Huai Kuang Tsai

Summary

Affiliation: Academia Sinica
Country: Taiwan

Publications

  1. pmc Impact of DNA-binding position variants on yeast gene expression
    Krishna B S Swamy
    Institute of Information Science, National Yang Ming University, Taiwan
    Nucleic Acids Res 37:6991-7001. 2009
  2. doi request reprint Associations between intronic non-B DNA structures and exon skipping
    Zing Tsung Yeh Tsai
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan, Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan and Institute of Biomedical Informatics, National Yang Ming University, Taipei, 112, Taiwan
    Nucleic Acids Res 42:739-47. 2014
  3. pmc Evolution of cis-regulatory elements in yeast de novo and duplicated new genes
    Zing Tsung Yeh Tsai
    Institute of Information Science, Academia Sinica, Taipei, Taiwan
    BMC Genomics 13:717. 2012
  4. pmc Evolutionary conservation of DNA-contact residues in DNA-binding domains
    Yao Lin Chang
    Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan
    BMC Bioinformatics 9:S3. 2008
  5. pmc Co-expression of neighboring genes in the zebrafish (Danio rerio) genome
    Huai Kuang Tsai
    Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan
    Int J Mol Sci 10:3658-70. 2009
  6. pmc Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system
    Huai Kuang Tsai
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    BMC Genomics 8:352. 2007
  7. pmc MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
    Huai Kuang Tsai
    Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
    Nucleic Acids Res 35:W221-6. 2007
  8. ncbi request reprint Method for identifying transcription factor binding sites in yeast
    Huai Kuang Tsai
    Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan
    Bioinformatics 22:1675-81. 2006
  9. doi request reprint Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast
    Chien Hao Su
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    Genomics 96:352-61. 2010
  10. pmc Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast
    Krishna B S Swamy
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
    BMC Evol Biol 11:150. 2011

Collaborators

Detail Information

Publications24

  1. pmc Impact of DNA-binding position variants on yeast gene expression
    Krishna B S Swamy
    Institute of Information Science, National Yang Ming University, Taiwan
    Nucleic Acids Res 37:6991-7001. 2009
    ..Our analysis supports the importance of nucleotide variants at variable positions of TFBSs in gene regulation...
  2. doi request reprint Associations between intronic non-B DNA structures and exon skipping
    Zing Tsung Yeh Tsai
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan, Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan and Institute of Biomedical Informatics, National Yang Ming University, Taipei, 112, Taiwan
    Nucleic Acids Res 42:739-47. 2014
    ..We thus show that, in addition to the well-known effects of RNA and protein structure, the relative positional arrangement of intronic non-B DNA structures may also impact exon skipping. ..
  3. pmc Evolution of cis-regulatory elements in yeast de novo and duplicated new genes
    Zing Tsung Yeh Tsai
    Institute of Information Science, Academia Sinica, Taipei, Taiwan
    BMC Genomics 13:717. 2012
    ..Here, we conducted a comprehensive investigation to depict the emergence and establishment of cis-regulatory elements in de novo yeast genes...
  4. pmc Evolutionary conservation of DNA-contact residues in DNA-binding domains
    Yao Lin Chang
    Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan
    BMC Bioinformatics 9:S3. 2008
    ..In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues...
  5. pmc Co-expression of neighboring genes in the zebrafish (Danio rerio) genome
    Huai Kuang Tsai
    Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan
    Int J Mol Sci 10:3658-70. 2009
    ..Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes' co-expression are also discussed...
  6. pmc Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system
    Huai Kuang Tsai
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    BMC Genomics 8:352. 2007
    ..iis.sinica.edu.tw/~mybs/, the ratios of TF-sharing pairs among all the adjacent pairs in yeast genomes were analyzed. The levels of co-expression in different adjacent patterns were also compared...
  7. pmc MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
    Huai Kuang Tsai
    Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
    Nucleic Acids Res 35:W221-6. 2007
    ..MYBS also allows users to identify target gene sets of each TF pair, which could be used as a starting point for further explorations of TF combinatorial regulation. MYBS is available at http://cg1.iis.sinica.edu.tw/~mybs/...
  8. ncbi request reprint Method for identifying transcription factor binding sites in yeast
    Huai Kuang Tsai
    Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan
    Bioinformatics 22:1675-81. 2006
    ..The abundance and the diversity of genomic data provide an excellent opportunity for identifying TFBSs. Developing methods to integrate various types of data has become a major trend in this pursuit...
  9. doi request reprint Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast
    Chien Hao Su
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    Genomics 96:352-61. 2010
    ..Our analysis suggests that genes in a divergent pair tend to be co-regulated in at least one condition; however, in most conditions, they may not be co-regulated...
  10. pmc Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast
    Krishna B S Swamy
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
    BMC Evol Biol 11:150. 2011
    ..Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites...
  11. pmc Statistical methods for identifying yeast cell cycle transcription factors
    Huai Kuang Tsai
    Genomics Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 102:13532-7. 2005
    ..In addition to the cell cycle, our methods are also applicable to other functions...
  12. doi request reprint MetaABC--an integrated metagenomics platform for data adjustment, binning and clustering
    Chien Hao Su
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    Bioinformatics 27:2298-9. 2011
    ..After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams...
  13. ncbi request reprint The impact of normalization and phylogenetic information on estimating the distance for metagenomes
    Chien Hao Su
    Academia Sinica, Taipei
    IEEE/ACM Trans Comput Biol Bioinform 9:619-28. 2012
    ..We conclude that incorporating rank-based normalization with phylogenetic information into the distance functions helps achieve reliable clustering results...
  14. doi request reprint Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast
    Sufeng Chiang
    Institute of Information Science, Academia Sinica, Taiwan
    Gene 491:237-45. 2012
    ..e., highly co-localized). Moreover, such associations were highly conserved between sensu stricto yeasts and also influenced gene expression, which were consistent with enriched functional categories...
  15. pmc Roles of trans and cis variation in yeast intraspecies evolution of gene expression
    Huang Mo Sung
    Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 26:2533-8. 2009
    ..Moreover, MIM genes are, on average, subject to stronger trans effects than SIM genes, though the difference between the two types of genes is not conspicuous...
  16. pmc The impact of trans-regulation on the evolutionary rates of metazoan proteins
    Yi Ching Chen
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    Nucleic Acids Res 41:6371-80. 2013
    ....
  17. doi request reprint De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae
    Mei Ju May Chen
    Department of Computer Science and Information Engineering, National Taiwan University and Institute of Information Science, Academia Sinica, Taipei, Taiwan
    Bioinformatics 28:701-8. 2012
    ..This article aims at improving the accuracy of inferring TF-TF interactions by incorporating motif discovery as a fundamental step when detecting overlapping targets of TFs based on ChIP-chip data...
  18. doi request reprint MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions
    Tse Yi Wang
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
    Bioinformatics 27:3341-7. 2011
    ..However, such estimated abundances might deviate from the true abundances in habitats due to sampling biases and other systematic artifacts in metagenomic data processing...
  19. pmc Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency
    Francis C Weng
    Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
    BMC Bioinformatics 11:565. 2010
    ..We also compared the consistency between our taxonomic binning and those reported in the original studies...
  20. ncbi request reprint Cysteine separations profiles on protein sequences infer disulfide connectivity
    East Zhao
    Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University, No 1, Sec 4, Roosevelt Rd, Taipei, Taiwan 106
    Bioinformatics 21:1415-20. 2005
    ..Here, by using an alternative scheme with global information for disulfide connectivity prediction, higher performance is obtained with respect to other approaches...
  21. ncbi request reprint An evolutionary approach for gene expression patterns
    Huai Kuang Tsai
    Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan, ROC
    IEEE Trans Inf Technol Biomed 8:69-78. 2004
    ..These results indicate that HeSGA has potential in analyzing gene expression patterns...
  22. pmc Discovering gapped binding sites of yeast transcription factors
    Chien yu Chen
    Department of Bio Industrial Mechatronics Engineering, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan
    Proc Natl Acad Sci U S A 105:2527-32. 2008
    ..Predictions on additional 54 TFs successfully discover 11 gapped and 38 ungapped motifs supported by literature. Our method achieves high sensitivity and specificity for predicting experimentally verified TFBSs...
  23. ncbi request reprint An evolutionary algorithm for large traveling salesman problems
    Huai Kuang Tsai
    Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan, ROC
    IEEE Trans Syst Man Cybern B Cybern 34:1718-29. 2004
    ..0074% above the optimum for each test problem. These findings imply that the proposed method can find tours robustly with a fixed small population and a limited family competition length in reasonable time, when used to solve large TSPs...
  24. pmc GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations
    Jinn Moon Yang
    Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao Tung University, Hsinchu, 30050, Taiwan
    Protein Sci 11:1897-907. 2002
    ..These results suggest that GEM is robust and can be used to examine the factors limiting the accuracy of protein side-chain prediction methods. Furthermore, it can be used to systematically evaluate and thus improve scoring functions...