Qin Ma

Research interests

Publications

• Single-cell biological network inference using a heterogeneous graph transformer

  Nature Communications · 2023 · 10.1038/s41467-023-36559-0

• A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

  Nature Neuroscience · 2022 · 10.1038/s41593-022-01104-7

• Androgen conspires with the CD8 + T cell exhaustion program and contributes to sex bias in cancer

  Science Immunology · 2022 · 10.1126/sciimmunol.abq2630

• Microglia coordinate cellular interactions during spinal cord repair in mice

  Nature Communications · 2022 · https://doi.org/10.1038/s41467-022-31797-0

• Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data

  Nature Communications · 2022 · 10.1038/s41467-022-34277-7

• scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

  Nature Communications · 2021 · https://doi.org/10.1038/s41467-021-22197-x

• A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

  Genome Research · 2021 · 10.1101/gr.271205.120

• Integrative Methods and Practical Challenges for Single-Cell Multi-omics

  Trends in biotechnology · 2020 · https://doi.org/10.1016/j.tibtech.2020.02.013

• Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier

  Computers in Biology and Medicine · 2020 · 10.1016/j.compbiomed.2020.103899

• Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources

  Metabolites · 2020 · 10.3390/metabo10050202

• Long-term high-P fertilizer input decreased the total bacterial diversity but not phoD-harboring bacteria in wheat rhizosphere soil with available-P deficiency

  Soil Biology and Biochemistry · 2020 · 10.1016/j.soilbio.2020.107918

• scREAD: A Single-Cell RNA-Seq Database for Alzheimer's Disease

  iScience · 2020 · 10.1016/j.isci.2020.101769

• Clustering and classification methods for single-cell RNA-sequencing data

  Briefings in Bioinformatics · 2019 · 10.1093/bib/bbz062

• LightGBM-PPI: Predicting protein-protein interactions through LightGBM with multi-information fusion

  Chemometrics and Intelligent Laboratory Systems · 2019 · https://doi.org/10.1016/j.chemolab.2019.06.003

• SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting

  Bioinformatics · 2019 · 10.1093/bioinformatics/btz734

• Transforming growth factor (TGF)-β1-induced miR-133a inhibits myofibroblast differentiation and pulmonary fibrosis

  Cell Death and Disease · 2019 · 10.1038/s41419-019-1873-x

• Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure

  Genomics · 2018 · 10.1016/j.ygeno.2018.12.007

• Interpretation of differential gene expression results of RNA-seq data: review and integration

  Briefings in Bioinformatics · 2018 · https://doi.org/10.1093/bib/bby067

• LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property

  Briefings in Bioinformatics · 2018 · 10.1093/bib/bby065

• Protein–protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique

  Bioinformatics · 2018 · 10.1093/bioinformatics/bty995

• Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

  Cell Research · 2015 · 10.1038/cr.2015.150

• DOOR 2.0: presenting operons and their functions through dynamic and integrated views

  Nucleic Acids Research · 2013 · 10.1093/nar/gkt1048

• QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

  Nucleic Acids Research · 2009 · 10.1093/nar/gkp491

Current projects

No projects listed.