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Shumin Li

A researcher who is passionate about bioinformatics, AI for genomics and running.

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My Publications

You can also browse my Google Scholar profile.

Publications

First or co-first authored (*), Corresponding(^)

  • Li, S.*, Ma, J.*, Zhao, T., Jia, Y., Liu, B., Luo, R.^, & Huang, Y.^ (2024).
    CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning.
    [Patterns] [GitHub]

  • Su, J.*^, Li, S.*, Zheng, Z, Lam, T.W., Luo, R.^ (2024).
    ClusterV-Web: A User-Friendly Tool for Profiling HIV Quasispecies and Generating Drug Resistance Reports from Nanopore Long-Read Data.
    [Bioinformatics Advances] [Web Service] [GitHub]

  • Li, S.*, Yan, B.*, Li, T. K.*, Lu, J., Gu, Y., Tan, Y., ... & Luo, R.^ (2023).
    Ultra-low-coverage genome-wide association study—insights into gestational age using 17,844 embryo samples with preimplantation genetic testing
    Genome Medicine, 15(1), 10.
    [Genome Med.] [medRxiv]

  • Li, S.*, Yan, B.*, Wu, B.*, Su, J., Lu, J., Lam, T. W., ... & Luo, R.^ (2023).
    Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics
    Stem Cell Research & Therapy, 14(1), 247.
    [Stem Cell Res. Ther] [Web Service]

  • Zheng, Z.*, Li, S.*, Su, J.*, Leung, A. W. S., Lam, T. W., & Luo, R.^ (2022).
    Symphonizing pileup and full-alignment for deep learning-based long-read variant calling.
    Nature Computational Science, 2(12), 797-803.
    [NatComputSci] [bioRxiv] [GitHub]

  • Li, S.*, Chen, J., & Liu, B^. (2017).
    Protein remote homology detection based on bidirectional long short-term memory
    BMC Bioinformatics, 18(1), 1-8.
    [BMC Bioinform.]

  • Liu, B.^, & Li, S. (2018).
    ProtDet-CCH: protein remote homology detection by combining long short-term memory and ranking methods.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics , 16(4), 1203-1210.
    [TCBB]

  • Chen, J., Guo, M., Li, S., & Liu, B^. (2017).
    ProtDec-LTR2. 0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.
    Bioinformatics, 33(21), 3473-3476.
    [Bioinform.]

  • Liu, B.^, Wang, S., Dong, Q., Li, S., & Liu, X. (2016).
    Identification of DNA-binding proteins by combining auto-cross covariance transformation and ensemble learning.
    IEEE transactions on nanobioscience , 15(4), 328-334.
    [IEEE T NANOBIOSCI.]

Working papers

  • Li, S.^*, Chow, F.W., Chen, L., Su, J., Ahmed, S., Luo, R.^ (2023).
    MirtronStructDB: A Comprehensive Database of Mirtrons with Predicted Secondary Structures.
    [Web Service]

  • Zheng, Y.*, Ye, S.*, Li, S.*, Liu, C., Luo, S., Xia, R., ... & Yang, D^. (2022)
    A self-blinking DNA probe for 3D superresolution imaging of native chromatin.
    [bioRxiv]

Written Theses

  • Ph.D. thesis
    New methods for studying massive and complex biological data : from ultra-low depth sequence to high resolution structure
    University of Hong Kong, Department of Computer Science, 2022
    [HKU Scholar Hub]

  • M.Eng. thesis
    Protein Remote Homology Detection Based on Deep Learning
    Harbin Institute of Technology (Shenzhen), Department of Computer Science, 2017
    [CNKI]