Difference between revisions of "Journal Club"
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+ | {|class=wikitable style="text-align:center;" | ||
+ | |+style="text-align:left;font-size:12pt" | 2024-2 scOmics | ||
+ | |- | ||
+ | !scope="col" style="padding:.4em" | Date | ||
+ | !scope="col" style="padding:.4em" | Team | ||
+ | !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|2025/1/21 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|25-2 | ||
+ | |style="padding:.4em;"|YL Jung | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.04.04.24305313 Single-cell RNA sequencing of human tissue supports successful drug targets] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2025/1/14 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|25-1 | ||
+ | |style="padding:.4em;"|EJ Sung | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2023.11.21.568145 ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2025/1/7 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-34 | ||
+ | |style="padding:.4em;"|IS Choi | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.09.24.614685 Evaluating the Utilities of Foundation Models in Single-cell Data Analysis] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/12/31 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-33 | ||
+ | |style="padding:.4em;"|SB Baek | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.09.24.614685 Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/12/24 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-32 | ||
+ | |style="padding:.4em;"|JH Cha | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.09.24.614685 scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/12/17 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-31 | ||
+ | |style="padding:.4em;"|HB Lee | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.09.09.611960 Mouse-Geneformer: A Deep Learning Model for Mouse Single-Cell Transcriptome and Its Cross-Species Utility] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/12/10 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-30 | ||
+ | |style="padding:.4em;"|YL Jung | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.08.16.608180 Quantized multi-task learning for context-specific representations of gene network dynamics] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/12/3 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-29 | ||
+ | |style="padding:.4em;"|EJ Sung | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.17632/wdxwy8gmrz.1 Systematic Functional Annotation and Visualization of Biological Networks] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/11/26 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-28 | ||
+ | |style="padding:.4em;"|IS Choi | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1038/s41592-024-02303-9 CellRank 2: unified fate mapping in multiview single-cell data] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/11/19 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-27 | ||
+ | |style="padding:.4em;"|SB Baek | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1101/2024.07.29.605556 scPRINT: pre-training on 50 million cells allows robust gene network predictions] | ||
+ | |- | ||
+ | |style="padding:.4em;" rowspan=1|2024/11/12 | ||
+ | |style="padding:.4em;" rowspan=1|Single-cell | ||
+ | |style="padding:.4em;"|24-26 | ||
+ | |style="padding:.4em;"|JH Cha | ||
+ | |style="padding:.4em;text-align:left"| | ||
+ | [https://doi.org/10.1038/s41467-024-46440-3 Bidirectional generation of structure and properties through a single molecular foundation model] | ||
+ | |} | ||
+ | |||
{|class=wikitable style="text-align:center;" | {|class=wikitable style="text-align:center;" | ||
|+style="text-align:left;font-size:12pt" | 2024-2 Microbiome | |+style="text-align:left;font-size:12pt" | 2024-2 Microbiome | ||
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|style="padding:.4em;"|24-25 | |style="padding:.4em;"|24-25 | ||
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[https://doi.org/10.1126/science.adj4857 A blueprint for tumor-infiltrating B cells across human cancers] | [https://doi.org/10.1126/science.adj4857 A blueprint for tumor-infiltrating B cells across human cancers] | ||
|- | |- | ||
− | |style="padding:.4em;" rowspan=1|2024/10/ | + | |style="padding:.4em;" rowspan=1|2024/10/29 |
|style="padding:.4em;" rowspan=1|Single-cell | |style="padding:.4em;" rowspan=1|Single-cell | ||
|style="padding:.4em;"|24-24 | |style="padding:.4em;"|24-24 |
Latest revision as of 16:15, 16 October 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 |