Difference between revisions of "Journal Club"

Latest revision as of 02:19, 27 October 2025

2025-2 Journal Club
Date	Paper index	Presenter	Paper title
2025/11/18	25-81	HJ Kim	Bidirectional subsethood of shared marker profiles enables accurate virus classification
2025/11/11	25-80	JY Ma	Self-supervised learning enables robust 1 microbiome predictions in data-limited and 2 cross-cohort settings
2025/11/11	25-79	JH Cha	Microbiome-wide PheWAS links gut microbial SNVs to human health and exposures
2025/11/04	25-78	IS Choi	BioLLM: A standardized framework for integrating and benchmarking single-cell foundation models
2025/11/04	25-77	SB Lim	Predicting functions of uncharacterized gene products from microbial communities
2025/10/28	25-76-2	HB Lee	OmniCellAgent: Towards AI Co-Scientists for Scientific Discovery in Precision Medicine
2025/10/28	25-76-1	HB Lee	Autonomous chemical research with large language models
2025/10/28	25-75	YR Jung	Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation
2025/9/30	25-74	YR Kim	GLM-Prior: a nucleotide transformer model reveals prior knowledge as the driver of GRN inference performance
2025/9/30	25-73-2	JY Kim	Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin
2025/9/30	25-73-1	JY Kim	Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites
2025/9/23	25-72	SH Ahn	Generanno: A Genomic Foundation Model for Metagenomic Annotation
2025/9/23	25-71	EJ Sung	Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
2025/9/16	25-70	JH Cha	Interpreting Attention Mechanisms in Genomic Transformer Models: A Framework for Biological Insights
2025/9/16	25-69	IS Choi	A large-scale foundation model for bulk transcriptomes
2025/9/9	25-68	HJ Kim	xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins
2025/9/9	25-67	JY Ma	Generalized biological foundation model with unified nucleic acid and protein language
2025/9/2	25-66	NY Kim	AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model
2025/9/2	25-65	YR Kim	Gut microbiome evolution from infancy to 8 years of age

2025-1 Journal Club
Date	Paper index	Presenter	Paper title
2025/8/29	25-64	HB Lee	Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions
2025/8/29	25-63	SH Ahn	SSAlign: Ultrafast and Sensitive Protein Structure Search at Scale
2025/8/29	25-62	YR Jung	Foundation Model Attributions Reveal Shared Inflammatory Program Across
2025/8/19	25-61	SB Lim	Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia
2025/8/19	25-60	JY Kim	Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease
2025/8/12	25-59	EJ Sung	scNET: learning context-specific gene and cell embeddings by integrating single-cell gene expression data with protein–protein interactions
2025/8/12	25-58	HJ Kim	Fine-Tuning Protein Language Models Unlocks the Potential of Underrepresented Viral Proteomes
2025/8/12	25-57	JY Ma	Orthology inference at scale with FastOMA
2025/8/8	25-56	JH Cha	Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut
2025/8/8	25-55	IS Choi	Cell2Sentence: Teaching Large Language Models the Language of Biology
2025/8/8	25-54	NY Kim	High‑resolution strain‑level microbiome composition analysis from short reads
2025/8/1	25-53	SB Lim	Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice
2025/8/1	25-52	HB Lee	A machine learning approach to leveraging electronic health records for enhanced omics analysis
2025/8/1	25-51	YR Jung	Predicting transcriptional outcomes of novel multigene perturbations with GEARS
2025/7/25	25-50	YR Kim	Nucleotide Transformer: building and evaluating robust foundation models for human genomics
2025/7/25	25-49	JY Kim	Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species
2025/7/25	25-48	SH Ahn	VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog
2025/7/18	25-47	NY Kim	Effects of gut microbiota on immune checkpoint inhibitors in multi-cancer and as microbial biomarkers for predicting therapeutic response
2025/7/18	25-46	HJ Kim	Highly accurate prophage island detection with PIDE
2025/7/18	25-45	JY Ma	Genome modeling and design across all domains of life with Evo 2
2025/7/11	25-44	JH Cha	Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease
2025/7/11	25-43	IS Choi	A cell atlas foundation model for scalable search of similar human cells
2025/7/11	25-42	EJ Sung	geneRNIB: a living benchmark for gene regulatory network inference
2025/7/4	25-41	JY Kim	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies
2025/7/4	25-40	HB Lee	SaprotHub: Making Protein Modeling Accessible to All Biologists
2025/7/4	25-39	YR Jung	Disentanglement of single-cell data with biolord
2025/6/27	25-38	YR Kim	Simulating 500 million years of evolution with a language model
2025/6/27	25-37	SB Lim	Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis
2025/6/27	25-36	WJ Kim	Predicting metabolite response to dietary intervention using deep learning
2025/6/13	25-35	SH Ahn	Ultra-fast and highly sensitive protein structure alignment with segment-level representations and block-sparse optimization
2025/6/13	25-34	EJ Sung	Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age
2025/6/13	25-33	HJ Kim	GOPhage: protein function annotation for bacteriophages by integrating the genomic context
2025/5/30	25-32	JY Ma	Fast, sensitive detection of protein homologs using deep dense retrieval
2025/5/30	25-31	JH Cha	ImmuneLENS characterizes systemic immune dysregulation in aging and cancer
2025/5/23	25-30	IS Choi	Mapping cells through time and space with moscot
2025/5/23	25-29	NY Kim	Human gut microbiota subspecies carry implicit information for in-depth microbiome research
2025/5/23	25-28	NY Kim	Intraspecies associations from strain-rich metagenome sample
2025/5/9	25-27	SB Lim	Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth
2025/5/9	25-26	HB Lee	Moving towards genome-wide data integration for patient stratification with Integrate Any Omics
2025/4/11	25-25	YR Jung	Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states
2025/4/11	25-24	YR Kim	Emergence of community behaviors in the gut microbiota upon drug treatment
2025/3/28	25-23	JY Kim	Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information
2025/3/28	25-22	WJ Kim	Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization
2025/3/21	25-21	SH Ahn	De novo discovery of conserved gene clusters in microbial genomes with Spacedust
2025/3/21	25-20	SH Ahn	Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer
2025/3/21	25-19	EJ Sung	Single-cell RNA sequencing of human tissue supports successful drug targets
2025/3/14	25-18	HJ Kim	MGM as a large-scale pretrained foundation model for microbiome analyses in diverse contexts
2025/3/14	25-17	JY Ma	Sequence modeling and design from molecular to genome scale with Evo
2025/3/7	25-16	JH Cha	Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson’s disease
2025/3/7	25-15	NY Kim	Quantifying Metagenomic Strain Associations from Microbiomes with Anpan

2024-2 scOmics
Date	Team	Paper index	Presenter	Paper title
2025/2/24	Single-cell	25-6	IS Choi	Evaluating the Utilities of Foundation Models in Single-cell Data Analysis
2025/2/19	Single-cell	25-5	SB Baek	Accurate predictions on small data with a tabular foundation model
2025/1/15	Single-cell	25-4	JH Cha	scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics
2025/1/8	Single-cell	25-3	HB Lee	TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions
2025/1/8	Single-cell	25-2	HB Lee	Topsy-Turvy: integrating a global view into sequence-based PPI prediction
2025/1/8	Single-cell	25-1	HB Lee	D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions
2024/12/17	Single-cell	24-30	YR Jung	Quantized multi-task learning for context-specific representations of gene network dynamics
2024/12/3	Single-cell	24-29	EJ Sung	ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces
2024/11/26	Single-cell	24-28	IS Choi	CellRank 2: unified fate mapping in multiview single-cell data
2024/11/19	Single-cell	24-27	SB Baek	scPRINT: pre-training on 50 million cells allows robust gene network predictions
2024/11/12	Single-cell	24-26	JH Cha	Bidirectional generation of structure and properties through a single molecular foundation model

2024-2 Microbiome
Date	Team	Paper index	Presenter	Paper title
2025/2/24	Microbiome	25-14	SB Lim	MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery
2025/2/24	Microbiome	25-13	HB Lee	Profiling lateral gene transfer events in the human microbiome using WAAFLE
2025/2/17	Microbiome	25-12	JY Ma	ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning
2025/2/17	Microbiome	25-11	JY Kim	The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution
2025/2/3	Microbiome	25-10	WJ Kim	pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes
2025/2/3	Microbiome	25-9	SH Ahn	A core microbiome signature as an indicator of health
2025/1/20	Microbiome	25-8	HJ Kim	Using artificial intelligence to document the hidden RNA virosphere
2025/1/20	Microbiome	25-7	YR Kim	Learning a deep language model for microbiomes: the power of large scale unlabeled microbiome data
2025/1/13	Microbiome	25-6	JH Cha	Accurate proteome-wide missense variant effect prediction with AlphaMissense
2025/1/13	Microbiome	25-5	NY Kim	A gut microbial signature for combination immune checkpoint blockade across cancer types
2025/1/6	Microbiome	25-4	YR Kim	Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders
2025/1/6	Microbiome	25-3	YR Kim	Multikingdom and functional gut microbiota markers for autism spectrum disorder
2025/1/6	Microbiome	25-2	JY Kim	A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies
2024/12/30	Microbiome	25-1	WJ Kim	Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut
2024/12/30	Microbiome	24-65	SH Ahn	Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants
2024/12/18	Microbiome	24-64	HJ Kim	VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes
2024/12/18	Microbiome	24-63	HJ Kim	Ultrafast and accurate sequence alignment and clustering of viral genomes
2024/12/18	Microbiome	24-62	JY Ma	The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling
2024/12/4	Microbiome	24-61	JH Cha	Genomic language model predicts protein co-regulation and function
2024/12/4	Microbiome	24-60	NY Kim	Protein Set 1 Transformer: A protein-based genome language model to power high diversity viromics
2024/11/20	Microbiome	24-59	YR Kim	Prophage-DB: A comprehensive database to explore diversity,distribution, and ecology of prophages
2024/11/20	Microbiome	24-58	JY Kim	Strain‑resolved de‑novo metagenomic assembly of viral genomes and microbial 16S rRNAs
2024/11/13	Microbiome	24-57	WJ Kim	Prokaryotic‑virus‑encoded auxiliary metabolic genes throughout the global oceans
2024/11/13	Microbiome	24-56	G Koh	Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome
2024/11/6	Microbiome	24-55	SH Ahn	Pangenomes of Human Gut Microbiota Uncover Links Between Genetic Diversity and Stress Response
2024/11/6	Microbiome	24-54	HJ Kim	vClassifier: a toolkit for species-level classification of prokaryotic viruses
2024/11/6	Microbiome	24-53	HJ Kim	GRAViTy-V2: a grounded viral taxonomy application
2024/10/16	Microbiome	24-52	JY Ma	Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures
2024/10/16	Microbiome	24-51	JH Cha	Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM)

2024-1 scOmics
Date	Team	Paper index	Presenter	Paper title
2024/11/12	Single-cell	24-25	HB Lee	A blueprint for tumor-infiltrating B cells across human cancers
2024/10/29	Single-cell	24-24	YR Jung	Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types
2024/10/08	Single-cell	24-23	EJ Sung	scDrugPrio: a framework for the analysis of single‑cell transcriptomics to address multiple problems in precision medicine in immune‑mediated inflammatory diseases
2024/09/24	Single-cell	24-22	IS Choi	A visual-language foundation model for computational pathology
2024/09/10	Single-cell	24-21	SB Baek	SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains
2024/09/03	Single-cell	24-20	HB Lee	Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lungcancer
2024/08/30	Single-cell	24-19	JH Cha	Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model
2024/08/16	Single-cell	24-18	YR 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 index	Presenter	Paper title
2024/10/02	Microbiome	24-51	NY Kim	Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes
2024/10/02	Microbiome	24-50	YR Kim	Gut virome-wide association analysis identifes cross-population viral signatures for infammatory bowel disease
2024/09/25	Microbiome	24-48-2	JY Kim	Efficient Low-rank Multimodal Fusion with Modality-Specific Factors
2024/09/25	Microbiome	24-48-1	JY Kim	Tensor Fusion Network for Multimodal Sentiment Analysis
2024/09/25	Microbiome	24-49	WJ Kim	Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway
2024/09/11	Microbiome	24-47	G Koh	Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation
2024/09/11	Microbiome	24-46	SH Ahn	Deep learning with multimodal representation for pancancer prognosis prediction
2024/09/04	Microbiome	24-45-2	HJ Kim	Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis
2024/09/04	Microbiome	24-45-1	HJ Kim	Pan-cancer integrative histology-genomic analysis via multimodal deep learning
2024/09/04	Microbiome	24-44	NY Kim	A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota
2024/08/21	Microbiome	24-43-2	JH Cha	BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs
2024/08/21	Microbiome	24-43-1	JH Cha	Learning Transferable Visual Models From Natural Language Supervision
2024/08/21	Microbiome	24-42	JY Ma	BIONIC: biological network integration using convolutions
2024/08/14	Microbiome	24-41	G Koh	Protein remote homology detection and structural alignment using deep learning
2024/08/14	Microbiome	24-41	YR Kim	Accurate structure prediction of biomolecular interactions with AlphaFold 3
2024/08/07	Microbiome	24-39	WJ Kim	Gut microbiome-metabolome interactions predict host condition
2024/08/07	Microbiome	24-38	JY kim	Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development
2024/07/31	Microbiome	24-37	SH Ahn	A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome
2024/07/31	Microbiome	24-36	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	24-35	JY Ma	Compositional Differential Abundance Testing: Defining and Finding a New Type of Health-Microbiome Associations
2024/07/24	Microbiome	24-34	JH Cha	Discovery of antimicrobial peptides in the global microbiome with machine learning
2024/07/17	Microbiome	24-33	NY Kim	Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome
2024/07/17	Microbiome	24-32	YR Kim	Paternal microbiome perturbations impact offspring fitness
2024/07/10	Microbiome	24-31	JY Kim	Interactions-based classification of a single microbial sample
2024/07/10	Microbiome	24-30	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

2024-1 Advanced scOmics Data Analysis
Date	Team	Paper index	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

2023-2 scOmics
Date	Team	Paper index	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 index	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

2023-1 ADVANCED MICROBIOME DATA ANALYSIS
Date	Team	Paper index	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 index	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 index	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 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
2021/06/03	-	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
2021/05/20	-	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
2021/05/13	-	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
2021/05/06	-	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
2021/04/29	-	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
2021/04/22	-	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
2021/02/22	Single-cell	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
2021/02/15	Single-cell	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
2021/02/08	Single-cell	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
2021/02/01	Single-cell	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
2020/06/09	-	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
2020/06/02	-	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
2020/05/26	-	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
2020/05/19	-	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
2020/05/12	-	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
2020/04/28	Single-cell	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
2019/10/15	Microbiome	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
2019/10/08	Single-cell	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
2019/10/01	Microbiome	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
2019/09/24	Single-cell	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
2019/09/17	Microbiome	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
2019/09/10	Single-cell	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
2019/09/03	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
2019/08/20	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
2019/08/13	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
2019/08/08	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
2019/08/07	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
2019/07/30	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.
2019/07/23	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.
2019/05/16	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.
2019/05/09	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.
2019/05/02	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.
2019/4/11	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.
2019/4/4	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.
2019/3/28	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
2019/3/14	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.
2018/06/14	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.
2018/06/07	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.
2018/05/31	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.
2018/05/24	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.
2018/05/17	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.
2018/05/10	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.
2017/06/28	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.
2017/06/14	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.
2017/06/07	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.
2017/05/31	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.
2017/05/24	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.
2017/05/17	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.
2017/04/26	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.
2017/04/12	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.
2017/04/05	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.
2017/03/29	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.
2017/03/22	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.
2017/03/15	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.
2017/02/28	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.
2017/02/21	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.
2017/02/07	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
2017/01/17	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
2016/6/8	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
2016/6/1	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
2016/5/18	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
2016/5/11	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
2016/5/4	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
2016/4/27	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.
2015/06/11	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.
2015/06/04	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.
2015/05/28	2015-50		GREAT improves functional interpretation of cis-regulatory regions.
2015/05/21	2015-49		Functional annotation of noncoding sequence variants.
2015/05/21	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.
2015/05/14	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.
2015/04/30	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.
2015/04/09	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.
2015/04/02	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.
2015/03/26	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.
2015/03/19	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.
2015/01/05	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.
2014/12/23	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.
2014/12/02	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.
2014/11/25	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.
2014/11/18	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.
2014/11/04	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.
2014/10/28	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.
2014/09/30	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.
2014/09/23	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.
2014/09/16	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.
2014/09/02	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.
2014/08/19	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.
2014/08/12	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.
2014/08/05	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.
2014/07/15	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
2013/06/26	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
2013/06/04	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
2013/05/28	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
2013/05/21	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
2013/05/14	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
2013/05/07	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
2013/01/18	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
2012/11/20	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
2012/11/06	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.
2012/01/09 2012/01/16	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
2011/09/19	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
2011/09/05	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
2011/09/22	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
2011/03/30	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
2011/03/16	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
2011/04/11	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
2011/03/28	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
2011/03/14	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
2011/02/28	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
2011/01/31	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
2010/12/27	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
2010/11/15	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
2010/11/01	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
2010/09/13	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
2010/04/07	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
2010/03/31	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

Difference between revisions of "Journal Club"

Latest revision as of 02:19, 27 October 2025

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 {|class=wikitable style="text-align:center;"
-|+style="text-align:left;font-size:12pt" | 2024-1 Advanced scOmics Data Analysis
+|+style="text-align:left;font-size:12pt" | 2025-2 Journal Club
+|-
+!scope="col" style="padding:.4em" | Date
+!scope="col" style="padding:.4em" | Paper<br/>index
+!scope="col" style="padding:.4em" | Presenter
+!scope="col" style="padding:.4em" | Paper title
+|-
+|style="padding:.4em;" rowspan=1|2025/11/18
+|style="padding:.4em;"|25-81
+|style="padding:.4em;"|HJ Kim
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1186/s40168-025-02159-x Bidirectional subsethood of shared marker profiles enables accurate virus classification]
+|-
+|style="padding:.4em;" rowspan=1|2025/11/11
+|style="padding:.4em;"|25-80
+|style="padding:.4em;"|JY Ma
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1101/2025.10.19.683269 Self-supervised learning enables robust 1 microbiome predictions in data-limited and 2 cross-cohort settings]
+|-
+|style="padding:.4em;" rowspan=1|2025/11/11
+|style="padding:.4em;"|25-79
+|style="padding:.4em;"|JH Cha
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.21203/rs.3.rs-5063726/v1 Microbiome-wide PheWAS links gut microbial SNVs to human health and exposures]
+|-
+|style="padding:.4em;" rowspan=1|2025/11/04
+|style="padding:.4em;"|25-78
+|style="padding:.4em;"|IS Choi
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1016/j.patter.2025.101326 BioLLM: A standardized framework for integrating and benchmarking single-cell foundation models]
+|-
+|style="padding:.4em;" rowspan=1|2025/11/04
+|style="padding:.4em;"|25-77
+|style="padding:.4em;"|SB Lim
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41587-025-02813-7 Predicting functions of uncharacterized gene products from microbial communities]
+|-
+|style="padding:.4em;" rowspan=1|2025/10/28
+|style="padding:.4em;"|25-76-2
+|style="padding:.4em;"|HB Lee
+|style="padding:.4em;text-align:left"|
+[https://www.biorxiv.org/content/10.1101/2025.07.31.667797v1.full OmniCellAgent: Towards AI Co-Scientists for Scientific Discovery in Precision Medicine]
+|-
+|style="padding:.4em;" rowspan=1|2025/10/28
+|style="padding:.4em;"|25-76-1
+|style="padding:.4em;"|HB Lee
+|style="padding:.4em;text-align:left"|
+[https://www.nature.com/articles/s41586-023-06792-0 Autonomous chemical research with large language models]
+|-
+|style="padding:.4em;" rowspan=1|2025/10/28
+|style="padding:.4em;"|25-75
+|style="padding:.4em;"|YR Jung
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41587-025-02777-8 Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation]
+|-
+|style="padding:.4em;" rowspan=1|2025/9/30
+|style="padding:.4em;"|25-74
+|style="padding:.4em;"|YR Kim
+|style="padding:.4em;text-align:left"|
+[https://www.biorxiv.org/content/10.1101/2025.06.29.662198v1 GLM-Prior: a nucleotide transformer model reveals prior knowledge as the driver of GRN inference performance]
+|-
+|style="padding:.4em;" rowspan=1|2025/9/30
+|style="padding:.4em;"|25-73-2
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+[https://www.nature.com/articles/s41564-025-01963-3 Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice]
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+[https://www.nature.com/articles/s42256-024-00974-9 A machine learning approach to leveraging electronic health records for enhanced omics analysis]
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+[https://www.biorxiv.org/content/10.1101/2024.01.10.575018v2 Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species]
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+|style="padding:.4em;"|SH Ahn
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+[https://www.biorxiv.org/content/10.1101/2025.02.26.640259v1 Highly accurate prophage island detection with PIDE]
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+|style="padding:.4em;"|JY Ma
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+[https://www.biorxiv.org/content/10.1101/2025.02.18.638918v1 Genome modeling and design across all domains of life with Evo 2]
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+|style="padding:.4em;"|JH Cha
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+[https://www.cell.com/cell/fulltext/S0092-8674(24)01429-6 Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease]
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+|style="padding:.4em;"|IS Choi
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+[https://www.nature.com/articles/s41586-024-08411-y A cell atlas foundation model for scalable search of similar human cells]
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+[https://www.biorxiv.org/content/10.1101/2025.02.25.640181v1 geneRNIB: a living benchmark for gene regulatory network inference]
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+[https://www.biorxiv.org/content/10.1101/2024.05.24.595648v1 SaprotHub: Making Protein Modeling Accessible to All Biologists]
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+[https://www.science.org/doi/10.1126/science.ads0018 Simulating 500 million years of evolution with a language model]
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+|style="padding:.4em;"|SB Lim
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+[https://pubmed.ncbi.nlm.nih.gov/39999841/ Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis]
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+[https://www.biorxiv.org/content/10.1101/2025.03.14.643159v1 Ultra-fast and highly sensitive protein structure alignment with segment-level representations and block-sparse optimization]
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+[https://www.nature.com/articles/s41590-024-02059-6 Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age]
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+[https://pubmed.ncbi.nlm.nih.gov/39123049/ Fast, sensitive detection of protein homologs using deep dense retrieval]
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+[https://www.nature.com/articles/s41588-025-02086-5 ImmuneLENS characterizes systemic immune dysregulation in aging and cancer]
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+|style="padding:.4em;"|IS Choi
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+[https://www.nature.com/articles/s41586-024-08453-2 Mapping cells through time and space with moscot]
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+|style="padding:.4em;"|NY Kim
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+[https://www.biorxiv.org/content/10.1101/2025.02.05.636567v1 Human gut microbiota subspecies carry implicit information for in-depth microbiome research]
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+|style="padding:.4em;"|25-28
+|style="padding:.4em;"|NY Kim
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+[https://www.biorxiv.org/content/10.1101/2025.02.07.636498v1 Intraspecies associations from strain-rich metagenome sample]
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+[https://doi.org/10.1101/2025.02.13.638109 Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth]
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+|style="padding:.4em;"|HB Lee
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+[https://www.nature.com/articles/s42256-024-00942-3 Moving towards genome-wide data integration for patient stratification with Integrate Any Omics]
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+[https://doi.org/10.1101/2024.11.18.624166 Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states]
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+[https://doi.org/10.1016/j.cell.2024.08.037 Emergence of community behaviors in the gut microbiota upon drug treatment]
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+[https://doi.org/10.1038/s41564-024-01832-5 Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information]
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+[https://doi.org/10.1101/2025.01.07.631807 Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization]
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+[https://doi.org/10.1101/2024.10.02.616292 De novo discovery of conserved gene clusters in microbial genomes with Spacedust]
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+[https://doi.org/10.1101/2024.04.14.589414 Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer]
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+[https://www.medrxiv.org/content/10.1101/2024.04.04.24305313v1 Single-cell RNA sequencing of human tissue supports successful drug targets]
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+[https://doi.org/10.1101/2024.12.30.630825 MGM as a large-scale pretrained foundation model for microbiome analyses in diverse contexts ]
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+[https://doi.org/10.1126/science.ado9336 Sequence modeling and design from molecular to genome scale with Evo]
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+[https://doi.org/10.1101/2024.12.18.629142 Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson’s disease]
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+[https://doi.org/10.1101/2025.01.06.631550 Quantifying Metagenomic Strain Associations from Microbiomes with Anpan]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41586-023-07011-6 Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory]
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-[https://doi.org/10.1038/s41467-021-22197-x scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses]
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+[https://doi.org/10.1101/2024.09.24.614685 scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics]
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+[https://doi.org/10.1093/bioinformatics/btac258 Topsy-Turvy: integrating a global view into sequence-based PPI prediction]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1126/science.abi4882 Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution]
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-[https://doi.org/10.1038/s41590-024-01792-2 Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy]
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-[https://doi.org/10.1038/s41467-021-27464-5 Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids]
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-[https://doi.org/10.1016/j.chom.2023.08.019 Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics]
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-[https://www.sciencedirect.com/science/article/pii/S1534580722002519?via%3Dihub The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves]
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-[https://doi.org/10.1038/s41588-022-01100-4 Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s42255-023-00876-x Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41587-023-01747-2 Multimodal spatiotemporal phenotyping of human retinal organoid development]
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 |-
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41586-024-07251-0 Immune microniches shape intestinal Treg function]
+[https://doi.org/10.1101/2024.12.30.630844 The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution]
 |-
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1016/j.devcel.2021.02.021 A single-cell analysis of the Arabidopsis vegetative shoot apex]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41467-023-40137-9 Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq]
+[https://doi.org/10.1016/j.cell.2024.09.019 A core microbiome signature as an indicator of health]
 |-
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-[https://doi.org/10.1038/s41564-023-01462-3 Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection]
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-[https://doi.org/10.1016/j.celrep.2022.111736 Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection]
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 |-
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41587-023-01979-2 Spatial metatranscriptomics resolves host–bacteria–fungi interactomes]
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 |-
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41467-023-36325-2 Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses]
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 |-
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41593-023-01452-y Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41593-023-01455-9 Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain]
+[https://doi.org/10.1038/s41564-024-01739-1 Multikingdom and functional gut microbiota markers for autism spectrum disorder]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41467-023-39933-0 Spatial cellular architecture predicts prognosis in glioblastoma]
+[https://doi.org/10.1186/s13059-024-03390-9 A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies]
 |-
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-[https://doi.org/10.1016/j.celrep.2024.113784 Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41467-022-30511-4 Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity]
+[https://doi.org/10.1038/s41467-024-52561-6 Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41467-021-26271-2 Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions]
+[https://doi.org/10.1186/s13059-024-03320-9 VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes]
 |-
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-[https://doi.org/10.1021/acscentsci.3c01169 Single-Cell Analysis Reveals Cxcl14+ Fibroblast Accumulation in Regenerating Diabetic Wounds Treated by Hydrogel-Delivering Carbon Monoxide]
+[https://doi.org/10.1101/2024.06.27.601020 Ultrafast and accurate sequence alignment and clustering of viral genomes]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41477-022-01291-y Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism]
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 |-
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+[https://doi.org/10.1038/s41467-024-46947-9 Genomic language model predicts protein co-regulation and function]
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+[https://doi.org/10.1101/2024.07.26.605391 Protein Set 1 Transformer: A protein-based genome language model to power high diversity viromics]
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 |style="padding:.4em;"|YR Kim
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-[https://doi.org/10.1038/s41556-023-01316-4 Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation]
+[https://doi.org/10.1101/2024.07.11.603044 Prophage-DB: A comprehensive database to explore diversity,distribution, and ecology of prophages]
 |-
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 |style="padding:.4em;"|JY Kim
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-[https://doi.org/10.1038/s41467-022-35319-w Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases]
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 |-
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 |style="padding:.4em;"|WJ Kim
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-[https://doi.org/10.1016/j.cmet.2022.07.010 Neuregulin 4 suppresses NASH-HCC development by restraining tumor-prone liver microenvironment]
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 |-
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 |style="padding:.4em;"|G Koh
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-[https://doi.org/10.1038/s41593-023-01334-3 Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease]
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 |-
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 |style="padding:.4em;"|SH Ahn
 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1136/gutjnl-2023-330243 Single-cell transcriptomic analysis deciphers heterogenous cancer stem-like cells in colorectal cancer and their organ-specific metastasis]
+[https://doi.org/10.1101/2024.04.17.589959 Pangenomes of Human Gut Microbiota Uncover Links Between Genetic Diversity and Stress Response]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41467-022-31519-6 Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis]
+[https://doi.org/10.1101/2024.05.28.596318 vClassifier: a toolkit for species-level classification of prokaryotic viruses]
 |-
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 |style="padding:.4em;"|HJ Kim
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-[https://doi.org/10.1016/j.ccell.2023.09.011 Progenitor-like exhausted SPRY1+CD8+ T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma]
+[https://doi.org/10.1101/2024.07.26.605250 GRAViTy-V2: a grounded viral taxonomy application]
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-[https://doi.org/10.1016/j.immuni.2024.02.007 CD4+ T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy]
+[https://doi.org/10.1126/science.adj4857 A blueprint for tumor-infiltrating B cells across human cancers]
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-[https://doi.org/10.1016/j.ccell.2023.12.012 Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer]
+[https://doi.org/10.1038/s41467-024-48310-4 Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types]
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-[https://doi.org/10.1016/j.cell.2023.11.037 A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma]
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-[https://doi.org/10.1038/s41467-024-48310-4 Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types]
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 [https://doi.org/10.1038/s41592-024-02175-z SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains]
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-[https://doi.org/10.1101/2024.06.04.597354 Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1016/j.ccell.2023.12.013 Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lungcancer]
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 [https://doi.org/10.1016/j.xgen.2023.100473 Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases]
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-[https://doi.org/10.1101/2024.06.16.599201 node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking]
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-[https://doi.org/10.1038/s41592-024-02305-7 Large-scale foundation model on single-cell transcriptomics]
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 [https://doi.org/10.1016/j.xgen.2023.100383 Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1016/j.chom.2024.03.005 A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota]
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-[https://doi.org/10.1038/s41586-024-07487-w Accurate structure prediction of biomolecular interactions with AlphaFold 3]
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 |style="padding:.4em;text-align:left"|
-[https://doi.org/10.1038/s41591-024-02963-2 Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development]
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 [https://doi.org/10.1101/2023.12.11.571168 Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression]
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 |style="padding:.4em;"|JY Ma
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 [https://doi.org/10.1101/2024.06.04.596112 Compositional Differential Abundance Testing: Defining and Finding a New Type of Health-Microbiome Associations]
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 |style="padding:.4em;"|NY Kim
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 [https://doi.org/10.1016/j.cell.2024.05.029 Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome]
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 [https://doi.org/10.1038/s41586-024-07336-w Paternal microbiome perturbations impact offspring fitness]
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 [https://doi.org/10.1073/pnas.2008731118 Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes]
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+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41467-021-26271-2 Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions]
+|-
+|style="padding:.4em;" rowspan=1|2024/05/14
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-9
+|style="padding:.4em;"|Q Zhen
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1021/acscentsci.3c01169 Single-Cell Analysis Reveals Cxcl14+ Fibroblast Accumulation in Regenerating Diabetic Wounds Treated by Hydrogel-Delivering Carbon Monoxide]
+|-
+|style="padding:.4em;" rowspan=1|2024/05/07
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-8
+|style="padding:.4em;"|CR Leenaars
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41477-022-01291-y Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism]
+|-
+|style="padding:.4em;" rowspan=1|2024/05/07
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-7
+|style="padding:.4em;"|YR Kim
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41556-023-01316-4 Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation]
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+|style="padding:.4em;" rowspan=1|2024/05/07
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-6
+|style="padding:.4em;"|JY Kim
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41467-022-35319-w Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases]
+|-
+|style="padding:.4em;" rowspan=1|2024/05/07
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-5
+|style="padding:.4em;"|WJ Kim
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1016/j.cmet.2022.07.010 Neuregulin 4 suppresses NASH-HCC development by restraining tumor-prone liver microenvironment]
+|-
+|style="padding:.4em;" rowspan=1|2024/04/23
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-4
+|style="padding:.4em;"|G Koh
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41593-023-01334-3 Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease]
+|-
+|style="padding:.4em;" rowspan=1|2024/04/23
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-3
+|style="padding:.4em;"|SH Ahn
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1136/gutjnl-2023-330243 Single-cell transcriptomic analysis deciphers heterogenous cancer stem-like cells in colorectal cancer and their organ-specific metastasis]
+|-
+|style="padding:.4em;" rowspan=1|2024/04/23
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-2
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+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1038/s41467-022-31519-6 Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis]
+|-
+|style="padding:.4em;" rowspan=1|2024/04/23
+|style="padding:.4em;" rowspan=1|Single-cell
+|style="padding:.4em;"|24-1
+|style="padding:.4em;"|HJ Kim
+|style="padding:.4em;text-align:left"|
+[https://doi.org/10.1016/j.ccell.2023.09.011 Progenitor-like exhausted SPRY1+CD8+ T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma]
+|}