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 CSB Laboratory 計算系統生物學實驗室  
 

「計算系統生物學實驗室(Computational Systems Biology Laboratory)」成立於2010年,由 李宗夷 教授 擔任本實驗室之指導教授,本實驗室以培育資訊、生物、統計等跨領域專業人才為宗旨。本實驗室專注於生物資訊與系統生物學相關研究,包含基因調控網路、蛋白質體學與蛋白質轉譯後修飾作用、Metagenomics and Metatranscriptomics、癌症生物標誌與藥物設計、訊息傳遞與代謝路徑等,並結合雲端運算與大數據技術建構高效能及高穩定度之生物資料庫與分析系統。

李宗夷老師非常重視學生品格學習態度(能力可以培養,但性格與態度決定你的未來發展),並強調實驗室向心力與團隊合作。老師亦非常鼓勵學生參加國際學術研討會,累積人生經歷與擴大國際視野,加強英文口說、寫作與表達能力,帶領學生找到自信心與成就感,更致力於提升台灣在生物資訊領域之國際能見度。

(實驗室於2010年成立,至今已發表超過 50 篇「SCI國際期刊」研究論文)


 News 最新消息

 
 

恭賀本實驗室指導教授 李宗夷 老師 榮獲「財團法人徐有庠紀念基金會」頒發 第十三屆有庠傑出教授獎(新聞連結)

本實驗室博士生 高慧茹 同學 於國際研討會 APBC2015 發表論文海報 "Characterization and identification of protein O-linked glycosylation sites based on glycotransferase substrate specificities",並獲得 Best Poster Presentation Award. (more ...)

2015.05.20 - 由 CSB Lab 發佈



研究方向與未來展望

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Protein Post-translational Modifications 蛋白質後轉譯修飾作用


ptm
Cheng-Tsung Lu†, Kai-Yao Huang†, Min-Gang Su† († joint first authorship), Tzong-Yi Lee* ,Neil Arvin Bretaña, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen, and Hsien-Da Huang*, 2013, "dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications," Nucleic Acids Research, 41:D295-305. (SCI, 2011 IF: 8.026 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

Related Publications

Tzong-Yi Lee*, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang and Yu-Ju Chen*, 2012, "dbSNO: a database of cysteine S-Nitrosylation," Bioinformatics, 28(17):2293-5. (SCI, 2011 IF:5.468; 1/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

Cheng-Tsung Lu, Neil Arvin Bretaña, Tzu-Hsiu Cheng, and Tzong-Yi Lee*, 2011, "Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites," Journal of Computer-Aided Molecular Design, 25(10):987-95. (SCI, 2010 IF:3.374; 4/97 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)

Tzong-Yi Lee*, Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Min-Gang Su, and Kai-Yao Huang, 2011, "Investigation and identification of protein γ-glutamyl carboxylation sites," BMC Bioinformatics, 12 Suppl 11, S10. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

Tzong-Yi Lee*, Yi-Ju Chen, Tsung-Cheng Lu, Hsien-Da Huang and Yu-Ju Chen*, 2011, "SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity," PLoS ONE, 6(7): e21849. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)

Tzong-Yi Lee*, Shu-An Chen, Hsin-Yi Hung, and Yu-Yen Ou, 2011, "Incorporating distant sequence features and radial basis function network to identify ubiquitin conjugation sites," PLoS ONE, 6(3): e17331. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)

Shu-An Chen†, Tzong-Yi Lee† († joint first authorship), and Yu-Yen Ou*, 2010, "Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins," BMC Bioinformatics, 11:536. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, and Hsien-Da Huang, 2010, "N-Ace: using solvent accessibility and physicochemical properties to identify protein N-Acetylation sites," Journal of Computational Chemistry, Vol. 31 (15), 2759-2771. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)

D.M. Shien†, Tzong-Yi Lee† († joint first authorship), W.C. Chang, J.B.K. Hsu, J.T. Horng, P.C. Hsu, T.Y. Wang and H.D. Huang*, 2009, Jul 15 "Incorporating Structural Characteristics for Identification of Protein Methylation Sites," Journal of Computational Chemistry, Vol. 30, No. 9, pp.1532-1543. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)

W.C. Chang†, Tzong-Yi Lee† († joint first authorship), D.M. Shien, J. B.K. Hsu, P.C. Hsu, T.Y. Wang, J.T. Horng, H.D. Huang* and R.L. Pan*, 2009, Nov 30 "Incorporating support vector machine for identifying protein tyrosine sulfation sites," Journal of Computational Chemistry, . (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)

Tzong-Yi Lee, J.B.K. Hsu, W.C. Chang, T.Y. Wang, P.C. Hsu, and H.D. Huang*, 2009, "A Comprehensive Resource for Integrating and Displaying Protein Post-Translational Modifications," BMC Research Notes, 2(1):111.

Tzong-Yi Lee, H.D. Huang*, J.H. Hung, Y.S. Yang, and T.H. Wang*, 2006, "dbPTM: An information repository of protein post-translational modification," Nucleic Acids Research, Vol. 34, D622-D627. (SCI, 2011 IF: 8.026 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)


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Protein Phosphorylation & Signal Transduction 蛋白質磷酸化與信息傳遞


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Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, and Hsien-Da Huang* , 2011, "RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans," Nucleic Acids Research, Vol. 39, D777-D787. (SCI, 2011 IF: 8.026; 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

Related Publications

Neil Arvin Bretaña, Cheng-Tsung Lu,Chiu-Yun Chiang, Min-Gang Su, Kai-Yao Huang, Tzong-Yi Lee* and Shun-Long Weng, 2012, "Identifying Protein Phosphorylation Sites with Kinase Substrate Specificity on Human Viruses," PLoS ONE, 7(7): e40694. (SCI, 2011 IF:4.092; 12/84 in BIOLOGY)


Tzong-Yi Lee*, Neil ARVIN Bretana, and Cheng-Tsung Lu, 2011, "PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity," BMC Bioinformatics, 12:261. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)


Y.H. Wong†, Tzong-Yi Lee† († joint first authorship), H.K. Liang, C.M. Huang, Y.H. Yang, C.H. Chu, H.D. Huang* , M.T. Ko, and J.K. Hwang, 2007, "KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns," Nucleic Acids Research, Vol 35, W588-594. (SCI, 2011 IF: 8.026 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)


H.D. Huang*, Tzong-Yi Lee, S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou, 2005, "Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites," Journal of Computational Chemistry, Vol. 26, pp.1032-1041. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)


H.D. Huang*, Tzong-Yi Lee, S.W. Tseng, and J.T. Horng, 2005, "KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites," Nucleic Acids Research, Vol. 33, W226-229. (SCI, 2011 IF: 8.026 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)



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Gene Transcriptional Regulation 基因轉錄調控


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Tzong-Yi Lee*, Wen-Chi Chang*, Justin BK Hsu, Tzu-Hao Chang and Dray-Ming Shien, 2012, January "GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group," BMC Genomics, 13(Suppl 1):S3. (SCI, 2011 IF: 4.073; 26/157 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

Related Publications

W.C. Chang, Tzong-Yi Lee, H.D. Huang*, H.Y. Huang, R.L. Pan*, 2008, "PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group," BMC Genomics, 9:561. (SCI, 2010 IF: 4.206; 24/160 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)


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Protein Functions & Structures 蛋白質功能與結構


structure
Justin Bo-Kai Hsu, Neil Arvin Bretaña, Tzong-Yi Lee* and Hsien-Da Huang*, 2011, "Incorporating evolutionary information and functional domains for identifying RNA splicing factors," PLoS ONE, 6(11): e27567. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)

Related Publications

Tzong-Yi Lee*, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, and Cheng-Tsung Lu, 2011, "Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences," Bioinformatics, 27(13): 1780-1787. (SCI, 2011 IF:5.468; 1/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)


Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee and M. Michael Gromiha*, 2011, June "Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties," Bioinformatics, 27(15):2062-7. (SCI, 2011 IF:5.468; 1/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)


J.H. Hung†, H.D. Huang†,* († joint first authorship), and Tzong-Yi Lee, 2006, "ProKware: an integrated software for presenting protein structural properties in protein tertiary structures," Nucleic Acids Research, Vol 34, W89-W94. (SCI, 2011 IF: 8.026 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)


Tzong-Yi Lee, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin, 2006, "An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints," Journal of Computational Chemistry, Vol. 27, No. 9, 1020-32. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)


H.D. Huang, Tzong-Yi Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou, 2005, "MultiProtIdent: identifying proteins using database search and protein-protein interactions," Journal of Proteome Research, Vol. 4(3), 690-697. (SCI, 2010 IF: 5.460; 9/71 in BIOCHEMICAL RESEARCH METHODS)



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High-throughput Technology & Cancer Biomarker 生物晶片與癌症生物標記


chip
C.H. Chien, Y.M. Sun, W.C. Chang, P.Y. Chiang-Hsieh, Tzong-Yi Lee, W.C. Tsai, J.T. Horng, A.P. Tsou*, H.D. Huang*, 2011, "Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data," Nucleic Acids Research, 39(21):9345-9356. (SCI, 2011 IF: 8.026; 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

Related Publications

Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee and Hsien-Da Huang*, 2011, "miRTar: an integrated system for identifying miRNA-target interactions in Human," BMC Bioinformatics, 12:300. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)



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