I am currently a postdoctoral fellow at the HKUCDS BioAI lab, School of Computing and Data Science, The University of Hong Kong. I work on bioinformatics algorithm development, deep learning, and genomics research, with extensive experience in Python, C, and C++. Feel free to visit my GitHub page for details.

I received my Ph.D. in Computer Science from The University of Hong Kong in September 2023, supervised by Prof. Ruibang Luo. Prior to that, I received my M.Eng. and B.Eng. in Software Engineering from the School of Computer Science and Engineering, Sun Yat-sen University.

My research interests include long-read variant calling, somatic variant detection, RNA variant calling, and third-generation sequencing data analysis. I develop the Clair series variant callers (Clair3, ClairS, ClairS-TO, Clair3-RNA, etc.), several of which are officially supported by Oxford Nanopore Technologies. I have published 15+ papers in peer-reviewed journals and conferences, including Nature Computational Science, Nature Communications, Bioinformatics, Briefings in Bioinformatics, and BMC Bioinformatics.

🔥 News

2026.04: 🎉🎉 Gungnir DNA storage codec was published in Nature Communications.
2025.12: 🎉🎉 Clair3-RNA was published in Nature Communications.
2025.10: 🎉🎉 ClairS-TO was published in Nature Communications.
2025.01: 🎉🎉 Repun was published in Briefings in Bioinformatics.
2023.09: 🎉🎉 I graduated from the Department of Computer Science, the University of Hong Kong.
2023.08: 🎉🎉 A preprint describing ClairS’s algorithms and results is at bioRxiv.
2023.05: 🎉🎉 ClairS was supported as an official somatic small variant caller tool by Oxford Nanopore Technologies, link here.
2023.04: 🎉🎉 I gave a talk in Recomb-Seq on our new somatic variant caller ClairS.
2023.02: 🎉🎉 Our paper Clair3 was accepted by Nature Computational Science.
2021.10: 🎉🎉 Our first bioinformatics software Clair3 was supported as official variant caller tool by Oxford Nanopore Technologies, link here.

📝 Publications

Selected Publications (^*equal contribution, ^#corresponding)

Z. Zheng^*, S. Li^*, J. Su^*, A. W. S. Leung, T. W. Lam, R. Luo^#. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nature Computational Science, 2022, 2(12): 797-803. Full text · Code
Z. Zheng^*, X. Yu^*, L. Chen, Y. L. Lee, C. Xin, A. O. K. Wong, M. Jain, R. K. Kesharwani, F. J. Sedlazeck^#, R. Luo^#. Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data. Nature Communications, 2025, 16(1): 11553. Full text · Code
Z. Zheng^*, L. Chen^*, J. Su^*, Y. L. Lee, T. W. Lam, R. Luo^#. ClairS: a deep-learning method for long-read somatic small variant calling. bioRxiv, 2023. Full text · Code
Z. Zheng, M. He, X. Yu, J. Li, L. Chen, A. O. K. Wong, J. Zhang, Y. Zhou, R. Luo^#. Accelerated long-read variant calling with Clair3 for whole-genome sequencing. Bioinformatics, 2026, 42(5): btag181. Full text · Code
Z. Zheng^*#, Y. Ren^*, L. Chen, A. O. K. Wong, S. Li, X. Yu, T. W. Lam, R. Luo^#. Repun: An accurate small variant representation unification method for multiple sequencing platforms. Briefings in Bioinformatics, 2025, 26(1): bbae613. Full text · Code
Z. Zheng, M. He, X. Yu, L. Chen, A. O. K. Wong, J. Zhang, Y. Zhou, R. Luo^#. T2T-CHM13 reveals missing truth variants and improves deep-learning-based variant calling in long-read sequencing data. Accepted by Quantitative Biology, 2026.
L. Chen^*, Z. Zheng^*#, J. Su, X. Yu, A. O. K. Wong, J. Zhang, Y. L. Lee, R. Luo^#. ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling. Nature Communications, 2025, 16(1): 9630. Full text · Code
J. Zhang^*, L. Chen^*, J. Sun^*, S. Li, Y. Zhou, Z. Wu, C. Li, Z. Zheng^#, R. Luo^#. Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power. Nature Communications, 2026. Full text · Code
J. Su^*, Z. Zheng^*, S. S. Ahmed, T. W. Lam, R. Luo^#. Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks. Briefings in Bioinformatics, 2022, 23(5): bbac301. Full text · Code
L. Chen^*, Z. Zheng^*#, M. He, A. O. K. Wong, X. Yu, J. Li, J. Zhang, Y. Zhou, R. Luo^#. Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling. bioRxiv, 2025. Full text · Code
H. Yu^*, Z. Zheng^*, J. Su^#, T. W. Lam^#, R. Luo^#. Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP. BMC Bioinformatics, 2023, 24: 308. Full text · Code
L. Chen^*, J. Su^*, Z. Zheng^*, T. W. Lam, R. Luo^#. Large-scale Dataset and Effective Model for Variant-Disease Associations Extraction. Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2023, 1-6. Full text

Please check my Google Scholar for all publications here.

🎖 Honors and Awards

2019 - 2023 University Postgraduate Fellowships
2019 - 2023 Postgraduate Scholarships
2018 Kaggle Competition silver medal and bronze medal
2018 First-class Graduate Academic Scholarship
2014 - 2016 First-class Undergraduate Academic Scholarship

📖 Educations

2019.09 - 2023.09, Ph.D., Department of Computer Science, The University of Hong Kong, Hong Kong.
2017.09 - 2019.06, M.Eng., School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou.
2013.09 - 2017.06, B.Eng., School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou.

💬 Presentations

2025.12, A deep learning-based small variant caller for long-read RNA sequencing data. GIW/ISCB-Asia 2025, Hong Kong, China.
2024.10, ClairS: a deep-learning method for long-read somatic small variant calling. APBJC 2024, Okinawa, Japan.
2023.04, Accurate haplotype-aware long-read somatic variant calling using deep learning-based synthetic data learning. RECOMB-SEQ 2023, Istanbul, Turkey.
2020.05, Claire: Clair-extended to support full alignment as input to a deep neural network for more accurate germline variant calling in low complexity genome regions. RECOMB-SEQ 2020, Padua, Italy.

💻 Internships

2018.05 - 2018.09, Summer intern, Intelligent Recommendation Center, Tencent.
2017.06 - 2017.09, Research intern, Medical Image Group, Sun Yat-sen University Cancer Center.

Zhenxian Zheng