Siyuan Chen (陈思远)
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Siyuan Chen

Siyuan Chen (陈思远) is currently a PhD. student 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:

  • Biochemical Image Analysis.
  • 3D Genomics Analysis and its implications for evolution, health, and disease.
  • Deep-Learning in Genomics .
  • Publications

    Journal(* equal contribution)

    1. 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

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

    3. 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

    4. 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

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

    6. 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 | code

    Preprint or under review(* equal contribution)

    1. YOLOOP: A Fast and Accurate Detection Framework for Genome-wide Chromatin Loop Mapping from Hi-C data
      Siyuan Chen*, Jiuming Wang∗, Xin Gao, and Yu Li

    2. 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 and Xin Gao.
      bioarxiv, 2022 | paper

    3. 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 and Yu Li
      arxiv, 2022 | paper


    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


    1. Sep 2023 - Nov 2023   Teaching Assistant (CS220-Data Analytics)   Ministry of Interior (MOI) 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 2023
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