I am a highly motivated Software Engineering graduate currently pursuing a Master's degree in Computational Biology. My academic journey has equipped me with a solid foundation in computer science, encompassing software development, algorithm design, and data structures, while my graduate research focuses on computational biology and model interpretability. By leveraging my expertise in bioinformatics, machine learning, and systems biology, I aim to develop innovative computational solutions for complex biological and medical challenges.

I have contributed to high-impact research as evidenced by my publications in top-tier journals, including Genome Biology, Computational Methods and Programs in Biomedicine and IEEE Journal of Biomedical and Health Informatics. These works highlight my commitment to interdisciplinary collaboration and advancing knowledge at the intersection of computational science and biology.

Selected Publications

You can also find my articles on my Google Scholar profile

†: Co-first Author

1. He Z, Sun Y, Li H, Sun C, Yang X, Chen H, Liao M, Bo X. CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model. Genome Biol. 2026 Jan; doi: 10.1186/s13059-026-03948-9. (IF=17.9, JCR Q1)
2. He Z, Zhang R, Qu P, Meng Y, Jia J, Wang Z, Wang P, Ni Y, Shan L, Liao M, Li Y. Development and validation of an explainable model of brain injury in premature infants: A prospective cohort study. Comput Methods Programs Biomed. 2025 Mar;260:108559. doi: 10.1016/j.cmpb.2024.108559. (IF=7.0, JCR Q1)
3. He Z, Wang C, Guo X, Sun H, Bi Y, Pitt ME, Li C, Song J, Coin LJM, Li F. MERITS: a web-based integrated Mycobacterial PE/PPE protein database. Bioinform Adv. 2024 Mar 2;4(1):vbae035. doi: 10.1093/bioadv/vbae035. (IF=2.4, JCR Q2)
4. Jia R†, He Z†, Wang C, Guo X, Li F. MetalPrognosis: A Biological Language Model-Based Approach for Disease-Associated Mutations in Metal-Binding Site Prediction. IEEE/ACM Trans Comput Biol Bioinform. 2024 Sep 25;PP. doi: 10.1109/TCBB.2024.3467093. (IF=4.5, JCR Q1)
5. Wang C, He Z, Jia R, Pan S, Coin LJ, Song J, Li F. PLANNER: a multi-scale deep language model for the origins of replication site prediction. IEEE J Biomed Health Inform. 2024 Jan 4;PP. doi: 10.1109/JBHI.2024.3349584. (IF=7.7, JCR Q1)