Siyuan Chen (陈思远)
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Siyuan Chen

Siyuan Chen (陈思远) is currently a PhD. candidate in Computer Science at King Abdullah University of Science and Technology(KAUST),supervised by Professor Xin Gao in Structural and Functional Bioinformatics (SFB) Group, I am co-supervised by Professor Yu Li from CUHK. I work on the intersection between computer science and biology. Before that,I did my bachelors at UESTC, advised by Professor Yang Hu, and Professor Yan Chen .

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Research Interests:

  • 3D Genomics Analysis and its implications for evolution, health, and disease.

  • Biochemical Image Analysis, Cytogenetics Research .

  • Deep-Learning in Genomics, Next Generation Sequencing .

    • Publications

    Journal(* equal contribution, # correspondance)

    1. A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
      Siyuan Chen*, Jiuming Wang*,Inkyung Jung,Zhaowen Qiu, Xin Gao#, Yu Li#
      Genome Research, 2024 | paper

    2. BR-CHromNet:Banding Resolution localization of CHromosome structural abnormality with conditional random field
      Siyuan Chen*, Tingting Hu*, Xin Gao, Yongguo Yu#
      Journal of Molecular Biology, 2024 | paper

    3. KaryoXpert: An accurate chromosome segmentation and classification framework for karyotyping analysis without training with manually labeled metaphase-image mask annotations
      Siyuan Chen*, Kaichuang Zhang*, Jingdong Hu, Na Li, Ao Xu, Haoyang Li, Juexiao Zhou, Chao Huang, Yongguo Yu#, Xin Gao#
      Computers in Biology and Medicine, 2024 | paper

    4. PPML-Omics: a Privacy-Preserving federated Machine Learning system protects patients’ privacy from omic data
      Juexiao Zhou*, Siyuan Chen*, Yulian Wu*, Haoyang Li, Bin Zhang, Longxi Zhou, Yan Hu, Zihang Xiang, Zhongxiao Li, Ningning Chen, Wenkai Han, Di Wang#, Xin Gao#.
      Science Advances, 2024 | paper | news

    5. An AI Agent for Fully Automated Multi-omic Analyses
      Juexiao Zhou, Bin Zhang, Guowei Li, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen,Liwei Liu, Xin Gao#
      Advanced Science, 2024 | paper

    6. ProNet DB: A proteome-wise database for protein surface property representations and RNA-binding profiles
      Junkang Wei* , Jin Xiao*, Siyuan Chen*, Licheng Zong, Xin Gao#, Yu Li#
      Database: The Journal of Biological Databases and Curation 2024 | paper

    7. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics
      Haoyang Li*, Juexiao Zhou*, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao#
      Nature Communications 2023 paper

    8. Deep learning identifies and quantifies recombination hotspot determinants
      Yu Li*, Siyuan Chen*, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao#
      Bioinformatics , 2022 | paper

    9. The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity
      Shaorong Fan,Wenju Sun, Ligang Fan,Nan Wu,Wei Sun,Haiqian Ma, Siyuan Chen, ZitongLi, Yu Li,Jilin Zhang, Jian Yan#
      Computational and Structural Biotechnology Journal, 2022 | paper

    10. Self-supervised contrastive learning for integrative single cell RNA-seq data analysis
      Wenkai Han, Yuqi Cheng, Jiayang Chen, Huawen Zhong, Zhihang Hu, Siyuan Chen, Licheng Zong, Ting-Fung Chan, Kevin Lip, Irwin King, Xin Gao#, Yu Li#
      Briefing in Bioinformatics, 2022 | paper

    11. Protein-RNA interaction prediction with deep learning: Structure matters
      Junkang Wei*, Siyuan Chen*, Licheng Zong*, Xin Gao#, Yu Li#
      Briefing in Bioinformatics, 2021 | paper

    12. Lunar features detection for energy discovery via deep learning
      Siyuan Chen*, Yu Li*, Tao Zhang, Xingyu Zhu, Shuyu Sun, Xin Gao#
      Applied Energy, 2021 | paper | news

    Preprint or under review(* equal contribution)

    1. NoTAC: A Noise-Tolerance Automatic Cleaning Framework for Bone Marrow Karyotyping Data
      Rihan Huang*, Siyuan Chen*, Yafei Li, Chunling Zhang, Yilan Zhang, Changchun Yang, Na Li, Jingdong Hu, Ao Xu, Junkai Su, Xin Gao#, Huidan Li#, Jiatao Lou#
      bioarxiv, 2025 | paper

    2. Large Language Models in Biomedicine and Healthcare
      Juexiao Zhou, Haoyang Li, Siyuan Chen, Zhongyi Han, Xin Gao#
      bioarxiv, 2024 | paper

    3. An Inclusive Foundation Model for Generalizable Cytogenetics in Precision Oncology
      Changchun Yang, Weiqian Dai1, Yilan Zhang, Siyuan Chen, Jingdong Hu, Junkai Su, Yuxuan Chen, Ao Xu, Na Li, Xin Gao, Yongguo Yu#
      2025 | paper

    Education

    1. Jan 2022 - Present,   Ph.D. candidate in Computer Science,   King Abdullah University of Science and Technology, Saudi Arabia

    2. Aug 2020 - Dec 2021,   M.S. in Computer Science,   King Abdullah University of Science and Technology, Saudi Arabia

    3. Sept 2016 - Jun 2020,   B.E. in Engineering,   University of Electronic Science and Technology of China, China

    4. Sept 2016 - Jun 2020,   B.E. in Finance,   University of Electronic Science and Technology of China, China

    Experiences

    1. Sep 2023 - Nov 2023   Teaching Assistant (CS220-Data Analytics)   Ministry of Interior (MOI) King Fahad Security College (KFSC),Riyadh, Saudi Arabia

    2. May 2023   Teaching Assistant (DSA009-Data Analytics)   Saudi Aramco Dammam, Saudi Arabia

    3. Jan 2023   Administrator,  The 21st International Conference on Bioinformatics (InCoB2022) KAUST, Saudi Arabia

    4. Jul 2022 - Sep 2022,   Visiting Scholar,   The Chinese University of Hong Kong, Hong Kong, China

    © Siyuan Chen 陈思远 | Last updated: May 2025
    Thanks the template from YunheWang .