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Date Team Paper
Presenter Paper title
2021/02/22 Single-cell 21-8 IS Choi

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity

21-7 JH Cha

Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy

2021/02/15 Single-cell 21-6 SB Baek

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

21-5 IS Choi

Trajectory-based differential expression analysis for single-cell sequencing data

2021/02/08 Single-cell 21-4 SB Baek

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

21-3 JH Cha

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

2021/02/01 Single-cell 21-2 JW Cho

Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

21-1 JW Cho

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

2020-1st semester
Date Team Paper
Presenter Paper title
2021/02/01 - 20-15 JW Cho

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

20-14 JW Choi

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment Within Human Melanoma

20-13 JW Seo

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

2020/06/09 - 20-12 JY Lee

Single-cell Transcriptional Diversity Is a Hallmark of Developmental Potential

20-11 JH Kim

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

2020/06/02 - 20-10 HY Seo

Peripheral T Cell Expansion Predicts Tumour Infiltration and Clinical Response

20-9 KH Hong

Defining T Cell States Associated With Response to Checkpoint Immunotherapy in Melanoma

2020/05/26 - 20-8 JY Seong

Rapid Non-Uniform Adaptation to Conformation-Specific KRAS(G12C) Inhibition

20-7 OY Min

Targeted Therapy Guided by Single-Cell Transcriptomic Analysis in Drug-Induced Hypersensitivity Syndrome: A Case Report

2020/05/19 - 20-6 SN Lee

Distinct Microbial and Immune Niches of the Human Colon

20-5 DJ Park

Massively Parallel Single-Cell Chromatin Landscapes of Human Immune Cell Development and Intratumoral T Cell Exhaustion

2020/05/12 - 20-4 SY Park

Single-cell Gene Expression Reveals a Landscape of Regulatory T Cell Phenotypes Shaped by the TCR

20-3 NY Kim

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

2020/04/28 Single-cell 20-2 SB Baek

scAI: An Unsupervised Approach for the Integrative Analysis of Parallel Single-Cell Transcriptomic and Epigenomic Profiles

20-1 JH Cha

Single-cell Multiomic Analysis Identifies Regulatory Programs in Mixed-Phenotype Acute Leukemia

2019-2nd semester
Date Team Paper
Presenter Paper title
2019/10/15 Microbiome 19-51 CY Kim

Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition

19-50 SH Lee

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease

2019/10/08 Single-cell 19-49 SB Baek

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

19-48 SB Baek

Assessment of computational methods for the analysis of single-cell ATAC-seq data

2019/10/01 Microbiome 19-47 MY Lee

Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet

19-46 NY Kim

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

2019/09/24 Single-cell 19-45 JH Cha

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

19-44 SB Baek

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

2019/09/17 Microbiome 19-43 SH Lee

A sparse covarying unit that describes healthy and impaired human gut microbiota development

19-42 CY Kim

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

2019/09/10 Single-cell 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 Microbiome 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

Date Paper
Presenter Paper title
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


Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation


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


A new genomic blueprint of the human gut microbiota


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.


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.


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.


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.


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.


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.


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.


A single-cell molecular map of mouse gastrulation and early organogenesis


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


Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

Date Paper
Presenter Paper title
2018/06/14 18-12

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.


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.


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.


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.

Date Paper
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.


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.


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.


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

Date Paper
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

Date Paper
Presenter Paper title
2015/06/11 2015-55

Improved exome prioritization of disease genes through cross-species phenotype comparison.


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.


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.


GREAT improves functional interpretation of cis-regulatory regions.

2015/05/21 2015-49

Functional annotation of noncoding sequence variants.


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.


Biological interpretation of genome-wide association studies using predicted gene functions.

2015/05/07 2015-45

Human symptoms-disease network.


A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.


Uncovering disease-disease relationships through the incomplete interactome.

2015/04/30 2015-42

The discovery of integrated gene networks for autism and related disorders.


Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.

2015/04/23 2015-40

Dissecting neural differentiation regulatory networks through epigenetic footprinting.


Cell-of-origin chromatin organization shapes the mutational landscape of cancer.


Integrative analysis of 111 reference human epigenomes.

2015/04/09 2015-37

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.


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.


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.


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.


Computational and analytical challenges in single-cell transcriptomics.

2015/03/12 2015-29

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.


Richness of human gut microbiome correlates with metabolic markers.


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.

Date Paper
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.

Date Paper
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


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
2012-31 (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.
2012-11 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
2012-05 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.
2012-02 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


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


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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