My Publications

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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]