Research Interests:
Biochemical Image Analysis.
3D Genomics Analysis and its implications for evolution, health, and disease.
Deep-Learning in Genomics .
Publications
Journal(* equal contribution)
- 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
- Deep learning identifies and quantifies recombination hotspot determinants
Yu Li*, Siyuan Chen*, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao
Bioinformatics , 2022 | paper
- 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
- 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
- Protein-RNA interaction prediction with deep learning: Structure matters
Junkang Wei*, Siyuan Chen*, Licheng Zong*, Xin Gao, Yu Li
Briefing in Bioinformatics, 2021 | paper
- 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)
- 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
- 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
- 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
- Jan 2022 - Present,   Ph.D. candidate in Computer Science,   King Abdullah University of Science and Technology, Saudi Arabia
- Aug 2020 - Dec 2021,   M.S. in Computer Science,   King Abdullah University of Science and Technology, Saudi Arabia
- Sept 2016 - Jun 2020,   B.E. in Engineering,   University of Electronic Science and Technology of China, China
- Sept 2016 - Jun 2020,   B.E. in Finance,   University of Electronic Science and Technology of China, China
Experiences
- Sep 2023 - Nov 2023   Teaching Assistant (CS220-Data Analytics)   Ministry of Interior (MOI) Riyadh, Saudi Arabia
- May 2023   Teaching Assistant (DSA009-Data Analytics)   Saudi Aramco Dammam, Saudi Arabia
- Jan 2023   Administrator,  The 21st International Conference on Bioinformatics (InCoB2022) KAUST, Saudi Arabia
- Jul 2022 - Sep 2022,   Visiting Scholar,   The Chinese University of Hong Kong, Hong Kong, China
© Siyuan Chen 陈思远 | Last updated: May 2023 Template from
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