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  1. Human iPSC-based model of COPD to investigate disease mechanisms, predict SARS-COV-2 outcome and test preventive immunotherapy

    Article • Stem Cells, January 2024, Oxford University Press (OUP)

    Dr. Yang Li

  2. CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq

    Article • Briefings in Bioinformatics, November 2023, Oxford University Press (OUP)

    Dr. Yang Li

  3. CD200R signaling contributes to unfavorable tumor microenvironment through regulating production of chemokines by tumor-associated myeloid cells

    Article • iScience, June 2023, Elsevier

    Dr. Yang Li

  4. CEMIG: Prediction of thecis-regulatory motif using the De Bruijn graph from ATAC-seq

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Dr. Yang Li

  5. A Weighted Two-stage Sequence Alignment Framework to Identify DNA Motifs from ChIP-exo Data

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr. Yang Li, Anjun Ma

  6. Single-cell biological network inference using a heterogeneous graph transformer

    Article • Nature Communications, February 2023, Springer Science + Business Media

    Dr. Yang Li, Anjun Ma

  7. Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease

    Article • Acta Neuropathologica Communications, December 2022, Springer Science + Business Media

    Dr. Yang Li

  8. Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Dr. Yang Li, Anjun Ma

  9. scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data

    Article • Bioinformatics, October 2022, Oxford University Press (OUP)

    Dr. Yang Li, Anjun Ma

  10. Microglia coordinate cellular interactions during spinal cord repair in mice

    Article • Nature Communications, July 2022, Springer Science + Business Media

    Dr. Yang Li, Anjun Ma

  11. Elucidation of Biological Networks across Complex Diseases Using Single-Cell Omics

    Article • Trends in Genetics, December 2020, Elsevier

    Dr. Yang Li, Anjun Ma

  12. Abstract 4409: Towards cell-type-specific gene regulation in heterogeneous cancer cells

    Article • Cancer Research, August 2020, American Association for Cancer Research (AACR)

    Dr. Yang Li, Anjun Ma

  13. Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites

    Article • Biochemical and Biophysical Research Communications, November 2019, Elsevier

    Dr. Yang Li

  14. Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework

    Article • Nucleic Acids Research, August 2019, Oxford University Press (OUP)

    Dr. Yang Li, Anjun Ma

  15. ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery

    Article • Bioinformatics, May 2019, Oxford University Press (OUP)

    Dr. Yang Li

  16. MiMod: A New Algorithm for Mining Biological Network Modules

    Article • IEEE Access, January 2019, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Yang Li

  17. Identification of lncRNAs-gene interactions in transcription regulation based on co-expression analysis of RNA-seq data

    Article • Mathematical Biosciences and Engineering, January 2019, American Institute of Mathematical Sciences (AIMS)

    Dr. Yang Li

  18. Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples

    Article • Advanced Science, December 2018, Wiley

    Dr. Yang Li

  19. Block-based characterization of protease specificity from substrate sequence profile

    Article • BMC Bioinformatics, October 2017, Springer Science + Business Media

    Dr. Yang Li

  20. Identification of driver modules in pan-cancer via coordinating coverage and exclusivity

    Article • Oncotarget, March 2017, Impact Journals, LLC

    Dr. Yang Li

  21. An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data

    Article • Briefings in Bioinformatics, March 2017, Oxford University Press (OUP)

    Dr. Yang Li