Systems Biology Team

Goal
  • Construction of the integrated database for human, mouse and rat genes that can be useful to genome annotation and to research the relation of gene and disease


  • Date
  • Weekly meeting : every Thursday 9:00 a.m
  • Members
  • 舛費層, 沿走汎(窓), 沿肯姥, 廃耕敬, 舛殿呪, 舛遂, 酵濁費 (7誤)


  • 2006. May(5)
    Date Name Title Material
    05.04 舛殿呪
    05.04 沿走汎 Similarity measure between lattices : toxicant data
    05.11 沿肯姥 Correlation dependent on third gene expression level
    05.11 廃耕敬 cDNA microarray & Proteomics (2託 歳汐)
    05.18 舛費層
    05.18 舛遂
    05.25 酵濁費
    05.25 舛費層
    2006. April(4)
    Date Name Title Material
    04.06 酵濁費 GRIP 働臓 舛軒 貢 昔斗凪戚什 呪舛 遭楳雌伐
    04.06 舛費層 Pathway mapping
    04.13 沿走汎 BioLattice as analysis viewer on BioCANDi
    04.13 沿肯姥 Temporal relation between GO
    04.20 廃耕敬 Multimarker predictive model using machine learning algorithm
    04.20 舛殿呪 BioLattice: similarity of lattices
    04.27 舛遂 Difficulty in importing GEO data into Xperanto
    04.27 酵濁費 Depth-First Search 奄鋼 Object Search & Drawing Object Network
    2006. March(3)
    Date Name Title Material
    03.03 舛殿呪 PathTalk: Visualization and evaluation of structural relationship between gene clusters and biological pathways
    03.03 舛遂 GEO, for better approach
    03.09 酵濁費 DB Update 貢 Interface 薄伐
    03.09 舛費層 PathMeSH + miRNA progress
    03.16 沿走汎 BioLattice application II
    03.16 沿肯姥 Functional enrichment of sequential pattern with MIPS functional category
    03.23 廃耕敬 Integrating Classification and Association Rule Mining
    03.30 舛殿呪 Geodesic distance in pathway graph
    03.30 舛遂 Present state of GEO Localization
    2006. February(2)
    Date Name Title Material
    02.03 舛費層
    02.03 舛殿呪 PathTalk: Visualization and evaluation of structural relationship between gene clusters and biological pathways
    02.10 廃耕敬 Applying rule mining and FCA to protein with profile & pattern
    02.10 沿走汎 Rule mining from concept lattice
    02.24 沿肯姥
    02.24 廃耕敬 Association Mining and Formal Concept Analysis
    2006. January(1)
    Date Name Title Material
    01.06 沿肯姥 Application of Genetic Algorithm to sequential pattern mining on gene expression data
    01.06 廃耕敬 Comparative analysis of array CGH algorithms
    01.13 舛殿呪 PathTalk: diameters of gene sets on topological structure of pathways
    01.13 舛費層 ArrayXPathIII: Implementation of Mutual Information
    01.20 沿走汎 Rule mining from Concept Lattice
    01.20 沿肯姥 Sequential pattern mining税 誤溌廃 轄軒穿鯵研 是廃 flow chart
    2005. December(12)
    Date Name Title Material
    12.02 沿走汎 Genome Annotation Report
    12.02 廃耕敬 政号章 AB chip 歳汐域塙
    12.16 沿耕薄 Evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data
    12.16 沿肯姥 Rationale for sequential pattern mining
    12.23 舛殿呪 PathTalk: Visualization and evaluation of structural relationship between gene clusters and biological pathways
    12.23 舛費層 ArrayXPathIII: localize KEGG pathways using KEGG API
    12.30 沿走汎 Orientia genome annotation update
    2005. November(11)
    Date Name Title Material
    11.04 酵濁費
    11.04 沿肯姥 spm税 竺究径赤澗 轄軒穿鯵
    11.11 廃耕敬 Plan for protein-ontology lattice
    11.18 沿耕薄 matrix factorization for clustering and pattern discovery 舛軒
    11.25 舛殿呪 DispLay: different sequential patterned moduLes in array data
    11.25 舛費層 Plan for ArrayXPath and add a function
    2005. October(10)
    Date Name Title Material
    10.07 沿走汎 research plan
    10.07 酵濁費 鉦弘政穿端 DB 呪舛 紫牌
    10.14 沿肯姥 Do you understand the rationale for SPM?
    10.14 廃耕敬 What is the next step?
    10.21 沿耕薄 (progress) Matrix factorization for clustering and molecular pattern discovery on Microarray
    10.21 舛殿呪 Kullback-Leibler divergence to measure the biological relevance of given cluster
    10.28 舛費層 Idea for ArrayXPath III
    10.28 沿走汎 correlation of transcriptome and interactome
    2005. September(9)
    Date Name Title Material
    09.02 廃耕敬
    09.02 舛殿呪 室匂税 耕持弘 神唇 照穿失 汝亜
    09.09 舛費層 Frame work of GRIP
    09.09 沿走汎 Short BioLattice Manuscript
    09.16 酵濁費 GRIP Pathway Mapping
    09.16 沿肯姥 Cluster viewer upgrade
    09.23 沿耕薄 Matrix factorization fo microarray data analysis
    09.23 廃耕敬 aCGH_GLAD
    09.30 舛殿呪
    09.30 舛費層 Idea of pathway merge
    2005. August(8)
    Date Name Title Material
    08.05 沿肯姥 Get the facts about SGD GO-slim
    08.05 廃耕敬 Molecule Role Ontology
    08.12 舛殿呪 Required analysis modules in Xperanto
    08.12 沿走汎 BioLattice manuscript (artworks)
    08.19 舛費層 newGRIP manuscript
    08.19 沿肯姥 The very first step in mouse lymphoma microarray analysis
    08.26 舛費層
    08.26 沿耕薄 Issues for application MF to microarray data analysis
    2005. July(7)
    Date Name Title Material
    07.01 沿肯姥 Temporal relation between GO terms
    07.08 廃耕敬 Further steps for protein classification
    07.08 舛殿呪 Filters in Xperanto-BioCANDI
    07.15 沿耕薄 Review of Matrix factorization (ICA人 搾嘘)
    07.15 星駁失 Heterogeneous Ensemble
    07.22 舛費層 Chip2Chip
    07.22 沿走汎 BioLattice work summary
    07.29 舛費層 Biological mode and knowledge based conversion for microarray
    07.29 沿秦姥 PhactaX税 SOAP 奄鋼 績雌獣蝿淫恵 切戟嘘発
    2005. June(6)
    Date Name Title Material
    06.13
    Monthly
    沿走汎 Biological interpretation of BioLattice results
    06.03 星駁失 Cluster Ensemble and Its Applications in Gene Expression Analysis
    06.03 舛殿呪 Learning Model for pathway extension
    06.10 舛費層 Summary GRIP concept for manuscript
    06.10 沿走汎 Biological interpretation of BioLattice results
    06.17 酵濁費 attributes of New GRIP
    06.17 沿秦姥 Microarray Analysis Component 娃 切戟妊薄 XML Schema 鯵降
    2005. May(5)
    Date Name Title Material
    05.06 舛費層 Item sets for newGRIP
    05.06 沿走汎 Representation and visualization of cluster relationship
    05.13 酵濁費 Gene 傾婚 & Gene Family 傾婚 遭楳雌伐
    05.13 沿秦姥 Microarray Analysis Component 娃 切戟妊薄 貢 嘘発号狛
    05.20 廃耕敬 Protein classification from protein domain composition and GO using formal concept analysis
    05.27 沿肯姥 Re-design and Re-implementation of BioGPS
    05.27 沿耕薄 review of issues for ICA
    2005. April(4)
    Date Name Title Material
    04.01 舛殿呪 RunDEDS
    04.01 舛費層 PathCross: the first step
    04.08 沿走汎 BioLattice analysis results
    04.08 酵濁費 Current Localized Sequence object status
    04.15 沿秦姥 Development plan for the component-based Microarray analysis environment
    04.15 沿肯姥 Summary of sequential pattern mining
    04.22 廃耕敬 Analysis & interpretation of tripartite lattice
    04.22 沿耕薄 Web-DEDS 左刃
    04.29 星駁失 Combining Multiple Clusterings
    04.29 舛殿呪 Plan to complete PathPlus

    2005. March(3)
    Date Name Title Material
    03.03 舛費層 Manuscript for AXP 2.0
    03.03 沿走汎 BioLattice work report
    03.10 酵濁費 GRIP Specs. (耕舛軒..)
    03.10 沿秦姥 Microarray High-Level Data Analysis Modeling (Use Case Modeling)
    03.17 沿肯姥 FESD: a Functional Element SNPs Database in human
    03.17 廃耕敬 Database localization & How to make matrix?
    03.24 沿耕薄 Progress in DEDS
    03.24 星駁失 Approaches to Discover Emerging Patterns in bio-data

    2005. February(2)
    Date Name Title Material
    02.03 沿走汎 Supporting evidence to modular organization
    02.03 沿肯姥 Current agenda and Overlap matrix visualization
    02.17 酵濁費
    02.17 廃耕敬 Three-way interpenetration among protein domain, protein, and GO using FCA
    02.24 沿耕薄 Algorithm of ICA - FastICA
    02.24 星駁失 Application of emerging patterns for multi-source data classification and analysis
    2005. January(1)
    Date Name Title Material
    01.06 酵濁費 MDS errors...
    01.06 沿肯姥 Manuscripting "sequential patterning mining in gene expression data"
    01.13 舛費層 The development present status of ArrayXPath 2.0
    01.13 沿耕薄 Algorithm of ICA
    01.20 廃耕敬 GOTree Machine (GOTM)
    01.20 酵濁費 GRIP object
    01.27 廃耕敬 Review GO tool
    01.27 沿秦姥 MAGE-OM 鎧 Highlevel Data Analysis 鳶徹走 溌舌
    01.27 舛費層 Strategy for ArrayXPath

    December(12)
    Date Name Title Material
    12.02 舛費層 ArrayXPath plan for NGIC project
    12.02 沿走汎(窓) GO-FCA work progress
    12.09 沿秦姥 績雌獣蝿切戟淫軒獣什奴 鎧 MGED 乞季元 切戟呪増
    12.09 廃耕敬 VitaPad: Visualization Tools for the Analysis of Pathway Data
    12.16 沿肯姥 Sequential pattern mining拭 企廃 奄沙鯵割引 砺滴莞級
    12.16 酵濁費 GRIP Object 税 property 衣舛
    12.23 沿耕薄 Estimating gene networks Using Bayesian network
    12.23 舛費層 Items of ArrayXPath 2.0
    12.30 沿走汎 Progress note for BioLattice
    12.30 沿秦姥 績雌獣蝿切戟淫軒獣什奴 鎧 MGED 切戟 脊径竺域

    November(11)
    Date Name Title Material
    11.04 舛費層 ArrayXPath: version 2.0
    11.04 沿走汎(窓) GO-based cluster annotation using Formal Concept Analysis
    11.11 沿肯姥 Relevant work review of k-gOPSM
    11.11 沿秦姥 績雌獣蝿切戟人 持弘叔蝿切戟税 尻衣号照
    11.18 舛殿呪 CGH-Explorer 貢 政紫 祷 軒坂
    11.18 酵濁費 GRIP Version 2 Intro
    ( GRIP Ver.2 税 modelling 引 open/closed integration issue 級拭 企廃 轄税 )
    11.25 廃耕敬 Searching pathway databases
    11.25 沿耕薄 Using BN for estimating gene networks from microarrays and biological knowledge

    October(10)
    Date Name Title Material
    10.07 沿肯姥 Order-based subspace clustering
    10.07 沿秦姥 績雌獣蝿切戟人 郊戚神切戟税 搭杯聖 是廃 汽戚斗 乞季
    10.14 舛殿呪 Determining differentially expressed genes in a microarray expression dataset
    10.14 酵濁費 GEO拭辞 Platform Description header 人 Sample Description header税 歳汐
    10.21 廃耕敬 Possibility of systematic Multiple-pathways
    10.21 沿耕薄 Bayesian Network & example of application

    September(9)
    Date Name Title Material
    09.23 舛費層 PathMesh - Writing manuscript -
    09.23 沿走汎(窓) Total context view of clusters using FCA


    Grip/PharmGKB Team Meeting

    Goal
    Construction of the integrated database for human, mouse and rat genes that can be useful to genome annotation and to research the relation of gene and disease
    Date
    Weekly meeting : every Thursday 10:00 A.M
    Monthly meeting: every firstTuesday 08:30 A.M.

    2004
     September
    9.07 沿走汎 Monthly Meeting
    9.02 沿走汎 Formal Concept Analysis & Application
    9.02 廃耕敬 PharmGKB parsing
    9.09 酵濁費 KPRN data repository site
     
    &lng patterns for multi-source data classification and analysis

     August
    8.10 戚駁据 (Monthly Meeting)
    8.12 酵濁費 GRIP Layer ( Object )
    8.19 沿奄据 Church vs Snubi
    8.19 沿肯姥 Modeling for BioGPS;
    8.26 戚駁据 Tissue Microarray Data Modeling
    2005. January(1)
    Date Name Title Material
    01.06 酵濁費 MDS errors... <
    6.29 舛費層 (Monthly Meeting)
    7.01 沿走汎 Current application in Literature Mining 1
    7.01 酵濁費 Open/closed database integration approach
    7.08 沿奄据 ToPNet
    7.08 戚駁据 Regulation at Chromatin level
    7.15 沿肯姥 Multiple mapping in BioGPS
    7.15 廃耕敬 HGNC parsing
    7.22 沿走汎 C20050127_okgu.ppt">
    01.27 舛費層 Strategy for ArrayXPath

    December(12)
    Date Name Title Material
    12.="3">
     June
    6.01 廃耕敬 Gene Family and Protein Family DataBases(Monthly meeting)
    6.03 沿走汎 State of art in Literature Mining
    6.03 舛費層 Link between pathway and disease
    6.10 酵濁費 Entrez Gene 生稽 昔廃 Gene Layer 仙 乞季元
    6.10 沿肯姥 lt;/tr>
    6.17<7_hyewon.ppt"> Databases containing the elements of gene structure
     
    Database of Association between disease and pathway
    6.24 沿奄据 Cytoband visualization
    6.24 廃耕敬 HGNC Gene Family parsing plan
     
     May
    5.04 沿肯姥 Koogle, the finale(Monthly meeting)
    5.06 戚駁据 Elements of Gene structure
    5.06 廃耕敬 Breast Cancer Risk Assessment Tool
    5.13 沿走汎 Review - Text Mining in Biology
    5.13 舛費層 Link between pathway and medical information
    5.20 沿奄据 Data Structure based on biological concepts
    5.20 沿肯姥 BioGPS, writing manuscript
    5.27 戚駁据 First step with a few genes to Gene Modeling
    5.27 廃耕敬 Gene Family and Protein Family
     

     April

    4.01 沿走汎 Frequency Finder
    4.06 酵濁費 Data Integrating Issue (Monthly meeting)
    4.22 酵濁費 GRIP full-text search
    4.28 沿肯姥 Network-based approach for identifier mapping
     

     March

    3.03 酵濁費 PharmGKB 姥繕人 庚薦繊 PharmGKB 姥繕人 庚薦繊聖 歳汐馬壱 鉦弘政穿端紫穣舘 data submission 号狽聖 持唖廃陥.
    3.09 戚駁据 Constructing PharmGKB with GRIP Monthly Meeting
    3.11 滅?lt;/td> Ontology Development for a Pharmacogenetics Knowledge base Pharmacogenetics Ontology 鯵降 鯉旋 貢 号狛経
    3.18 沿肯姥 Koogle Development Graph algoritm聖 戚遂背辞 辞稽 陥献 id研 resolve背 左壱 唖唖税 algorithm聖 旋遂梅聖 凶税 税耕拭 企背 持唖背 沙陥. web interface研 亜遭 prototype聖 獣薄廃陥.
    3.25 廃耕敬 GRIP Contents 呪舛 薄仙 GRIP 拭辞 薦因馬澗 Content級税 採膳廃繊級聖 左刃馬壱 New interface 研 歯稽 姥雌廃? ( 戚 鎧遂聖 塘企稽 叔薦 interface 郊蝦依績 )
     

     February

    2.04 廃耕敬 Guidance for Industry Pharmacogenomic Data Submissions FDA拭辞 蟹紳 Draft Guidance Document 研 凧壱馬食 薄仙 PharmGKB data submission 舛奪 貢 闘兄球研 歳汐廃陥.
    2.10 沿肯姥 From Gene to Pharmacogenetics Monthly Meeting
    2.11 酵濁費 PharmGKB 竺域 左壱 貢 瀬 昔斗凪戚什 鯵降 域塙 PharmGKB 竺域拭 悦暗馬食 鉦弘政穿端尻姥舘 data研 嬢胸惟 煽舌拝依昔走 , 瀬 昔斗凪戚什 姥失精 嬢胸惟 拝依昔走拭 企廃 轄税研 廃陥.
    2.18 舛費層 BioSVG + GRIP 置曽舛軒 益疑照 旭戚 尻姥梅揮 採歳級聖 舛軒馬壱 DB Management 採歳拭辞 持奄澗 庚薦繊級引 背衣奪聖 乞事廃陥.
    2.25 沿肯姥 Koogle: Id chaining, key resolving 陥丞廃 id研 resolve馬澗 service研 幻窮陥.
     

     January 

    1.06 酵濁費 GRIP Interface 姥失引 Ensembl localize  
    1.07 酵濁費 Gene Symbol 搭杯 域塙照 Monthly Meeting
    1.14 舛費層 GRIP weekly meeting  
    1.28 戚駁据 Ensembl Localize人 statistics ensembl id 稽 級嬢神澗 input 拭 企背 GRIP拭辞 resolving 戚 亜管馬惟 廃陥.
    1.28 沿肯姥 LocusLink 人 UniGene 鎧拭 赤澗 Gene Symbol 搭杯 LocusLink 人 UniGene 拭 糎仙馬澗 Symbol 級聖 搭杯敗生稽辞 GRIP 鎧拭辞 匂胤旋昔 Symbol search 貢 full text search 亜 亜管馬惟 廃陥.

     

    2003
    Date Presenter Title
    8.08 酵濁費 GRIP 域塙
    8.22 酵濁費 Introduction MGD
    9.05 戚駁据 comparison of SOURCE and GRIP
    9.19 沿肯姥 SWISSPROT -> GRIP
    10.01 沿走汎 dbSNP parsing strategy
    10.08 滅?lt;/td> interface 遭楳雌伐
    10.21(monthly) 酵濁費 Swissprot/TrEMBL in GRIP
    10.22 酵濁費 GRIP税 bug 左壱
    10.29 酵濁費 GRIP interface 噺税
    11.05 舛費層 BIOSVG -Method of Search and Match-Making
    11.12 沿走汎 dbSNP parsing 穿繰
    11.18(monthly) 酵濁費 GRIP monthly report
    11.19 沿走汎 dbSNP parsing result
    12.03 沿走汎 dbSNP parsing
    12.10 酵濁費 Gene Symbol in BioSVG
    12.17 酵濁費 Genome Research Informatics Pipeline
    12.24 戚駁据 Ensembl localize