518-523. (Single Author)

(8) Li-Yeh Chuang, Yu-Huei Cheng, and Cheng-Hong Yang (2012). URPD: A Specific Product Primer Design Tool. BMC Research Notes, Jun 19;5:306. [SCIE/Scopus/EI] [PMID: 22713312] (http://www.biomedcentral.com/1756-0500/5/306)

(9) Cheng-Hong Yang, Yu-Huei Cheng*, Hsueh-Wei Chang, and Li-Yeh Chuang (2010). Primer Design with Specific PCR Product using Particle Swarm Optimization, International Journal of Chemical and Biological Engineering, vol. 3, pp. 18-23. [SCIE/Scopus/EI] (https://www.waset.org/journals/ijcbe/v3/v3-1-4.pdf)

(10) Hsueh-Wei Chang, Li-Yeh Chuang, Yu-Huei Cheng, Yu-Chen Hung, Cheng-Hao Wen, De-Leung Gu, and Cheng-Hong Yang (2009). Prim-SNPing: a primer designer for cost-effective SNP genotyping. Biotechniques, May;46(6):421-31. [SCIE/Scopus/EI] [PMID: 19480636] (http://www.biotechniques.com/BiotechniquesJournal/2009/May/Prim-SNPing-a-primer-designer-for-cost-effective-SNP-genotyping/biotechniques-140957.html)

(11) Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang (2009). Specific PCR product primer design using memetic algorithm. Biotechnology progress, May-Jun;25(3):745-53. [SCIE/Scopus/EI] [PMID: 19405106] (http://onlinelibrary.wiley.com/doi/10.1002/btpr.169/full)

6. DNA methylation analysis

DNA methylation is a epigenetic mechanism and is a chemical modification of DNA chemical modification. DNA methylation can change gene expression in the prerequisite of keeping the DNA sequence. In a mature somatic cell, DNA methylation usually occurs on the positions of CpG dinucleotide. The region of CpG dinucleotide repeating highly is called as CpG islands. CpG islands mostly locate the region of promoter. In order to analyze the DNA methylation, we integrated DBTSS (Database of Transcriptional Start Sites), NCBI RefSeq and UCSC In Silico PCR, and employ CpG Island Searcher to provide an available DNA methylation system for PCR-RFLP genotyping.

(1) Cheng-Hong Yang, Li-Yeh Chuang, Yu-Huei Cheng, De-Leung Gu, Chung-Ho Chen, and Hsueh-Wei Chang (2010). Methyl-Typing: An improved and visualized COBRA software for epigenomic studies. FEBS Letters, Feb 19;584(4):739-44. [SCIE/Scopus/EI] [PMID: 20026327] (http://www.sciencedirect.com/science/article/pii/S0014579309010722)

7. Mitochondrial visualization and analysis

Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. We provided a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Furthermore, visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI were also developed for an ideal and complete visualization interface for human mtSNPs association studies.

(1) Li-Yeh Chuang, Cheng-Hong Yang, Yu-Huei Cheng, De-Leung Gu, Phei-Lang Chang, Ke-Hung Tsui, and Hsueh-Wei Chang (2006). V-MitoSNP: visualization of human mitochondrial SNPs. BMC Bioinformatics, Aug 15;7:379. [SCIE/Scopus/EI] [PMID: 16907992] (http://www.biomedcentral.com/1471-2105/7/379))