Chuan Yi Tang

Summary

Affiliation: National Tsing Hua University
Country: Taiwan

Publications

  1. pmc Identification of degenerate motifs using position restricted selection and hybrid ranking combination
    Chien Hua Peng
    Department of Computer Science, Institute of Molecular and Cellular Biology, National Tsing Hua University, Taiwan 300, Republic of China
    Nucleic Acids Res 34:6379-91. 2006
  2. pmc GeneAlign: a coding exon prediction tool based on phylogenetical comparisons
    Shu Ju Hsieh
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, 300, ROC
    Nucleic Acids Res 34:W280-4. 2006
  3. pmc Feature amplified voting algorithm for functional analysis of protein superfamily
    Che Lun Hung
    Department of Computer Science, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Hsinchu, Taiwan
    BMC Genomics 11:S14. 2010
  4. pmc A parallel and incremental algorithm for efficient unique signature discovery on DNA databases
    Hsiao Ping Lee
    Department of Computer Science and Communication Engineering, Providence University, Taichung, 43301 Taiwan, ROC
    BMC Bioinformatics 11:132. 2010
  5. ncbi request reprint Constrained multiple sequence alignment tool development and its application to RNase family alignment
    Chuan Yi Tang
    Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC
    J Bioinform Comput Biol 1:267-87. 2003
  6. ncbi request reprint Constrained multiple sequence alignment tool development and its application to RNase family alignment
    Chuan Yi Tang
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R O C
    Proc IEEE Comput Soc Bioinform Conf 1:127-37. 2002
  7. pmc Hydrophilic aromatic residue and in silico structure for carbohydrate binding module
    Wei Yao Chou
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
    PLoS ONE 6:e24814. 2011
  8. pmc SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations
    Yen Lin Huang
    Department of Computer Science, National Tsing Hua University, Taiwan, R O C
    Nucleic Acids Res 38:W221-7. 2010
  9. pmc RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
    Yun Sheng Chung
    Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan
    Nucleic Acids Res 35:W639-44. 2007
  10. pmc Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome
    Hsiu Yu Wang
    Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
    BMC Mol Biol 8:89. 2007

Collaborators

Detail Information

Publications38

  1. pmc Identification of degenerate motifs using position restricted selection and hybrid ranking combination
    Chien Hua Peng
    Department of Computer Science, Institute of Molecular and Cellular Biology, National Tsing Hua University, Taiwan 300, Republic of China
    Nucleic Acids Res 34:6379-91. 2006
    ..The high applicability of MotifSeeker to biological data is further demonstrated experimentally on regulons of Saccharomyces cerevisiae and liver-specific genes with experimentally verified regulatory elements...
  2. pmc GeneAlign: a coding exon prediction tool based on phylogenetical comparisons
    Shu Ju Hsieh
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, 300, ROC
    Nucleic Acids Res 34:W280-4. 2006
    ..The rates of missing exons and wrong exons are smaller than 1%. GeneAlign is a free tool available at http://genealign.hccvs.hc.edu.tw...
  3. pmc Feature amplified voting algorithm for functional analysis of protein superfamily
    Che Lun Hung
    Department of Computer Science, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Hsinchu, Taiwan
    BMC Genomics 11:S14. 2010
    ..In this study, the amidohydrolase superfamily was an interesting case for verifying the proposed approach because it contains divergent enzymes and proteins...
  4. pmc A parallel and incremental algorithm for efficient unique signature discovery on DNA databases
    Hsiao Ping Lee
    Department of Computer Science and Communication Engineering, Providence University, Taichung, 43301 Taiwan, ROC
    BMC Bioinformatics 11:132. 2010
    ..However, existing discovery algorithms do not address the need to discover all implicit signatures...
  5. ncbi request reprint Constrained multiple sequence alignment tool development and its application to RNase family alignment
    Chuan Yi Tang
    Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC
    J Bioinform Comput Biol 1:267-87. 2003
    ..The resulting alignments illustrate the practicability of our method...
  6. ncbi request reprint Constrained multiple sequence alignment tool development and its application to RNase family alignment
    Chuan Yi Tang
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R O C
    Proc IEEE Comput Soc Bioinform Conf 1:127-37. 2002
    ..The resulting alignments illustrate the practicability of our method...
  7. pmc Hydrophilic aromatic residue and in silico structure for carbohydrate binding module
    Wei Yao Chou
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
    PLoS ONE 6:e24814. 2011
    ..Finally, the pre-simulated CBM structures have been deposited in the Database of Simulated CBM structures (DS-CBMs). The web service is publicly available at http://dscbm.life.nthu.edu.tw/ and http://dscbm.cs.ntou.edu.tw/...
  8. pmc SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations
    Yen Lin Huang
    Department of Computer Science, National Tsing Hua University, Taiwan, R O C
    Nucleic Acids Res 38:W221-7. 2010
    ..SoRT(2) is available online at http://bioalgorithm.life.nctu.edu.tw/SORT2/...
  9. pmc RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
    Yun Sheng Chung
    Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan
    Nucleic Acids Res 35:W639-44. 2007
    ..Experiments demonstrate that RE-MuSiC can be used to help predict important residues and locate phylogenetically conserved structural elements. RE-MuSiC is available on-line at http://140.113.239.131/RE-MUSIC...
  10. pmc Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome
    Hsiu Yu Wang
    Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
    BMC Mol Biol 8:89. 2007
    ..Although they are generated by gene duplication event, distinct edn and ecp expression profile in various tissues have been reported...
  11. doi request reprint Design of novel FLT-3 inhibitors based on dual-layer 3D-QSAR model and fragment-based compounds in silico
    Kuei Chung Shih
    Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
    J Chem Inf Model 52:146-55. 2012
    ..This dual-layer 3D-QSAR model constitutes a valuable tool to easily and quickly screen and optimize novel potential FLT-3 inhibitors for the treatment of acute myeloid leukemia...
  12. pmc A reinforced merging methodology for mapping unique peptide motifs in members of protein families
    Hao Teng Chang
    Institute of Molecular and Cellular Biology, Department of Life Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
    BMC Bioinformatics 7:38. 2006
    ..The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family...
  13. ncbi request reprint ROBIN: a tool for genome rearrangement of block-interchanges
    Chin Lung Lu
    Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, ROC
    Bioinformatics 21:2780-2. 2005
    ..If the input is sequence data, ROBIN will automatically search for the identical landmarks that are the homologous/conserved regions shared by all the input sequences...
  14. pmc SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges
    Ying Chih Lin
    Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC
    Nucleic Acids Res 34:W696-9. 2006
    ..In addition, SPRING shows phylogenetic trees that are reconstructed based on the rearrangement and breakpoint distance matrixes...
  15. doi request reprint GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects
    Chi Ching Lee
    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
    Gene 518:114-23. 2013
    ..This pre-analytic system can provide useful information for finishing a genome sequencing project...
  16. doi request reprint Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules
    Wei Yao Chou
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan 300, Republic of China
    Bioinformatics 26:1022-8. 2010
    ..Therefore, we propose a feature-incorporated alignment (FIA) to flexibly align conserved signatures in CBMs. Then, an FIA-based target-template prediction model was further implemented to identify functional ligand-binding residues...
  17. doi request reprint Pharmacophore modeling and virtual screening to identify potential RET kinase inhibitors
    Kuei Chung Shih
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    Bioorg Med Chem Lett 21:4490-7. 2011
    ..The hits were docked to RET with GOLD and CDOCKER after filtering by Lipinski's rules. Ultimately, 24 molecules were selected as potential RET inhibitors for further investigation...
  18. pmc A genetic algorithm-based Boolean delay model of intracellular signal transduction in inflammation
    Chu Chun Kang
    Department of Computer Science, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
    BMC Bioinformatics 12:S17. 2011
    ..Thus, a systematic approach to integrate experimental data and qualitative knowledge to identify the physiological consequences of environmental stimuli is needed...
  19. pmc Simpute: an efficient solution for dense genotypic data
    Yen Jen Lin
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    Biomed Res Int 2013:813912. 2013
    ..Simpute is suitable for regular screening of the large-scale SNP genotyping particularly when the sample size is large, and efficiency is a major concern in the analysis...
  20. pmc Reconstruction of phyletic trees by global alignment of multiple metabolic networks
    Cheng Yu Ma
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    BMC Bioinformatics 14:S12. 2013
    ..In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information...
  21. pmc Enzyme reaction annotation using cloud techniques
    Chuan Ching Huang
    Department of Computer Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
    Biomed Res Int 2013:140237. 2013
    ..Our tool is designed as a single execution file; thus, it could be applied to any cloud platform in which multiple queries are supported. ..
  22. pmc A novel molecular signature identified by systems genetics approach predicts prognosis in oral squamous cell carcinoma
    Chien Hua Peng
    Resource Center for Clinical Research, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan, Republic of China
    PLoS ONE 6:e23452. 2011
    ..This study identified a candidate molecular signature associated with poor prognosis in OSCC patients, which may ultimately facilitate patient-tailored selection of therapeutic strategies...
  23. pmc Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling
    Chun Tien Chang
    Department of Computer Science, National Tsing Hua University, Hsin Chu, Taiwan
    ScientificWorldJournal 2012:365104. 2012
    ....
  24. pmc Metabolic classification of microbial genomes using functional probes
    Chi Ching Lee
    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
    BMC Genomics 13:157. 2012
    ....
  25. doi request reprint Development of novel 3D-QSAR combination approach for screening and optimizing B-Raf inhibitors in silico
    Kuei Chung Shih
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    J Chem Inf Model 51:398-407. 2011
    ..78% and 80%, and the goodness of hit test score of 0.675 and 0.699, respectively. These results indicate that our combination approach could effectively identify diverse B-Raf inhibitors and predict the activity...
  26. pmc HaplotypeCN: copy number haplotype inference with Hidden Markov Model and localized haplotype clustering
    Yen Jen Lin
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    PLoS ONE 9:e96841. 2014
    ..The clinical association carried out with our fractional estimate of copy numbers in the cancer samples provides better detection power than that with integer copy number states. ..
  27. pmc Development of a human dihydroorotate dehydrogenase (hDHODH) pharma-similarity index approach with scaffold-hopping strategy for the design of novel potential inhibitors
    Kuei Chung Shih
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    PLoS ONE 9:e87960. 2014
    ..This approach provides a useful tool for the discovery and design of potential inhibitors of hDHODH, and does not require docking analysis; thus, our method can assist medicinal chemists in their efforts to identify novel inhibitors...
  28. pmc A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle
    Jeh Ting Hsu
    Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
    BMC Bioinformatics 12:281. 2011
    ..Although a number of approaches have been used to predict gene functions and interactions, tools that analyze the essential coordination of functional components in cellular processes still need to be developed...
  29. pmc Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation
    Shih Chi Peng
    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC
    BMC Bioinformatics 11:308. 2010
    ..Thus, a systematic approach is needed to integrate experimental data and theoretical hypotheses to identify the physiological consequences of environmental stimuli...
  30. pmc An efficient RNA interference screening strategy for gene functional analysis
    Chih Hung Chang
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    BMC Genomics 13:491. 2012
    ..This phenomenon implies that it is possible to silence several genes simultaneously with a carefully designed siRNA...
  31. pmc Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques
    Chia Han Chu
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
    PLoS ONE 5:e13361. 2010
    ..The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications...
  32. doi request reprint Angle-distance image matching techniques for protein structure comparison
    Chia Han Chu
    Department of Computer Science, National Tsing Hua University, Taiwan, ROC
    J Mol Recognit 21:442-52. 2008
    ..Moreover, for proteins with low sequence identity that share high structure similarity, the proposed algorithms are an efficient and effective method for structural comparison...
  33. ncbi request reprint Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems with new architectures, updated compilers, and libraries
    Jen Shiang K Yu
    Department of Biological Science and Technology, National Chiao Tung University, No 75, Po Ai Street, Hsinchu 300, Taiwan
    J Chem Inf Comput Sci 44:635-42. 2004
    ..Resultant performance impact suggests that IA64 and AMD64 architectures are able to fulfill significantly higher throughput than the IA32, which is consistent with the SpecFPrate2000 benchmarks...
  34. pmc PreZon: prediction by zone and its application to egg productivity in chickens
    Yen Jen Lin
    Department of Computer Science, National Tsing Hua University, Hsinchu City 30013, Taiwan
    ScientificWorldJournal 2012:785187. 2012
    ..It can be used to find low and improve egg productivity in TRFCCs by selecting the best chickens before they reach maturity...
  35. pmc Whole-exome sequencing to identify a novel LMNA gene mutation associated with inherited cardiac conduction disease
    Chun Chi Lai
    Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
    PLoS ONE 8:e83322. 2013
    ..Inherited cardiac conduction diseases (CCD) are rare but are caused by mutations in a myriad of genes. Recently, whole-exome sequencing has successfully led to the identification of causal mutations for rare monogenic Mendelian diseases...
  36. pmc Phylogenomic and domain analysis of iterative polyketide synthases in Aspergillus species
    Shu Hsi Lin
    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
    Evol Bioinform Online 8:373-87. 2012
    ..High rates of gene duplication and divergence were frequent. All data are accessible through our web database at http://metabolomics.jp/wiki/Category:PK...
  37. doi request reprint Identification of essential residues of human alpha-L-fucosidase and tests of its mechanism
    Sheng Wen Liu
    Department of Applied Chemistry, National Chiao Tung University, Institute of Biological Chemistry, Academia Sinica, Hsinchu, Taiwan
    Biochemistry 48:110-20. 2009
    ..As direct evidence to prove the function of Glu(289), an accumulation of fucosyl-enzyme intermediate was detected directly through ESI/MS analysis...
  38. ncbi request reprint An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species
    Ying Chih Lin
    Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, R O C
    J Comput Biol 12:102-12. 2005
    ....