Journal Club

2023 scOmics

Date	Team	Paper index	Presenter	Paper title
2023/03/14	Single-cell	23-9	G Koh	Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment
2023/03/07	Single-cell	23-8	JW Yu	MetaTiME: Meta-components of the Tumor Immune Microenvironment
2023/02/28	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
2022/02/07	Single-cell	23-4	IS Choi	Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment
2023/01/31	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 Microbiome Date Team Paper index Presenter Paper title 2023/02/14 Microbiome 23-5 NY Kim Phage–host coevolution in natural populations 2023/02/07 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 2023/01/31 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 index 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 index 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 index 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 index 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 index 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 2021 Date Team Paper index 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 index 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 index 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 2019 Date Paper index 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 19-21 Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation 19-20 Microbial network disturbances in relapsing refractory Crohn's disease. 2019/05/23 19-19 New insights from uncultivated genomes of the global human gut microbiome 19-18 A new genomic blueprint of the human gut microbiota 19-17 Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. 2019/05/16 19-16 Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. 19-15 Metatranscriptome of human faecal microbial communities in a cohort of adult men. 2019/05/09 19-14 Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. 19-13 Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. 2019/05/02 19-12 Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy. 19-11 Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. 2019/4/11 19-10 Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. 19-9 Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. 2019/4/4 19-8 Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. 19-7 Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing 2019/3/28 19-6 Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. 19-5 Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. 2019/3/21 19-4 Phenotype molding of stromal cells in the lung tumor microenvironment. 19-3-1 A single-cell molecular map of mouse gastrulation and early organogenesis 19-3 The single-cell transcriptional landscape of mammalian organogenesis 2019/3/14 19-2 Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 19-1 Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer 2018 Date Paper index Presenter Paper title 2018/06/14 18-12 A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. 18-11 Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. 2018/06/07 18-10 Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. 18-9 Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing. 2018/05/31 18-8 Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. 18-7 A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. 2018/05/24 18-6 CY Kim Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs. 18-5 HJ Han FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map. 2018/05/17 18-4 KS Kim A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. 18-3 SH Lee A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. 2018/05/10 18-2 JW Cho Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. 18-1 DS Bae Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. 2017 Date Paper index Presenter Paper title 2017/06/28 17-36 HJ Han Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. 17-35 JW Cho Landscape of tumor-infiltrating T cell repertoire of human cancers. 2017/06/14 17-34 JW Cho The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression. 17-33 MY Lee A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. 2017/06/07 17-32 Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis. 17-31 MY Lee Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. 2017/05/31 17-30 DS Bae Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. 17-29 JW Cho Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. 2017/05/24 17-28 EB Kim Systemic Immunity Is Required for Effective Cencer Immunotherapy. 17-27 CY Kim Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. 2017/05/17 17-26 Host and Environmental Factors Influencing Individual Human Cytokine Responses. 17-25 A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. 2017/04/26 17-24 Pooled CRISPR screening with single-cell transcriptome readout. 17-23 Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. 2017/04/12 17-22 SH Lee Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. 17-21 CY Kim Wishbone identifies bifurcating developmental trajectories from single-cell data. 2017/04/05 17-20 KS Kim Reversed graph embedding resolves complex single-cell developmental trajectories. 17-19 SH Lee Single-cell mRNA quantification and differential analysis with Census. 2017/03/29 17-18 Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage. 17-17 DS Bae Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis. 2017/03/22 17-16 Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. 17-15 EB Kim Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. 2017/03/15 17-14 Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. 17-13 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. 2017/02/28 17-12 KS Kim A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. 17-11 JE Shim Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types. 2017/02/21 17-10 EB Kim Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer. 17-09 EB Kim Chromatin structure-based prediction of recurrent noncoding mutations in cancer. 2017/02/07 17-08 DS Bae Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. 17-07 MY Lee Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer. 2017/01/31 17-06 CY Kim Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. 2017/01/24 17-05 JW Cho Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells. 2017/01/17 17-04 HJ Han Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C 17-03 EB Kim CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. 2017/01/10 17-02 JE Shim ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis 2017/01/03 17-01 SH Lee Single-cell messenger RNA sequencing reveals rare intestinal cell types 2016 Date Paper index Presenter Paper title 2016/12/27 2016-31 EB Kim Decoding the regulatory network of early blood development from single-cell gene expression measurements. 2016/12/6 2016-30 KS Kim Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. 2016/11/29 2016-29 DS Bae The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. 2016/11/22 2016-28 CY Kim Classification of low quality cells from single-cell RNA-seq data. 2016/11/15 2016-27 MY Lee Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. 2016/11/8 2016-26 JW Cho Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. 2016/11/1 2016-25 HJ Han Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. 2016/10/25 2016-24 MY Lee Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. 2016/10/11 2016-23 JE Shim Widespread parainflammation in human cancer 2016/9/27 2016-22 ER Kim Analysis of protein-coding genetic variation in 60,706 humans 2016/9/20 2016-21 SM Yang Functional characterization of somatic mutations in cancer using network-based inference of protein activity pubmed fulltext 2016/9/13 2016-20 KS Kim Exploiting single-cell expression to characterize co-expression replicability. 2016/9/6 2016-19 T Lee Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade 2016/8/31 2016-18 DS Bae A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors 2016/8/16 2016-17 JW Cho The landscape of accessible chromatin in mammalian preimplantation embryos 2016/8/8 2016-16 EB Kim Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin 2016/8/1 2016-15 MY Lee Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients 2016/7/25 2016-14 CY Kim Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets 2016/7/18 2016-13 HJ Han Identification of transcriptional regulators in the mouse immune system 2016/6/8 2016-12 DS Bae, CY Kim Mapping the effects of drugs on the immune system 2016-11 DS Bae, CY Kim Elucidating compound mechanism of action by network perturbation analysis 2016/6/1 2016-10 MY Lee,SM Cho Integrative approaches for large-scale transcriptome-wide association studies 2016-9 MY Lee,SM Cho Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases 2016/5/18 2016-8 CY Kim,SJ Kwon Survey of variation in human transcription factors reveals prevalent DNA binding changes 2016-7 CY Kim,SJ Kwon Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo 2016/5/11 2016-6 DS Bae, CY Kim Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality 2016-5 DS Bae, CY Kim Dynamic regulatory network controlling Th17 cell differentiation 2016/5/4 2016-4 MY Lee,SM Cho Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy 2016-3 MY Lee,SM Cho Regulators of genetic risk of breast cancer identified by integrative network analysis 2016/4/27 2016-2 CY Kim,SJ Kwon A predictive computational framework for direct reprogramming between human cell types 2016-1 CY Kim,SJ Kwon CellNet: Network biology applied to stem cell engineering 2015 Date Paper index Presenter Paper title 2015/06/11 2015-55 Improved exome prioritization of disease genes through cross-species phenotype comparison. 2015-54 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. 2015/06/04 2015-53 eXtasy: variant prioritization by genomic data fusion. 2015-52 A probabilistic disease-gene finder for personal genomes. 2015/05/28 2015-51 Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. 2015-50 GREAT improves functional interpretation of cis-regulatory regions. 2015/05/21 2015-49 Functional annotation of noncoding sequence variants. 2015-48 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. 2015/05/14 2015-47 Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. 2015-46 Biological interpretation of genome-wide association studies using predicted gene functions. 2015/05/07 2015-45 Human symptoms-disease network. 2015-44 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. 2015-43 Uncovering disease-disease relationships through the incomplete interactome. 2015/04/30 2015-42 The discovery of integrated gene networks for autism and related disorders. 2015-41 Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. 2015/04/23 2015-40 Dissecting neural differentiation regulatory networks through epigenetic footprinting. 2015-39 Cell-of-origin chromatin organization shapes the mutational landscape of cancer. 2015-38 Integrative analysis of 111 reference human epigenomes. 2015/04/09 2015-37 Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. 2015-36 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. 2015/04/02 2015-35 Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. 2015-34 Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. 2015/03/26 2015-33 Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. 2015-32 Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. 2015/03/19 2015-31 Decoding the regulatory network of early blood development from single-cell gene expression measurements. 2015-30 Computational and analytical challenges in single-cell transcriptomics. 2015/03/12 2015-29 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species. 2015-28 Richness of human gut microbiome correlates with metabolic markers. 2015-27 A metagenome-wide association study of gut microbiota in type 2 diabetes. 2015/03/09 2015-26 HJ Han Practical guidelines for the comprehensive analysis of ChIP-seq data. 2015-25 T Lee Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. 2015-24 ER Kim Rapid neurogenesis through transcriptional activation in human stem cells. 2015/03/02 2015-23 DS Bae Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. 2015-22 CY Kim Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies. 2015-21 ER Kim The Genotype-Tissue Expression (GTEx) project. 2015/02/24 2015-20 ER Kim Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. 2015-19 KS Kim Principles of regulatory information conservation between mouse and human. 2015-18 BH Kang Conservation of trans-acting circuitry during mammalian regulatory evolution. 2015/02/16 2015-17 T Lee Genetic and epigenetic fine mapping of causal autoimmune disease variants. 2015-16 CY Kim A general framework for estimating the relative pathogenicity of human genetic variants. 2015-15 CY Kim A probabilistic model to predict clinical phenotypic traits from genome sequencing. 2015/02/02 2015-14 BH Kang Relating the metatranscriptome and metagenome of the human gut. 2015-13 BH Kang Alterations of the human gut microbiome in liver cirrhosis. 2015-12 CY Kim An integrated catalog of reference genes in the human gut microbiome. 2015-11 CY Kim Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. 2015/01/26 2015-10 HH Kim Computational meta'omics for microbial community studies. 2015-09 HH Kim Functional profiling of the gut microbiome in disease-associated inflammation. 2015-08 BH Kang Biodiversity and functional genomics in the human microbiome. 2015-07 BH Kang Chapter 12: Human Microbiome Analysis. 2015-06 BH Kang Conducting a Microbiome Study. 2015/01/12 2015-05 KS Kim Small RNA changes en route to distinct cellular states of induced pluripotency. 2015-04 DS Bae Genome-wide characterization of the routes to pluripotency. 2015-03 DS Bae Divergent reprogramming routes lead to alternative stem-cell states. 2015/01/05 2015-02 HJ Han Global view of enhancer-promoter interactome in human cells. 2015-01 HJ Han Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. 2014 Date Paper index Presenter Paper title 2014/12/23 2014-41 CY Kim Super-enhancers in the control of cell identity and disease. 2014-40 CY Kim Master transcription factors and mediator establish super-enhancers at key cell identity genes. 2014/12/09 2014-39 HH Kim Unraveling the biology of a fungal meningitis pathogen using chemical genetics. 2014-38 JE Shim A proteome-scale map of the human interactome network. 2014-37 JE Shim The role of the interactome in the maintenance of deleterious variability in human populations. 2014-36 HS Shim Integrative annotation of variants from 1092 humans: application to cancer genomics. 2014/12/02 2014-35 HJ Han Mapping functional transcription factor networks from gene expression data. 2014-34 KS Kim In pursuit of design principles of regulatory sequences. 2014/11/25 2014-33 KS Kim Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease. 2014-32 HJ Han Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. 2014/11/18 2014-31 SM Yang The 'dnet' approach promotes emerging research on cancer patient survival. 2014-30 HJ Han Determination and inference of eukaryotic transcription factor sequence specificity. 2014/11/11 2014-29 DS Bae Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles. 2014-28 HH Kim Dissecting engineered cell types and enhancing cell fate conversion via CellNet. 2014-27 HH Kim CellNet: network biology applied to stem cell engineering. 2014/11/04 2014-26 HS Shim Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality. 2014-25 JH Shin Phen-Gen: combining phenotype and genotype to analyze rare disorders. 2014/10/28 2014-24 HJ Han A community effort to assess and improve drug sensitivity prediction algorithms. 2014-23 HS Shim Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. 2014/09/30 2014-22 JE Shim Network-based stratification of tumor mutations. 2014-21 KS Kim Synonymous mutations frequently act as driver mutations in human cancers. 2014/09/23 2014-20 CY Kim VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data. 2014-19 HJ Han DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. 2014/09/16 2014-18 JH Shin Integrated analysis of recurrent properties of cancer genes to identify novel drivers. 2014-17 AR Cho Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. 2014/09/02 2014-16 JE Shim A network module-based method for identifying cancer prognostic signatures. 2014-15 AR Cho Realizing the promise of cancer predisposition genes. 2014/08/19 2014-14 JE Shim Assessing the clinical utility of cancer genomic and proteomic data across tumor types. 2014-13 HS Shim Mutational landscape and significance across 12 major cancer types. 2014/08/12 2014-12 HS Shim Signatures of mutational processes in human cancer. 2014-11 HJ Kim Discovery and saturation analysis of cancer genes across 21 tumour types. 2014/08/05 2014-10 CY Kim Comprehensive identification of mutational cancer driver genes across 12 tumor types. 2014-9 JE Shim IntOGen-mutations identifies cancer drivers across tumor types. 2014/07/29 2014-8 CY Kim Computational approaches to identify functional genetic variants in cancer genomes. 2014-7 AR Cho Mutational heterogeneity in cancer and the search for new cancer-associated genes. 2014-6 AR Cho Cancer genomes: discerning drivers from passengers 2014/07/22 2014-5 AR Cho The Cancer Genome Atlas Pan-Cancer analysis project. 2014-4 AR Cho Cancer genome landscapes. 2014-3 AR Cho Distinguishing driver and passenger mutations in an evolutionary history categorized by interference. 2014/07/15 2014-2 HJ Han A promoter-level mammalian expression atlas. 2014-1 HJ Han An atlas of active enhancers across human cell types and tissues. 2013 Date Paper index Presenter Paper title 2013/06/26 2013-31 HJ Han Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages 2013-30 YH Ko Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli 2013/06/04 2013-29 KS Kim Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding 2013-28 ER Kim Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples 2013/05/28 2013-27 YH Ko Discovering statistically significant pathways in expression profiling studies 2013-26 JE Shim Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses 2013/05/21 2013-25 HJ Han Dynamic regulatory network controlling TH17 cell differentiation 2013-24 T Lee Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions 2013/05/14 2013-23 JE Shim Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci 2013-22 HJ Kim Chromatin marks identify critical cell types for fine mapping complex trait variants 2013/05/07 2013-21 ER Kim Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues 2013-20 HS Shim Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression 2013/04/09 2013-19 HJ Kim Annotation of functional variation in personal genomes using RegulomeDB 2013/04/02 2013-18 HJ Kim The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression 2013/03/12 2013-17 ER Kim Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation 2013/03/05 2013-16 ER Kim ChIP–seq: advantages and challenges of a maturing technology 2013/02/21 2013-15 KS Kim Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density 2013-14 KS Kim A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells 2013-13 HJ Han Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. 2013/02/15 2013-12 HJ Han Chromatin accessibility pre-determines glucocorticoid receptor binding patterns 2013-11 JE Shim, CY Kim Interpreting noncoding genetic variation in complex traits and human disease 2013-10 HJ Han, JH Kim Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data 2013/02/08 2013-09 HJ Kim Widespread Site-Dependent Buffering of Human Regulatory Polymorphism 2013-08 JE Shim, CY Kim Linking disease associations with regulatory information in the human genome 2013-07 HJ Han, JH Kim Understanding transcriptional regulation by integrative analysis of transcription factor binding data 2013/01/25 2013-06 HJ Han, JH Kim The long-range interaction landscape of gene promoters 2013-05 ER Kim, HS Shim Landscape of transcription in human cells 2013-04 HJ Han, JH Kim Architecture of the human regulatory network derived from ENCODE data 2013/01/18 2013-03 KS Kim, TH Kim An expansive human regulatory lexicon encoded in transcription factor footprints 2013-02 HJ Han, JH Kim The accessible chromatin landscape of the human genome 2013/01/11 2013-01 JE Shim, CY Kim An integrated encyclopedia of DNA elements in the human genome 2012 Date Paper index Paper title 2013/01/11 2012-81 (TH Kim) MuSiC: identifying mutational significance in cancer genomes. 2012/12/04 2012-80 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation 2012/11/20 2012-79 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks 2012-78 (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins 2012/11/06 2012-77 (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA 2012-76 (KS Kim) A public resource facilitating clinical use of genomes 2012/07/19 2012-75 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks 2012-74 (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People 2012-73 (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes 2012-72 (SH Hwang) Network-based classification of breast cancer metastasis 2012-71 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants 2012-70 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data 2012/07/16 2012-69 (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data 2012-66 (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools 2012-65 (ER Kim&TH Kim)The Variant Call Format and VCFtools 2012-64 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View 2012-63 (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions 2012-62 (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System 2012-61 (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome 2012-60 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective 2012/07/13 2012-59 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome 2012-58 (JH Shin&HJ Kim)A framework for human microbiome research 2012-57 (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome 2012/07/12 2012-56 (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines 2012-55 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes 2012-54 (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity 2012-53 (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups 2012/07/09 2012-52 (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity 2012-51 (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells 2012-50 (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer 2012-49 (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism 2012-48 (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders 2012-47 (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations 2012/07/06 2012-46 (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS) 2012-45 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases 2012-44 (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners 2012-43 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans 2012-42 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes 2012-41 (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits 2012/07/02 2012-40 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions 2012-39 (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer 2012-38 (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas 2012-37 (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine 2012-36 (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype 2012-35 (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets 2012/03/05 2012-34 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq. 2012-33 (11,Go&Ju)Differential expression analysis for sequence count data 2012-32 (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data 2012/02/27 2012/02/28 2012-31 (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics 2012-30 (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq 2012-29 (3,HJ Han)From RNA-seq reads to differential expression results 2012-28 (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods 2012-27 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq 2012-26 (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation 2012-25 (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq 2012/02/06 2012-24 mirConnX: condition-specific mRNA-microRNA network integrator 2012-23 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data 2012-22 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures 2012-21 Reprogramming of miRNA networks in cancer and leukemia 2012-20 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma 2012/01/30 2012-19 Principles and Strategies for Developing Network Models in Cancer 2012-18 Reverse engineering of regulatory networks in human B cells 2012-17 Variations in DNA elucidate molecular networks that cause disease 2012-16 Harnessing gene expression to identify the genetic basis of drug resistance 2012-15 An Integrated Approach to Uncover Drivers of Cancer 2012/01/09 2012-14 Genetic variation in an individual human exome. 2012-13 Predicting phenotypic variation in yeast from individual genome sequences. 2012-12 Clinical assessment incorporating a personal genome. 2012/01/09 2012/01/16 2012-11 Human allelic variation: perspective from protein function, structure, and evolution. 2012-10 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. 2012-09 Prediction of deleterious human alleles. 2012-08 Human non-synonymous SNPs: server and survey. 2012-07 A method and server for predicting damaging missense mutations. 2012-06 SNAP: predict effect of non-synonymous polymorphisms on function 2012/01/09 2012/01/16 2012-05 Computational and statistical approaches to analyzing variants identified by exome sequencing. 2012-04 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. 2012-03 Targeted capture and massively parallel sequencing of 12 human exomes. 2012/01/09 2012/01/16 2012-02 The distribution of fitness effects of new mutations. 2012-01 Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies 2011 Date Paper_index Paper_title 2011/11/28 2011-49 (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events 2011-48 (Shin)Network pharmacology: the next paradigm in drug discovery 2011-47 (Oh)Systematic exploration of synergistic drug pairs 2011-46 (Shim)Chemogenomic profiling predicts antifungal synergies 2011-45 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery 2011-44 (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines 2011/11/14 2011-43 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets 2011-42 Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole 2011-41 Analysis of multiple compound–protein interactions reveals novel bioactive molecules 2011/11/07 2011-40 Drug—target network 2011-39 A side effect resource to capture phenotypic effects of drugs 2011-38 Quantitative systems-level determinants of human genes targeted by successful drugs 2011-37 Drug Target Identification Using Side-Effect Similarity 2011/11/07 2011-36 Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data 2011-35 Exploiting drug–disease relationships for computational drug repositioning 2011-34 Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks 2011/10/05 2011-33 Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families 2011-32 Quantifying environmental adaptation of metabolic pathways in metagenomics 2011-31 Quantitative assessment of protein function prediction from metagenomics shotgun sequences 2011/10/04 2011-30 A human gut microbial gene catalogue established by metagenomic sequencing 2011-29 Molecular eco-systems biology: towards an understanding of community function 2011-28 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges 2011-27 Unravelling the effects of the environment and host genotype on the gut microbiome 2011/09/19 2011-26 independently evolved virulence effectors converge onto hubs in a plant immune system Network 2011-25 Evidence for network evolution in an arabidopsis interactome Map 2011/09/05 2011-24 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy 2011-23 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers 2011/09/22 2011-22 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks 2011-21 From expression QTLs to personalized transcriptomics 2011/06/20 2011-20 a user's guide to the encyclopedia of DNA elements(ENCODE) 2011/03/30 2011-19 enterotypes of the human gut microbiome 2011-18 toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data 2011/03/16 2011-17 variable pathogenicity determines individual lifespan in caenorhabditis elegans 2011-16 a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue 2011/04/25 2011-15 Hallmarks of Cancer : The next generation 2011-14 Mapping Cancer Origins 2011-13 Genetic Interactions in Cancer Progression and Treatment 2011/04/11 2011-12 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology 2011-11 ***Changed!*** Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions 2011/03/28 2011-10 profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis 2011-09 cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control 2011/03/14 2011-08 phenotypic landscape of a bacterial cell 2011-07 cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action 2011/02/28 2011-06 genomic patterns of pleiotropy and the evolution of complexity 2011-05 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway 2011/02/21 2011-04 dynamic interaction networks in a hierarchically organized tissue 2011/02/14 2011-03 rewiring of genetic networks in response to DNA damage 2011/01/31 2011-02 Applying mass spectrometry-based proteomics to genetics, genomics and network biology 2011-01 Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics 2010 Date Paper_index Paper_title 2010/12/27 2010-29 Functional_roles_fornoise_in_genetic_circuits 2010-28 Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries 2010/11/15 2010-27 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes 2010-26 It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks 2010/11/01 2010-25 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes 2010-24 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster 2010/10/11 2010-23 Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders 2010/09/13 2010-22 Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells 2010-21 Limits_of_sequence_and_functional_conservation 2010/05/26 2010-20 network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf 2010/05/19 2010-19 interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf 2010/04/21 2010-18 identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf 2010/04/14 2010-17 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man 2010/04/07 2010-16 systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes 2010-15 genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines 2010/03/31 2010-14 toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf 2010-13 systems_biology_of_stem_cell_fate_and_cellular_reprogramming 2010/03/24 2010-12 dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome 2010/01/18 2010-11 JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies 2010/01/16 2010-10 systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells 2010/01/15 2010-09 distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions 2010/01/14 2010-08 chemogenomic_profiling_predicts_antifungal_synergies 2010/01/13 2010-07 edgetic_perturbation_models_of_human_inherited_disorders 2010/01/12 2010-06 analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans 2010/01/11 2010-05 predicting_new_molecular_targets_for_known_drugs.pdf Reference:SEA(Similarity Ensemble Approach) 2010/01/09 2010-04 harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance 2010/01/08 2010-03 an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer 2010/01/07 2010-02 a_phenotypic_profile_of_the_candida_albicans_regulatory_network 2010/01/06 2010-01 a_global_view_of_protein_expression_in_human_cells_tissues_and_organs