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2024-1 Advanced scOmics Data Analysis
Date Team Paper
Presenter Paper title
2024/06/18 Single-cell 24-32 EB Hong

Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory

2024/06/18 Single-cell 24-31 JJ Heo

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

2024/06/18 Single-cell 24-30 SM Han

Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

2024/06/18 Single-cell 24-29 HJ Choi

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

2024/06/11 Single-cell 24-28 SA Choi

Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids

2024/06/11 Single-cell 24-27 HJ Cha

Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics

2024/06/11 Single-cell 24-26 YK Jung

The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

2024/06/11 Single-cell 24-25 HJ Lee

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

2024/06/04 Single-cell 24-24 HK Lee

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

2024/06/04 Single-cell 24-23 JI Lee

Multimodal spatiotemporal phenotyping of human retinal organoid development

2024/06/04 Single-cell 24-22 JH Lee

Immune microniches shape intestinal Treg function

2024/06/04 Single-cell 24-21 JH Lee

A single-cell analysis of the Arabidopsis vegetative shoot apex

2024/05/28 Single-cell 24-20 JH Lee

Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq

2024/05/28 Single-cell 24-19 YH Lee

Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection

2024/05/28 Single-cell 24-18 EB Yu

Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection

2024/05/28 Single-cell 24-17 DY Won

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

2024/05/21 Single-cell 24-16 SG Oh

Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses

2024/05/21 Single-cell 24-15 SY Park

Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition

2024/05/21 Single-cell 24-14 HS Moon

Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain

2024/05/21 Single-cell 24-13 JH Nam

Spatial cellular architecture predicts prognosis in glioblastoma

2024/05/14 Single-cell 24-12 HS Na

Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease

2024/05/14 Single-cell 24-11 PK Kim

Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity

2024/05/14 Single-cell 24-10 SH Kwon

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

2024/05/14 Single-cell 24-9 Q Zhen

Single-Cell Analysis Reveals Cxcl14+ Fibroblast Accumulation in Regenerating Diabetic Wounds Treated by Hydrogel-Delivering Carbon Monoxide

2024/05/07 Single-cell 24-8 CR Leenaars

Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism

2024/05/07 Single-cell 24-7 YR Kim

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

2024/05/07 Single-cell 24-6 JY Kim

Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases

2024/05/07 Single-cell 24-5 WJ Kim

Neuregulin 4 suppresses NASH-HCC development by restraining tumor-prone liver microenvironment

2024/04/23 Single-cell 24-4 G Koh

Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease

2024/04/23 Single-cell 24-3 SH Ahn

Single-cell transcriptomic analysis deciphers heterogenous cancer stem-like cells in colorectal cancer and their organ-specific metastasis

2024/04/23 Single-cell 24-2 EJ Sung

Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis

2024/04/23 Single-cell 24-1 HJ Kim

Progenitor-like exhausted SPRY1+CD8+ T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma

2024-1 scOmics
Date Team Paper
Presenter Paper title
2024/09/20 Single-cell 24-21 HB Lee

CD4+ T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy

2024/09/20 Single-cell 24-21 YL Jung

Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer

2024/09/20 Single-cell 24-21 EJ Sung

A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

2024/09/13 Single-cell 24-21 IS Choi

Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types

2024/09/06 Single-cell 24-21 SB Baek

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains

2024/08/30 Single-cell 24-20 JH Cha

Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model

2024/08/23 Single-cell 24-19 HB Lee

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lungcancer

2024/08/16 Single-cell 24-18 YL Jung

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

2024/08/09 Single-cell 24-17 EJ Sung

Population-level comparisons of gene regulatory networks modeled on highthroughput single-cell transcriptomics data

2024/08/02 Single-cell 24-16 IS Choi

node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking

2024/07/26 Single-cell 24-15 SB Baek

Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning

2024/07/19 Single-cell 24-14 JH Cha

Contextual AI models for single-cell protein biology

2024/07/12 Single-cell 24-13 EJ Sung

Nicheformer: a foundation model for single-cell and spatial omics

2024/07/05 Single-cell 24-12 IS Choi

Large Scale Foundation Model on Single-cell Transcriptomics

2024/06/28 Single-cell 24-11 SB Baek

scGPT: toward building a foundation modelfor single-cell multi-omics using generative AI

2024/06/21 Single-cell 24-10 JH Cha

Transfer learning enables predictions in network biology

2024/06/07 Single-cell 24-9 EJ Sung

The Web-Based Portal SpatialTME Integrates Histological Images with Single-Cell and Spatial Transcriptomics to Explore the Tumor Microenvironment

2024/05/17 Single-cell 24-8 IS Choi

SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes

2024/05/10 Single-cell 24-7 SB Baek

A relay velocity model infers cell-dependent RNA velocity

2024/05/03 Single-cell 24-5 EJ Sung

Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity

2024/04/26 Single-cell 24-6 JH Cha

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

2024/04/05 Single-cell 24-4 IS Choi

Automatic cell-type harmonization and integration across Human Cell Atlas datasets

2024/03/22 Single-cell 24-3 SB Baek

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

2024/03/15 Single-cell 24-2 JH Cha

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

2024/03/08 Single-cell 24-1 EJ Sung

Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data

2024-1 Microbiome
Date Team Paper
Presenter Paper title
2024/08/21 Microbiome 24-23 NY Kim

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

2024/08/14 Microbiome 24-23 YR Kim

Accurate structure prediction of biomolecular interactions with AlphaFold 3

2024/08/14 Microbiome 24-23 JY kim

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

2024/08/07 Microbiome 24-23 WJ Kim

Gut microbiome-metabolome interactions predict host condition

2024/08/07 Microbiome 24-23 G Koh

Protein remote homology detection and structural alignment using deep learning

2024/07/31 Microbiome 24-23 SH Ahn

A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome

2024/07/31 Microbiome 24-23 HJ Kim

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

2024/07/24 Microbiome 24-23 JY Ma

Compositional Differential Abundance Testing: Defining and Finding a New Type of Health-Microbiome Associations

2024/07/24 Microbiome 24-23 JH Cha

Discovery of antimicrobial peptides in the global microbiome with machine learning

2024/07/17 Microbiome 24-23 NY Kim

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome

2024/07/17 Microbiome 24-23 YR Kim

Paternal microbiome perturbations impact offspring fitness

2024/07/10 Microbiome 24-23 JY Kim

Interactions-based classification of a single microbial sample

2024/07/10 Microbiome 24-23 NY Kim

Accurate estimation of intraspecificmicrobial gene content variation inmetagenomic data with MIDAS v3 andStrainPGC

2024/07/03 Microbiome 24-29 WJ Kim

A pan-cancer analysis of the microbiome inmetastatic cancer

2024/07/03 Microbiome 24-28 G Koh

A specific enterotype derived from gut microbiomeof older individuals enables favorable responses toimmune checkpoint blockade therapy

2024/06/26 Microbiome 24-27 SH Ahn

Stratification of Fusobacterium nucleatum by localhealth status in the oral cavity defines its subspeciesdisease association

2024/06/26 Microbiome 24-26 HJ Kim

A universe of human gut-derived bacterialprophages: unveiling the hidden viral players inintestinal microecology

2024/06/19 Microbiome 24-25 JY Ma

Robustness of cancer microbiome signals over a broad range of methodological variation

2024/06/19 Microbiome 24-24 JY Cha

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

2024/06/05 Microbiome 24-22 YR Kim

A cryptic plasmid is among the most numerous genetic elements in the human gut

2024/06/05 Microbiome 24-21 JY Kim

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

2024/05/29 Microbiome 24-20 WJ Kim

Fecal microbial load is a major determinant of gut microbiome variation and aconfounder for disease associations

2024/05/29 Microbiome 24-19 G Koh

A host-microbiota interactome reveals extensive transkingdom connectivity

2024/05/22 Microbiome 24-18 SH Ahn

Metagenomic estimation of dietary intake from human stool

2024/05/22 Microbiome 24-17 HJ Kim

A metagenomic catalog of the early-life human gut virome

2024/05/08 Microbiome 24-16 JY Ma

Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

2024/05/08 Microbiome 24-15 JH Cha

Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’

2024/05/01 Microbiome 24-14 NY Kim

Gut microbial structural variation associates with immune checkpoint inhibitor response

2024/05/01 Microbiome 24-13 YR Kim

Fungal signature differentiates alcohol-associated liver disease from nonalcoholic fatty liver disease

2024/04/24 Microbiome 24-12 JY Kim

Incorporating metabolic activity, taxonomy and community structure to improve microbiome based predictive models for host phenotype prediction

2024/04/24 Microbiome 24-11 WJ Kim

Disease-specific loss of microbial cross feeding interactions in the human gut

2024/04/03 Microbiome 24-7 JY Ma

Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures

2024/04/03 Microbiome 24-9 SH Ahn

Microdiversity of the vaginal microbiome is associated with preterm birth

2024/03/27 Microbiome 24-8 HJ Kim

Large language models improve annotation of prokaryotic viral proteins

2024/03/27 Microbiome 24-10 G Koh

Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide

2024/03/20 Microbiome 24-6-2 JH Cha

Visualizing ’omic feature rankings and log-ratios using Qurro

2024/03/20 Microbiome 24-6-1 JH Cha

Establishing microbial composition measurement standards with reference frames

2024/03/20 Microbiome 24-5 NY Kim

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

2024/03/13 Microbiome 24-4 YR Kim

Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults

2024/03/13 Microbiome 24-3 JY Kim

Effective binning of metagenomic contigs using contrastive multi-view representation learning

2024/03/06 Microbiome 24-2 WJ Kim

Polarization of microbial communities between competitive and cooperative metabolism

2024/03/06 Microbiome 24-1-2 G Koh

Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome

2024/03/06 Microbiome 24-1-1 G Koh

Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes

2023-2 scOmics
Date Team Paper
Presenter Paper title
2024/02/20 Single-cell 23-40 IS Choi

Population-level integration of single-cell datasets enables multi-scale analysis across samples

2024/02/06 Single-cell 23-39 SB Baek

scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

2024/01/30 Single-cell 23-38 JH Cha

Modeling intercellular communication in tissues using spatial graphs of cells

2024/01/16 Single-cell 23-37 EJ Sung

Precise identification of cell states altered in disease using healthy single-cell references

2024/01/09 Single-cell 23-36 IS Choi

Learning Individual Survival Models from PanCancer Whole Transcriptome Data

2024/01/02 Single-cell 23-35 SB Baek

Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics

2023/12/12 Single-cell 23-34 JH Cha

Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti–PD-1 in head and neck cancer

2023/12/05 Single-cell 23-33 EJ Sung

MHC II immunogenicity shapes the neoepitope landscape in human tumors

2023/11/28 Single-cell 23-32 IS Choi

Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours

2023/11/21 Single-cell 23-31 JW Yu

Pan-cancer classification of single cells in the tumour microenvironment

2023/10/31 Single-cell 23-30 JH Cha

Single-cell mapping of combinatorial target antigens for CAR switches using logic gates

2023/10/24 Single-cell 23-29 SB Baek

Comparative analysis of cell–cell communication at single-cell resolution

2023/09/26 Single-cell 23-28 EJ Sung

Phenotypic diversity of T cells in human primary and metastatic brain tumors revealed by multiomic interrogation

2023/09/19 Single-cell 23-27 IS Choi

An integrated tumor, immune and microbiome atlas of colon cancer

2023/09/12 Single-cell 23-26 SB Baek

Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

2023/09/05 Single-cell 23-25 JH Cha

Recruitment of epitope-specific T cell clones with a low-avidity threshold supports efficacy against mutational escape upon re-infection

2023-2 Microbiome
Date Team Paper
Presenter Paper title
2024/02/21 Microbiome 23-66 HJ Kim

Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

2024/02/21 Microbiome 23-65 JH Cha

A predicted CRISPR-mediated symbiosis between uncultivated archaea

2024/02/14 Microbiome 23-64 SH Ahn

Integrating compositional and functional content to describe vaginal microbiomes in health and disease

2024/02/14 Microbiome 23-63 JY Ma

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

2024/02/07 Microbiome 23-62 NY Kim

Mapping the T cell repertoire to a complex gut bacterial community

2024/02/07 Microbiome 23-61 YR Kim

Multi-view integration of microbiome data for identifying disease-associated modules

2024/01/24 Microbiome 23-60 JY Kim

Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis

2024/01/24 Microbiome 23-59 WJ Kim

Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

2024/01/17 Microbiome 23-58 G Koh

Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome

2024/01/17 Microbiome 23-57 SH Ahn

Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines

2024/01/10 Microbiome 23-56 HJ Kim

Fast and robust metagenomic sequence comparison through sparse chaining with skani

2024/01/10 Microbiome 23-55 JY Ma

Bacterial SNPs in the human gut microbiome associate with host BMI

2023/01/03 Microbiome 23-54 JH Cha

Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer

2023/01/03 Microbiome 23-53 NY Kim

Multi-kingdom gut microbiota analyses define bacterial-fungal interplay and microbial markers of pan-cancer immunotherapy across cohorts

2023/12/27 Microbiome 23-52 YR Kim

Prior antibiotic administration disrupts anti-PD-1 responses in advanced gastric cancer by altering the gut microbiome and systemic immune response

2023/12/27 Microbiome 23-51 JY Kim

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

2023/12/13 Microbiome 23-50 WJ Kim

Altered infective competence of the human gut microbiome in COVID-19

2023/12/13 Microbiome 23-49 G Koh

Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning

2023/12/06 Microbiome 23-48 SH Ahn

A data-driven approach for predicting the impact of drugs on the human microbiome

2023/12/06 Microbiome 23-47 HJ Kim

Activation of programmed cell death and counter-defense functions of phage accessory genes

2023/11/29 Microbiome 23-46 JH Cha

Top-down identification of keystone taxa in the microbiome

2023/11/29 Microbiome 23-45 JY Ma

Pitfalls of genotyping microbial communities with rapidly growing genome collections

2023/11/22 Microbiome 23-44 NY Kim

Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

2023/11/22 Microbiome 23-43 SH Lee

Generation of accurate, expandable phylogenomic trees with uDance

2023/11/08 Microbiome 23-42 WJ Kim

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

2023/11/08 Microbiome 23-41 JY Kim

Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures

2023/11/01 Microbiome 23-40 G Koh

Consistency across multi-omics layers in a drug-perturbed gut microbial community

2023/11/01 Microbiome 23-39 HJ Kim

Identification of mobile genetic elements with geNomad

2023/10/25 Microbiome 23-38 SH Ahn

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer

2023/10/11 Microbiome 23-37 JH Cha

The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans

2023/10/11 Microbiome 23-36 JY Ma

Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy

2023/09/27 Microbiome 23-35 NY Kim

The defensome of complex bacterial communities

2023/09/27 Microbiome 23-34 SH Lee

Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment

2023/09/20 Microbiome 23-33 WJ Kim

Toward an improved definition of a healthy microbiome for healthy aging

2023/09/20 Microbiome 23-32 JY Kim

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults

2023/09/13 Microbiome 23-31 G Koh

Statistical modeling of gut microbiota for personalized health status monitoring

2023/09/13 Microbiome 23-30 SH Ahn

Adjusting for age improves identification of gut microbiome alterations in multiple diseases

2023/09/06 Microbiome 23-29 HJ Kim

Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan

2023/09/06 Microbiome 23-28 JH Cha

Longitudinal comparison of the developing gut virome in infants and their mothers

Date Team Paper
Presenter Paper title
2023/06/13 Microbiome 23-24 JY Kim

Structure of the Mucosal and Stool Microbiome in Lynch Syndrome

2023/06/13 Microbiome 23-23 WJ Kim

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

2023/06/13 Microbiome 23-22 SH Ahn

Roles of oral microbiota and oral-gut microbial transmission in hypertension

2023/05/30 Microbiome 23-21 SY Lim

Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain

2023/05/30 Microbiome 23-20 BS Kim

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease

2023/05/30 Microbiome 23-19 JY Kim

Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS

2023/05/23 Microbiome 23-18 EJ Sung

Gut microbiota-mediated nucleotide synthesis attenuates the response to neoadjuvant chemoradiotherapy in rectal cancer

2023/05/23 Microbiome 23-17 G Koh

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease

2023/05/23 Microbiome 23-16 SH Lee

Identification of trypsin-degrading commensals in the large intestine

2023/05/16 Microbiome 23-15 JP Hong

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

2023/05/16 Microbiome 23-14 MR Jang

Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance

2023/05/16 Microbiome 23-13 JW Yu

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

2023/05/09 Microbiome 23-12 NY Kim

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors

2023/05/09 Microbiome 23-11 HR Shin

Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts

2023/05/09 Microbiome 23-10 SG Oh

The antitumour effects of caloric restriction are mediated by the gut microbiome

2023/05/02 Microbiome 23-9 WJ Kim

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

2023/05/02 Microbiome 23-8 SM Han

Drivers and determinants of strain dynamics following fecal microbiota transplantation

2023/05/02 Microbiome 23-7 YY Kim

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

2023/04/18 Microbiome 23-6 SH Heo

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites

2023/04/18 Microbiome 23-5 SY Yang

Population-level impacts of antibiotic usage on the human gut microbiome

2023/04/18 Microbiome 23-4 YH Yoon

Enterococci enhance Clostridioides difficile pathogenesis

2023/04/11 Microbiome 23-3 DH Lee

Targeting keystone species helps restore the dysbiosis of butyrate‐producing bacteria in nonalcoholic fatty liver disease

2023/04/11 Microbiome 23-2 YJ Roh

Differential Oral Microbial Input Determines Two Microbiota Pneumo-Types Associated with Health Status

2023/04/11 Microbiome 23-1 SH Ahn

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

2023-1 scOmics
Date Team Paper
Presenter Paper title
2023/08/30 Single-cell 23-24 JW Yu

Decoupling the correlation between cytotoxic and exhausted T lymphocyte transcriptomic signatures enhances melanoma immunotherapy response prediction from tumor expression

2023/08/09 Single-cell 23-23 IS Choi

Major data analysis errors invalidate cancer microbiome findings

2023/08/02 Single-cell 23-22 EJ Sung

A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets

2023/07/26 Single-cell 23-21 G Koh

Single-cell meta-analyses reveal responses of tumor-reactive CXCL13+ T cells to immune-checkpoint blockade

2023/07/19 Single-cell 23-20 JW Yu

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression

2023/07/12 Single-cell 23-19 JH Cha

DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data

2023/07/05 Single-cell 23-18 SB Baek

Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance

2023/06/28 Single-cell 23-17 EJ Sung

Self-supervised graph representation learning integrates multiple molecular networks and decodes gene-disease relationships

2023/06/21 Single-cell 23-16 IS Choi

High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

2023/06/14 Single-cell 23-15 G Koh

Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment

2023/05/31 Single-cell 23-14 JW Yu

Mutated processes predict immune checkpoint inhibitor therapy benefit in metastatic melanoma

2023/05/24 Single-cell 23-13 JH Cha

Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer

2023/05/17 Single-cell 23-12 SB Baek

Integrative single-cell analysis of cardiogenesis indentifies developmental trajectories and non-conding mutations in congenital heart disease

2023/05/10 Single-cell 23-11 EJ Sung

Supervised discovery of interpretable gene programs from single-cell data

2023/05/03 Single-cell 23-10 IS Choi

Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer

2023/04/26 Single-cell 23-9 G Koh

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

2023/03/22 Single-cell 23-8 JW Yu

MetaTiME: Meta-components of the Tumor Immune Microenvironment

2023/03/08 Single-cell 23-7 JH Cha

Pre-encoded responsiveness to type I interferon in the peripheral immune system defines outcome of PD1 blockade therapy

2023/02/21 Single-cell 23-6 SB Baek

Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating T cells

2023/02/14 Single-cell 23-5 EJ Sung

A T cell resilience model associated with response to immunotherapy in multiple tumor types

2022/01/31 Single-cell 23-4 IS Choi

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

2023/01/25 Single-cell 23-3 G Koh

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

2023/01/17 Single-cell 23-2 JW Yu

Pan-cancer integrative histology-genomic analysis via multimodal deep learning

2023/01/11 Single-cell 23-1 JH Cha

Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy

2023-1 Microbiome
Date Team Paper
Presenter Paper title
2023/08/25 Microbiome 23-27 JY Ma

Enterosignatures define common bacterial guilds in the human gut microbiome

2023/08/25 Microbiome 23-26 NY Kim

PhyloMed: a phylogeny-based test of mediation effect in microbiome

2023/08/18 Microbiome 23-25 SH Lee

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

2023/08/18 Microbiome 23-24 WJ Kim

Measurement of bacterial replication rates in microbial communities

2023/08/11 Microbiome 23-23 JY Kim

Skin microbiome diferentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons

2023/08/11 Microbiome 23-22 SH Ahn

Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype

2023/08/04 Microbiome 23-21 HJ Kim

Profiling the human intestinal environment under physiological conditions

2023/07/28 Microbiome 23-20 JH Cha

Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system

2023/07/14 Microbiome 23-19 JY Ma

Enhanced metagenomic deep learning for disease prediction and consistent signature recognition by restructured microbiome 2D representations

2023/07/07 Microbiome 23-18 NY Kim

Gene fow and introgression are pervasive forces shaping the evolution of bacterial species

2023/06/30 Microbiome 23-17 JH Cha

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi‑omic analyses

2023/06/23 Microbiome 23-16 HJ Kim

Deciphering microbial gene function using natural language processing

2023/06/16 Microbiome 23-15 SH Lee

Rethinking bacterial relationships in light of their molecular abilities

2023/06/02 Microbiome 23-14 JY Ma

The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn’s disease

2023/05/26 Microbiome 23-13 NY Kim

Antigen discovery and specification of immunodominance hierarchies for MHCIIrestricted epitopes

2023/05/19 Microbiome 23-12 SH Lee

Single Cell Transcriptomics Reveals the Hidden Microbiomes of Human Tissues

2023/05/12 Microbiome 23-11 JY Kim

Stability of the human faecal microbiome in a cohort of adult men

2023/04/28 Microbiome 23-10 WJ Kim

Metatranscriptome of human faecal microbial communities in a cohort of adult men

2023/03/24 Microbiome 23-9 SH Ahn

Tumor microbiome links cellular programs and immunity in pancreatic cancer

2023/03/17 Microbiome 23-8 HJ Kim

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

2023/03/10 Microbiome 23-7 JH Cha

The person-to-person transmission landscape of the gut and oral microbiomes

2023/02/21 Microbiome 23-6 JY Ma

BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations

2023/02/14 Microbiome 23-5 NY Kim

Phage–host coevolution in natural populations

2023/01/31 Microbiome 23-4 SH Lee

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease

2023/01/25 Microbiome 23-3 SH Ahn

Scalable power analysis and effect size exploration of microbiome community differences with Evident

2023/01/17 Microbiome 23-2 HJ Kim

Phanta: Phage-inclusive profiling of human gut metagenomes

2023/01/11 Microbiome 23-1 JH Cha

Computational approach to modeling microbiome landscapes associated with chronic human disease progression

2022 scOmics
Date Team Paper
Presenter Paper title
2022/12/28 Single-cell 22-32 EJ Sung

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

2022/11/29 Single-cell 22-31 JH Cha, SB Baek, IS Choi

Representation learning of RNA velocity reveals robust cell transitions UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference Mapping transcriptomic vector fields of single cells

2022/11/22 Single-cell 22-30 IS Choi

Network-based machine learning approach to predict immunotherapy response in cancer patients

2022/11/08 Single-cell 22-29 SB Baek

Modeling fragment counts improves single-cell ATAC-seq analysis

2022/10/11 Single-cell 22-28 G Koh

Extricating human tumour immune alterations from tissue inflammation

2022/09/13 Single-cell 22-25 JW Yu

T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies

2022/09/06 Single-cell 22-26 JH Cha

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

2022/09/01 Single-cell 22-27 SB Baek

MIRA: Joint regulatory modeling of multimodal expression and chromatin accessibility in single cells

2022/08/25 Single-cell 22-24 EJ Sung

Immune phenotypic linkage between colorectal cancer and liver metastasis

2022/08/18 Single-cell 22-23 IS Choi

Biologically informed deep learning to infer gene program activity in single cells

2022/08/11 Single-cell 22-22 SB Baek

Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology

2022/07/28 Single-cell 22-21 JH Cha

Mapping single-cell data to reference atlases by transfer learning

2022/07/21 Single-cell 22-20 JW Yu

Pan-cancer mapping of single T cell profiles reveals a TCF1:CXCR6-CXCL16 regulatory axis essential for effective anti-tumor immunity

2022/07/14 Single-cell 22-19 IS Choi

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics

2022/07/07 Single-cell 22-18 EJ Sung

Metacells untangle large and complex single-cell transcriptome networks MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions Metacell‑2: a divide‑and‑conquer metacell algorithm for scalable scRNA‑seq analysis

2022/06/23 Single-cell 22-17 SB Baek

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics

2022/06/09 Single-cell 22-16 JH Cha

Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)

2022/06/02 Single-cell 22-15 JW Yu

Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial

2022/05/19 Single-cell 22-14 EJ Sung

Effect of imputation on gene network reconstruction from single-cell RNA-seq data

2022/05/12 Single-cell 22-13 IS Choi

Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

2022/04/07 Single-cell 22-12 SB Baek

Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19

2022/03/25 Single-cell 22-11 JH Cha

Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy

2022/03/18 Single-cell 22-10 JW Yu

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels

2022/03/04 Single-cell 22-9 EJ Sung

Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses

2022/02/25 Single-cell 22-8 SB Baek

MultiMAP: dimensionality reduction and integration of multimodal data

2022/02/18 Single-cell 22-7 IS Choi

CellRank for directed single-cell fate mapping

2022/02/11 Single-cell 22-6 JH Cha

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

2022/02/04 Single-cell 22-5 IS Choi

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

2022/01/28 Single-cell 22-4 EJ Sung

Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

2022/01/28 Single-cell 22-3 JH Cha

Pan-cancer single-cell landscape of tumor-infiltrating T cells

2022/01/14 Single-cell 22-2 JW Yu

Atlas of clinically distinct cell states and ecosystems across human solid tumors

2022/01/07 Single-cell 22-1 SB Baek

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

2022 Microbiome
Date Team Paper
Presenter Paper title
2022/12/28 Microbiome 22-34 JY Ma

A novel in silico method employs chemical and protein similarity algorithms to accurately identify chemical transformations in the human gut microbiome

2022/11/29 Microbiome 22-33 NY Kim

Inference of disease-associated microbial biomarkers based on metagenomic and metatranscriptomic data

2022/11/22 Microbiome 22-32 SH Lee

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance

2022/10/11 Microbiome 22-31 SH Ahn

Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration

2022/09/27 Microbiome 22-30 HJ Kim

Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans

2022/09/13 Microbiome 22-29 JH Cha

SynTracker: a synteny based tool for tracking microbial strains

2022/09/06 Microbiome 22-28 JY Ma

Identification of antimicrobial peptides from the human gut microbiome using deep learning

2022/09/01 Microbiome 22-27 NY Kim

Discovery of bioactive microbial gene products in inflammatory bowel disease

2022/08/25 Microbiome 22-26 SH Lee

Large-scale microbiome data integration enables robust biomarker identification

2022/08/18 Microbiome 22-25 SH Ahn

Predicting cancer prognosis and drug response from the tumor microbiome

2022/08/11 Microbiome 22-24 HJ Kim

Thousands of small, novel genes predicted in global phage genomes

2022/08/04 Microbiome 22-23 JH Cha

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

2022/07/28 Microbiome 22-22 NY Kim

Biosynthetic potential of the global ocean microbiome

2022/07/14 Microbiome 22-21 JY Ma

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

2022/07/07 Microbiome 22-20 SH Lee

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit disease Critical Assessment of Metagenome Interpretation: the second round of challenges

2022/06/24 Microbiome 22-19 SH Ann

Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer’s-type dementia

2022/06/10 Microbiome 22-18 HJ Kim

Microbiome and metabolome features of the cardiometabolic disease spectrum

2022/06/03 Microbiome 22-17 JH Cha

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

2022/05/27 Microbiome 22-16 NY Kim

Integrating phylogenetic and functional data in microbiome studies

2022/05/20 Microbiome 22-15 MY Ma

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

2022/05/13 Microbiome 22-14 SH Lee

Multivariable association discovery in population-scale meta-omics studies

2022/04/08 Microbiome 22-13 SH Ahn

Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

2022/04/01 Microbiome 22-12 HJ Kim

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

2022/03/18 Microbiome 22-11 JH Cha

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

2022/03/04 Microbiome 22-10 JY Ma

Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling

2022/02/25 Microbiome 22-9 NY Kim

Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

2022/02/18 Microbiome 22-8 SH Lee

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

2022/02/11 Microbiome 22-7 SH Ahn

Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis

2022/02/04 Microbiome 22-6 JH Cha

Gut microbiota modulates weight gain in mice after discontinued smoke exposure

2022/01/28 Microbiome 22-5 JY Ma

The human microbiome encodes resistance to the antidiabetic drug acarbose

2022/01/28 Microbiome 22-4 SH Lee

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis

2022/01/14 Microbiome 22-3 HJ Kim

The influence of the gut microbiome on BCG-induced trained immunity

2022/01/07 Microbiome 22-2 JY Ma

Towards the biogeography of prokaryotic genes

2022/01/07 Microbiome 22-1 NY Kim

ReprDB and panDB: minimalist databases with maximal microbial representation

2022 Microbiome Special JC
Date Team Paper
Presenter Paper title
2022/08/30 Microbiome 22-15 HY Kang

Maast: genotyping thousands of microbial strains efficiently

2022/08/30 Microbiome 22-14 YJ Roh

MIDAS2: Metagenomic Intra-species Diversity Analysis System

2022/08/30 Microbiome 22-13 SC Yang

Scalable microbial strain inference in metagenomic data using StrainFacts

2022/08/26 Microbiome 22-12 SH Ahn

StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

2022/08/26 Microbiome 22-11 HJ Kim

Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation

2022/08/26 Microbiome 22-10 JY Ma

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

2022/08/19 Microbiome 22-9 JH Cha

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

2022/08/19 Microbiome 22-8 NY Kim

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

2022/08/19 Microbiome 22-7 SH Lee

Dispersal strategies shape persistence and evolution of human gut bacteria

2022/08/09 Microbiome 22-6 SH Ahn

The long-term genetic stability and individual specificity of the human gut microbiome

2022/08/09 Microbiome 22-5 HJ Kim

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

2022/08/09 Microbiome 22-4 JY Ma

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

2022/07/29 Microbiome 22-3 JH Cha

Extensive transmission of microbes along the gastrointestinal tract

2022/07/29 Microbiome 22-2 NY Kim

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

2022/07/29 Microbiome 22-1 SH Lee

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

2021-2nd semester
Date Team Paper
Presenter Paper title
2021/11/23 Single-cell 21-39 IS Choi

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

2021/11/16 Single-cell 21-38 SB Back

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer

2021/11/09 Single-cell 21-37 JH Cha

Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci

2021/11/02 Single-cell 21-36 SB Baek

Functional Inference of Gene Regulation using Single-Cell Multi-Omics

2021/10/26 Single-cell 21-35 IS Choi

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

2021/10/19 Single-cell 21-34 JH Cha

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

2021/10/05 Single-cell 21-33 JH Cha

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

2021/09/28 Single-cell 21-32 SB Baek

Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

2021/09/14 Single-cell 21-31 IS Choi

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

2021/09/07 Single-cell 21-30 JH Cha

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

2021/08/31 Single-cell 21-29 IS Choi

Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma

2021/08/24 Single-cell 21-28 SB Baek

Interpreting type 1 diabetes risk with genetics and single-cell epigenomics

2021-1st semester
Date Team Paper
Presenter Paper title
2021/06/03 - 21-27 HJ Kim

Massive expansion of human gut bacteriophage diversity

21-26 JY Ma

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

2021/05/27 - 21-25 JK Yoon

Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation

2021/05/20 - 21-24 NY Kim

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

21-23 IS Choi

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

2021/05/13 - 21-22 SA Kim

Gut microbiome structure and metabolic activity in inflammatory bowel disease

21-21 HJ Kim

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

2021/05/06 - 21-20 JY Ma

A predictive index for health status using species-level gut microbiome profiling

21-19 JH Cha

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

2021/04/29 - 21-18 SB Baek

Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis

21-17 SR You

Structure of the Mucosal and Stool Microbiome in Lynch Syndrome

2021/04/22 - 21-16 HH Eom

Cross-reactivity between tumor MHC class 1-restricted antigens and an enterococcal bacteriophage

21-15 JH Park

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice

2021/04/15 - 21-14 MH Lee

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk

2021/04/08 - 21-13 YY Jang

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

2021/04/01 - 21-12 NY Kim

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

2021/03/25 - 21-11 JM Lee

Mining the Human Gut Microbiota for Immunomodulatory Organisms

2021/03/18 - 21-10 JH Cha

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

2021/03/11 - 21-9 JH Cha

The human tumor microbiome is composed of tumor type-specific intracellular bacteria

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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