Difference between revisions of "Journal Club"

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|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]
 
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]
 
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|style="padding:.4em;" rowspan=2|2013/03/05
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|style="padding:.4em;" rowspan=2|'''2013/03/05'''
 
|style="padding:.4em;"|2013-17
 
|style="padding:.4em;"|2013-17
 
|style="padding:.4em;"| ER Kim
 
|style="padding:.4em;"| ER Kim
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|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html  Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]
 
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html  Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]
 
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|style="padding:.4em;" rowspan=3|'''2013/02/08'''
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|style="padding:.4em;" rowspan=3|2013/02/08
 
|style="padding:.4em;"|2013-09
 
|style="padding:.4em;"|2013-09
 
|style="padding:.4em;"|HJ Kim
 
|style="padding:.4em;"|HJ Kim

Revision as of 10:28, 5 March 2013

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-xx HJ Kim Annotation of functional variation in personal genomes using RegulomeDB
2013-xx HJ Kim The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
2013/03/05 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
2013-16 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



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