Journal Club

Date	Paper_index	Paper_title
2012/03/05	2012-34	(8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
	2012-33	(11,Go&Ju)Differential expression analysis for sequence count data
	2012-32	(12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
2012/02/27 2012/02/28	2012-31	(1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
	2012-30	(2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
	2012-29	(3,HJ Han)From RNA-seq reads to differential expression results
	2012-28	(4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
	2012-27	(5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
	2012-26	(6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
	2012-25	(7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
2012/02/06	2012-24	mirConnX: condition-specific mRNA-microRNA network integrator
	2012-23	Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
	2012-22	A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
	2012-21	Reprogramming of miRNA networks in cancer and leukemia
	2012-20	An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
2012/01/30	2012-19	Principles and Strategies for Developing Network Models in Cancer
	2012-18	Reverse engineering of regulatory networks in human B cells
	2012-17	Variations in DNA elucidate molecular networks that cause disease
	2012-16	Harnessing gene expression to identify the genetic basis of drug resistance
	2012-15	An Integrated Approach to Uncover Drivers of Cancer
2012/01/09	2012-14	Genetic variation in an individual human exome.
	2012-13	Predicting phenotypic variation in yeast from individual genome sequences.
	2012-12	Clinical assessment incorporating a personal genome.
2012/01/09 2012/01/16	2012-11	Human allelic variation: perspective from protein function, structure, and evolution.
	2012-10	Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
	2012-09	Prediction of deleterious human alleles.
	2012-08	Human non-synonymous SNPs: server and survey.
	2012-07	A method and server for predicting damaging missense mutations.
	2012-06	SNAP: predict effect of non-synonymous polymorphisms on function
2012/01/09 2012/01/16	2012-05	Computational and statistical approaches to analyzing variants identified by exome sequencing.
	2012-04	Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
	2012-03	Targeted capture and massively parallel sequencing of 12 human exomes.
2012/01/09 2012/01/16	2012-02	The distribution of fitness effects of new mutations.
	2012-01	Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies
2011/11/28	2011-49	(Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
	2011-48	(Shin)Network pharmacology: the next paradigm in drug discovery
	2011-47	(Oh)Systematic exploration of synergistic drug pairs
	2011-46	(Shim)Chemogenomic profiling predicts antifungal synergies
	2011-45	(Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
	2011-44	(Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
2011/11/14	2011-43	Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
	2011-42	Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
	2011-41	Analysis of multiple compound–protein interactions reveals novel bioactive molecules
2011/11/07	2011-40	Drug—target network
	2011-39	A side effect resource to capture phenotypic effects of drugs
	2011-38	Quantitative systems-level determinants of human genes targeted by successful drugs
	2011-37	Drug Target Identification Using Side-Effect Similarity
2011/11/07	2011-36	Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
	2011-35	Exploiting drug–disease relationships for computational drug repositioning
	2011-34	Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
2011/10/05	2011-33	Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
	2011-32	Quantifying environmental adaptation of metabolic pathways in metagenomics
	2011-31	Quantitative assessment of protein function prediction from metagenomics shotgun sequences
2011/10/04	2011-30	A human gut microbial gene catalogue established by metagenomic sequencing
	2011-29	Molecular eco-systems biology: towards an understanding of community function
	2011-28	Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
	2011-27	Unravelling the effects of the environment and host genotype on the gut microbiome
2011/09/19	2011-26	independently evolved virulence effectors converge onto hubs in a plant immune system Network
	2011-25	Evidence for network evolution in an arabidopsis interactome Map
2011/09/05	2011-24	Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
	2011-23	Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
2011/09/22	2011-22	Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
	2011-21	From expression QTLs to personalized transcriptomics
2011/06/20	2011-20	a user's guide to the encyclopedia of DNA elements(ENCODE)
2011/03/30	2011-19	enterotypes of the human gut microbiome
	2011-18	toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
2011/03/16	2011-17	variable pathogenicity determines individual lifespan in caenorhabditis elegans
	2011-16	a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
2011/04/25	2011-15	Hallmarks of Cancer : The next generation
	2011-14	Mapping Cancer Origins
	2011-13	Genetic Interactions in Cancer Progression and Treatment
2011/04/11	2011-12	Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
	2011-11	***Changed!*** Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions
2011/03/28	2011-10	profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
	2011-09	cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
2011/03/14	2011-08	phenotypic landscape of a bacterial cell
	2011-07	cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
2011/02/28	2011-06	genomic patterns of pleiotropy and the evolution of complexity
	2011-05	simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
2011/02/21	2011-04	dynamic interaction networks in a hierarchically organized tissue
2011/02/14	2011-03	rewiring of genetic networks in response to DNA damage
2011/01/31	2011-02	Applying mass spectrometry-based proteomics to genetics, genomics and network biology
	2011-01	Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
2010/12/27		Functional_roles_fornoise_in_genetic_circuits
		Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
2010/11/15		Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
		It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
2010/11/01		A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
		A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
2010/10/11		Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
2010/09/13		Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells
		Limits_of_sequence_and_functional_conservation
2010/05/26		network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
2010/05/19		interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
2010/04/21		identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
2010/04/14		an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
2010/04/07		systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes
		genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines
2010/03/31	2010-14	toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf
	2010-13	systems_biology_of_stem_cell_fate_and_cellular_reprogramming
2010/03/24	2010-12	dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
2010/01/18	2010-11	JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
2010/01/16	2010-10	systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
2010/01/15	2010-09	distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
2010/01/14	2010-08	chemogenomic_profiling_predicts_antifungal_synergies
2010/01/13	2010-07	edgetic_perturbation_models_of_human_inherited_disorders
2010/01/12	2010-06	analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
2010/01/11	2010-05	predicting_new_molecular_targets_for_known_drugs.pdf Reference:SEA(Similarity Ensemble Approach)
2010/01/09	2010-04	harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
2010/01/08	2010-03	an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
2010/01/07	2010-02	a_phenotypic_profile_of_the_candida_albicans_regulatory_network
2010/01/06	2010-01	a_global_view_of_protein_expression_in_human_cells_tissues_and_organs