Journal Club

2019

Date	Paper index	Presenter	Paper title
2019/09/03	19-41	KS Kim	Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
	19-40	IS Choi	Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
2019/09/03	19-39	NY Kim	The Landscape of Genetic Content in the Gut and Oral Human Microbiome
	19-38	CY Kim	Benchmarking Metagenomics Tools for Taxonomic Classification
2019/08/20	19-37	JH Cha	Coexpression uncovers a unified single-cell transcriptomic landscape
	19-36	MY Lee	Single-cell interactomes of the human brain reveal cell-type specific convergence of brain disorders
2019/08/14	19-35	SH Lee	Proportionality: a valid alternative to correlation for relative data
	19-34	SH Lee	propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
	19-33	HJ Han	Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma
2019/08/13	19-32	KS Kim	A test metric for assessing single-cell RNA-seq batch correction
	19-31	KS Kim	Comprehensive Integration of Single-Cell Data
2019/08/08	19-30	JH Cha	Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
	19-29	KS Kim	High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy
2019/08/07	19-28	HJ Han	A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease
	19-27	IS Choi	Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma
2019/07/30	19-26	IS Choi	High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy
	19-25	JW Cho	A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade
2019/07/23	19-24	HJ Han	COMPASS identifies T-cell subsets correlated with clinical outcomes.
	19-23	HJ Han	Sensitive detection of rare disease-associated cell subsets via representation learning
2019/05/30	19-22		Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
	19-21		Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
	19-20		Microbial network disturbances in relapsing refractory Crohn's disease.
2019/05/23	19-19		New insights from uncultivated genomes of the global human gut microbiome
	19-18		A new genomic blueprint of the human gut microbiota
	19-17		Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
2019/05/16	19-16		Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.
	19-15		Metatranscriptome of human faecal microbial communities in a cohort of adult men.
2019/05/09	19-14		Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT.
	19-13		Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features.
2019/05/02	19-12		Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy.
	19-11		Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade.
2019/4/11	19-10		Lineage tracking reveals dynamic relationships of T cells in colorectal cancer.
	19-9		Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma.
2019/4/4	19-8		Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.
	19-7		Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing
2019/3/28	19-6		Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
	19-5		Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.
2019/3/21	19-4		Phenotype molding of stromal cells in the lung tumor microenvironment.
	19-3-1		A single-cell molecular map of mouse gastrulation and early organogenesis
	19-3		The single-cell transcriptional landscape of mammalian organogenesis
2019/3/14	19-2		Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
	19-1		Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

2018

Date	Paper index	Presenter	Paper title
2018/06/14	18-12		A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.
	18-11		Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.
2018/06/07	18-10		Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.
	18-9		Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.
2018/05/31	18-8		Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.
	18-7		A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.
2018/05/24	18-6	CY Kim	Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.
	18-5	HJ Han	FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.
2018/05/17	18-4	KS Kim	A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.
	18-3	SH Lee	A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.
2018/05/10	18-2	JW Cho	Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.
	18-1	DS Bae	Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.

2017

Date	Paper index	Presenter	Paper title
2017/06/28	17-36	HJ Han	Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.
	17-35	JW Cho	Landscape of tumor-infiltrating T cell repertoire of human cancers.
2017/06/14	17-34	JW Cho	The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression.
	17-33	MY Lee	A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.
2017/06/07	17-32		Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.
	17-31	MY Lee	Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
2017/05/31	17-30	DS Bae	Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.
	17-29	JW Cho	Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.
2017/05/24	17-28	EB Kim	Systemic Immunity Is Required for Effective Cencer Immunotherapy.
	17-27	CY Kim	Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
2017/05/17	17-26		Host and Environmental Factors Influencing Individual Human Cytokine Responses.
	17-25		A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.
2017/04/26	17-24		Pooled CRISPR screening with single-cell transcriptome readout.
	17-23		Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.
2017/04/12	17-22	SH Lee	Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
	17-21	CY Kim	Wishbone identifies bifurcating developmental trajectories from single-cell data.
2017/04/05	17-20	KS Kim	Reversed graph embedding resolves complex single-cell developmental trajectories.
	17-19	SH Lee	Single-cell mRNA quantification and differential analysis with Census.
2017/03/29	17-18		Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.
	17-17	DS Bae	Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.
2017/03/22	17-16		Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.
	17-15	EB Kim	Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.
2017/03/15	17-14		Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
	17-13		Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.
2017/02/28	17-12	KS Kim	A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.
	17-11	JE Shim	Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.
2017/02/21	17-10	EB Kim	Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.
	17-09	EB Kim	Chromatin structure-based prediction of recurrent noncoding mutations in cancer.
2017/02/07	17-08	DS Bae	Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.
	17-07	MY Lee	Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.
2017/01/31	17-06	CY Kim	Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.
2017/01/24	17-05	JW Cho	Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.
2017/01/17	17-04	HJ Han	Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
	17-03	EB Kim	CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
2017/01/10	17-02	JE Shim	ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis
2017/01/03	17-01	SH Lee	Single-cell messenger RNA sequencing reveals rare intestinal cell types

2016

Date	Paper index	Presenter	Paper title
2016/12/27	2016-31	EB Kim	Decoding the regulatory network of early blood development from single-cell gene expression measurements.
2016/12/6	2016-30	KS Kim	Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.
2016/11/29	2016-29	DS Bae	The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
2016/11/22	2016-28	CY Kim	Classification of low quality cells from single-cell RNA-seq data.
2016/11/15	2016-27	MY Lee	Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
2016/11/8	2016-26	JW Cho	Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
2016/11/1	2016-25	HJ Han	Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.
2016/10/25	2016-24	MY Lee	Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.
2016/10/11	2016-23	JE Shim	Widespread parainflammation in human cancer
2016/9/27	2016-22	ER Kim	Analysis of protein-coding genetic variation in 60,706 humans
2016/9/20	2016-21	SM Yang	Functional characterization of somatic mutations in cancer using network-based inference of protein activity pubmed fulltext
2016/9/13	2016-20	KS Kim	Exploiting single-cell expression to characterize co-expression replicability.
2016/9/6	2016-19	T Lee	Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade
2016/8/31	2016-18	DS Bae	A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors
2016/8/16	2016-17	JW Cho	The landscape of accessible chromatin in mammalian preimplantation embryos
2016/8/8	2016-16	EB Kim	Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
2016/8/1	2016-15	MY Lee	Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients
2016/7/25	2016-14	CY Kim	Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
2016/7/18	2016-13	HJ Han	Identification of transcriptional regulators in the mouse immune system
2016/6/8	2016-12	DS Bae, CY Kim	Mapping the effects of drugs on the immune system
	2016-11	DS Bae, CY Kim	Elucidating compound mechanism of action by network perturbation analysis
2016/6/1	2016-10	MY Lee,SM Cho	Integrative approaches for large-scale transcriptome-wide association studies
	2016-9	MY Lee,SM Cho	Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases
2016/5/18	2016-8	CY Kim,SJ Kwon	Survey of variation in human transcription factors reveals prevalent DNA binding changes
	2016-7	CY Kim,SJ Kwon	Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo
2016/5/11	2016-6	DS Bae, CY Kim	Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality
	2016-5	DS Bae, CY Kim	Dynamic regulatory network controlling Th17 cell differentiation
2016/5/4	2016-4	MY Lee,SM Cho	Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy
	2016-3	MY Lee,SM Cho	Regulators of genetic risk of breast cancer identified by integrative network analysis
2016/4/27	2016-2	CY Kim,SJ Kwon	A predictive computational framework for direct reprogramming between human cell types
	2016-1	CY Kim,SJ Kwon	CellNet: Network biology applied to stem cell engineering

2015

Date	Paper index	Presenter	Paper title
2015/06/11	2015-55		Improved exome prioritization of disease genes through cross-species phenotype comparison.
	2015-54		Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.
2015/06/04	2015-53		eXtasy: variant prioritization by genomic data fusion.
	2015-52		A probabilistic disease-gene finder for personal genomes.
2015/05/28	2015-51		Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.
	2015-50		GREAT improves functional interpretation of cis-regulatory regions.
2015/05/21	2015-49		Functional annotation of noncoding sequence variants.
	2015-48		FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.
2015/05/14	2015-47		Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.
	2015-46		Biological interpretation of genome-wide association studies using predicted gene functions.
2015/05/07	2015-45		Human symptoms-disease network.
	2015-44		A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.
	2015-43		Uncovering disease-disease relationships through the incomplete interactome.
2015/04/30	2015-42		The discovery of integrated gene networks for autism and related disorders.
	2015-41		Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.
2015/04/23	2015-40		Dissecting neural differentiation regulatory networks through epigenetic footprinting.
	2015-39		Cell-of-origin chromatin organization shapes the mutational landscape of cancer.
	2015-38		Integrative analysis of 111 reference human epigenomes.
2015/04/09	2015-37		Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.
	2015-36		A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
2015/04/02	2015-35		Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
	2015-34		Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
2015/03/26	2015-33		Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.
	2015-32		Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.
2015/03/19	2015-31		Decoding the regulatory network of early blood development from single-cell gene expression measurements.
	2015-30		Computational and analytical challenges in single-cell transcriptomics.
2015/03/12	2015-29		Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.
	2015-28		Richness of human gut microbiome correlates with metabolic markers.
	2015-27		A metagenome-wide association study of gut microbiota in type 2 diabetes.
2015/03/09	2015-26	HJ Han	Practical guidelines for the comprehensive analysis of ChIP-seq data.
	2015-25	T Lee	Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.
	2015-24	ER Kim	Rapid neurogenesis through transcriptional activation in human stem cells.
2015/03/02	2015-23	DS Bae	Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.
	2015-22	CY Kim	Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.
	2015-21	ER Kim	The Genotype-Tissue Expression (GTEx) project.
2015/02/24	2015-20	ER Kim	Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.
	2015-19	KS Kim	Principles of regulatory information conservation between mouse and human.
	2015-18	BH Kang	Conservation of trans-acting circuitry during mammalian regulatory evolution.
2015/02/16	2015-17	T Lee	Genetic and epigenetic fine mapping of causal autoimmune disease variants.
	2015-16	CY Kim	A general framework for estimating the relative pathogenicity of human genetic variants.
	2015-15	CY Kim	A probabilistic model to predict clinical phenotypic traits from genome sequencing.
2015/02/02	2015-14	BH Kang	Relating the metatranscriptome and metagenome of the human gut.
	2015-13	BH Kang	Alterations of the human gut microbiome in liver cirrhosis.
	2015-12	CY Kim	An integrated catalog of reference genes in the human gut microbiome.
	2015-11	CY Kim	Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
2015/01/26	2015-10	HH Kim	Computational meta'omics for microbial community studies.
	2015-09	HH Kim	Functional profiling of the gut microbiome in disease-associated inflammation.
	2015-08	BH Kang	Biodiversity and functional genomics in the human microbiome.
	2015-07	BH Kang	Chapter 12: Human Microbiome Analysis.
	2015-06	BH Kang	Conducting a Microbiome Study.
2015/01/12	2015-05	KS Kim	Small RNA changes en route to distinct cellular states of induced pluripotency.
	2015-04	DS Bae	Genome-wide characterization of the routes to pluripotency.
	2015-03	DS Bae	Divergent reprogramming routes lead to alternative stem-cell states.
2015/01/05	2015-02	HJ Han	Global view of enhancer-promoter interactome in human cells.
	2015-01	HJ Han	Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.

2014

Date	Paper index	Presenter	Paper title
2014/12/23	2014-41	CY Kim	Super-enhancers in the control of cell identity and disease.
	2014-40	CY Kim	Master transcription factors and mediator establish super-enhancers at key cell identity genes.
2014/12/09	2014-39	HH Kim	Unraveling the biology of a fungal meningitis pathogen using chemical genetics.
	2014-38	JE Shim	A proteome-scale map of the human interactome network.
	2014-37	JE Shim	The role of the interactome in the maintenance of deleterious variability in human populations.
	2014-36	HS Shim	Integrative annotation of variants from 1092 humans: application to cancer genomics.
2014/12/02	2014-35	HJ Han	Mapping functional transcription factor networks from gene expression data.
	2014-34	KS Kim	In pursuit of design principles of regulatory sequences.
2014/11/25	2014-33	KS Kim	Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.
	2014-32	HJ Han	Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.
2014/11/18	2014-31	SM Yang	The 'dnet' approach promotes emerging research on cancer patient survival.
	2014-30	HJ Han	Determination and inference of eukaryotic transcription factor sequence specificity.
2014/11/11	2014-29	DS Bae	Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.
	2014-28	HH Kim	Dissecting engineered cell types and enhancing cell fate conversion via CellNet.
	2014-27	HH Kim	CellNet: network biology applied to stem cell engineering.
2014/11/04	2014-26	HS Shim	Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.
	2014-25	JH Shin	Phen-Gen: combining phenotype and genotype to analyze rare disorders.
2014/10/28	2014-24	HJ Han	A community effort to assess and improve drug sensitivity prediction algorithms.
	2014-23	HS Shim	Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.
2014/09/30	2014-22	JE Shim	Network-based stratification of tumor mutations.
	2014-21	KS Kim	Synonymous mutations frequently act as driver mutations in human cancers.
2014/09/23	2014-20	CY Kim	VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.
	2014-19	HJ Han	DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
2014/09/16	2014-18	JH Shin	Integrated analysis of recurrent properties of cancer genes to identify novel drivers.
	2014-17	AR Cho	Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.
2014/09/02	2014-16	JE Shim	A network module-based method for identifying cancer prognostic signatures.
	2014-15	AR Cho	Realizing the promise of cancer predisposition genes.
2014/08/19	2014-14	JE Shim	Assessing the clinical utility of cancer genomic and proteomic data across tumor types.
	2014-13	HS Shim	Mutational landscape and significance across 12 major cancer types.
2014/08/12	2014-12	HS Shim	Signatures of mutational processes in human cancer.
	2014-11	HJ Kim	Discovery and saturation analysis of cancer genes across 21 tumour types.
2014/08/05	2014-10	CY Kim	Comprehensive identification of mutational cancer driver genes across 12 tumor types.
	2014-9	JE Shim	IntOGen-mutations identifies cancer drivers across tumor types.
2014/07/29	2014-8	CY Kim	Computational approaches to identify functional genetic variants in cancer genomes.
	2014-7	AR Cho	Mutational heterogeneity in cancer and the search for new cancer-associated genes.
	2014-6	AR Cho	Cancer genomes: discerning drivers from passengers
2014/07/22	2014-5	AR Cho	The Cancer Genome Atlas Pan-Cancer analysis project.
	2014-4	AR Cho	Cancer genome landscapes.
	2014-3	AR Cho	Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.
2014/07/15	2014-2	HJ Han	A promoter-level mammalian expression atlas.
	2014-1	HJ Han	An atlas of active enhancers across human cell types and tissues.

2013

Date	Paper index	Presenter	Paper title
2013/06/26	2013-31	HJ Han	Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages
	2013-30	YH Ko	Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
2013/06/04	2013-29	KS Kim	Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding
	2013-28	ER Kim	Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
2013/05/28	2013-27	YH Ko	Discovering statistically significant pathways in expression profiling studies
	2013-26	JE Shim	Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses
2013/05/21	2013-25	HJ Han	Dynamic regulatory network controlling TH17 cell differentiation
	2013-24	T Lee	Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions
2013/05/14	2013-23	JE Shim	Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci
	2013-22	HJ Kim	Chromatin marks identify critical cell types for fine mapping complex trait variants
2013/05/07	2013-21	ER Kim	Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues
	2013-20	HS Shim	Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression
2013/04/09	2013-19	HJ Kim	Annotation of functional variation in personal genomes using RegulomeDB
2013/04/02	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