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
  • 정희준, 김지훈(쥰), 김민구, 한미령, 정태수, 정용, 박찬희 (7명)


    •
    2006. May(5)
    Date Name Title Material
    05.04 정태수
    05.04 김지훈 Similarity measure between lattices : toxicant data
    05.11 김민구 Correlation dependent on third gene expression level
    05.11 한미령 cDNA microarray & Proteomics (2차 분석)
    05.18 정희준
    05.18 정용
    05.25 박찬희
    05.25 정희준
    2006. April(4)
    Date Name Title Material
    04.06 박찬희 GRIP 특징 정리 및 인터페이스 수정 진행상황
    04.06 정희준 Pathway mapping
    04.13 김지훈 BioLattice as analysis viewer on BioCANDi
    04.13 김민구 Temporal relation between GO
    04.20 한미령 Multimarker predictive model using machine learning algorithm
    04.20 정태수 BioLattice: similarity of lattices
    04.27 정용 Difficulty in importing GEO data into Xperanto
    04.27 박찬희 Depth-First Search 기반 Object Search & Drawing Object Network
    2006. March(3)
    Date Name Title Material
    03.03 정태수 PathTalk: Visualization and evaluation of structural relationship between gene clusters and biological pathways
    03.03 정용 GEO, for better approach
    03.09 박찬희 DB Update 및 Interface 현황
    03.09 정희준 PathMeSH + miRNA progress
    03.16 김지훈 BioLattice application II
    03.16 김민구 Functional enrichment of sequential pattern with MIPS functional category
    03.23 한미령 Integrating Classification and Association Rule Mining
    03.30 정태수 Geodesic distance in pathway graph
    03.30 정용 Present state of GEO Localization
    2006. February(2)
    Date Name Title Material
    02.03 정희준
    02.03 정태수 PathTalk: Visualization and evaluation of structural relationship between gene clusters and biological pathways
    02.10 한미령 Applying rule mining and FCA to protein with profile & pattern
    02.10 김지훈 Rule mining from concept lattice
    02.24 김민구
    02.24 한미령 Association Mining and Formal Concept Analysis
    2006. January(1)
    Date Name Title Material
    01.06 김민구 Application of Genetic Algorithm to sequential pattern mining on gene expression data
    01.06 한미령 Comparative analysis of array CGH algorithms
    01.13 정태수 PathTalk: diameters of gene sets on topological structure of pathways
    01.13 정희준 ArrayXPathIII: Implementation of Mutual Information
    01.20 김지훈 Rule mining from Concept Lattice
    01.20 김민구 Sequential pattern mining의 명확한 논리전개를 위한 flow chart
    2005. December(12)
    Date Name Title Material
    12.02 김지훈 Genome Annotation Report
    12.02 한미령 유방암 AB chip 분석계획
    12.16 김미현 Evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data
    12.16 김민구 Rationale for sequential pattern mining
    12.23 정태수 PathTalk: Visualization and evaluation of structural relationship between gene clusters and biological pathways
    12.23 정희준 ArrayXPathIII: localize KEGG pathways using KEGG API
    12.30 김지훈 Orientia genome annotation update
    2005. November(11)
    Date Name Title Material
    11.04 박찬희
    11.04 김민구 spm의 설득력있는 논리전개
    11.11 한미령 Plan for protein-ontology lattice
    11.18 김미현 matrix factorization for clustering and pattern discovery 정리
    11.25 정태수 DispLay: different sequential patterned moduLes in array data
    11.25 정희준 Plan for ArrayXPath and add a function
    2005. October(10)
    Date Name Title Material
    10.07 김지훈 research plan
    10.07 박찬희 약물유전체 DB 수정 사항
    10.14 김민구 Do you understand the rationale for SPM?
    10.14 한미령 What is the next step?
    10.21 김미현 (progress) Matrix factorization for clustering and molecular pattern discovery on Microarray
    10.21 정태수 Kullback-Leibler divergence to measure the biological relevance of given cluster
    10.28 정희준 Idea for ArrayXPath III
    10.28 김지훈 correlation of transcriptome and interactome
    2005. September(9)
    Date Name Title Material
    09.02 한미령
    09.02 정태수 세포의 미생물 오염 안전성 평가
    09.09 정희준 Frame work of GRIP
    09.09 김지훈 Short BioLattice Manuscript
    09.16 박찬희 GRIP Pathway Mapping
    09.16 김민구 Cluster viewer upgrade
    09.23 김미현 Matrix factorization fo microarray data analysis
    09.23 한미령 aCGH_GLAD
    09.30 정태수
    09.30 정희준 Idea of pathway merge
    2005. August(8)
    Date Name Title Material
    08.05 김민구 Get the facts about SGD GO-slim
    08.05 한미령 Molecule Role Ontology
    08.12 정태수 Required analysis modules in Xperanto
    08.12 김지훈 BioLattice manuscript (artworks)
    08.19 정희준 newGRIP manuscript
    08.19 김민구 The very first step in mouse lymphoma microarray analysis
    08.26 정희준
    08.26 김미현 Issues for application MF to microarray data analysis
    2005. July(7)
    Date Name Title Material
    07.01 김민구 Temporal relation between GO terms
    07.08 한미령 Further steps for protein classification
    07.08 정태수 Filters in Xperanto-BioCANDI
    07.15 김미현 Review of Matrix factorization (ICA와 비교)
    07.15 윤혜성 Heterogeneous Ensemble
    07.22 정희준 Chip2Chip
    07.22 김지훈 BioLattice work summary
    07.29 정희준 Biological mode and knowledge based conversion for microarray
    07.29 김옥구 PhactaX의 SOAP 기반 임상시험관련 자료교환
    2005. June(6)
    Date Name Title Material
    06.13
    Monthly    		 김지훈 Biological interpretation of BioLattice results
    06.03 윤혜성 Cluster Ensemble and Its Applications in Gene Expression Analysis
    06.03 정태수 Learning Model for pathway extension
    06.10 정희준 Summary GRIP concept for manuscript
    06.10 김지훈 Biological interpretation of BioLattice results
    06.17 박찬희 attributes of New GRIP
    06.17 김옥구 Microarray Analysis Component 간 자료표현 XML Schema 개발
    2005. May(5)
    Date Name Title Material
    05.06 정희준 Item sets for newGRIP
    05.06 김지훈 Representation and visualization of cluster relationship
    05.13 박찬희 Gene 레벨 & Gene Family 레벨 진행상황
    05.13 김옥구 Microarray Analysis Component 간 자료표현 및 교환방법
    05.20 한미령 Protein classification from protein domain composition and GO using formal concept analysis
    05.27 김민구 Re-design and Re-implementation of BioGPS
    05.27 김미현 review of issues for ICA
    2005. April(4)
    Date Name Title Material
    04.01 정태수 RunDEDS
    04.01 정희준 PathCross: the first step
    04.08 김지훈 BioLattice analysis results
    04.08 박찬희 Current Localized Sequence object status
    04.15 김옥구 Development plan for the component-based Microarray analysis environment
    04.15 김민구 Summary of sequential pattern mining
    04.22 한미령 Analysis & interpretation of tripartite lattice
    04.22 김미현 Web-DEDS 보완
    04.29 윤혜성 Combining Multiple Clusterings
    04.29 정태수 Plan to complete PathPlus

    2005. March(3)
    Date Name Title Material
    03.03 정희준 Manuscript for AXP 2.0
    03.03 김지훈 BioLattice work report
    03.10 박찬희 GRIP Specs. (미정리..)
    03.10 김옥구 Microarray High-Level Data Analysis Modeling (Use Case Modeling)
    03.17 김민구 FESD: a Functional Element SNPs Database in human
    03.17 한미령 Database localization & How to make matrix?
    03.24 김미현 Progress in DEDS
    03.24 윤혜성 Approaches to Discover Emerging Patterns in bio-data

    2005. February(2)
    Date Name Title Material
    02.03 김지훈 Supporting evidence to modular organization
    02.03 김민구 Current agenda and Overlap matrix visualization
    02.17 박찬희
    02.17 한미령 Three-way interpenetration among protein domain, protein, and GO using FCA
    02.24 김미현 Algorithm of ICA - FastICA
    02.24 윤혜성 Application of emerging patterns for multi-source data classification and analysis
    2005. January(1)
    Date Name Title Material
    01.06 박찬희 MDS errors...
    01.06 김민구 Manuscripting "sequential patterning mining in gene expression data"
    01.13 정희준 The development present status of ArrayXPath 2.0
    01.13 김미현 Algorithm of ICA
    01.20 한미령 GOTree Machine (GOTM)
    01.20 박찬희 GRIP object
    01.27 한미령 Review GO tool
    01.27 김옥구 MAGE-OM 내 Highlevel Data Analysis 패키지 확장
    01.27 정희준 Strategy for ArrayXPath

    December(12)
    Date Name Title Material
    12.02 정희준 ArrayXPath plan for NGIC project
    12.02 김지훈(쥰) GO-FCA work progress
    12.09 김옥구 임상시험자료관리시스템 내 MGED 모델링 자료수집
    12.09 한미령 VitaPad: Visualization Tools for the Analysis of Pathway Data
    12.16 김민구 Sequential pattern mining에 대한 기본개념과 테크닉들
    12.16 박찬희 GRIP Object 의 property 결정
    12.23 김미현 Estimating gene networks Using Bayesian network
    12.23 정희준 Items of ArrayXPath 2.0
    12.30 김지훈 Progress note for BioLattice
    12.30 김옥구 임상시험자료관리시스템 내 MGED 자료 입력설계

    November(11)
    Date Name Title Material
    11.04 정희준 ArrayXPath: version 2.0
    11.04 김지훈(쥰) GO-based cluster annotation using Formal Concept Analysis
    11.11 김민구 Relevant work review of k-gOPSM
    11.11 김옥구 임상시험자료와 생물실험자료의 연결방안
    11.18 정태수 CGH-Explorer 및 유사 툴 리뷰
    11.18 박찬희 GRIP Version 2 Intro
    ( GRIP Ver.2 의 modelling 과 open/closed integration issue 들에 대한 논의 )
    11.25 한미령 Searching pathway databases
    11.25 김미현 Using BN for estimating gene networks from microarrays and biological knowledge

    October(10)
    Date Name Title Material
    10.07 김민구 Order-based subspace clustering
    10.07 김옥구 임상시험자료와 바이오자료의 통합을 위한 데이터 모델
    10.14 정태수 Determining differentially expressed genes in a microarray expression dataset
    10.14 박찬희 GEO에서 Platform Description header 와 Sample Description header의 분석
    10.21 한미령 Possibility of systematic Multiple-pathways
    10.21 김미현 Bayesian Network & example of application

    September(9)
    Date Name Title Material
    09.23 정희준 PathMesh - Writing manuscript -
    09.23 김지훈(쥰) 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 김지훈 Monthly Meeting
    9.02 김지훈 Formal Concept Analysis & Application
    9.02 한미령 PharmGKB parsing
    9.09 박찬희 KPRN data repository site
     
    &lng patterns for multi-source data classification and analysis

     August
    8.10 이혜원 (Monthly Meeting)
    8.12 박찬희 GRIP Layer ( Object )
    8.19 김기원 Church vs Snubi
    8.19 김민구 Modeling for BioGPS;
    8.26 이혜원 Tissue Microarray Data Modeling
    2005. January(1)
    Date Name Title Material
    01.06 박찬희 MDS errors... <
    6.29 정희준 (Monthly Meeting)
    7.01 김지훈 Current application in Literature Mining 1
    7.01 박찬희 Open/closed database integration approach
    7.08 김기원 ToPNet
    7.08 이혜원 Regulation at Chromatin level
    7.15 김민구 Multiple mapping in BioGPS
    7.15 한미령 HGNC parsing
    7.22 김지훈 C20050127_okgu.ppt">
    01.27 정희준 Strategy for ArrayXPath

    December(12)
    Date Name Title Material
    12.="3">
     June
    6.01 한미령 Gene Family and Protein Family DataBases(Monthly meeting)
    6.03 김지훈 State of art in Literature Mining
    6.03 정희준 Link between pathway and disease
    6.10 박찬희 Entrez Gene 으로 인한 Gene Layer 재 모델링
    6.10 김민구 lt;/tr>
    6.17<7_hyewon.ppt"> Databases containing the elements of gene structure
     
    Database of Association between disease and pathway
    6.24 김기원 Cytoband visualization
    6.24 한미령 HGNC Gene Family parsing plan
     
     May
    5.04 김민구 Koogle, the finale(Monthly meeting)
    5.06 이혜원 Elements of Gene structure
    5.06 한미령 Breast Cancer Risk Assessment Tool
    5.13 김지훈 Review - Text Mining in Biology
    5.13 정희준 Link between pathway and medical information
    5.20 김기원 Data Structure based on biological concepts
    5.20 김민구 BioGPS, writing manuscript
    5.27 이혜원 First step with a few genes to Gene Modeling
    5.27 한미령 Gene Family and Protein Family
     

     April
    4.01 김지훈 Frequency Finder
    4.06 박찬희 Data Integrating Issue (Monthly meeting)
    4.22 박찬희 GRIP full-text search
    4.28 김민구 Network-based approach for identifier mapping
     

     March
    3.03 박찬희 PharmGKB 구조와 문제점 PharmGKB 구조와 문제점을 분석하고 약물유전체사업단 data submission 방향을 생각한다.
    3.09 이혜원 Constructing PharmGKB with GRIP Monthly Meeting
    3.11 鎌煊?lt;/td> Ontology Development for a Pharmacogenetics Knowledge base Pharmacogenetics Ontology 개발 목적 및 방법론
    3.18 김민구 Koogle Development Graph algoritm을 이용해서 서로 다른 id를 resolve해 보고 각각의 algorithm을 적용했을 때의 의미에 대해 생각해 본다. web interface를 가진 prototype을 시현한다.
    3.25 한미령 GRIP Contents 수정 현재 GRIP 에서 제공하는 Content들의 부족한점들을 보완하고 New interface 를 새로 구상한? ( 이 내용을 토대로 실제 interface 바꿀것임 )
     

     February
    2.04 한미령 Guidance for Industry Pharmacogenomic Data Submissions FDA에서 나온 Draft Guidance Document 를 참고하여 현재 PharmGKB data submission 정책 및 트렌드를 분석한다.
    2.10 김민구 From Gene to Pharmacogenetics Monthly Meeting
    2.11 박찬희 PharmGKB 설계 보고 및 웹 인터페이스 개발 계획 PharmGKB 설계에 근거하여 약물유전체연구단 data를 어떻게 저장할것인지 , 웹 인터페이스 구성은 어떻게 할것인지에 대한 논의를 한다.
    2.18 정희준 BioSVG + GRIP 최종정리 그동안 같이 연구했던 부분들을 정리하고 DB Management 부분에서 생기는 문제점들과 해결책을 모색한다.
    2.25 김민구 Koogle: Id chaining, key resolving 다양한 id를 resolve하는 service를 만든다.
     

     January 
    1.06 박찬희 GRIP Interface 구성과 Ensembl localize  
    1.07 박찬희 Gene Symbol 통합 계획안 Monthly Meeting
    1.14 정희준 GRIP weekly meeting  
    1.28 이혜원 Ensembl Localize와 statistics ensembl id 로 들어오는 input 에 대해 GRIP에서 resolving 이 가능하게 한다.
    1.28 김민구 LocusLink 와 UniGene 내에 있는 Gene Symbol 통합 LocusLink 와 UniGene 에 존재하는 Symbol 들을 통합함으로서 GRIP 내에서 포괄적인 Symbol search 및 full text search 가 가능하게 한다.

     

    2003
    Date Presenter Title
    8.08 박찬희 GRIP 계획
    8.22 박찬희 Introduction MGD
    9.05 이혜원 comparison of SOURCE and GRIP
    9.19 김민구 SWISSPROT -> GRIP
    10.01 김지훈 dbSNP parsing strategy
    10.08 鎌煊?lt;/td> interface 진행상황
    10.21(monthly) 박찬희 Swissprot/TrEMBL in GRIP
    10.22 박찬희 GRIP의 bug 보고
    10.29 박찬희 GRIP interface 회의
    11.05 정희준 BIOSVG -Method of Search and Match-Making
    11.12 김지훈 dbSNP parsing 전략
    11.18(monthly) 박찬희 GRIP monthly report
    11.19 김지훈 dbSNP parsing result
    12.03 김지훈 dbSNP parsing
    12.10 박찬희 Gene Symbol in BioSVG
    12.17 박찬희 Genome Research Informatics Pipeline
    12.24 이혜원 Ensembl localize