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Tsai, Huai-Kuang ޼Ӻᔊʧ Research Description
Research Description
޼Ӻᔊʧ

ᎇഹ͛ي߅ҦٙආӉd͛ي޴ᗫ༟ࣘҞ஺ଢ଼ Along with biotechnological progress, massive croarray experiment to identify important genes in
biological data accumulates that urges further coop- yeast fermentation.
ጐdڮԴ͛يኪ࢕ၾ༟ৃኪ࢕ٙආɓӉΥЪfҢ০ eration between biologists and computer scientists.
My colleagues and I have participated in several The transcription of genes is controlled by
࿁஢εࠠࠅٙ͛ي༟ৃ޴ᗫਪᕚਂཀɓӻΐٙ޴ᗫ bioinformatics-related studies, including protein interaction between transcription factors (TFs) and
structure prediction, microarray and sequence analy- their binding sites (TFBSs) (or cis-regulatory ele-
޼Ӻdͦۃ޼Ӻ˙Σ˴ࠅ̙ʱމஐͣሯഐ࿴ཫ಻e ments). Inferring the function of a TF and identify-
sis, and regulatory networks.
͛ي౺˪ၾҏΐʱؓ˸ʿܔͭਿΪሜછၣ༩f ing its binding sites are helpful for understanding
In protein structure prediction, we proposed the mechanism of transcriptional regulation. We
an evolutionary approach combined by a rotamer developed an integrated computational approach to
ίஐͣሯഐ࿴ཫ಻௅ʱdҢࡁ౤̈ɓစʷό library to predict protein side-chain conformations. identify regulatory elements in the yeast cell cycle. Research Fellows
The proposed method is robust and can be used to The method utilizes several data sources, including
ࠇၑٙ˙جdഐΥ༟ࣘࢫԸЪஐͣሯ˕ᗡʘഐ࿴ཫ DNA sequences, phylogenetic information, microar-
examine the factors limiting the accuracy of protein
಻fה౤̈ʘ˙جʔසঐϓ̌ཫ಻˕ᗡd͵̙˸ܛ side-chain prediction methods. We also proposed an ray data and chromatin immunoprecipitation - DNA
algorithm to detect the disulfide connectivity of pro- chip (ChIP-chip) data. The essential idea is that
ࠈίஐͣሯ˕ᗡഐ࿴ཫ಻˙ج΢၇Ϊ९࿁ഐ؈ʘᅂ teins using cysteine separation profiles. We are cur- genes regulated by a cell cycle TF should have high-
rently investigating ways to integrate protein side- er (lower, if it is a repressor) expression levels than
ᚤfϤ̮ᔟ͟ᝈ࿀޴Νᕐିᒟٙஹഐً࿒dҢࡁ೯ chain conformations and disulfide bonds to predict genes not regulated by it during one or more phases
the protein structure. of the cell cycle. We predict 50 cell cycle TFs and
ତՉஐͣሯҏΐʕdՇՇ̒আऄაʘගٙ൷ᕎϞ޴
Research Fellows
ਿ ͉ ༟ ࣘ
ਿ ͉ ༟ ࣘ 80 synergistic TF pairs and describe the behaviors
ʝ࿁ᏐٙᗫڷdҢࡁ౤̈ɓ˙ج̙˸͍ᆽཫ಻ᕐି In microarray and sequence analysis, we in- of 50 known or inferred cell cycle TFs in each cell
vestigated the optimal array sets for microarray ex- cycle phase in terms of activation/repression and
ᒟٙஹഐً࿒fͦۃҢࡁ͍޼ӺνО዆Υஐͣሯ˕ perimental design and utilized the microarray data potential positive/negative interactions between
ᔖcc၈j п޼Ӻࡰ
to identify discriminative genes in diseases. We also TFs. We further developed software, TFBSﬁ nder, to
Assistant Research Fellow (2006/7--) ᗡၾᕐିᒟஹഐٙഐ؈Ըཫ಻ஐͣሯͭ᜗ഐ࿴f designed a novel approach that significantly reduced identify TFBS, outperforming well-known methods.
the number of primers in the multiplex polymerase We are now studying to modify our methods for ap-
௰৷ኪዝj Ph.D., Computer Science and ί͛ي౺˪ʿҏΐʱؓ˙ࠦ, Ңࡁਗ਼రҬ͛ي chain reaction experiments. We are currently col- plications to other functions in order to build up the
Information Engineering, National laborating with biologists to design an optimal mi- whole regulatory networks.
Taiwan University (2003) ౺˪௰Գྼ᜕ணࠇᔷʷϓɓࡈतᅄ፯՟ٙਪᕚdԨ
౤̈ɓࡈϞࣖٙ˙جԸరҬՉ௰Գྼ᜕ணࠇfҢࡁ
Selected Publications
ཥcc༑j+886-2-2788-3799 ext. 1718 Selected Publications
Ԩ˲༶͛͜ي౺˪༟ࣘԸ፫ᗆίࠠࠅशषʕdϞ׼
ෂccॆj+886-2-2782-4814 ᜑࢨйڌତٙࠠࠅਿΪfϤ̮d০࿁ልΥDNAၳΥ 1. Tsai, H.K. and Kao, C.Y. (2000) Using Genetic Algorithms to Con- ence on Mathematics and Engineering Techniques in Medicine and
struct Physical Maps of Chromosomes with Unique Probes, Interna-
Biological Sciences (METMBS), 243-249.
ཥɿڦᇌjhktsai@iis.sinica.edu.tw 㺛ஹᕁˀᏐdҢࡁ౤̈ɓࡈอ˙جԸணࠇ௰ˇࡈᅰ tional conference on Computational Biology (RECOMB), Currents in 12. Huang, Y.C., Chao, Y.C., Lin, S.B., Tsai, H.K. and Kao C.Y. (2004) A

Computational Molecular Biology. Tool to Determine the Speciﬁcity of Antisense Oligonucleotide, The
ၣccࠫjhttp://www.iis.sinica.edu.tw/pages/hktsai ٙˏɿdɽඎࠥЭ༈ྼ᜕הცϓ͉fҢࡁͦۃၾ͛ 2. Tsai, C.H., Yang, J.M., Hwang, M.J., Tsai, H.K. and Kao, C. Y. (2001) 2004 International Conference on Mathematics and Engineering Tech-
Protein Side-chain Prediction by Evolutionary Algorithm, Medical niques in Medicine and Biological Sciences (METMBS), 447-449.
يኪ࢕ΥЪdᏍпணࠇྼ᜕ԨҬ̈ί჏͎ഽ೯჏ཀ Infromatics Symposium/Show(MIST2001), Taiwan, 2001. 13. Chuang, H.Y., Tsai, H.K. and Kao, C.Y. (2004) Optimal designs for
th
3. Tsai, H.K., Yang, J.M., and Kao, C.Y. (2001) A genetic algorithm for microarray experiments, The 7 International Symposium on Parallel
೻ʕҲစࠠࠅԉЍٙਿΪf traveling salesman problems, Proceedings of the Genetic and Evolution- Architectures, Algorithms, and Networks (I-SPAN), 619-624.
• Postdoctoral Fellow, Genome Research Center, ary Computation Conference (GECCO), 687-693. 14. Huang Y.C., Chuang H.Y., Tsai, H.K., Chang C.F. and Kao C.Y. (2004)
Academia Sinica, May 2004- June 2005. 4. Tsai, H.K., Yang, J.M. and Kao, C.Y. (2002) Solving traveling sales- Designing multiple-use primer set for multiplex PCR by using com-
ͦۃ౷ཁႩމਿΪᔷ፽݊աՑᔷ፽ΪɿʿՉ man problems by combining global and local search mechanisms, pact GAs, Lecture Notes in Computer Science, 3242, 511-523. (Impact
• Postdoctoral Fellow, Department of Computer Sci- ഐΥЗໄהሜછdʱؓᔷ፽Ϊɿٙ̌ঐၾՉ࿁Ꮠٙ 5. Congress of Evolutionary Computation (CEC), 1290-1295. 15. factor 0.513)
Tsai, Y.F., Tsai, H.K. and Kao, C.Y. (2004) Clustering analysis of
Tsai, H.K., Yang, J.M. and Kao, C.Y. (2002) Applying genetic algo-
ence and Information Engineering, National Taiwan rithms to ﬁnding the optimal gene order in displaying the microarray debris ﬂ ow streams, International Journal of Sediment Research, 19,

ഐΥЗໄਗ਼Ϟп׵ᐝ༆ਿΪᔷ፽ٙዚՓfҢࡁഐΥ data, Proceedings of the Genetic and Evolutionary Computation Confer- 37-46. (corresponding author)
University, Oct. 2003- Apr. 2004. ence (GECCO), 610-617. 16. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y. (2004) Some issues
DNAҏΐeਿΪ౺˪eစʷᗫڷձݑЍ࠽еޥӏዠ 6. Yang, J.M., Tsai, C.H., Hwang, M.J., Tsai, H.K., Hwang, J.K. and Kao, of designing genetic algorithms for traveling salesman problems, Soft
• Ph.D., Department of Computer Science and Infor- C.Y. (2002) GEM: a Gaussian Evolutionary Method for predicting Comput, 8, 689-697. (Impact factor 0.333)
౺˪d౤̈ɓࡈϞࣖٙ޼ӺԸ፫ᗆሜછ჏͎ഽ୚ߤ
mation Engineering, National Taiwan University, protein side-chain conformations, Protein Sci, 11, 1897-1907. (Impact 17. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y. (2004) An evolution-
factor 4.116)
ary approach for gene expression patterns, IEEE Trans Inf Technol
1998-2003. ඄ಂٙᔷ፽ΪɿʿՉഐΥЗໄfਿ͉ٙᝈׂމj஗ 7. Tsai, Y.F., Tsai, H.K. and Shieh, C.L. (2002) Hazard zone mapping of Biomed, 8, 69-78. (Impact factor 1.575)
ሜછ୚ߤ඄ಂʘᔷ፽ΪɿሜછٙਿΪڌତึձӚϞ debris ﬂ ow, The Chinese Journal of Mechanics, part B, 18, 91-102. (in 18. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y. (2004) An evolution-
• M.S., Department of Computer Science and Infor- Chinese) ary algorithm for large traveling salesman problems, IEEE Trans Syst
mation Engineering, National Taiwan University, ஗ՉሜછٙਿΪڌତɽʔ޴Νfл͜ϤɓᝈׂdҢ 8. Chuang, H.Y., Tsai, H.K., Tsai, Y.F. and Kao, C.Y. (2003) Rank- 19. Man Cybern B Cybern, 34, 1718-1729. (Impact factor 1.052)
Chan, C.H., Lee, S.A., Kao, C.Y. and Tsai, H.K. (2005) Improving
ing genes for discriminability on microarray data, J Inf Sci Eng, 19,
1996-1998. ࡁϓ̌ٙҬՑ50ࡈሜછ୚ߤ඄ಂʘᔷ፽Ϊɿ˸ʿՉ 953-966. (corresponding author) (Impact factor 0.163) EAX with restricted 2-opt, Proceedings of the 2005 Genetic and Evolu-
9. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y. (2003) Heterogeneous tionary Computation (GECCO), 1471-1476.
• B.S., Department of Computer Science and Infor- ʹʝЪ͜ᗫڷdԨ๟ᆽٙ౜ࠑՉݺʷၾҵՓЪ͜f selection genetic algorithms for traveling salesman problems, Eng Op- 20. Tsai, H.K., Lu, H.H. and Li, W.H. (2005) Statistical methods for iden-
timiz, 35, 297-311. (Impact factor 0.544) tifying yeast cell cycle transcription factors, Proc Natl Acad Sci U S A,
mation Engineering, National Taiwan University, ҢࡁԨආɓӉྼЪ̈TFBSfinderழ᜗˸፫ᗆᔷ፽Ϊ 10. Tsai, C.H., Tsai, H.K., Chen, S.C. and Kao, C.Y. (2004) Disulﬁ de con- 102, 13532-13537. (Impact factor 10.452)
1992-1996. ɿʘഐΥЗໄdՉഐ؈ჃᎴ׵ͦۃ੬͜ʘՉ˼ழ nectivity prediction using support vector machine and novel features, 21. Zhao, E., Liu, H.L., Tsai, C.H., Tsai, H.K., Chan, C.H. and Kao, C.Y.
The 2004 International Conference on Mathematics and Engineering
(2005) Cysteine separations proﬁles on protein sequences infer disul-

Techniques in Medicine and Biological Sciences (METMBS), 391-395. ﬁ de connectivity, Bioinformatics, 21, 1415-1420. (Impact factor 5.742)
᜗fͦۃҢࡁ͍዆ΥϤɓ˙ج˸Ꮠ͜ՑՉ˼͛يࠠ 11. Chiu, H.S., Chuang, H.Y., Tsai, H.K., Huang, T.W. and Kao, C.Y. 22. Tsai, H.K., Huang, Grace T., Chou, M.Y., Lu, Henry, H.S. and Li, W.H.
(2004) Discovering Statistically Signiﬁ cant Clusters by Using Genetic (2006) Method for identifying transcription factor binding sites in
ࠅ̌ঐɪԸܔͭ዆ࡈਿΪሜછၣ༩f
Algorithms in Gene Expression Data”, The 2004 International Confer- yeast, Bioinformatics, advance published online. (Impact factor 5.742)
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