gmbd tbi 1 bioinformatics core for genomic medicine and biotechnology development i-shou chang,...
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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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GMBDTBI
Training and EducationTraining and Education
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GMBDTBI
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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GMBDTBI
Research and DevelopmentResearch and Development
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GMBDTBI
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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GMBDTBI
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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GMBDTBI
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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GMBDTBI
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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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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GMBDTBI
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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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!
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