Journal Club

Date	Paper_index	Paper_title
2012/03/05		(8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
		(11,Go&Ju)Differential expression analysis for sequence count data
		(12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
2012/02/27~2012/02/28		(1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
		(2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
		(3,HJ Han)From RNA-seq reads to differential expression results
		(4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
		(5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
		(6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
		(7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
2012/02/06		mirConnX: condition-specific mRNA-microRNA network integrator
		Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
		A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
		Reprogramming of miRNA networks in cancer and leukemia
		An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
2012/01/30		Principles and Strategies for Developing Network Models in Cancer
		Reverse engineering of regulatory networks in human B cells
		Variations in DNA elucidate molecular networks that cause disease
		Harnessing gene expression to identify the genetic basis of drug resistance
		An Integrated Approach to Uncover Drivers of Cancer
	January 9 Mon, 2012 January 16 Mon, 2012		Genetic variation in an individual human exome.
			Predicting phenotypic variation in yeast from individual genome sequences.
			Clinical assessment incorporating a personal genome.
	January 9 Mon, 2012 January 16 Mon, 2012		Human allelic variation: perspective from protein function, structure, and evolution.
			Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
			Prediction of deleterious human alleles.
			Human non-synonymous SNPs: server and survey.
			A method and server for predicting damaging missense mutations.
			SNAP: predict effect of non-synonymous polymorphisms on function
	January 9 Mon, 2012 January 16 Mon, 2012		Computational and statistical approaches to analyzing variants identified by exome sequencing.
			Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
			Targeted capture and massively parallel sequencing of 12 human exomes.
	January 9 Mon, 2012 January 16 Mon, 2012		The distribution of fitness effects of new mutations.
			Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies
	November 28 Mon, 2011	TY Oh, SH Hwang, JE Shim, S Beck, JH Shin	(Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
			(Shin)Network pharmacology: the next paradigm in drug discovery
			(Oh)Systematic exploration of synergistic drug pairs
			(Shim)Chemogenomic profiling predicts antifungal synergies
			(Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
			(Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
	November 14 Mon, 2011	HH Kim & AR Cho	Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
			Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
			Analysis of multiple compound–protein interactions reveals novel bioactive molecules
	November 7 Mon, 2011	YH Ko	Drug—target network
			A side effect resource to capture phenotypic effects of drugs
			Quantitative systems-level determinants of human genes targeted by successful drugs
			Drug Target Identification Using Side-Effect Similarity
	November 7 Mon, 2011	JW Song	Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
			Exploiting drug–disease relationships for computational drug repositioning
			Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
	October 5 Mon, 2011	HH Kim	Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
			Quantifying environmental adaptation of metabolic pathways in metagenomics
			Quantitative assessment of protein function prediction from metagenomics shotgun sequences
	October 4 Mon, 2011	S Beck	A human gut microbial gene catalogue established by metagenomic sequencing
			Molecular eco-systems biology: towards an understanding of community function
			Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
			Unravelling the effects of the environment and host genotype on the gut microbiome
	September 19 Mon, 2011	TY Oh	independently evolved virulence effectors converge onto hubs in a plant immune system Network
			Evidence for network evolution in an arabidopsis interactome Map
	September 5 Mon, 2011	SG Ji	Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
		SH Hwang	Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
	August 22 Mon, 2011	ER Kim	Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
		T Lee	From expression QTLs to personalized transcriptomics
	June 20 Mon, 2011	JH Shin	a user's guide to the encyclopedia of DNA elements(ENCODE)
	May 30 Mon, 2011	HH Kim	enterotypes of the human gut microbiome
			toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
	May 16 Mon, 2011	AR Cho	variable pathogenicity determines individual lifespan in caenorhabditis elegans
			a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
	April 25 Mon, 2011	S Beck	Hallmarks of Cancer : The next generation
			Mapping Cancer Origins
			Genetic Interactions in Cancer Progression and Treatment
	April 11 Mon, 2011	JE Shim	Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
		T Lee	***Changed!*** Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions
	March 28 Mon, 2011	TY Oh	profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
			cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
	March 14 Mon, 2011	JW Song	phenotypic landscape of a bacterial cell
			cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
	February 28 Mon, 2011	KS Kim	genomic patterns of pleiotropy and the evolution of complexity
		HJ Han	simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
	February 21 Mon, 2011	MH Lee	dynamic interaction networks in a hierarchically organized tissue
	February 14 Mon, 2011	AR Cho	rewiring of genetic networks in response to DNA damage
	January 31 Mon, 2011	JW Song	Applying mass spectrometry-based proteomics to genetics, genomics and network biology
			Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
	December 27 Mon, 2010	ER Kim	Functional_roles_fornoise_in_genetic_circuits
		T Lee	Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
	November 15 Mon, 2010	AR Cho	Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
		SG Ji	It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
	November 1 Mon, 2010	HH Kim	A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
		JH Shin	A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
	October 11 Mon, 2010	JE Shim	Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
	September 13 Mon, 2010	SH Hwang	Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells Limits_of_sequence_and_functional_conservation
	May 26 Wed, 2010	AR Cho	network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
	May 19 Wed, 2010	SG Ji	interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
	April 21 Wed, 2010	JH Shin	identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
	April 14 Wed, 2010	TY Oh	an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
	April 7 Wed, 2010	HHkim	systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes
		T Lee	genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines
	Mar 31 Wed, 2010	JE Shim	toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf systems_biology_of_stem_cell_fate_and_cellular_reprogramming
	Mar 24 Wed, 2010	SH Hwang	dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
	Jan 18 Mon, 2010	TY Oh(T Lee)	JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
	Jan 16 Sat, 2010	JE Shim(MH Lee)	systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
	Jan 15 Fri, 2010	SG Ji	distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
	Jan 14 Thu, 2010	HH kim	chemogenomic_profiling_predicts_antifungal_synergies
	Jan 13 Wed, 2010	JH Shin(ER Kim)	edgetic_perturbation_models_of_human_inherited_disorders
	Jan 12 Tue, 2010	TY Oh(T Lee)	analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
	Jan 11 Mon, 2010	JE Shim(MH Lee)	predicting_new_molecular_targets_for_known_drugs.pdf Reference:SEA(Similarity Ensemble Approach)
	Jan 09 Sat, 2010	SG Ji	harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
	Jan 08 Fri, 2010	AR Cho	an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
	Jan 07 Thu, 2010	HH Kim	a_phenotypic_profile_of_the_candida_albicans_regulatory_network
	Jan 06 Wed, 2010	JH Shin(ER Kim)	a_global_view_of_protein_expression_in_human_cells_tissues_and_organs

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	March 5 Mon, 2012		(8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
			(11,Go&Ju)Differential expression analysis for sequence count data
			(12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
***	February 27 Mon~28 Tue, 2012		(1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
			(2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
			(3,HJ Han)From RNA-seq reads to differential expression results
			(4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
			(5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
			(6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
			(7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
	February 6 Mon, 2012		mirConnX: condition-specific mRNA-microRNA network integrator
			Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
			A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
			Reprogramming of miRNA networks in cancer and leukemia
			An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
	January 30 Mon, 2012		Principles and Strategies for Developing Network Models in Cancer
			Reverse engineering of regulatory networks in human B cells
			Variations in DNA elucidate molecular networks that cause disease
			Harnessing gene expression to identify the genetic basis of drug resistance
			An Integrated Approach to Uncover Drivers of Cancer
	January 9 Mon, 2012 January 16 Mon, 2012		Genetic variation in an individual human exome.
			Predicting phenotypic variation in yeast from individual genome sequences.
			Clinical assessment incorporating a personal genome.
	January 9 Mon, 2012 January 16 Mon, 2012		Human allelic variation: perspective from protein function, structure, and evolution.
			Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
			Prediction of deleterious human alleles.
			Human non-synonymous SNPs: server and survey.
			A method and server for predicting damaging missense mutations.
			SNAP: predict effect of non-synonymous polymorphisms on function
	January 9 Mon, 2012 January 16 Mon, 2012		Computational and statistical approaches to analyzing variants identified by exome sequencing.
			Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
			Targeted capture and massively parallel sequencing of 12 human exomes.
	January 9 Mon, 2012 January 16 Mon, 2012		The distribution of fitness effects of new mutations.
			Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies
	November 28 Mon, 2011	TY Oh, SH Hwang, JE Shim, S Beck, JH Shin	(Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
			(Shin)Network pharmacology: the next paradigm in drug discovery
			(Oh)Systematic exploration of synergistic drug pairs
			(Shim)Chemogenomic profiling predicts antifungal synergies
			(Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
			(Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
	November 14 Mon, 2011	HH Kim & AR Cho	Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
			Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
			Analysis of multiple compound–protein interactions reveals novel bioactive molecules
	November 7 Mon, 2011	YH Ko	Drug—target network
			A side effect resource to capture phenotypic effects of drugs
			Quantitative systems-level determinants of human genes targeted by successful drugs
			Drug Target Identification Using Side-Effect Similarity
	November 7 Mon, 2011	JW Song	Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
			Exploiting drug–disease relationships for computational drug repositioning
			Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
	October 5 Mon, 2011	HH Kim	Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
			Quantifying environmental adaptation of metabolic pathways in metagenomics
			Quantitative assessment of protein function prediction from metagenomics shotgun sequences
	October 4 Mon, 2011	S Beck	A human gut microbial gene catalogue established by metagenomic sequencing
			Molecular eco-systems biology: towards an understanding of community function
			Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
			Unravelling the effects of the environment and host genotype on the gut microbiome
	September 19 Mon, 2011	TY Oh	independently evolved virulence effectors converge onto hubs in a plant immune system Network
			Evidence for network evolution in an arabidopsis interactome Map
	September 5 Mon, 2011	SG Ji	Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
		SH Hwang	Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
	August 22 Mon, 2011	ER Kim	Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
		T Lee	From expression QTLs to personalized transcriptomics
	June 20 Mon, 2011	JH Shin	a user's guide to the encyclopedia of DNA elements(ENCODE)
	May 30 Mon, 2011	HH Kim	enterotypes of the human gut microbiome
			toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
	May 16 Mon, 2011	AR Cho	variable pathogenicity determines individual lifespan in caenorhabditis elegans
			a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
	April 25 Mon, 2011	S Beck	Hallmarks of Cancer : The next generation
			Mapping Cancer Origins
			Genetic Interactions in Cancer Progression and Treatment
	April 11 Mon, 2011	JE Shim	Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
		T Lee	***Changed!*** Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions
	March 28 Mon, 2011	TY Oh	profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
			cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
	March 14 Mon, 2011	JW Song	phenotypic landscape of a bacterial cell
			cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
	February 28 Mon, 2011	KS Kim	genomic patterns of pleiotropy and the evolution of complexity
		HJ Han	simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
	February 21 Mon, 2011	MH Lee	dynamic interaction networks in a hierarchically organized tissue
	February 14 Mon, 2011	AR Cho	rewiring of genetic networks in response to DNA damage
	January 31 Mon, 2011	JW Song	Applying mass spectrometry-based proteomics to genetics, genomics and network biology
			Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
	December 27 Mon, 2010	ER Kim	Functional_roles_fornoise_in_genetic_circuits
		T Lee	Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
	November 15 Mon, 2010	AR Cho	Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
		SG Ji	It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
	November 1 Mon, 2010	HH Kim	A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
		JH Shin	A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
	October 11 Mon, 2010	JE Shim	Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
	September 13 Mon, 2010	SH Hwang	Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells Limits_of_sequence_and_functional_conservation
	May 26 Wed, 2010	AR Cho	network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
	May 19 Wed, 2010	SG Ji	interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
	April 21 Wed, 2010	JH Shin	identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
	April 14 Wed, 2010	TY Oh	an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
	April 7 Wed, 2010	HHkim	systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes
		T Lee	genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines
	Mar 31 Wed, 2010	JE Shim	toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf systems_biology_of_stem_cell_fate_and_cellular_reprogramming
	Mar 24 Wed, 2010	SH Hwang	dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
	Jan 18 Mon, 2010	TY Oh(T Lee)	JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
	Jan 16 Sat, 2010	JE Shim(MH Lee)	systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
	Jan 15 Fri, 2010	SG Ji	distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
	Jan 14 Thu, 2010	HH kim	chemogenomic_profiling_predicts_antifungal_synergies
	Jan 13 Wed, 2010	JH Shin(ER Kim)	edgetic_perturbation_models_of_human_inherited_disorders
	Jan 12 Tue, 2010	TY Oh(T Lee)	analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
	Jan 11 Mon, 2010	JE Shim(MH Lee)	predicting_new_molecular_targets_for_known_drugs.pdf Reference:SEA(Similarity Ensemble Approach)
	Jan 09 Sat, 2010	SG Ji	harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
	Jan 08 Fri, 2010	AR Cho	an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
	Jan 07 Thu, 2010	HH Kim	a_phenotypic_profile_of_the_candida_albicans_regulatory_network
	Jan 06 Wed, 2010	JH Shin(ER Kim)	a_global_view_of_protein_expression_in_human_cells_tissues_and_organs

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