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2012-03:
27 Summary and Overview of Personal Genome Deciphers team  SysBiol

2012-02:
07 Previous seminar summary & current seminar overview  Seminar

2011-12:
06 Phenotypic Signature  Seminar
24 SNPedia: a wiki supporting personal genome annotation, interpretation and analysis     J.Club

2011-11:
02 Genetic risk reporting  SysBiol

2011-10:
13 Previous seminar summary & current seminar overview  Seminar
13 Predicting phenotype from genotype  Seminar
29 Correlated genotypes in friendship networks     J.Club

2011-09:
07 SNPedia data structure & Variant annotation  Seminar

2011-08:
27 Automated validation of genetic variants from large databases ensuring that variant references refer to the same genomic locations     J.Club

2011-07:
02 The use of VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency     J.Club
29 Personal genome variants annotation  SysBiol

2011-06:
10 Building SNP-Phenotype association database     SysBiol
29 Personal Genome Deciphers team progress report   TopicSem

2011-05:
21 Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics     J.Club

2011-04:
02 Improving disease gene prioritization using the semantic similarity of Gene Ontology terms       J.Club

2011-03:
14 To improve the semantic signature work  TopicSem

2008-10:
06 Lattice on BMA semantic space  Seminar
23 Lattices on BMA semantic space  Seminar

2008-09:
01 Evaluation plan for term-wise and geneset-wise semantic measure  Seminar
25 Evaluation of semantic measure I  Seminar

2008-08:
14 Application of a new geneset-wise measure for building semantic space  Seminar

2008-07:
03 BioCLASS : Semantic space checks  Seminar
14 BioCLASS-Biological Concept Lattice on Annotated Semantic Space  Seminar
28 Semantic distance distribution for re-selected geneset  Seminar

2008-06:
20 BioCLASS work progress 0620  Seminar

2008-05:
16 BioLattice work progress  Seminar
30 BioCLASS work progress  Seminar

2008-04:
11 BioLattice software update & analysis plan  Seminar
25 BioLattice software update  Seminar

2008-03:
03 Unified GO annotation  Seminar
21 Question of biological interpretation of distance map for toxicant lattices  Seminar
29 NetworkBLAST: Comparative analysis of protein networks     J.Club

2008-02:
02 PathExpress: a web-based tool to identify relevant pathways in gene expression data     J.Club
05 BioLattice Update & To do  Seminar
19 SNUBI Unified GO Annotator  Seminar
25 Unified solution for GO annotation  Seminar

2008-01:
04 Incomplete issues in BioLattice  Seminar

2007-12:
11 Current issues on semantic similarity in Bioinformatics  Seminar
22 Evaluation of high-throughput functional categorization of human disease genes       J.Club
28 BioCLASS : A semantic comparison of microarray gene expression data  Seminar

2007-11:
02 BioLattice update  Seminar
03 BioCLASS : A semantic comparison of microarray gene expression data  J.Club
17 Strategy for encoding and comparison of gene expression signatures       J.Club
20 Work summary  Seminar

2007-10:
16 Microarray analysis of C.parvum  Seminar

2007-09:
07 geneset extension for semantic distance  Seminar
28 Biolattice future directions  Seminar
29 Quantitative assessment of relationship between sequence similarity and function similarity     J.Club

2007-08:
08 Working plan for BioCLASS  Seminar
11 A New Method to Measure the Semantic Similarity of GO terms     J.Club
24 BioCLASS work progress  Seminar

2007-07:
04 BioCLASS : work progress  Seminar
07 Developing a similarity measure in biological function space       J.Club
20 BioCLASS work progress  Seminar

2007-06:
02 FatiGO and GAzer  J.Club
15 BioCLASS : Biological Concept Lattice on Annotated Semantic Space  Seminar

2007-05:
04 geneset functional space using gene ontology  Seminar
25 CLASS : Concept Lattice on Annotated Semantic Space  Seminar

2007-04:
07 Weighted Cohesiveness for Identification of Functional Modules and their Interconnectivity     J.Club
11 Geneset functional space using gene ontology  Seminar
16 Revision about BioLattice Article  Seminar

2007-03:
07 Lattice application on geneset functional space II  Seminar
23 Lattice application on geneset functional space III  Seminar

2007-02:
09 Lattice aplication on geneset functional space  Seminar
24 Identifying clusters of functionally related genes in genome       J.Club

2007-01:
06 Combining functional and topological properties to identify core modules in protein interaction networks       J.Club
17 semantic similarity between concepts in lattice with human pathways  Seminar

2006-12:
06 semantic similarity between concepts in lattice with pathways  Seminar
27 semantic similarity between concepts in lattice with pathways II  Seminar

2006-11:
04 A new measure for functional similarity of gene products based on Gene Ontology [semantic map]      J.Club
13 Semantic similarity between concepts in lattices  Seminar
15 Would you give me a word of advice for geneset-wise lattices?  Seminar

2006-10:
16 Lattice similarity measure  Seminar
25 Progress in lattice similarity measure  Seminar

2006-09:
30 Assessing semantic similarity measures for the characterization of human regulatory pathways [Semantic distance]      J.Club

2006-06:
01 similarity among normal tissues and cancer by biological context  SysBiol
17 From XML to RDF: how semantic web technologies will change the design of omic standards [XML RDF]      J.Club
22 Lattice similarity work progress [biolattice] SysBiol

2006-05:
04 Similarity measure between lattices : toxicant data [BioLattice] SysBiol
20 A System Based Approach to Interpret Dose and Time-dependent Microarray Data: Quantitative Integration of GO Ontology Analysis for Risk Assessment [microarray]      J.Club

2006-04:
08 Integrated analysis of gene expression by Association Rules Discovery       J.Club
10 Similarity measures for lattices  Seminar

2006-03:
04 Instance-based concept learning from multiclass DNA microarray data       J.Club
16 BioLattice application II  SysBiol

2006-02:
10 Rule mining from concept lattice  SysBiol
27 BioLattice Application - relational pattern -  Seminar

2006-01:
20 Rule mining from Concept Lattice  SysBiol
21 Biological profiling of gene groups utilizing gene ontology       J.Club

2005-12:
02 Genome Annotation Report  SysBiol
05 Comparative Genomics for Orientia  Seminar
26 Rule mining from BioLattice  Seminar
30 Orientia genome annotation update  SysBiol

2005-11:
07 BioLattice ü  Seminar

2005-10:
07 research plan  SysBiol
15 PAGE: Parametric Analysis of Gene Set Enrichment       J.Club
24 microBLAST  Seminar
28 correlation of transcriptome and interactome  SysBiol

2005-09:
09 Short BioLattice Manuscript  SysBiol

2005-08:
12 BioLattice manuscript (artworks)  SysBiol
27 Using process diagrams for the graphical representation of biological networks       J.Club

2005-07:
23 Comparison of computational methods for the identification of cell cycle-regulated genes       J.Club

2005-06:
10 Biological interpretation of BioLattice results  SysBiol
13 Biological interpretation of BioLattice results [SysBiol] Seminar

2005-05:
06 Representation and visualization of cluster relationship  SysBiol

2005-04:
08 BioLattice analysis results  SysBiol

2005-03:
03 BioLattice work report  SysBiol
26 CLOE Identification of putative functional relationships among genes by comparison of expression profiles between two species       J.Club

2005-02:
03 Supporting evidence to modular organization  SysBiol

2005-01:
10 A function-based framework for understanding biological systems     J.Club

2004-12:
02 GO-FCA work progress  SysBiol
30 Progress note for BioLattice  SysBiol

2004-11:
04 GO-based cluster annotation using Formal Concept Analysis  SysBiol
08 Formal concept analysis for GO-based cluster annotation  Seminar
20 Transcriptional regulatory code of a eukaryotic genome       J.Club

2004-10:
16 Using the gene ontology for microarray data mining       J.Club

2004-09:
07 Formal Concept Analysis and Application  Seminar
23 Total context view of clusters using FCA  SysBiol

2004-08:
07 Predicting Gene Expression from Sequence       J.Club

2004-07:
03 Methods for automated concept mapping between medical databases       J.Club
14 Bioconductor Basics  MAInfo

2004-06:
09 DIB-C  MAInfo

2004-05:
15 Quantifying the relationship between co-expression, co-regulation and gene function       J.Club
19 Difference-Based Clustering of Time Series Data  MAInfo

2004-04:
03 Inferring transcriptional regulation relationship from microarray time series data       J.Club
14 Analysis of responsive genes after Low-Dose Ionizing Radiation Using Evolutionary Algorithm  MAInfo

2004-02:
07 Statistical resynchronization and Bayesian detection of periodically expressed genes       J.Club
19 Simulation study to measure cyclicity in microarray expression profile  MAInfo

2004-01:
27 Monthly report  MAInfo
29 Preprocessing cell-cycle microarray data using PERL  MAInfo

2003-12:
04 What should I make bed? T.T  MAInfo
13 Computational discovery of gene modules and regulatory networks       J.Club

2003-10:
02 Gemone-wide analysis relatiing expression level with protein subcelluler localization  MAInfo
18 Phase-independent rhythmic analysis of genome-wide expression patterns       J.Club
30 Using gene effect to identify periodical genes  MAInfo

2003-09:
08 Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations       J.Club

2003-08:
01 Questions about microarray data analysis  Seminar

2003-06:
03 The consistency related problems to handle microarray data  Seminar

2003-05:
16 Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization       J.Club

2003-04:
08 Genome-wide expression analysis  Seminar

2003-03:
13 A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription       J.Club

2003-02:
18 Genome browser implementation  Seminar

2003-01:
07 Annotation work summary  Seminar
16 Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level       J.Club

2002-11:
12 "Genome annotation framework [pdf] Seminar
21 The meaning of it all: web-based resources for large-scale functional annotation and visualization of DNA microarray data       J.Club

2002-10:
29 Genome annotation strategy  Seminar

2002-09:
12 A motif-based profile scanning approach for genome-wide prediction of signaling pathways       J.Club
16 Identification of regulatory elements using a feature selection method       J.Club
17 Identification of regulatory elements  Seminar

2002-08:
27 Chronobiological analysis for the reliable identification of cell-cycle regulated genes from gene expression profiles  Seminar

2002-06:
20 Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm       J.Club
25 Chronobiological analysis for the reliable identification of cell-cycle regulated genes
from gene expression profiles
 
Seminar

2002-05:
07 Automation of Annotation  Seminar

2002-04:
16 Re-annotation of genome microbial coding-sequence: finding new genes and inaccurately annotated genes       J.Club

2002-03:
14 Introduction to Affymetrix Chip Algorithm  Seminar

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