scInterpreter: Training Large Language Models to Interpret scRNA-seq Data for Cell Type Annotation
Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences（中国科学院动物研究所干细胞与生殖生物学国家重点实验室）；University of Chinese Academy of Sciences（中国科学院大学）
Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to train and adapt the Large Language Model with the capability to interpret and distinguish cell types in single-cell RNA sequencing data. Our preliminary research results indicate that these foundational models excel in accurately categorizing known cell types, demonstrating the potential of the Large Language Models as effective tools for uncovering new biological insights.
scReader: Prompting Large Language Models to Interpret scRNA-seq Data
Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences（中国科学院动物研究所干细胞与生殖生物学国家重点实验室）；University of Chinese Academy of Sciences（中国科学院大学）
Partial domain adaptation enables cross domain cell type annotation between scRNA-seq and snRNA-seq
Shandong Jianzhu University（山东建筑大学）；University of Electronic Science and Technology of China（电子科技大学）；Chongqing Jiaotong University（重庆交通大学）；Westlake University（西湖大学）
Bipartite Graph Attention-based Clustering for Large-scale scRNA-seq Data
Institute of Intelligent Information Processing, Shanxi University（山西大学智能信息处理研究院）；Alliance Manchester Business School, The University of Manchester（曼彻斯特大学阿联酋商业学院）
A Hybrid Computational Intelligence Framework for scRNA-seq Imputation: Integrating scRecover and Random Forests
University of Technology Sydney, Australia（悉尼科技大学）；University of Sydney, Australia（悉尼大学）；Asia Pacific International College (APIC), Parramatta, NSW, Australia（亚太国际学院）；Lincoln Institute of Higher Education (LIHE), Sydney, Australia（林肯高等教育研究所）；The Institute of International Studies (TIIS), Sydney, Australia（国际研究学院）
Application of Deep Learning on Single-Cell RNA-sequencing Data Analysis: A Review
Weill Cornell Medicine（威尔康奈尔医学院）；Cornell University（康奈尔大学）；Institute for Computational Biomedicine（计算生物医学研究所）；Caryl and Israel Englander Institute for Precision Medicine（卡里尔与以色列·英格兰德精准医学研究所）；Temple University（天普大学）
SpaDiT: Diffusion Transformer for Spatial Gene Expression Prediction using scRNA-seq
the School of Information Science；Engineering , Yunnan University , 650091 , Kunming, Yunnan , China；College of Nursing Health Sciences , Yunnan Open University , 650599 , Kunming , China
scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering
Sichuan University（四川大学）；University of International Business and Economics（对外经济贸易大学）；Great Bay University（大湾区大学）；The Education University of Hong Kong（香港教育大学）
Graph Structure Learning for Tumor Microenvironment with Cell Type Annotation from non-spatial scRNA-seq data
School of Computer Science, Northwestern Polytechnical University（西北工业大学计算机学院）；Research & Development Institute of Northwestern Polytechnical University in Shenzhen（西北工业大学深圳研究院）；School of Engineering, The University of Sydney（悉尼大学工程学院）；College of Life Sciences, Northwest University（西北大学生命科学学院）；Research Office, City University of Hong Kong (Dongguan)（香港城市大学（东莞）研究办公室）
scCDCG: Efficient Deep Structural Clustering for single-cell RNA-seq via Deep Cut-informed Graph Embedding
Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；University of Chinese Academy of Sciences（中国科学院大学）；Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences（中国科学院大学杭州先进研究所）；State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences（中国科学院动物研究所干细胞与生殖生物学重点实验室）；Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Science（中国科学院干细胞与再生医学研究所）；Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Science（中国科学院北京干细胞与再生医学研究所）
A Multi-Modal AI Copilot for Single-Cell Analysis with Instruction Following
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；ZJU-Hangzhou Global Scientific and Technological Innovation Center（浙大杭州国际科创中心）；College of Pharmaceutical Sciences, Zhejiang University（浙江大学药学院）；School of Software Technology, Zhejiang University（浙江大学软件学院）；Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine（浙江大学创新中心（国家中药复方重点实验室））
scRNA-seq of preeclamptic trophoblasts identifies EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia markers: validation of neuradapt as a superior mimetic to cobalt chloride
HSE University（高等经济大学）；Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences（俄罗斯科学院谢米亚金-奥夫钦尼科夫生物有机化学研究所）
Integrating gene regulatory priors into Transformer attention with scTransformer for interpretable scRNA-seq analysis
Department of Information Engineering, University of Padova（信息工程系，帕多瓦大学）；Department of Neuroscience, University of Padova（神经科学系，帕多瓦大学）；Padova Neuroscience Center（帕多瓦神经科学中心）；Information Systems Institute, University of Applied Sciences Western Switzerland, HES-SO Valais（应用科学西瑞士信息系统研究所，HES-SO瓦莱大学）；Department of Comparative Biomedicine and Food Science, University of Padova（比较生物医学与食品科学系，帕多瓦大学）；Padua Center for Network Medicine, University of Padova（帕维亚网络医学中心，帕多瓦大学）
scKDGM: KAN-guided Dynamic Graph Masked Learning for Single-Cell RNA-seq Clustering
College of Computer and Information Science, Southwest University（西南大学计算机与信息科学学院）；Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences（中国科学院新疆物理化学研究所）
scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing
Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；University of Chinese Academy of Sciences（中国科学院大学）；Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences（中国科学院大学杭州高等研究院）；School of Computing and Information Technology, Great Bay University（大湾区大学计算机科学与技术学院）；School of Engineering, Westlake University（西湖大学工学院）
scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data
Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；University of Chinese Academy of Sciences（中国科学院大学）；College of Life Science, Northeast Agricultural University（东北农业大学生命科学学院）；SKL-IOTSC and Department of CIS, University of Macau（澳门大学SKL-IOTSC和CIS系）；Jilin University（吉林大学）
