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݄ॱ௫

Shih, Arthur Chun-Chieh ޼Ӻᔊʧ Research Description
Research Description
޼Ӻᔊʧ
(also known as Chwen-Jye Sze)
My current research is concerned with the fol- domestic GMP plant to produce local flu vaccines.
ͦۃҢٙ޼Ӻ˴ᕚd˴ࠅϞഹࠠί͛ي༟ৃٙ
lowing topics related to bioinformatics: Beginning in 2006 we participate in a three-year
ɨΐ఻ࡈ˴ᕚj CDC (Center for Disease Control, Taiwan) project
1. Large-scale and large-number sequence align- for development of influenza vaccine. We are going
ment and the visualization tool development to study the evolutionary mechanisms of influenza
ɽˉܓ̶ඎҏΐʱؓʿൖᙂʷʈՈʘක೯ķί
In the post-genomic era, the number of se- viruses from sequence data as well as to establish
ܝਿΪଡ଼ٙࣛ˾ʕd̙˸͜ԸࠠܔစʷᗫڷٙਿΪ a computational model that can predict potentially
quences available for reconstructing the evolution-
ʿي၇စʷዝ̦ٙҏΐdᅰඎʊ຾ᄣ̋Ցڢ੬ᜓɛ ary history of genes and species has increased emerging strains in coming epidemic seasons. One
20-fold in the past decade. But most tools available of our goals is to be able to provide a quantitative
ٙήӉfෂ୕ٙࠇၑʈՈே̥ঐஈଣˇඎٙҏΐ༟ model for vaccine strain selection.
to date are limited to processing only small data
ৃdतй྅݊˸௰Գʷοʩ˙όܔͭစʷዓᗫڷٙ sets. In this project, we focus on the study and pro- Research Fellows
cessing of large-number sequence alignments and 3. Plant mitochondrial genomes: annotation and
˙جdცࠅ޴຅ɽඎٙࠇၑi຅ҏΐᅰͦᄣ̋ࣛd molecular evolution study
their phylogenies. We are going to develop efficient
ఱ఻˷ೌجίϞࠢٙࠇၑ༟๕ɨࠇၑҁϓfίவࡈ algorithms for constructing large-scale phylogenetic To date, only few of plant mitochondrial DNA
trees, such as supertrees, as well as to develop effec- genomes (mtDNAs) have been completely sequenc-
ࠇ೥ʕdҢࡁ޼Ӻձஈଣ̶ඎҏΐર዆ԨઞীνО
tive visualization tools for visualizing these data. So ing because the sizes of mtDNAs are not only
ܔͭ˼ࡁٙစʷᗫڷfͦۃҢࡁʊ຾೯࢝̈ɓࢁൖ far, we have developed a versatile alignment visual- greatly expanded but also highly variable in size. To
ization system, SinicView (Sequence-aligning INno- explore the diversity of complete mtDNA structures
ᙂʷӻ୕d౤Զɽˉܓҏΐર዆ʘˢ༰ʈՈd၈މ vative and Interactive Comparison VIEWer), which during the evolution of the major seed plants and
Research Fellows
ਿ
ਿ ͉ ༟ ࣘ SinicViewfவࡈʈՈ̙˸ᜫԴ͜٫Դ͜Іʉٙҏΐ enables users to efficiently compare and evaluate as- to understand the mtDNA genomic organization in
༟
͉
ࣘ
sorted alignment results obtained by different tools the gymnosperm lineages, Dr. Shu-Miaw Chaw, a
༟ࣘdˢ༰ʔΝҏΐર዆೻όהପ͛ٙഐ؈ʘගٙ
in the initial stage of sequence analysis. research fellow of Research Center for Biodiver-
ᔖcc၈j п޼Ӻࡰ ࢨମdԨ፯኿௰ቇΥٙഐ؈ආБܝᚃٙʱؓʈЪf sity, Academia Sinica, chose Taitung cycad (Cycas

Assistant Research Fellow Aug. 2002- 2. Influenza virus study and vaccine strain selec- taitungensis), an endangered and rare cycad, as a
tion
ݴชषݭʱؓၾޥߴषݭࣺཫ಻ķʱؓݴชޥ model of the cycads and has completely sequenced
௰৷ኪዝj Ph.D., Computer Science and ߴਞϽषݭࣺձՉ˼อጳषݭࣺٙᜊମdމݴБष In recent years, the study of molecular phylog- the mitochondrial genome. We have cooperated
Information Engineering, National enies of influenza viruses has become increasingly with Dr. Chaw to analyze and annotate the whole
genome as well as to study possible evolutionary
important for epidemiologists and evolutionary
Central University, ኪɪ޴຅ࠠࠅٙᙄᕚfሊ͛໇މᒒеຬɓί೯͛Ό biologists. To avoid a lack of drugs and vaccines mechanisms of some newly discovered elements in
Taiwan (1998) ଢɽݴБࣛd̙ঐೌج౤Զԑ੄ٙޥߴʿᖹيԶ਷ in case of a global flu outbreak, the Department of the cycad.
ɛԴ͜dΪϤʊ຾ක֐ࠇ೥ІБ͛ପݴชޥߴfҢ Health, Executive Yuan, has planned to establish a
ཥcc༑j+886-2-2788-3799 ext. 1719 ࡁί2006ϋਞ̋श၍҅ٙݴชޥߴ޼೯ࠇ೥މಂɧ
Selected Publications
ෂccॆj+886-2-2782-4814 ϋfҢࡁཫࠇᔟ͟ʱؓ͟ᑗґ՟੻ٙषݭࣺd੽ࣨ Selected Publications
ཥɿڦᇌjarthur@iis.sinica.edu.tw 㹷აҏΐɪٙ߉ᜊᒈැdܔͭޥߴषݭࣺձอጳष 1. Chwen-Jye Sze, Hong-Yaun Mark Liao, Kuo-Chin Fan, Ming-Yang 10. Chun-Chieh Shih, Hsiao-Rong Tyan and Hong-Yaun Mark Liao, “Shot
ݭࣺٙʱɿစʷᜊମᅼόdආϾཫ಻ݴชޥߴਞϽ Chern, and Chen-Kuo Tsao, “ Fractal image coding system based on Change Detection based on the Reynolds Transport Theorem,” Proc.

ၣccࠫj http://www.iis.sinica.edu.tw/pages/arthur an adaptive side-coupling quadtree structure,” Image and Vision Com- Second IEEE Pacific Rim Conference on Multimedia, Oct.24-26, Bei-
षݭࣺ݊щʊ຾ჃᕎͦۃݴБٙषݭࣺૄ໊dપ಻ puting, vol.14, pp. 401-415, 1996. jing, China, LNCS 2195, pp.819-824, 2001.
2. Chwen-Jye Sze, Hong-Yaun Mark Liao, Hai-Lung Hung, Kuo-Chin 11. Chwen-Jye Sze, Hong-Yaun Mark Liao, and Kuo-Chin Fan, “A New
̙ঐอጳݴБٙषݭࣺૄ໊d౤ԶԣޥఊЗһอޥ Fan, and Jun-Wei Hsieh, “Multiscale Edge Detection on Range Images Image Flux Conduction Model and It’s Application to Selective Im-
via Normal Changes,” IEEE Trans. on Circuits and Systems II, Special age Smoothing,” IEEE Trans. on Image Processing, vol.10, no.2,
ߴषݭࣺٙ༟ৃf issue on Multirate Systems, Filter Banks, Wavelets, and Applications, pp.296-306, 2001.
• Postdoctoral Fellow, Ecology and Evolution, vol. 45, no. 8, pp.1087-1092, 1998. 12. Ming-Shing Su, Chun-Yen Chen, Chun-Chieh Shih, and K. Y. Cheng,
University of Chicago, USA (2001/04 ~ 2002/02), ಔي୐ᇞ᜗ਿΪଡ଼ʘൗ༆ၾʱɿစʷዚՓٙઞী 3. Chwen-Jye Sze, Hong-Yaun Mark Liao, Shih-Kun Huang and Chun- “Smoothing of 3D Polygon Meshes Using Non-Linear Diffusion
Equations,” Computer Graphics Workshop, Taiwan, 24-24, 2002.
Shieh Lu, “Selective Image Smoothing via Dyadic Wavelet-based
Conduction Equation,” IEEE Workshop on Neural Network for Signal 13. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-Shieh
• Postdoctoral Fellow, IIS, Academia Sinica, ķ୐ᇞ᜗ί୚ߤʫҲစࠠࠅٙԉЍfಔيٙ୐ᇞ᜗ Processing, pp.400-408, 1999. Lu, “Dyadic Wavelet-based Nonlinear Conduction Equation: Theory
Taiwan (1998/10 ~ 2001/03 and 2002/03~2002/07), ਿΪଡ଼DNAҏΐڗܓ޴ମޟɽd੽60 KBՑ400KB 4. Chwen-Jye Sze, Hsiao-Rong Tyan, Hong-Yuan Mark Liao, Chun- and Applications,” IEEE Trans. on Image Processing, vol. 12, no.4,
pp.466-476, 2003.
Shieh Lu and Shih-Kun Huang, “Shape-based Retrieval on a Fish Da-
Ph.D., Computer Science and Information ேϞfͦۃස฽ˇᅰٙ৷ഃي၇ٙ୐໗᜗ਿΪଡ଼஗ tabase of Taiwan,” Tamkang Journal of Science and Engineering, Vol. 14. Lian-Hua Chen, Chih-Wen Su, Hong-Yuan Liao, and Chun-Chieh
2, No.3, pp.163-173, 2000. Shih, "On the Preview of Digital Movies," Journal of Visual Commu-
Engineering, National Central University, ֛ҏҁϓfίႠɿಔيژձጹᗳಔيژdͦۃ֠͊ 5. Chun-Shieh Lu, Hong-Yuan Mark Liao, Shih-Kun Huang, and Chwen- nication and Image Representation, vol. 14, pp.358-368, 2003.
Taiwan (1998), Ϟ΂Оٙ˾ڌي၇ʘ୐ᇞ᜗ਿΪଡ଼஗֛ҏf͟׵ᘽ Jye Sze, “Cocktail watermarking for digital image protection,” IEEE 15. C. H. Wang, H. C. Lin, C. C. Shih, H. R. Tyan, C. F. Lin and H. Y.
Trans. on Multimedia, Vol. 2, No.4, December 2000.
Mark Liao, "Querying Image Database by Video Content," Journal of
6. Chun-Shieh Lu, Shih-Kun Huang, Chwen-Jye Sze, and Hong-Yuan Information Science and Engineering, Vol.19 No.6, pp.967-987, 2003.
• M.S., Electrical Engineering, National Chung Cheng ᚛ಔيίစʷɪʿ͛يεᅵʷٙሙᕚʕҲစ޴຅ࠠ Mark Liao, “A new watermarking technique for multimedia protec- 16. Arthur Chun-Chieh Shih and Wen-Hsiung Li, “GS-Aligner: A Novel
tion, in Multimedia Image and Video Processing, eds. Ling Guan, Tool for Aligning Genomic Sequences Using Bit-Level Operations,”
University, Taiwan (1994), ࠅٙԉЍdʱؓՉ୐໗᜗ਿΪଡ଼d̙˸՘пҢࡁ੻ Jan Larsen, and S. Y. Kung, CRC Press Inc., Chapter 18, pp.507-530, Mol. Biol. Evol., vol. 20, pp.1299-1309, 2003.
2000. 17. Yu-Ming Liang, Arthur Chun-Chieh Shih, Hsiao-Rong Tyan, and
ٝᘽ᚛ಔيί͛նዓٙፋᇝᗫڷʿಔيٙစʷཀ೻ 7. Chwen-Jye Sze, Hong-Yaun Mark Liao, Chun-Shieh Lu, and Shih- Hong-Yuan Mark Liao, “Background Modeling Using Phase Space for
• B.S., Electrical Engineering, Chinese Culture Kun Huang, “Dyadic Wavelet-based Nonlinear Conduction Equation: Day and Night Video Surveillance Systems,” 5th IEEE Pacific-Rim
ၾዚՓfͦۃ͉ࠇ೥ၾʕ޼৫͛يεᅵ׌ʕː޼Ӻ
University, Taiwan (1992). Theory and Applications,” 2000 International Conference on Image Conference on Multimedia, Lecture Note in Computer Science, pp. I.
ɛࡰ΍ΝΥЪdᔟ͟˼ࡁҁϓ̨؇ᘽ᚛୐ᇞ᜗ਿΪ 8. Processing, vol. I, pp. 880-883, 2000. 18. 206-213, 2004.
Jung-Shiong Chang, Arthur Chun-Chieh Shih, Hong-Yuan Mark Liao,
Chwen-Jye Sze, Hong-Yaun Mark Liao, Chun-Shieh Lu, and Simon
ଡ଼ٙҏΐdආБਿΪൗ༆ٙʈЪdΝࣛʱؓɓԬ C. Li, “Shape-based Retrieval on A Fish Database of Taiwan,” Fourth and Wen-Hsien Fang, “Using Normal Vectors for Stereo Correspon-
Asian Conference on Computer Vision, vol.I, pp.370-375, 2000. (in- dence Construction,” KES 2005 Lecture Notes in Artifi cial Intelligence
ʩ९€νtransposonsձtandem repeatsٙʱбၾԸ vited paper). (LNAI) 3681 (1), pp.381-387, 2005.
9. Chwen-Jye Sze, Hong-Yaun Mark Liao, and Kuo-Chin Fan, “Selec- 19. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng ,
๕dઞীί୐໗᜗ਿΪଡ଼စʷʕהҲစ̙ٙঐዚ tive Image Smoothing Based on An Image Flux Conduction Model”, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou,
Fourth Asian Conference on Computer Vision, vol.I, pp.553-558, Tze-Chang Shiao, and Mu-Fen Hsieh, “SinicView: A visualization en-
Փf 2000. vironment for comparisons of multiple nucleotide sequence alignment
tools,” BMC Bioinformatics,7:103, 2006.
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