A dataset of small protein conformational ensembles from all-atom molecular dynamics simulations

Ying Hu, Xin Yang, Xinlei Zhu, Zhixiang Sui, Pingping Sun, Ming Ni, Xiaochen Bo, Longjia Jia, Zhiguo Fu, Zilin Ren

Scientific Data

Co-first authors: Ying Hu, Xin Yang · Corresponding author: Zilin Ren

Genome-guided generative adversarial learning enables nanopore adaptive sequencing

Yixiang Zhang, Pingping Sun, Jiarong Zhang, Zhiguo Fu, Xiaochen Bo, Di Guan, Ming Ni, Zilin Ren

Nature Communications · 17 · 7097

Co-first authors: Yixiang Zhang · Corresponding author: Zilin Ren

Genomic-epidemiological analysis of 15 million SARS-CoV-2 genomes reveals accelerated fitness gain of JN.1 lineage

Zhong-yi Lei, Qian-tong Jin, Xiao-min Zhang, Xiao-chen Bo, Zi-lin Ren, Yi-gang Tong, Ming Ni

Virologica Sinica · 41 · 2 · 382–391

Corresponding author: Zilin Ren

MuFaDDG: a sequence-based multiscale feature fusion framework for protein stability changes prediction

Jianting Gong, Pengjia Ma, Zilin Ren, Si Li, Zhiguo Fu, Pingping Sun, Ming Ni, Xiaochen Bo

Bioinformatics · 42 · 5 · btag196

Co-first authors: Jianting Gong, Pengjia Ma

Efficient exploration of conformational ensembles via protein interaction-informed deep learning

Zilin Ren, Duo Liu, Qianyi Jia, Qiantong Jin, Yubin Liu, Chan Liu, Zhixiang Sui, Luyao Han, Yixiang Zhang, Xin Yang, Pingping Sun, Zhiguo Fu, Chengkun Wu, Ming Ni, Xiaochen Bo

Research Square

First author: Zilin Ren

Multimodal AI unveils a billion-scale microbial enzyme atlas

Ming Ni, Jianting Gong, Pengjia Ma, Wanyi Chen, Yibo Zhang, Lingchun Qiao, Xiaomin Zhang, Haoyue Gu, Junling Yang, Songyang Diao, Wanlin Liu, Zilin Ren, Yunming Fang, Xiaochen Bo, Tianwei Tan

Research Square

Co-first authors: Jianting Gong, Pengjia Ma

A T cell-based ubiquitin-mediated mRNA vaccine provides cross-protection against H1N1 and B influenza viruses in mice

Yaxin Di, Ziliang Wang, Zilin Ren, Haixin Huang, Songhui Yang, Chenchao Zhang, Shibo Liang, Pengyuan Dong, Wanbo Tai, Xinyu Zhuang, Mingyao Tian

Current Research in Microbial Sciences · 9 · 100457

Co-first authors: Zilin Ren

Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing

Fuqiang Ye, Juanjuan Zhu, Xiaomin Zhang, Jiarong Zhang, Zihan Xie, Tingting Yang, Yifang Han, Xiaohong Yang, Zilin Ren, Ming Ni

GigaScience · 14 · giaf018

Corresponding author: Zilin Ren

DeepPFP: a multi-task-aware architecture for protein function prediction

Han Wang, Zilin Ren, Jinghong Sun, Yongbing Chen, Xiaochen Bo, JiGuo Xue, Jingyang Gao, Ming Ni

Briefings in Bioinformatics · 26 · 1 · bbae579

Co-first authors: Zilin Ren · Corresponding author: Zilin Ren

Integrating genomic epidemiology and deep mutational scanning data for prevalence forecasting of SARS-CoV-2 Omicron lineages

Zhong-yi Lei, Xiao-min Zhang, Jia-lu Han, Ji-guo Xue, Jia-yi Xu, Zi-lin Ren, Yi-gang Tong, Xiao-chen Bo, Ming Ni

PLOS One · 20 · 11 · e0335520

Corresponding author: Zilin Ren

N-terminal PEGylation enhances organophosphorus hydrolase catalysis for a promising fast and long-acting prophylactic candidate

Ming Ma, Yanan Zhai, Qiantong Jin, Dan Wang, Shunye Wang, Zhuang Liu, Ziyang Wang, Chengcai Wang, Yanwei Xie, Zilin Ren, Xiang Gao, Jing Gao

Journal of Hazardous Materials · 488 · 137336

Corresponding author: Zilin Ren

PLMABFW: A deep learning framework for predicting Antibody–Antigen interactions using protein language model

Yongbing Chen, Qianyi Jia, Xinyue Jia, Zhiguo Fu, Pingping Sun, Bo Li, Zilin Ren

Journal of Bioinformatics and Computational Biology · 23 · 06

First author: Yongbing Chen

A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity

Jiayi Xu, Jianting Gong, Xiaochen Bo, Yigang Tong, Zilin Ren, Ming Ni

Biophysical Chemistry · 311 · 107253

Corresponding author: Zilin Ren

CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism

Zilin Ren, Lili Jiang, Yaxin Di, Dufei Zhang, Jianli Gong, Jianting Gong, Qiwei Jiang, Zhiguo Fu, Pingping Sun, Bo Zhou, Ming Ni

Bioinformatics · 40 · 7 · btae330

Co-first authors: Zilin Ren, Lili Jiang

NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm

Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang, Pingping Sun, Jiguo Xue, Xiaochen Bo, Bo Zhou, Jiangwei Yan, Ming Ni

Briefings in Bioinformatics · 25 · 6 · bbae472

Co-first authors: Zilin Ren, Yixiang Zhang · Corresponding author: Zilin Ren

Deciphering and identifying pan-cancer RAS pathway activation based on graph autoencoder and ClassifierChain

Jianting Gong, Yingwei Zhao, Xiantao Heng, Yongbing Chen, Pingping Sun, Fei He, Zhiqiang Ma, Zilin Ren

Electronic Research Archive · 31 · 8 · 4951-4967

First author: Jianting Gong · Corresponding author: Zilin Ren

MTNA: A deep learning based predictor for identifying multiple types of N-terminal protein acetylated sites

Yongbing Chen, Wenyuan Qin, Tong Liu, Ruikun Li, Fei He, Ye Han, Zhiqiang Ma, Zilin Ren

Electronic Research Archive · 31 · 9 · 5442-5456

First author: Yongbing Chen · Corresponding author: Zilin Ren

Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data

Zilin Ren, Quan Li, Kajia Cao, Marilyn M. Li, Yunyun Zhou, Kai Wang

BMC Bioinformatics · 23 · Suppl 3 · 572

First author: Zilin Ren

PLMTHP: An Ensemble Framework for Tumor Homing Peptide Prediction based on Protein Language Model

Yongbing Chen, Han Qin, Xiaodan Cui, Tianhui Yang, Pingping Sun, Jianting Gong, Zilin Ren

2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · 841-846

First author: Yongbing Chen

THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model

Jianting Gong, Lili Jiang, Yongbing Chen, Yixiang Zhang, Xue Li, Zhiqiang Ma, Zhiguo Fu, Fei He, Pingping Sun, Zilin Ren, Mingyao Tian

Bioinformatics · 39 · 11 · btad646

First author: Jianting Gong · Corresponding author: Zilin Ren

Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance

Yanfeng Lin, Yan Dai, Yuqi Liu, Zhuli Ren, Hao Guo, Zhenzhong Li, Jinhui Li, Kaiying Wang, Lang Yang, Shuang Zhang, Hongbo Liu, Leili Jia, Ming Ni, Peng Li, Hongbin Song

Frontiers in Microbiology · 13 · 929241

Co-first authors: Zilin Ren

Author-name note: Zilin Ren is printed as “Zhuli Ren” in the original article.

Forensic nanopore sequencing of STRs and SNPs using Verogen’s ForenSeq DNA Signature Prep Kit and MinION

Zi-Lin Ren, Jia-Rong Zhang, Xiao-Meng Zhang, Xu Liu, Yan-Feng Lin, Hua Bai, Meng-Chun Wang, Feng Cheng, Jin-Ding Liu, Peng Li, Lei Kong, Xiao-Chen Bo, Sheng-Qi Wang, Ming Ni, Jiang-Wei Yan

International Journal of Legal Medicine · 135 · 5 · 1685–1693

First author: Zilin Ren