Junhao Su

Ph.D. in Computer Science, Department of Computer Science, Faculty of Engineering, HKU

Rm307, Haking Wong Bldg
The University of Hong Kong
Pokfulam Road, Hong Kong

Tel: (+852) 5643-3527
Email: jhsu (at) connect (dot) hku (dot) hk

[Google Scholar] [ORCiD] [GitHub] [ResearchGate] [LinkedIn]


Junhao Su obtained his Ph.D. in Computer Science degree from the University of Hong Kong (HKU) in 2023, under the supervision of Dr. Ruibang Luo and Prof. Tak-Wah Lam. Previously, he completed his Bachelor's degree in Bioinformatics in 2017 and Master's degree in Computer Science and Technology in 2019, both from Harbin Institute of Technology (HIT).
His work focuses on developing algorithms and tools for analyzing genomics data, with a primary emphasis on third-generation ONT long-read data and its applications in various medical practices. His research findings have been published in prestigious peer-reviewed journals, including Nature Computational Science, Briefings in Bioinformatics, and NAR Genomics and Bioinformatics.

personal pic

Research Interests

Bioinformatics Algorithms

Education

Ph.D. in Computer Science, The University of Hong Kong Sept. 2019 – Oct. 2023

Surpervisor: Ruibang Luo

M. Eng. in Computer Science and Technology, Harbin Institute of Technology Sept. 2017 – Jun. 2019

Surpervisor: Yadong Wang

B. Eng. in Bioinformatics, Harbin Institute of Technology Sept. 2013 – Jun. 2017

Work Experience

► Post-doctoral Fellow, Laboratory of Data Discovery for Health (Hong Kong) Nov. 2023 - Present

► Honorary Research Associate, The University of Hong Kong Feb. 2024 - Present

► Teaching Assistant, The University of Hong Kong Spring 2023

     COMP2501, Introduction to Data Science and Engineering, Undergraduate Course

► Teaching Assistant, The University of Hong Kong Spring 2020,2021,2022

     CCST9047, The Age of Big Data, Undergraduate Course, Common Core

► Teaching Assistant, Harbin Institute of Technology Fall 2018

     Bioinformatics, Undergraduate Course

► Bioinformatics Intern, WeGene (ShenZhen) Summer 2016,2017; Spring 2018

Publications

Co-first (*), Co-corresponding(^)

  • Junhao Su*, Shumin Li*, Zhenxian Zheng, Tak-Wah Lam, and Ruibang Luo^. "ClusterV-Web: A User-Friendly Tool for Profiling HIV Quasispecies and Generating Drug Resistance Reports from Nanopore Long-Read Data." Bioinformatics Advances 4.1 (2024): vbae006. [Bioinformatics Advances], [GitHub]
  • Timothy Ting Leung Ng*, Junhao Su*, et al. "Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies." Clinical Chemistry hvad108 (2023). (IF 2022: 9.3, JCR Q1) [Clinical Chemistry], **EDITOR'S CHOICE**, [GitHub]
  • Junhao Su*, Wui Wang Lui*, YanLam Lee*, et al. "Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling." Scientific Reports 13, no. 1 (2023): 5237. (IF 2022: 4.6, JCR Q2) [Scientific Reports] [GitHub]
  • Huijing Yu*, Zhenxian Zheng*, Junhao Su^, Tak-Wah Lam^, and Ruibang Luo^. "Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP." BMC Bioinformatics 24, 308 (2023). (IF 2022: 3.0, JCR Q3) [BMC Bioinformatics] [GitHub]
  • Lei Chen, Junhao Su^, Zhenxian Zheng^, Tak-Wah Lam, and Ruibang 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) [ACM BCB]
  • Lei Chen^, Junhao Su, Tak-Wah Lam, and Ruibang Luo^. "Exploring Pair-Aware Triangular Attention for Biomedical Relation Extraction." Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (2023) [ACM BCB]
  • Shumin Li*, Bin Yan*, Binbin Wu*, Junhao Su, et al. "Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics." Stem Cell Research & Therapy 14.1 (2023): 1-17. (IF 2022: 7.5, JCR Q1)
  • Zhenxian Zheng*, Shumin Li*, Junhao Su*, Amy Wing-Sze Leung, Tak-Wah Lam, and Ruibang Luo^. "Symphonizing pileup and full-alignment for deep learning-based long-read variant calling." Nature Computational Science 2, no. 12 (2022): 797-803. (IF 2022: 11.3) [Nature Computational Science] [GitHub]
  • Junhao Su*, Zhenxian Zheng*, Syed Shakeel Ahmed, Tak-Wah Lam, and Ruibang Luo^. "Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks." Briefings in Bioinformatics 23, no. 5 (2022): bbac301. (IF 2021: 13.994, JCR Q1) [Briefings in Bioinformatics] [GitHub]
  • Junhao Su*, Ye Wu*, Hing-Fung Ting, Tak-Wah Lam, and Ruibang Luo^. "RENET2: high-performance full-text gene–disease relation extraction with iterative training data expansion." NAR Genomics and Bioinformatics 3, no. 3 (2021): lqab062. (IF 2022: 4.6) [NAR Genomics and Bioinformatics] [GitHub]
  • Yadong Liu, Jiang Tao, Junhao Su, Bo Liu, Tianyi Zang, and Yadong Wang. "SKSV: ultrafast structural variation detection from circular consensus sequencing reads." Bioinformatics 37, no. 20 (2021): 3647-3649. (IF 2020: 6.937, JCR Q1) [Bioinformatics]

Working Papers or Papers Under Review:

  • Zhenxian Zheng*, Junhao Su*, Lei Chen*, YanLam Lee, Tak-Wah Lam, and Ruibang Luo^. "ClairS: a deep-learning method for long-read somatic small variant calling." (2023) [bioRxiv]
  • Junhao Su*, Zhenxian Zheng*, Tak-Wah Lam, and Ruibang Luo^. "Accurate Nanopore long-read de novo variant calling in family trios with deep neural networks " (2024)

Softwares

► Clair3-Trio: deep-learning, ONT long read, small germline variant calling, bioconda/docker supported

► RENET2: deep-learning, text mining, gene-disease relation extraction, bioconda supported

► ClusterV: deep-learning, ONT long read, HIV sequencing data, Illumina data, drug resistance report, docker supported

► ONT-TB-NF: ONT long read, Nextflow pipeline, metagenomic samples, ONT adaptive sequencing

Presentations

June 2023 – Presenter at TRS (Theme-based Research Scheme) Symposium, The University of Hong Kong, Hong Kong
"ONT adaptive sequencing and its application in metagenomic samples"

April 2023 – Poster at RECOMB-SEQ, Istanbul, Turkey
"ClusterV: Accurate Detection of HIV Quasispecies and Drug Resistance Mutations using ONT Sequencing Data"

December 2022 – Presenter at HKU Bioinfo-seminars, The University of Hong Kong, Hong Kong
"Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks"

Skills

Languages: Mandarin, Cantonese, English