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, 2024 | paper

    2. Large Language Models in Biomedicine and Healthcare
      Juexiao Zhou, Haoyang Li, Siyuan Chen, Zhongyi Han, Xin Gao#
      bioarxiv, 2024 | 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: Aug 2024
    Thanks the template from YunheWang .