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GMBDTBI

Bioinformatics Core for Genomic Medicine Bioinformatics Core for Genomic Medicine and Biotechnology Developmentand Biotechnology Development

I-Shou Chang, I-Shou Chang, Ping-Chiang LyuPing-Chiang Lyu,

Chao A. Hsiung, Jenn-Kang Hwang, H. Sunny Sun

National Health Research Institutes, National Tsing Hua University,National Chiao Tung University, and National Cheng Kung University

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GMBDTBI

GMBDTBI

Statistical Genetics

Computational proteomics

Comparative Genomics and Interactomes

Structural Bioinformatics

Applied Medical Genomics

GMBD Core

Services

Collaborative Research

Education and Training

Dissemination

R & D

Infectious diseases

Highly heritable diseases

Cancer research

Innovative research

Supporting NRPGM

NRPGM Core Facilities

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GMBDTBI

Web portal Web portal http://www.tbi.org.tw

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GMBDTBI

Online ServicesOnline Services

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GMBDTBI

Mirror sites and DatabasesMirror sites and Databases

Mirror sitesPDB -Protein Data BankSCOP -Structural Classification of ProteinsPredictProtein server –Secondary structure, solvent accessible area prediction

In-house DatabasesSNP -SNP value-added databaseRegRNA -Regulatory RNA Motifs and Elements Database miRNAMap - Genomic Maps for microRNACDSPD -CoDing region Sequence and Proteomic Database TAG-Tumor Associated Gene FlyDPI -Drosophila Database of Protein Interactomeshp-DPI -H. pylori Database of protein interactomesGPDB -Genome Profile DatabasedbPTM - Protein Post-Translational Modification Database Virtual 2D gel -Simulated 2D Gel for complete sequenced microbial genomes IM2PD -Integrated Microbial Metabolic Pathway Database SSDB -Disulfide Proteins Database pKnot –Protein knot structure database

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GMBDTBI

Analysis ToolsAnalysis Tools Homology & Similarity

BLAST -Basic Local Alignment Search Tool         BLAST servers      PDB-BLAST -BLAST against PDB protein databank         RPS-BLAST -BLAST against Motif/Domain database     

FASTA -Pair-wise Sequences Alignment

Sequence AnalysisClustalW -Web-based Multiple Sequence Alignment    PDA -Primer Design Assistant   RepeatMasker -Screening for low complexity DNA sequences [mirror ]   GPRM - Genetic Programming for RNA MotifsGenePredict -Web-based gene prediction service KinasePhos -Predict phosphorylation sites within given protein sequences     SpliceInfo -An information repository for mRNA alternative splicing ProSplicer -An Alternative Splicing Database based on Protein, mRNA, and EST Se

quences     MuSiC -Multiple Sequence Alignment with Constraints GPRM Genetic Programm

ing for RNA Motifs RNAMST -An efficient and flexible search tool for RNA structural homologs CELLO -Prediction of protein subcellular localization

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GMBDTBI

Analysis ToolsAnalysis Tools RegRNA A Regulatory RNA Motifs and Elements Finder ESTviewer A Web interface for visualizing ESTs PSEP System A Comparative Method for Identification of Gene Structures and Alternatively Splic

ed Variants ENACE System Identification and evolutionary analysis of novel exons and alternative splicing ev

ents

Phylogenetic Analysis

POWER -Phylogenetic Web Repeater

Proteomics KPST -Pathway search tool for KEGG RMA - A Reinforced Merging methodology for mapping unique peptide Tm Predictor - Melting Temperature Prediction : Predict thermal stability of proteins

Structural Analysis SARST -Structure Alignment by Ramachandran Search Tool StEQ - Structural Entropy Query SDSE - Sequence Derived Structure Entropy (PS)2 -Protein Structure Prediction Server GEMDOCK -Generic Evolutionary Method for molecular DOCKing ProKware -A graphic web server for presenting protein structural properties

GMBD

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GMBDTBI

Analysis ToolsAnalysis Tools

Miscellaneous Tools － GCG -Wisconsin Sequence Analysis Package    － SeqWeb -Web-based GCG － EMBOSS -European Molecular Biology Open Software Suite    － JEMBOSS -Java user interface of EMBOSS － EMBOSS GUI -Web-based service of EMBOSS

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GMBDTBI

SoftwareSoftware

Incorporating endophenotypes in linkage analysis Break point search based on array-CGH data Segregation analysis based on onset time Time course transcription profile of virus genome

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GMBDTBI

Accumulative visits of hp-DPI, Nov. 2004 to Nov. 2007

Usage of hp-DPI : Usage of hp-DPI : H. pylori Database of protein interactomes

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GMBDTBI

Accumulative sequences submitted to/visits of PDA, Jul. 2003 to Nov. 2007

Usage of PDA-Primer Design AssistantUsage of PDA-Primer Design Assistant

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Training and EducationTraining and Education

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Activities Activities 2003-20072003-2007

Microarray analysis workshop, held in Academia Sinica, 2004 (122)Bioinformatics and applied medical genomics, held in NCKU, 2004Workshop on Virus Evolution and Molecular Epidemiology, NHRI, Zhunan, 2005 (157)Workshop on Statistical Genomics, held in NHRI Zhunan Campus, 2006 (119)Structural Bioinformatics Workshop, held in NCKU, 2006From Sequences, Structure to Systems

Mini symposia

GMBD Core Services Workshop(471) Workshop on sequence analysis tools: The Wisconsin Package and EMNOSS suite(1,281) Workshop on Genetics, Evolution and BioinformaticsStructural bioinformatics and drug design workshopWorkshop on Analysis Methods of Genomic Research (65)Bioinformatics in medical applicationPhylogenetic Analysis Workshop(319)Workshop in systems biology and in genetic regulatory networks (in BIT2005)

Courses and Hands-on Workshop held island-wide Bioinformatics workshops: 3,037 participants

International symposium: 1255 people attended

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GMBDTBI

Course NewsCourse News

結構生物資訊學研習會 (2008.09)

課程時間：九月四日 ( 星期四 ) 至九月五日 ( 星期五 )

上課地點：中國醫藥大學互助大樓 7F 電腦教室 課程大綱：

由蛋白質基本概念、功能以及結構介紹起，接著介紹世界上與蛋白質研究相關的資料庫及各式工具，同時搭配 GMBD Core Servi

ce Website 中的工具，輔助介紹蛋白質功能與結構分析上的各項研究。

親緣演化分析研習會 (2008.10)

介紹親緣演化分析基本理論、建構演化樹之方法，以及不同演化樹所代表的意義，並配合常用之親緣演化分析軟體的實際操作

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Systems Biology Package WorkshopSystems Biology Package Workshop (NCKU)(NCKU)

Course NewsCourse News

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Research and DevelopmentResearch and Development

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Translate developments into web services: • Provide 14 in-house databases and 26 in-house tools• Published 102 papers in years 2003-2007• There are 28 tools/databases under development

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Web services under development

Statistical Genetics, Comparative Genomics and Interactomes

CDSPD － CoDing Sequence and Proteomics Database studies.

EFG － Extractor of Feature sequence from GenBank

MOLAS-Lite － Microarray OnLine Analysis System

UPS － Unique Probe Selector

My BLAST － Customized BLAST server

Hubba-Hubba － Hub Object Analyzer

AMP － Automatic Model Selector for Phylogenetic Analysis

Hum-DPI － Interactome of Human

Yeast-DPI － Interactome of yeast

Caption － Interactome of C. ablicans

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GMBDTBI

Computational Proteomics

GPTB － Genome/Proteom Tree Builder

IP-SARST － Integrated Protein Search Aided by Ramachandran Sequential Transformation

CELLO II － An integrated method to predict protein subcellular localization using SVM and sequence alignment

Re-MUSIC － The web tool for multiple sequence alignment with regular expression constraints

KinasePhos 2.0 － A web server for identifying protein kinase-specific phosphorylation sites

Web services under development

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GMBDTBI

Structural Bioinformatics

3D partner － A web server to predict interacting partners and binding models

Sspred － Disulfide connectivity predictor

Fast structure alignment server － A web server to provide fast protein structure alignment

The Protein Knot Server － A web server for detecting protein knots as well as the database of all knotted proteins

Automatic structure recognition server － A web server to automatically recognize protein structure domains

Database of protein fluctuations － Computation of protein dynamics and correlated motions using weighted protein contact model

Web services under development

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Applied Medical Genomics

SNP-VAD － SNP value-added database

LCR database － Low-copy-repeat (LCR) database

BEST － The binding element searching tools

Methylome － Genome-wide methylation tagging map

Repetitome － Whole genome repetitive elements map

ViTa － A database of host microRNA targets on viruses

Web services under development

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Research HighlightsResearch Highlights

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GMBDTBI General bioinformatics tools to General bioinformatics tools to

facilitate GM researchfacilitate GM research

Nucleic Acids Res. 2003, 31: 3751-3754

Sequence analysis and value-added databases

PDA （ Primer Design Assistant ） POWER （ Phylogenetic Web Repeater ） Molecular typing of enterovirus Human-specific indels : Comparative genomics approach Predicting antigenic variants of Influenza A virus CDSPD （ CoDing region Sequence and Proteomic Databas

e ） TAG (Tumor Associated Genes) LCR (Low-copy Repeats Database) The BEST (Binding Element Searching Tool) Value-added SNP (single nucleotide polymorphism) database

Nucleic Acids Res. 2005, 33: 553-556

Genome Res. 2007, 17:16-22

NAR Molecular Database Online #922, 2007

Gemomics 2006, 87:290-297

Nucleic Acids Res. 2005, 33: 5190-5198

Virus Genet. 2005, 21(3)337-347

Bioinformatics, under revision

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GMBDTBI General bioinformatics tools to General bioinformatics tools to

facilitate GM researchfacilitate GM research Transcriptome analysis-Microarray Studies

MOLAS （ Microarray on-line Analysis System ） Array CGH analysis Time course analysis for virus genes

Protein interactomes Hp-DPI (H. pylori Database of protein interactomes) Fly-DPI (Drosophila Database of Protein Interactomes) C. albicans-DPI EBV-DPI

Genetic analysis Incorporating endophenotypes into allele-sharing based linkage te

sts Genetic statistic server

Bioinformatics 2005, 21: 1288-1290

BMC Bioinformatics, 2006, 7: S18

Stat. Appl. In Gen. & Mol. Biol. 2006

J. of Virol. 2006, 80(18):8989-99

Genet. Epid., 2006

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GMBDTBI

NATURE REVIEWSMicrobiology(2006) 4, 741-751Methods for predicting bacterialprotein subcellular localization

(1) A review article in Nat Rev Microbiol introduced CELLO in 2006.

(2) The world largest human vaccine company Sanofi Pasteur has requested a site licenses of CELLO from our core.

Yu et al. Protein Science (2004); Proteins (2006)

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GMBDTBI

The The TAGTAG

NAR Molecular Database Online #922, 2007

Visitors around the world

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GMBDTBI NRPGM Bioinformatics CoresNRPGM Bioinformatics Cores

Impact on ResearchImpact on Research

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Collaborative ResearchCollaborative Research

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Collaborative Research Collaborative Research

Serves as partner in bioinformatics to the research community

Collaborated with 31 PIs in 21 institutions

Participated in NRPGM and many other research projects

Published 46 papers in years 2003-2007

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Collaborative Research Collaborative Research

NRPGM Research Projects

Highly Heritable Diseases

Infectious Diseases

Liver Cancer

Lung Cancer

Innovative Researches

NRPGM Core Facilities

Proteomics and Structural Biology Research Core

High-field Macromolecular NMR Core Facility

RNAi Core

Tumor Tissue Bank Core

Collaboration with NRPGM projects

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Collaboration with other National Research Projects

National Research Program for Nano sciences and technologies

National Research Program for Biotechnology and Drug Development

National Science and Technology Program for Agricultural Biotechnology

GMBD Collaborative Research Collaborative Research

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GMBDTBI

2E122GBZ

2GSC

2E11

2FA5

2CMH 2FUK

1ZUH2DYU 2BQXCollaboration in Stuctural Genomics projects have generated more than 30 protein structures and 20 papers.

1XS3 2CMG2GU9 2FUJ2BO3Innovative research: structural genomics

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GMBDTBI

PNAS (2006) 103, 14412

Collaborative Research with Collaborative Research with other National Research Program projectsother National Research Program projects

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GMBDTBI

Collaborative researchCollaborative research

GemDOCK has been cited more than 50 times since published

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GMBDTBI Collaborative researchCollaborative research

Klebsiella pneumoniaehttp://kp.life.nthu.edu.tw/

Stenotrophomonas maltophilia http://sm.life.nthu.edu.tw/

Helicobacter pylori http://hp.life.nthu.edu.tw/

Xanthomonas campestrishttp://xcc.life.nthu.edu.tw/

Structural Genomics ProjectsStructural Genomics Projects

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GMBDTBI

ContactContact For Collaboration National Health Research Institutes

Dr. I-Shou Chang ( 張憶壽教授 ), Dr. Chao Agnes Hsiung ( 熊昭教授 )

National Tsing-Hua University

Dr. Ping-Chiang Lyu ( 呂平江教授 )

National Chiao-Tung University

Dr. Jenn-Kang Hwang ( 黃鎮剛教授 )

National Cheng Kung University

Dr. H. Sunny Sun ( 孫孝芳教授 )

Help Desk: Phone: 037-246166 ext 33621

Fax: 037-586410

email : service@tbi.org.tw

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GMBDTBI

Thank you!Thank you!