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Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective

单细胞和空间转录组学数据分析中的深度学习：数据科学视角下的进展与挑战

期刊:Briefings in Bioinformatics

影响因子:7.7

doi:10.1093/bib/bbaf136

Ge, Shuang; Sun, Shuqing; Xu, Huan; Cheng, Qiang; Ren, Zhixiang

Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence

利用双视角集成学习从单序列预测突变后蛋白质稳定性变化

期刊:Briefings in Bioinformatics

影响因子:7.7

doi:10.1093/bib/bbaf319

Nie, Zhiwei; Ma, Yiming; Liu, Yutian; Huang, Xiansong; Liu, Zhihong; Yang, Peng; Xu, Fan; Yin, Feng; Li, Zigang; Fu, Jie; Ren, Zhixiang; Zhang, Wen-Bin; Chen, Jie

发表日期：2025

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A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-Î±/JAK inhibitor.

用 TNF-α/JAK 抑制剂治疗类风湿性关节炎患者的滑液单细胞 RNA-seq 数据集

期刊:Scientific Data

影响因子:6.9

doi:10.1038/s41597-025-05339-4

He Chenjia, Ren Zhixiang, Xia Xuyang, Xue Zhinan, Zhang Feng, Qian Maoxiang, Shu Yang, Yin Geng, Xie Qibing, Xu Heng

Single-cell and spatial transcriptomics profile the interaction of SPP1(+) macrophages and FAP(+) fibroblasts in non-small cell lung cancer.

单细胞和空间转录组学分析了非小细胞肺癌中 SPP1(+) 巨噬细胞和 FAP(+) 成纤维细胞的相互作用

期刊:Translational Lung Cancer Research

影响因子:3.5

doi:10.21037/tlcr-2025-244

Xiao Minqin, Deng Yiqi, Guo Hang, Ren Zhixiang, He Yajiao, Ren Xia, Huang Li-Bin, Zhang Wei-Han, Chen Hai-Ning, Shu Yang, Zeng Fanxin, Zhang Yan, Xu Heng, Wang Lanlan

Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction

对来自72种脊椎动物的数百万条RNA一级序列进行自监督学习，可提高基于序列的RNA剪接预测能力。

期刊:Briefings in Bioinformatics

影响因子:7.7

doi:10.1093/bib/bbae163

Chen, Ken; Zhou, Yue; Ding, Maolin; Wang, Yu; Ren, Zhixiang; Yang, Yuedong

发表日期：2024

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CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction

CELA-MFP：一种用于多功能治疗肽预测的对比增强型标签自适应框架

期刊:Briefings in Bioinformatics

影响因子:7.7

doi:10.1093/bib/bbae348

Fang, Yitian; Luo, Mingshuang; Ren, Zhixiang; Wei, Leyi; Wei, Dong-Qing

CEL

发表日期：2024

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TCMM: A unified database for traditional Chinese medicine modernization and therapeutic innovations

TCMM：中医药现代化和治疗创新统一数据库

期刊:Computational and Structural Biotechnology Journal

影响因子:4.1

doi:10.1016/j.csbj.2024.04.016

Ren, Zhixiang; Ren, Yiming; Li, Zeting; Xu, Huan

多发性骨髓瘤

发表日期：2024

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A Large-Scale Dataset of Three-Dimensional Solar Magnetic Fields Extrapolated by Nonlinear Force-Free Method

利用非线性无力方法外推的大规模三维太阳磁场数据集

期刊:Scientific Data

影响因子:6.9

doi:10.1038/s41597-023-02091-5

Zhao, Zhongrui; Xu, Long; Zhu, Xiaoshuai; Zhang, Xinze; Liu, Sixuan; Huang, Xin; Ren, Zhixiang; Tian, Yonghong

发表日期：2023

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Electrically driven lasing from a dual-cavity perovskite device

双腔钙钛矿器件的电驱动激光发射

Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution

利用计算机模拟病毒进化对现实世界中流行的SARS-CoV-2突变进行生成式预测

Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective

单细胞和空间转录组学数据分析中的深度学习：数据科学视角下的进展与挑战

Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence

利用双视角集成学习从单序列预测突变后蛋白质稳定性变化

A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-Î±/JAK inhibitor.

用 TNF-α/JAK 抑制剂治疗类风湿性关节炎患者的滑液单细胞 RNA-seq 数据集

Single-cell and spatial transcriptomics profile the interaction of SPP1(+) macrophages and FAP(+) fibroblasts in non-small cell lung cancer.

单细胞和空间转录组学分析了非小细胞肺癌中 SPP1(+) 巨噬细胞和 FAP(+) 成纤维细胞的相互作用

Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction

对来自72种脊椎动物的数百万条RNA一级序列进行自监督学习，可提高基于序列的RNA剪接预测能力。

CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction

CELA-MFP：一种用于多功能治疗肽预测的对比增强型标签自适应框架

TCMM: A unified database for traditional Chinese medicine modernization and therapeutic innovations

TCMM：中医药现代化和治疗创新统一数据库

A Large-Scale Dataset of Three-Dimensional Solar Magnetic Fields Extrapolated by Nonlinear Force-Free Method

利用非线性无力方法外推的大规模三维太阳磁场数据集