Journal Club

2013

Date	Paper index	Presenter	Paper title
Undecided	2013-xx	HJ Kim	Chromatin marks identify critical cell types for fine mapping complex trait variants
	2013-xx	T Lee	Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions
	2013-xx	JE Shim	Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci
	2013-xx	HS Shim	Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression
	2013-xx	ER Kim	Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues
2013/04/01	2013-19	HJ Kim	Annotation of functional variation in personal genomes using RegulomeDB
	2013-18	HJ Kim	The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
2013/03/12	2013-17	ER Kim	Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation
2013/03/05	2013-16	ER Kim	ChIP–seq: advantages and challenges of a maturing technology
2013/02/21	2013-15	KS Kim	Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
	2013-14	KS Kim	A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells
	2013-13	HJ Han	Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.
2013/02/15	2013-12	HJ Han	Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
	2013-11	JE Shim, CY Kim	Interpreting noncoding genetic variation in complex traits and human disease
	2013-10	HJ Han, JH Kim	Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
2013/02/08	2013-09	HJ Kim	Widespread Site-Dependent Buffering of Human Regulatory Polymorphism
	2013-08	JE Shim, CY Kim	Linking disease associations with regulatory information in the human genome
	2013-07	HJ Han, JH Kim	Understanding transcriptional regulation by integrative analysis of transcription factor binding data
2013/01/25	2013-06	HJ Han, JH Kim	The long-range interaction landscape of gene promoters
	2013-05	ER Kim, HS Shim	Landscape of transcription in human cells
	2013-04	HJ Han, JH Kim	Architecture of the human regulatory network derived from ENCODE data
2013/01/18	2013-03	KS Kim, TH Kim	An expansive human regulatory lexicon encoded in transcription factor footprints
	2013-02	HJ Han, JH Kim	The accessible chromatin landscape of the human genome
2013/01/11	2013-01	JE Shim, CY Kim	An integrated encyclopedia of DNA elements in the human genome

2012

Date	Paper index	Paper title
2013/01/11	2012-81	(TH Kim) MuSiC: identifying mutational significance in cancer genomes.
2012/12/04	2012-80	(CY KIM) Human genomic disease variants: A neutral evolutionary explanation
2012/11/20	2012-79	(HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks
	2012-78	(HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
2012/11/06	2012-77	(HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
	2012-76	(KS Kim) A public resource facilitating clinical use of genomes
2012/07/19	2012-75	(HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
	2012-74	(JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
	2012-73	(JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
	2012-72	(SH Hwang) Network-based classification of breast cancer metastasis
	2012-71	(T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants
	2012-70	(ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
2012/07/16	2012-69	(ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data
	2012-66	(ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools
	2012-65	(ER Kim&TH Kim)The Variant Call Format and VCFtools
	2012-64	(YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View
	2012-63	(T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions
	2012-62	(AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System
	2012-61	(SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome
	2012-60	(SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective
2012/07/13	2012-59	(JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
	2012-58	(JH Shin&HJ Kim)A framework for human microbiome research
	2012-57	(JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome
2012/07/12	2012-56	(AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines
	2012-55	(YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
	2012-54	(YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity
	2012-53	(JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
2012/07/09	2012-52	(ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
	2012-51	(ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells
	2012-50	(ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer
	2012-49	(JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism
	2012-48	(JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders
	2012-47	(JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
2012/07/06	2012-46	(T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)
	2012-45	(T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases
	2012-44	(AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners
	2012-43	(AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans
	2012-42	(JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes
	2012-41	(JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits
2012/07/02	2012-40	(JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions
	2012-39	(ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer
	2012-38	(YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
	2012-37	(SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine
	2012-36	(SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype
	2012-35	(JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets
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

Date	Paper_index	Paper_title
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

Date	Paper_index	Paper_title
2010/12/27	2010-29	Functional_roles_fornoise_in_genetic_circuits
	2010-28	Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
2010/11/15	2010-27	Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
	2010-26	It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
2010/11/01	2010-25	A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
	2010-24	A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
2010/10/11	2010-23	Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
2010/09/13	2010-22	Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells
	2010-21	Limits_of_sequence_and_functional_conservation
2010/05/26	2010-20	network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
2010/05/19	2010-19	interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
2010/04/21	2010-18	identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
2010/04/14	2010-17	an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
2010/04/07	2010-16	systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes
	2010-15	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