Siyuan Chen (陈思远)
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Siyuan Chen

Siyuan Chen (陈思远) is currently a first-year PhD. student in Computer Science at King Abdullah University of Science and Technology(KAUST), co-supervised by Professor Yu Li from CUHK, and Professor Xin Gao in Structural and Functional Bioinformatics (SFB) Group. 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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News

  • Mar 2022, One paper accepted by Bioinformatics (IF=6.93).

  • Jan 2022, Begin my journey as Ph.D. student at KAUST.

  • Nov 2021, One paper accepted by Briefing in Bioinformatics (IF=11.620).

  • Jul 2021, My work reported as "Training an AI eye on the Moon" was published by KAUST Discovery .

  • Jun 2021, One paper accepted by Applied Energy (IF=9.746).

  • Aug 2020, Begin my journey as Ms studnet at KAUST.

    • Publications

    Journal(* equal contribution)

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

    2. 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

    3. 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

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

    5. 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

    4. Benchmarking and guidelines of cellular deconvolution for spatial transcriptomics.
      Haoyang Li*, Juexiao Zhou*, Zhongxiao Li, Hanmin Li, Siyuan Chen, Xin Gao

    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

    © Siyuan Chen 陈思远 | Last updated: Oct 2022
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