All Stories

  1. A cross model single-cell atlas reveals conserved involvement of osteopontin in polycystic kidney disease

    Article • JCI Insight, July 2026, American Society for Clinical Investigation

    Anjun Ma

  2. GARP+ Erythroid Regulatory Cells (G-ERCs) define spatially organized immunosuppressive niches that restrain anti-tumor immunity 2259805

    Article • The Journal of Immunology, July 2026, Oxford University Press (OUP)

    Anjun Ma

  3. An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid

    Article • July 2026, openRxiv

    Anjun Ma

  4. SpaFlow depicts the dynamics of ligand-receptor interaction in spatial transcriptomics data

    Article • April 2026, openRxiv

    Anjun Ma

  5. ZFP148 is a transcriptional repressor of cytolytic effector CD8+ T cell differentiation

    Article • Nature Immunology, March 2026, Springer Science + Business Media

    Anjun Ma

  6. A multi-agent platform for assessment and improvement of bioinformatics software documentation

    Article • February 2026, openRxiv

    Anjun Ma

  7. Transcriptomics-based modeling of methionine metabolism effectively estimates sample-wise DNA methylation activity and epigenetic aging

    Article • February 2026, openRxiv

    Anjun Ma

  8. Harnessing the power of single-cell large language models with parameter-efficient fine-tuning using scPEFT

    Article • Nature Machine Intelligence, December 2025, Springer Science + Business Media

    Anjun Ma

  9. Epigenetic Modulation, Intratumoral Microbiome, and Immunity in Early-Onset Colorectal Cancer

    Article • Cancer Research Communications, November 2025, American Association for Cancer Research (AACR)

    Anjun Ma

  10. Heightened protein synthesis and aggregation, coupled with futile protein quality control, underlie a novel mechanism of CD8+ T cell exhaustion 3479

    Article • The Journal of Immunology, November 2025, Oxford University Press (OUP)

    Anjun Ma

  11. ZFP148 is a transcriptional checkpoint for effector CD8+ T cell differentiation 3939

    Article • The Journal of Immunology, November 2025, Oxford University Press (OUP)

    Anjun Ma

  12. Proteotoxic stress response drives T cell exhaustion and immune evasion

    Article • Nature, October 2025, Springer Science + Business Media

    Anjun Ma

  13. Ad hoc, post hoc and intrinsic-hoc in bioinformatics

    Article • Nature Biotechnology, October 2025, Springer Science + Business Media

    Anjun Ma

  14. Advancing biological understanding of cellular senescence with computational multiomics

    Article • Nature Genetics, September 2025, Springer Science + Business Media

    Dr Paul Robson, Anjun Ma

  15. Data from Tumor-associated NK Cells Regulate Distinct CD8<sup>+</sup> T-cell Differentiation Program in Cancer and Contribute to Resistance against Immune Checkpoint Blockers

    Article • September 2025, American Association for Cancer Research (AACR)

    Anjun Ma

  16. Supplementary Figures S1-S16 from Tumor-associated NK Cells Regulate Distinct CD8<sup>+</sup> T-cell Differentiation Program in Cancer and Contribute to Resistance against Immune Checkpoint Blockers

    Article • September 2025, American Association for Cancer Research (AACR)

    Anjun Ma

  17. Supplementary Tables S1-S4 from Tumor-associated NK Cells Regulate Distinct CD8<sup>+</sup> T-cell Differentiation Program in Cancer and Contribute to Resistance against Immune Checkpoint Blockers

    Article • September 2025, American Association for Cancer Research (AACR)

    Anjun Ma

  18. The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes

    Article • Nature Chemical Biology, September 2025, Springer Science + Business Media

    Anjun Ma

  19. Analysis of head and neck cancer scRNA-seq data identified PRDM6 promotes tumor progression by modulating immune gene expression

    Article • Frontiers in Immunology, August 2025, Frontiers

    Anjun Ma

  20. TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues

    Article • Nature Communications, August 2025, Springer Science + Business Media

    Anjun Ma

  21. O-GlcNAc transferase plays dual antiviral roles by integrating innate immunity and lipid metabolism

    Article • Nature Communications, August 2025, Springer Science + Business Media

    Anjun Ma

  22. Characterizing Cellular Heterogeneity and Transcriptomic Features of Senotype Using Deep Graph Representation Learning

    Article • July 2025, openRxiv

    Anjun Ma

  23. Tumor-associated NK Cells Regulate Distinct CD8+ T-cell Differentiation Program in Cancer and Contribute to Resistance against Immune Checkpoint Blockers

    Article • Cancer Discovery, June 2025, American Association for Cancer Research (AACR)

    Anjun Ma

  24. TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues

    Article • January 2025, Springer Science + Business Media

    Anjun Ma

  25. 934 ZFP148 represses effector differentiation and cytotoxicity of CD8+ T cells during chronic viral infection and cancer

    Article • November 2024, BMJ

    Anjun Ma

  26. Graph Fourier transform for spatial omics representation and analyses of complex organs

    Article • Nature Communications, August 2024, Springer Science + Business Media

    Anjun Ma

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

    Article • Briefings in Bioinformatics, July 2024, Oxford University Press (OUP)

    Anjun Ma

  28. A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)

    Article • Nature Communications, June 2024, Springer Science + Business Media

    Anjun Ma

  29. Graph Fourier transform for spatial omics representation and analyses of complex organs

    Article • February 2024, Springer Science + Business Media

    Anjun Ma

  30. Data from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  31. Data from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  32. FIGURE 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  33. FIGURE 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  34. FIGURE 2 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  35. FIGURE 2 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  36. FIGURE 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  37. FIGURE 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  38. Supplementary Figure 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  39. Supplementary Figure 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  40. Supplementary Table 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  41. Supplementary Table 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  42. Supplementary Table 2 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  43. Supplementary Table 2 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  44. Supplementary Table 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  45. Supplementary Table 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  46. Supplementary Table 4 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  47. Supplementary Table 4 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  48. Supplementary Table 5 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  49. Supplementary Table 5 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  50. Supplementary Table 6 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  51. Supplementary Table 6 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  52. Supplementary Table 7 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  53. Supplementary Table 7 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  54. A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

    Article • Cancer Research Communications, February 2024, American Association for Cancer Research (AACR)

    Anjun Ma

  55. MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer

    Article • Nature Communications, January 2024, Springer Science + Business Media

    Anjun Ma

  56. A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)

    Article • September 2023, openRxiv

    Anjun Ma

  57. MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer

    Article • August 2023, openRxiv

    Anjun Ma

  58. Computational methods and challenges in analyzing intratumoral microbiome data

    Article • Trends in Microbiology, July 2023, Elsevier

    Anjun Ma

  59. A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset

    Article • May 2023, openRxiv

    Anjun Ma

  60. An explainable graph neural framework to identify cancer-associated intratumoral microbial communities

    Article • April 2023, openRxiv

    Anjun Ma

  61. 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

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

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

    Dr. Yang Li, Anjun Ma

  63. Explainable Deep Hypergraph Learning Modeling the Peptide Secondary Structure Prediction

    Article • Advanced Science, February 2023, Wiley

    Anjun Ma

  64. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

    Article • Nature Aging, December 2022, Springer Science + Business Media

    Dr Paul Robson, Anjun Ma

  65. 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

  66. Spatial omics representation and functional tissue module inference using graph Fourier transform

    Article • December 2022, openRxiv

    Anjun Ma

  67. Machine learning development environment for single-cell sequencing data analyses

    Article • December 2022, Institute of Electrical & Electronics Engineers (IEEE)

    Anjun Ma

  68. 943 Harnessing anti-tumor metabolic sensing switch GPR84 on macrophages for cancer immunotherapy

    Article • November 2022, BMJ

    Anjun Ma

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

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

    Anjun Ma

  70. SUSD2 suppresses CD8+ T cell antitumor immunity by targeting IL-2 receptor signaling

    Article • Nature Immunology, October 2022, Springer Science + Business Media

    Anjun Ma

  71. 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

  72. MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data

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

    Anjun Ma

  73. Single Cell RNA sequencing (scRNAseq) of fresh human lung cell suspension v1

    Article • July 2022, Springer Science + Business Media

    Anjun Ma

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

    Article • Science Immunology, July 2022, American Association for the Advancement of Science

    Anjun Ma

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

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

    Dr. Yang Li, Anjun Ma

  76. Deep learning analysis of single‐cell data in empowering clinical implementation

    Article • Clinical and Translational Medicine, July 2022, Wiley

    Anjun Ma

  77. Biological aging of CNS-resident cells alters the clinical course and immunopathology of autoimmune demyelinating disease

    Article • JCI Insight, June 2022, American Society for Clinical Investigation

    Anjun Ma

  78. The use of single-cell multi-omics in immuno-oncology

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

    Anjun Ma

  79. Author Correction: scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

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

    Anjun Ma

  80. Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology

    Article • Journal of Hematology & Oncology, January 2022, Springer Science + Business Media

    Anjun Ma

  81. DESSO-DB: A web database for sequence and shape motif analyses and identification

    Article • Computational and Structural Biotechnology Journal, January 2022, American Association for the Advancement of Science

    Anjun Ma

  82. Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning

    Article • Computational and Structural Biotechnology Journal, January 2022, American Association for the Advancement of Science

    Anjun Ma

  83. Assessing deep learning methods in cis -regulatory motif finding based on genomic sequencing data

    Article • Briefings in Bioinformatics, October 2021, Oxford University Press (OUP)

    Anjun Ma

  84. Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data

    Article • September 2021, openRxiv

    Anjun Ma

  85. Prediction of protein–protein interactions based on elastic net and deep forest

    Article • Expert Systems with Applications, August 2021, Elsevier

    Anjun Ma

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

    Article • Nature Communications, March 2021, Springer Science + Business Media

    Anjun Ma

  87. scGMAI: a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder

    Article • Briefings in Bioinformatics, December 2020, Oxford University Press (OUP)

    Anjun Ma

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

    Article • Trends in Genetics, December 2020, Elsevier

    Dr. Yang Li, Anjun Ma

  89. DeepMal: Accurate prediction of protein malonylation sites by deep neural networks

    Article • Chemometrics and Intelligent Laboratory Systems, December 2020, Elsevier

    Anjun Ma

  90. Single-Cell Techniques and Deep Learning in Predicting Drug Response

    Article • Trends in Pharmacological Sciences, December 2020, Elsevier

    Anjun Ma

  91. Integrative Methods and Practical Challenges for Single-Cell Multi-omics

    Article • Trends in Biotechnology, September 2020, Elsevier

    Anjun Ma

  92. 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

  93. IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq

    Article • Nucleic Acids Research, May 2020, Oxford University Press (OUP)

    Anjun Ma

  94. WFhb1-1 plays an important role in resistance against Fusarium head blight in wheat

    Article • Scientific Reports, May 2020, Springer Science + Business Media

    Anjun Ma

  95. DNNAce: Prediction of prokaryote lysine acetylation sites through deep neural networks with multi-information fusion

    Article • Chemometrics and Intelligent Laboratory Systems, May 2020, Elsevier

    Anjun Ma

  96. Network analyses in microbiome based on high-throughput multi-omics data

    Article • Briefings in Bioinformatics, February 2020, Oxford University Press (OUP)

    Anjun Ma

  97. Inductive inference of gene regulatory network using supervised and semi-supervised graph neural networks

    Article • Computational and Structural Biotechnology Journal, January 2020, American Association for the Advancement of Science

    Anjun Ma

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

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

    Anjun Ma

  99. MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome

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

    Anjun Ma

  100. QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data

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

    Anjun Ma

  101. 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

  102. Clustering and classification methods for single-cell RNA-sequencing data

    Article • Briefings in Bioinformatics, July 2019, Oxford University Press (OUP)

    Anjun Ma

  103. MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome

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

    Anjun Ma

  104. The Genetics and Genome-Wide Screening of Regrowth Loci, a Key Component of Perennialism in Zea diploperennis

    Article • G3 Genes Genomes Genetics, May 2019, Oxford University Press (OUP)

    Anjun Ma

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

    Article • Bioinformatics, December 2018, Oxford University Press (OUP)

    Anjun Ma

  106. A Central Edge Selection Based Overlapping Community Detection Algorithm for the Detection of Overlapping Structures in Protein–Protein Interaction Networks

    Article • Molecules, October 2018, MDPI AG

    Anjun Ma

  107. RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis

    Article • Genes, May 2018, MDPI AG

    Anjun Ma

  108. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data

    Article • Briefings in Bioinformatics, February 2018, Oxford University Press (OUP)

    Anjun Ma

  109. A Review of Matched-pairs Feature Selection Methods for Gene Expression Data Analysis

    Article • Computational and Structural Biotechnology Journal, January 2018, American Association for the Advancement of Science

    Anjun Ma