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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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

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: Mar 2023
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