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− | [https://doi.org/10. | + | [https://doi.org/10.1126/science.adj4857 A blueprint for tumor-infiltrating B cells across human cancers] |
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− | [https://doi.org/10.1038/ | + | [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:// | + | [https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01314-7 scDrugPrio: a framework for the analysis of single‑cell transcriptomics to address multiple problems in precision medicine in immune‑mediated inflammatory diseases] |
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− | [https://doi.org/10.1038/ | + | [https://doi.org/10.1038/s41591-024-02856-4 A visual-language foundation model for computational pathology] |
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− | [https://doi.org/10. | + | [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. | + | [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. | + | [https://doi.org/10.1101/2024.06.04.597354 Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model] |
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− | [https://doi.org/10.1016/j. | + | [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/10.1038/ | + | [https://doi.org/10.1038/s43588-024-00597-5 Population-level comparisons of gene regulatory networks modeled on highthroughput single-cell transcriptomics data] |
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− | |style="padding:.4em;"| | + | |style="padding:.4em;"|IS Choi |
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− | [https://doi.org/10. | + | [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. | + | [https://doi.org/10.1016/j.xgen.2024.100553 Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1101/2023.07.18.549602 Contextual AI models for single-cell protein biology] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1101/2024.04.15.589472 Nicheformer: a foundation model for single-cell and spatial omics] |
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− | |style="padding:.4em;"| | + | |style="padding:.4em;"|IS Choi |
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− | [https://doi.org/10. | + | [https://doi.org/10.1101/2023.05.29.542705 Large Scale Foundation Model on Single-cell Transcriptomics] |
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− | [https://doi.org/10.1038/ | + | [https://doi.org/10.1038/s41592-024-02201-0 scGPT: toward building a foundation modelfor single-cell multi-omics using generative AI] |
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− | [https://doi.org/10.1038/ | + | [https://doi.org/10.1038/s41586-023-06139-9 Transfer learning enables predictions in network biology] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1158/0008-5472.CAN-23-2650 The Web-Based Portal SpatialTME Integrates Histological Images with Single-Cell and Spatial Transcriptomics to Explore the Tumor Microenvironment] |
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− | [https://doi.org/10.1038/ | + | [https://doi.org/10.1038/s41592-023-02117-1 SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes] |
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− | [https://doi.org/10.1038/ | + | [https://doi.org/10.1038/s41587-023-01728-5 A relay velocity model infers cell-dependent RNA velocity] |
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− | [https://doi.org/10.1038/s41467- | + | [https://doi.org/10.1038/s41467-023-44206-x Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1038/s41587-023-01734-7 Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1016/j.cell.2023.11.026 Automatic cell-type harmonization and integration across Human Cell Atlas datasets] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1038/s41592-023-01994-w Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells] |
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− | |style="padding:.4em;"| | + | |style="padding:.4em;"|JH Cha |
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− | [https://doi.org/10.1038/ | + | [https://doi.org/10.1038/s41587-021-00896-6 Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID] |
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− | [https://doi.org/10.1016/j. | + | [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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− | [https://doi.org/10. | + | [https://doi.org/10.1038/s41591-024-03067-7 Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes] |
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− | [https://doi.org/10. | + | [https://doi.org/10.1186/s40168-024-01832-x Gut virome-wide association analysis identifes cross-population viral signatures for infammatory bowel disease] |
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− | [https://doi.org/10. | + | [https://doi.org/10.48550/arXiv.1806.00064 Efficient Low-rank Multimodal Fusion with Modality-Specific Factors] |
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− | [https://doi.org/10. | + | [https://doi.org/10.48550/arXiv.1707.07250 Tensor Fusion Network for Multimodal Sentiment Analysis] |
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[https://doi.org/10.1016/j.chom.2024.02.010 Stratification of Fusobacterium nucleatum by localhealth status in the oral cavity defines its subspeciesdisease association] | [https://doi.org/10.1016/j.chom.2024.02.010 Stratification of Fusobacterium nucleatum by localhealth status in the oral cavity defines its subspeciesdisease association] | ||
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[https://doi.org/10.1038/s41388-024-02974-w Robustness of cancer microbiome signals over a broad range of methodological variation] | [https://doi.org/10.1038/s41388-024-02974-w Robustness of cancer microbiome signals over a broad range of methodological variation] | ||
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[https://doi.org/10.1038/s41586-024-07182-w A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche] | [https://doi.org/10.1038/s41586-024-07182-w A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche] | ||
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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] | [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/s41587-023-01979-2 Spatial metatranscriptomics resolves host–bacteria–fungi interactomes] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/21 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-16 | ||
+ | |style="padding:.4em;"|SG Oh | ||
+ | |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] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/21 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-15 | ||
+ | |style="padding:.4em;"|SY Park | ||
+ | |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] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/21 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-14 | ||
+ | |style="padding:.4em;"|HS Moon | ||
+ | |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] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/21 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-13 | ||
+ | |style="padding:.4em;"|JH Nam | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1038/s41467-023-39933-0 Spatial cellular architecture predicts prognosis in glioblastoma] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/14 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-12 | ||
+ | |style="padding:.4em;"|HS Na | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1016/j.celrep.2024.113784 Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/14 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-11 | ||
+ | |style="padding:.4em;"|PK Kim | ||
+ | |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] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/05/14 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-10 | ||
+ | |style="padding:.4em;"|SH Kwon | ||
+ | |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] | ||
+ | |- | ||
+ | |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 | ||
+ | |style="padding:.4em;"|EJ Sung | ||
+ | |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] | ||
+ | |} | ||
+ | |||
Latest revision as of 20:36, 27 August 2024
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 | |
2024/06/11 | Single-cell | 24-28 | SA Choi | |
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 | |
2024/06/11 | Single-cell | 24-25 | HJ Lee | |
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 | |
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 | |
2024/05/28 | Single-cell | 24-18 | EB Yu | |
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 | |
2024/05/21 | Single-cell | 24-15 | SY Park | |
2024/05/21 | Single-cell | 24-14 | HS Moon | |
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 | |
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 | |
2024/05/14 | Single-cell | 24-9 | Q Zhen | |
2024/05/07 | Single-cell | 24-8 | CR Leenaars | |
2024/05/07 | Single-cell | 24-7 | YR Kim | |
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 | |
2024/04/23 | Single-cell | 24-2 | EJ Sung | |
2024/04/23 | Single-cell | 24-1 | HJ Kim |
Date | Team | Paper index |
Presenter | Paper title |
---|---|---|---|---|
2023/08/30 | Single-cell | 23-24 | JW Yu | |
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 | |
2023/07/26 | Single-cell | 23-21 | G Koh | |
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 | |
2023/06/21 | Single-cell | 23-16 | IS Choi | |
2023/06/14 | Single-cell | 23-15 | G Koh | |
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 | |
2023/05/17 | Single-cell | 23-12 | SB Baek | |
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 | |
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 | |
2023/02/21 | Single-cell | 23-6 | SB Baek | |
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 | |
2023/01/25 | Single-cell | 23-3 | G Koh | |
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 |
Date | Team | Paper index |
Presenter | Paper title |
---|---|---|---|---|
2021/11/23 | Single-cell | 21-39 | IS Choi | |
2021/11/16 | Single-cell | 21-38 | SB Back | |
2021/11/09 | Single-cell | 21-37 | JH Cha | |
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 | |
2021/10/19 | Single-cell | 21-34 | JH Cha | |
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 | |
2021/09/14 | Single-cell | 21-31 | IS Choi | |
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 |
Date | Team | Paper index |
Presenter | Paper title |
---|---|---|---|---|
2021/02/22 | Single-cell | 21-8 | IS Choi |
Functional CRISPR dissection of gene networks controlling human regulatory T cell identity |
21-7 | JH Cha |
Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy | ||
2021/02/15 | Single-cell | 21-6 | SB Baek | |
21-5 | IS Choi |
Trajectory-based differential expression analysis for single-cell sequencing data | ||
2021/02/08 | Single-cell | 21-4 | SB Baek |
Genetic determinants of co-accessible chromatin regions in activated T cells across humans |
21-3 | JH Cha |
Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer | ||
2021/02/01 | Single-cell | 21-2 | JW Cho | |
21-1 | JW Cho |