Applied Genomics

 Mail to AG team members

Weekly meeting : every Wednesday 9:00 A.M.
Members : 조성범,박유랑,정희준, 이혜원, 나영지,김민구, 정용, 박찬희(helper)
Major Project : Cord-Blood , PkarmGKB , Xperanto, Xperanto-TMA, GoChase 2
Order(7명) :나영지,정용, 김민구, 조성범,정희준,박유랑, 이혜원
May PresenterTitle
2006.05.03 정희준 CC2Path progress
2006.05.03 박유랑 CTMS (Clinical Trial Management System) 개발 계획
2006.05.10.이혜원 TG2-Knockout mouse Data Analysis
2006.05.10나영지 Breastome : Meta-analytic approach of breast cancer
2006.05.17정용
2006.05.17김민구
2006.05.24 조성범
2006.05.24 정희준

April PresenterTitle
2006.04.05 조성범 Mantel test between gene sets
2006.04.05정희준 CC2Path Progress
2006.04.12 나영지 Comparison of Meta Analysis Methods
2006.04.12 이혜원 Progress in Cybrid Data Analysis
2006.04.19 박유랑 암 표준용어체계 및 메타데이터 저장소 개발과 이에 기반한 임상시험 정보시스템 개발
2006.04.19 김민구 Correlation changes in module genes across experimental conditions
2006.04.26 정용 Plan : Importing GEO data into Xperanto
2006.04.26 조성범 Mantel test with pathway gene set

March PresenterTitle
2006.03.08김민구 spm 결과정리
2006.03.08 박유랑 유방암센터 EMR 자료 분석
2006.03.15조성범 Integration of Mantel test & MDR algorithm
2006.03.15정희준 PahtMeSH + miRNA progress
2006.03.22정용 GEO localization
2006.03.22나영지 CCD data analysis
2006.03.29이혜원 Progress in Cybrid data analysis
2006.03.29김민구 Interpretation of inter-module relationship in SPM

February PresenterTitle
2006.02.07조성범 BMT data analysis
2006.02.07 박유랑 Review of Knowledge Management System
2006.02.14정희준 PathMeSH+miRNA
2006.02.14박유랑 Ontology and relational model in PharmGKB
2006.02.21이혜원 Progress in Liver Cancer Data Analysis
2006.02.21우정훈 A novel approach for finding differentially co-regulated gene sets
2006.02.28나영지 Functional association from time-series microarray data
2006.02.28정용 GEO progress

January PresenterTitle
2006.01.03 조성범 Result of the survival analysis of liver cancer microarray data
2006.01.03 박유랑 GOChase 2 progress
2006.01.10 정희준 PathMeSH: gene-centric pathway view
2006.01.10 이혜원 Mitochondria Cybrid Data Analysis
2006.01.17 우정훈 Gene factoring with modified R-mode factor analysis
2006.01.17 나영지 Analysis of Time Series Gene Expression Data
2006.01.24 정용 약물유전체 DB 입력 현황 재정리
2006.01.24 김민구 Order-preserving tendency of BP, MF, CC GO-slim term in SMD dataset

December PresenterTitle
2005.12.06 김민구 Cluster viewer demonstration
2005.12.06 조성범 Survival analysis of liver cancer microarray data
2005.12.13 정희준 Association between disease and pathway
2005.12.13이혜원 Xperanto-TMA: Templates and Data Elements
2005.12.20 박유랑 GOChase 2
2005.12.20 우정훈 Applying Factor analysis to microarray data
2005.12.27 나영지 BMT data analysis results
2005.12.27 김민구 Measuring order-preserving tendency of co-regulated genes with Kullback-Leibler divergence

November PresenterTitle
2005.11.01 우정훈 Estimate genetic subnetwork with SEM
2005.11.01 나영지 Radiation Data Analysis
2005.11.08 김민구 독성유전체 자료분석
2005.11.08 이혜원 Liver Cancer Data Analysis: focusing on Recurrence
2005.11.15 박유랑 Cancer Genomics Object Model :An Object Model for Cancer Research using Functional Genomics Data
2005.11.15우정훈 Get over biological problem in statistical microarray analysis
2005.11.22조성범 Survival analysis of liver cancer microarray data
2005.11.29 박유랑 Cancer Genomics Object Model :An Object Model for Cancer Research using Functional Genomics Data
2005.11.29 나영지 Uncovering transcriptional regulation of metabolism by using metabolic network topology

October PresenterTitle
2005.10.04 나영지 Bone Marrow Transplantation Microarray Analysis
2005.10.04 김민구 Fisher's exact test to higher dimensional contingency table
2005.10.11 박유랑 Cancer Genomics Object Model: An Object Model for Cancer Research using functional genomics data
2005.10.11 우정훈 Extensive information for SNP chip analysis
2005.10.18 이혜원 Liver cancer data analysis using BIOCANDI
2005.10.18정희준 PathMeSH 정리
2005.10.25조성범 Survival analysis of liver cancer data

SeptemberPresenterTitle
2005.09.06이혜원 Data Analysis: Hepatocelluar Carcinoma Data
2005.09.06박유랑 GOChase 2 progress - (manuscript & web interface)
2005.09.13정희준 Construction of GRIP
2005.09.13 조성범 Analysis of Hapatocellular Carcinoma Data
2005.09.27박찬희 약물유전체 DB 수정 사항 정리

AugustPresenterTitle
2005.08.02 나영지 Affy chip Analysis in BioCANDi
2005.08.02 김민구 Multiple test corrections in SPM
2005.08.09 우정훈 Existing and emerging toxicogenomics databases
2005.08.09 박유랑 XPERANTO (Recent advances & migration)
2005.08.16 정희준 Summary of CC2Path
2005.08.16 조성범 GSEA(gene set enrichment analysis) package
2005.08.23우정훈 Toxicogenomic issues of microarray experiment (review)
2005.08.30박찬희 Sequence-Gene , Gene-Protein Category Association table 작성
2005.08.30김민구 Mouse lymphoma microarray analysis 2

JulyPresenterTitle
2005.07.05 박찬희 Gene Identifier 를 부여 할 수 있는 idea
2005.07.05 나영지 An error in using FDR
2005.07.12 김민구 terminal GO의 시간적 관계 추론
2005.07.12 박유랑 GOChase 2 progress (web interface)
2005.07.19 이혜원 Hepatocelluar carcinoma data analysis : Preprocessing
2005.07.19 정희준 Scoring of clustered data using Mutual Information
2005.07.26 조성범 Identification of Pathways related to Pathologic Status in Lung cancer using Global Test
2005.07.26 박찬희
2005.07.04조성범 Monthly Seminar

JunePresenterTitle
2005.06.07김민구 K-means clustering for filtering large number of sequential patterns
2005.06.07이혜원 Integration of TMA-OM and MAGE-OM: Scenario and draft model
2005.06.14박유랑 XPERANTO Progress (Biocandi 2 and Project)
2005.06.14나영지 Biological Interpretation of Radiation Data
2005.06.21정희준 PathTalks: the fourth step
2005.06.28이수연 글리벡 데이터 분석 및 ABI 분석
2005.06.28조성범 Identification of Pathways related to the lymph node metastasis in lung cancer using Global test
2005.05.30박찬희 Monthly Seminar

MayPresenterTitle
2005.05.03조성범 Identification of Pathway related to the Clinical Outcome within Microarray data using Global Test
2005.05.03이혜원 Summary of TMA-OM and Xperanto-TMA
2005.05.10박찬희 Sequence Level & Gene Level 진행상황
2005.05.10박유랑 Progress of GOChase 2
2005.05.17나영지 Liver Cancer 데이터 분석
2005.05.24김민구 How to conclude sequential pattern mining
2005.05.24정희준 PathTalk: the third step
2005.05.31조성범 Identification of pathways related to the pathologic status of squamous cell carcinoma of uterine cervix using global test
2005.05.31박찬희 New_GRIP :Prosite and Pfam
2005.05.02 이혜원 Monthly Seminar

AprilPresenterTitle
2005.04.12이수연 독성유전체 데이터 분석
2005.04.12나영지 [Plan]Extension of Venn Diagram
2005.04.19 김민구 Java api를 이용한 Ensembl 접근
2005.04.19 박유랑 Progress of GOChase 2- Error (redundant and inconsistent annotation error) confirm
2005.04.26 이혜원 visualization of ontology data - EMAP browser
2005.04.26 정희준 PathTalk: the second step
2005.04.04 김민구 Monthly Seminar

MarchPresenterTitle
2005.03.04박찬희 Finding human SNPs miRNA genomic position related
2005.03.04이수연 Research topic
2005.03.11나영지 Normalization of cDNA at SNUBI
2005.03.11이혜원 MISFISHIE review
2005.03.18김민구 Sequential pattern mining with gap limit & 심규석교수님의 아이디어 구현
2005.03.22박유랑 GOChase 2: additional errors (implicit and true path rule errors) in GO-based annotations for gene products
2005.03.22정희준 MapGO progress
2005.03.29조성범 Analysis of gastric cancer tissue microarray data-II
2005.03.29박찬희 GRIP Progress ( sequence )

FebruaryPresenterTitle
2005.02.04정태수 Secondary analysis of arrary CGH data
2005.02.04박유랑 Progress in Cancer Genomics Object Model
2005.02.18ㅘ珠?lt;/td> Manuscript for AXP 2.0
2005.02.18김민구 New dataset from SMD
2005.02.25조성범 Analysis of gastric cancer tissue microarray data

JanuaryPresenterTitle
2005.01.07박찬희 BAC Clones resolved
2005.01.07이혜원 object model and relational database for tissue microarray
2005.01.14정태수 array CGH data analysis
2005.01.14박유랑 Cancer Genomics Object Model
2005.01.21정희준 Implement MapGO
2005.01.21김민구 Sequential pattern mining of gene expression profile에서 해야 할 두 가지
2005.01.28박찬희 Web based ArrayCGH data analysis tool 구현(1/2)
2005.01.28이혜원 [TMA] 진행상황 보고

DecemberPresenterTitle
2004.12.03박유랑 MIAME/Onc 진행사항
2004.12.03정희준 GOFCA - apply cell cycle data and liver cancer data -
2004.12.10이석호 BioCandi : Further Plan
2004.12.10김민구 Techniques in sequential pattern mining
2004.12.17이혜원 [TMA] web interface 진행상황
2004.12.24박찬희 ArrayCGH with GLAD & Gene info annotation
2004.12.24박유랑 Comparison of XPERANTO and mAdb
2004.12.31정희준 MapGO
2004.12.31김민구 Deterministic sequential pattern mining
NovemberPresenterTitle
2004.11.05이혜원 An Object model and relational database for tissue microarray
2004.11.05정희준 PathFCA: applied Mouse Kidney Data
2004.11.12서화정 Clinical-Genomic integration within CDA - INTRO.
2004.11.12박유랑 Define MIAME/Onc using NAACCR, CDE
2004.11.19김민구 Sequential pattern - related work review
2004.11.19이석호 BioCandi Reformulation - 2
2004.11.26김옥구 PK Profile 예측 시스템 연구
2004.11.26박찬희 약물유전체 genotype data 를 human whole genome 에 mapping 시켜 display 하기
OctoberPresenterTitle
2004.10.01박유랑 Affy data in XPERANTO(XPERANTO Release plan –1)
2004.10.01정희준 Clustering Analysis using FCA
2004.10.08서화정 Extraction of standardized XML DTD (structural constraints) from clinical document
2004.10.08김민구 Biological justification of order-preserving submatrix
2004.10.22이혜원 Object model for Tissue microarray
2004.10.22이석호 BioCandi Reformulation
2004.10.29김옥구 PharmacoGenomics 관심분야 및 공부현황
2004.10.29박찬희 KPRN data 입력 페이지
SeptemberPresenterTitle
2004.09.17김민구 The Biginning
2004.09.24박찬희 Beginning of AppGen


 
 
 
 
 
 
 
 
Xperanto/BioPathway Team
Mail to team members
Xperanto BBS
 
 
     
 
Goal
- Developing an infrastructure to support microarray research
- Developing a knowledge base for pharmacogenomics research
Date
- Weekly meeting : every Friday 9:00 A.M.
- Monthly meeting: every second Tuesday 08:30 A.M.
- Members (8명) : 정희준, 정태수, 서?? 박찬희, 김민구, 박유랑, 김미현, 김옥구

 

Date(9월)NameTitleMaterial
2004.09.10박찬희 import GEO into MAGE-ML(brief)
2004.09.10서화정 FCA-based Ontology Extension in a Medical Domain
2004.09.03박유랑 Apply MIAME/Tox to XPERANTO(1)
2004.09.03김민구 Genes with high global correlation
Date(8월)NameTitleMaterial
2004.08.31
Monthly
박찬희
2004.08.27정태수 Modeling of pathways
2004.08.27정희준 Plan to rebuild ArrayXPath 2.0
2004.08.20김옥구 임상시험 수행 및 자료 관리시스템 개발
2004.08.20김미현 Introduction to PATIKA
2004.08.13박찬희 GEO localize
2004.08.13서화정 병원의 산업적 발전 방향
Date(7월)NameTitleMaterial
2004.07.20
Monthly
박유랑 Integration of MAGE-OM and CDA using CDE(create template & CDA xml document)
2004.07.23정희준 [ISMB poster] ArrayXPath
2004.07.23정태수 [ISMB] PathPlus
2004.07.16김지훈 Xperanto Extension for the Affymetrix Data
2004.07.09박유랑 GOChase: Correcting Errors from Gene Ontology-based Annotations for Gene Products
2004.07.09김지훈 Introduction to Affymetrix Data
2004.07.02정태수 Pathway as a patterned graph
2004.07.02김민구 Biological interpretation of Gene-Gene plot
Date(6월)NameTitleMaterial
2004.06.22
Monthly
김민구
2004.06.25정희준 ArrayXPath 수정
2004.06.25박찬희 Gene Expression Omnibus NCBI gene expression and hybridization array data repository Part 2
2004.06.18박유랑 Group and project for the Integration MI and BI
2004.06.18서화정 Presentation of document constraints for structured discharge note
2004.06.11김지훈 Biological Validation of Clustering
2004.06.11정태수 Scoring Models for CAP
2004.06.04김민구 Beyond co-expression, co-regulation
2004.06.04정희준 CAP(Cluster Assignment using Pathway)
Date(5월)NameTitleMaterial
2004.05.28박찬희 GEO Data Analysis 와 Xperanto
2004.05.28박유랑 MIAME or MIAME/TOX compliant Microarray Databases
2004.05.21서화정 Evaluation strategy of clinical document prototype
2004.05.21김지훈 Assessment of the DIfference-Based Clustering(DIB-C)
2004.05.14정태수 Determining DEGs in a microarray data using pathway information
2004.05.14김민구 Classification of pathway relations using global expression profile
2004.05.07박찬희 Gene Expression Omnibus NCBI gene expression and hybridization array data repository
2004.05.07정희준 Plan of ArrayXPath upgrade
Date(4월)NameTitleMaterial
2004.04.30김민구 Characterize each type of relations in biological pathways with mircroarray data
2004.04.30서화정 Presenting of document constraints for structured discharge note
2004.04.23김지훈
2004.04.23정태수 A prediction model for pathway extension using microarray expression profiles
2004.04.16김미현 Pathway activity inference using microarray data
2004.04.16정희준 ArrayXpath modification& pathway modeling
2004.04.09박찬희 Locuslink에서 Entrez-Gene으로의 변환
2004.04.09박지연 Restoration of MAGE- ML service in Xperanto system
2004.04.02서화정 Make the best use of a data transfer utility
2004.04.02김지훈 The response of row dose radiation
Date(3월)NameTitleMaterial
2004.03.26김혜진 Biological interpretation of gene clusters
2004.03.26김민구 Building Koogle manuscript
2004.03.19정태수 pathway extension through microarray data
2004.03.19정희준 ArrayXPath-modified point
2004.03.12김민구 graph algorithmic approaches for elucidating complex relationship between IDs
2004.03.12박지연 Initial steps toward performance experiment for XML-RDB mapping schema
2004.03.05정희준 Future direction of ArrayXPath
2004.03.05박유랑 GOChase
Date(2월)NameTitleMaterial
2004.02.27김지훈 Finding Factor Specific Generative Pattern(FSGP) from the Breast Cancer Data
2004.02.27정태수 Constructing network of pathways in S.cerevisiae
2004.02.20김민구 ArrayXpath -> Id chaining
2004.02.20박유랑Progress in xperanto website
2004.02.17이혜원Introduction to Xperanto: Microarray Data System
2004.02.13정희준ArrayXpath-Arrangement for writing paper
2004.02.13박지연Formailism of MAGE-ML storage strategies and Implementation of Edge approach
2004.02.06김지훈Hands_On Tutorial of Microarray Data Analysis Using R
2004.02.06서화정Generating of XML DTD
Date(1월)NameTitleMaterial
2004.01.30박지연MAGE-ML data import 현황 및 evaluation 진행상황
2004.01.30김지훈Associating microarray data with pathway information
2004.01.16김민구How to write BioSVG manuscript
2004.01.16박유랑Progress in xperanto website
2004.01.09정희준BioSVG Part 3
2004.01.09정태수Extracting active pathways from gene expression data
Date(2003)NameTitleMaterial
2003.12.26김지훈BIOCANDI Extension & Personal use
2003.12.26이혜원Microarray Image Processing
2003.12.26박지연MIAME-bassed template for microarray information
2003.12.19박지연Mapping MAGE-ML DTA to Relational Schema
2003.12.12정희준BioSVG summary.2
2003.12.05김민구BioSVG -Pathway Modeling
2003.11.28박지연MAGE-ML and Storage Strategies
2003.11.21정희준BioSVG-Summary
2003.11.21박유량GO를 제공하는 Biological DB들의 에러
2003.11.14정태수Review on Xperanto
2003.11.14김지훈Finalizing Xperanto: the last step in analysis
2003.11.07김민구SBML --> BioSVG
2003.11.07박지연Making Generic Program for MAGE-ML Import
2003.10.24박지연MGED Ontology Incorporation in Xperanto System
2003.10.24박유랑Microarray data management in Xperanto
2003.10.17정희준BioSVG -Plan about arrangement-
2003.10.14박지연(SEMINAR) Xperanto Progress
2003.10.14정희준(SEMINAR) BioSVG -Current and Future-
2003.10.10김지훈Analysis Techniques for Epidemiology Studies
2003.10.10김민구Systems Biology Markup Language (SBML)