Hongli Ma

About

I am currently an Associate Researcher in the School of Mathematics at the Harbin Institute of Technology. Prior to this, I was trained as a postdoc in RNA bioinformatics and machine learning at the Zhi John Lu Lab in Tsinghua University (2 yrs). I obtained my Ph.D. in Mathematics from Shandong University (2 yrs in Financial Mathematics, 2 yrs in bioinfo(sequencing&omics) algorithms), and was a joint Ph.D. student in Computational Biology (molecular structure & interactions) at the University of Toronto, where I was fortunate to be advised by Prof. Zhaolei Zhang (2 yrs). My current research interests lie in the computational modeling of biomolecules, with a particular focus on RNA structures, RNA-ligand interactions, and interpretable machine learning. My Erdos number is 4.

Word cloud illustrating Hongli Ma's research interests

Selected Projects

RNAsmol

RNA-ligand interaction scoring via data perturbation and augmentation modeling.

Full text Code

RNANetMotif

A network-based method for discovering enriched RNA sequence-structure motifs.

Full text Code Webserver

KSP

An integrated network method for predicting catalyzing kinases of protein phosphorylation sites.

Full text Code

Publications

^† Equal contribution; ^* Corresponding author

2026

Conserved 3' Stem-Loop Structures Enable Comprehensive Analysis of Bacterial Transcription Termination in Metagenomes

Yunfan Jin^†, Jiyun Cui^†, Rulong Liu, Hongli Ma, Xiaomin Xu, Shufang Wu, Fei Gan^*, Zhi John Lu^*, Zhenjiang Zech Xu^*

Microbiome, 2026 / Full text

2025

RNA-ligand interaction scoring via data perturbation and augmentation modeling

Hongli Ma, Letian Gao, Yunfan Jin, Jianwei Ma, Yilan Bai, Xiaofan Liu, Pengfei Bao, Ke Liu, Zhenjiang Zech Xu^*, Zhi John Lu^*

Nature Computational Science, 2025 / Full text Code

News & Views highlight: What’s so hard about RNA-targeting drug discovery? by Carlos Oliver and Jérôme Waldispühl, Nature Computational Science, 2025.

Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential

Pengfei Bao^†, Taiwei Wang^†, Xiaofan Liu^†, Shaozhen Xing, Hanjin Ruan, Hongli Ma, Yuhuan Tao, Qing Zhan, Efres Belmonte-Reche, Lizheng Qin, Zhengxue Han, Minghui Mao^*, Mengtao Li^*, Zhi John Lu^*

Genome Biology, 2025 / Full text

Discovery of RNA-Targeting Small Molecules: Challenges and Future Directions

Zhengguo Cai^†,*, Hongli Ma^†, Fengcan Ye^†, Dingwei Lei^†, Zhenfeng Deng, Yongge Li, Ruichu Gu, Han Wen^*

MedComm, 2025 / Full text

2024

Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data

Xiaofan Liu^†, Yuhuan Tao^†, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li^*, Yunping Zhu^*, Zhi John Lu^*

Bioinformatics, 2024 / Full text

2022

RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites

Hongli Ma^†, Han Wen^†, Zhiyuan Xue, Guojun Li^*, Zhaolei Zhang^*

PLOS Computational Biology, 2022 / Full text Code Webserver

HCRNet: high-throughput circRNA-binding event identification from CLIP-seq data using deep temporal convolutional network

Yuning Yang^†, Zilong Hou^†, Yansong Wang, Hongli Ma, Pingping Sun, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li^*

Briefings in Bioinformatics, 2022 / Full text

Predicting Ligand-RNA Binding Using E3-Equivariant Network and Pretraining

Zhenfeng Deng^†, Ruichu Gu^†, Hangrui Bi^†, Hongli Ma, Xinyan Wang, Zhaolei Zhang^*, Han Wen^*

NeurIPS Machine Learning in Structural Biology Workshop, 2022 / Poster

2020

KSP: an integrated method for predicting catalyzing kinases of phosphorylation sites in proteins

Hongli Ma, Guojun Li^*, Zhengchang Su

BMC Genomics, 2020 / Full text Code