JOURNAL CLUB

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2003

2002


2004.	January (1)
3	서화정	XPERANTO: Publishing Object-Relational Data as XML [Reference] Querying XML Views of Relational Data
3	정희준	GenePublisher: Automated analysis of DNA microarray data
10	이혜원	Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice
10	김민구	A protein interaction map of Drosophila melanogaster
17	한미령	Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis
17	박유랑	caCORE: A common infrastructure for cancer informatics
31	김기원	Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
31	김지훈(H)	EVALUATION AND COMPARISON OF CLUSTERING ALGORITHMS IN ANGLYZING ES CELL GENE EXPRESSION DATA

2004.	February (2)
7	김지훈(쥰)	Statistical resynchronization and Bayesian detection of periodically expressed genes
7	박찬희	Automatic extraction of mutations from Medline and cross-validation with OMIM
14	박지연	A Mapping Schema and Interface for XML Stores
14	서화정	Presenting XML-based medical discharge letters according to CDA
21	윤혜성	CloseGraph: Mining Closed Frequent Graph Patterns
21	이정애	Towards linking patients and clinical information: detecting UMLS concepts in e-mail
28	정태수	ESPD: a pattern detection model underlying gene expression profiles
28	정희준	Computational knowledge integration in biopharmaceutical research

2004.	March (3)
6	이혜원	Molecular profiling of mouse lung tumors: association with tumor progression, lung development, and human lung adenocarcinomas
6	김민구	Meta-databases providing collection of hyperlinks
13	한미령	Gene expression predictors of breast cancer outcomes
13	박유랑	Ontology Versioning as an Element of an Ontology-Management Framework
20	김기원	Chipping away at the chip bias: RNA degradation in microarray analysis
20	정희준	The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
27	윤혜성	A new distributed data mining model based on similarity
27	박찬희	Pharmacogenetics: potential for individualized drug therapy through genetics

2004.	April (4)
3	박지연	Biological detection of low radiation doses by combining results of two microarray analysis methods
3	김지훈(쥰)	Inferring transcriptional regulation relationship from microarray time series data
10	서화정	UML-XML-RDB Model Mapping Solution for Facilitating Information Standardization and Sharing in Construction Industry
10	이정애	Selective automated indexing of findings and diagnoses in radiology reports
17	정태수	Discovering molecular pathways from protein interaction and gene expression data
17	김지훈(H)	Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress
24	이혜원	Common structural patterns in human genes.
24	김민구	Network-based approach for the comprehensive mapping between biological identifiers

2004.	May (5)
1	한미령	Expression profiling to predict postoperative prognosis for estrogen receptor-negative breast cancers by analysis of 25,344 genes on a cDNA microarray
1	박유랑	Development of common data elements: the experience of and recommendations from the early detection research network
8	김기원	Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes
8	김지훈(H)	Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference.
15	김지훈(쥰)	Quantifying the relationship between co-expression, co-regulation and gene function
15	박찬희	GoMiner: a resource for biological interpretation of genomic and proteomic data
22	정태수	Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
22	윤혜성	An Architecture for Biological Information Extraction and Representation
29	이정애	PubMatrix: a tool for multiplex literature mining.

2004	June(6)
5	김지훈(H)	Microarray data clustering based on temporal variation: FCV with TSD preclustering
5	박유랑	ArrayTrack.Supporting Toxicogenomic Research at the U.S. Food and Drug Administration National Center for Toxicological Research
12	서화정	XML as standard for communicating in a document-based electronic patient record: a 3 years experiment.
12	김민구	Transcriptional regultory networks in Saccharomyces cerevisiae
19	한미령
19	김기원
26	이혜원
26	정희준


2003.	January (1)
9	김지훈(H)	Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
16	김지훈(쥰)	Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
23	박찬희	SNPper: retrieval and analysis of human SNPs

		PSB 2003 Review
8	박지연	Linking Molecular Imaging Terminology to the Gene Ontology (GO)
8	정희준	Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networks
8	이혜원	PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype DataDIGIT: A Novel Gene Finding Program by Combining Gene-Finders
8	박찬희	Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases
8	서화정	Linking Biomedical Language Information and Knowledge Resources in the 21st Century: GO and UMLS
8	이정애	Evaluation of the Vector Space Representation in Text-Based Gene Clustering
8	김지훈(H)	Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses with Applications to Mammary Development
8	김지훈(쥰)	DIGIT: A Novel Gene Finding Program by Combining Gene-Finders

2003.	February (2)
6	박지연	MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
13	서화정	A user-centered model for web site design: needs assessment, user interface design, and rapid prototyping
20	윤혜성	Mining gene expression databases for association rules
27	이정애	Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature

2003.	March (3)
6	김지훈(H)	Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer
13	김지훈(쥰)	A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription
20	박지연	Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
27	박찬희	A database on alternative splice forms on the Integrated Genetic Map Service (IGMS)

2003.	April (4)
3	윤혜성	Gene Functional classification by Semi-supervised Learning from Heterogeneous Data
10	이정애	A literature-based method for assessing the functional coherence of a gene group
14	서화정	Designing and implementing special-purpose databases: lessons from the pharmacogenetic network
24	김지훈(H)	Diagnosis of multiple cancer types by shrunken centroids of gene expression

2003.	May (5)
16	김지훈(쥰)	Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization
22	서화정	Data extraction and ad hoc query of an entity-attribute-value database
26	박지연	The application of the unified modeling language in object-oriented analysis of healthcare information systems

2003.	June (6)
5	이정애	The Role of Domain Knowledge in Automating Medical Text Report Classification
19	김지훈(H)	Genetics of gene expression surveyed in maize, mouse and man
26	김지훈(쥰)	Identifying Periodically Expressed Transcripts in Microarray Time Series Data

2003.	July (7)
3	박지연	An approach to object-relational mapping in bioscience domains
10	박찬희	Gene interaction in DNA microarray data is decomposed by information geometric measure
24	윤혜성	Active Learning with Strong and Weak Views: A Case Study on Wrapper Induction
31	서화정	Using the XML-Based Clinical Document Architecture for Exchange of Structured Discharge Summaries

2003.	August (8)
9	이정애	The creation of an ontology of clinical document names
9	정태수	Subnetwork hierarchies of biochemical pathways
16	김지훈(H)	Clustering of housekeeping genes provides a unified model of gene order in the human genome
16	정희준	Global functional profiling of gene expression
23	김민구	Meta-Analysis of Microarrays: Interstudy Validation of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer

2003.	September (9)
6	박유랑	ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis
6	박지연	The Design and Performance Evaluation of Alternative XML Storage Strategies
8	김지훈(쥰)	Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations
8	이혜원	Molecular Profiling of Non-Small Cell Lung Cancer and Correlation with Disease-free Survival
8	서화정	Using the eXtensible Markup Language (XML) in a regional electronic patient record for patients with malignant diseases
20	정태수	The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae
20	이정애	A Pilot Study of Contextual UMLS(R) Indexing to Improve the Precision of Concept-Based Representation in XML-Structured Clinical Radiology Reports
27	윤혜성	Improving Information Extraction through Biological Correlation
27	이혜원	Association of genes to genetically inherited diseases using data mining

2003.	October (10)
4	정희준	Pathways database system: an integrated system for biological pathways
4	김민구	Comparing protein abundance and mRNA expression levels on a genomic scale
11	한미령	Gene expression profiles of human breast cancer progression
11	박유랑	Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies
18	김지훈(H)	Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity
18	김지훈(쥰)	Phase-independent rhythmic analysis of genome-wide expression patterns
25	박찬희	Personalized and Automated dbSNP Surveillance System
25	박지연	A Generic Load/Extract Utility for Data Transfer between XML Documents and Relational Databases

2003.	November (11)
8	정태수	Using Bayesian Networks to Analyze Expression Data
8	윤혜성	Artificial gene networks for objective comparison of analysis algorithms
15	이정애	Information extraction from full text scientific articles: where are the keywords?
15	서화정	Discharge and referral data exchange using global standards--the SCIPHOX project in Germany
22	정희준	PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis
22	이혜원	A training-testing approach to the molecular classification of resected non-small cell lung cancer
29	김민구	Genome-wide pathway analysis and visualization using gene expression data
29	한미령	Molecular classification of familial non-BRCA1/BRCA2 breast cancer

2003.	December (12)
6	박유랑	GOChase: Correcting Errors from Gene Ontology-based Annotations for Gene Products
6	김지훈(H)	Statistical tests for identifying differentially expressed genes in time-course microarray experiments
13	김지훈(쥰)	Computational discovery of gene modules and regulatory networks
13	박찬희	Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans
20	박지연	A New Inlining Algorithm for Mapping XML DTDs to Relational Schemas
20	정태수	Scoring clustering solutions by their biological relevance
27	윤혜성	Deriving phylogenetic trees from the similarity analysis of metabolic pathways
27	이정애	A Study of Biomedical Concept Identification: MetaMap vs. People

2002.	April (4)
2	온정헌	Gene expression analysis with universal n-mer arrays
9	김지훈(H)	Significance analysis of microarrays applied to the ionizing radition response
16	김지훈(쥰)	Re-annotation of genome microbial coding-sequence: finding new genes and inaccurately annotated genes
23	박찬희	Prediction of probable genes by Fourier analysis of genomic sequences

2002.	May (5)
2	박지연	Argus--a new database system for Web-based analysis of multiple microarray data sets
9	윤혜성	XML documentation of biopathways and their simulations in Genomic Object Net
16	서화정	Standard method for describing an electronic patient record template: application of XML to share domain knowledge
23	온정헌	Systematic determination of genetic network architecture
30	김지훈(H)	Missing value estimation methods for DNA microarrays

2002.	June (6)
20	김지훈(쥰)	Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm
25	박찬희	A cluster validity framework for genome expression data

2002.	July (7)
4	박지연	Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML
11	윤혜성	Active + Semi-Supervised Learning = Robust Multi-View Learning

2002.	August (8)
22	온정헌	Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks
29	서화정	An update on HL7's XML-based document representation standards

2002.	September (9)
5	김지훈(H)	Large-scale prediction of Saccharomyces cerevisize gene function using overlapping transcriptional clusters
12	김지훈(쥰)	A motif-based profile scanning approach for genome-wide prediction of signaling pathways
16	김지훈(쥰)	Identification of regulatory elements using a feature selection method
26	박지연	The Binding Database: data management and interface design

2002.	October (10)
10	박찬희	A bioinformatic strategy to rapidly characterize cDNA libraries
17	서화정	Plug-and-play XML: a health care perspective
24	윤혜성	Handling Very Large Numbers of Association Rules in the Analysis of Microarray Data
31	김지훈(H)	Variance stabilization applied to microarray data calibration and to the quantification of differential expression

2002.	November (11)
7	온정헌	Binary analysis and optimization-based normalization of gene expression data
14	박지연	Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis
21	김지훈(쥰)	The meaning of it all: web-based resources for large-scale functional annotation and visualization of DNA microarray data

2002.	December (12)
5	이정애	XML for electronic clinical communications in Scotland
12	서화정	Integrating medical information and knowledge in the HL7 RIM
26	윤혜성	Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees