All Stories

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

    Article • February 2026, openRxiv

    Anjun Ma

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

    Article • February 2026, openRxiv

    Anjun Ma

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

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

    Anjun Ma

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

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

    Anjun Ma

  5. 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

  6. 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

  7. 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

  8. 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

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

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

    Anjun Ma

  10. 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

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

    Article • January 2025, Springer Science + Business Media

    Anjun Ma

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

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

    Anjun Ma

  13. 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

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

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

    Anjun Ma

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

    Article • February 2024, Springer Science + Business Media

    Anjun Ma

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

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

    Anjun Ma

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

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

    Anjun Ma

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

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

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

    Anjun Ma

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

    Article • September 2023, openRxiv

    Anjun Ma

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

    Article • August 2023, openRxiv

    Anjun Ma

  44. Computational methods and challenges in analyzing intratumoral microbiome data

    Article • Trends in Microbiology, July 2023, Elsevier

    Anjun Ma

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

    Article • May 2023, openRxiv

    Anjun Ma

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

    Article • April 2023, openRxiv

    Anjun Ma

  47. 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

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

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

    Dr. Yang Li, Anjun Ma

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

    Article • Advanced Science, February 2023, Wiley

    Anjun Ma

  50. 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

  51. 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

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

    Article • December 2022, openRxiv

    Anjun Ma

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

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

    Anjun Ma

  54. 943 Harnessing anti-tumor metabolic sensing switch GPR84 on macrophages for cancer immunotherapy

    Article • November 2022, BMJ

    Anjun Ma

  55. 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

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

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

    Anjun Ma

  57. 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

  58. 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

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

    Article • July 2022, Springer Science + Business Media

    Anjun Ma

  60. 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

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

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

    Dr. Yang Li, Anjun Ma

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

    Article • Clinical and Translational Medicine, July 2022, Wiley

    Anjun Ma

  63. 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

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

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

    Anjun Ma

  65. 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

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

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

    Anjun Ma

  67. 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

  68. 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

  69. 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

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

    Article • September 2021, openRxiv

    Anjun Ma

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

    Article • Expert Systems with Applications, August 2021, Elsevier

    Anjun Ma

  72. 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

  73. 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

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

    Article • Trends in Genetics, December 2020, Elsevier

    Dr. Yang Li, Anjun Ma

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

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

    Anjun Ma

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

    Article • Trends in Pharmacological Sciences, December 2020, Elsevier

    Anjun Ma

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

    Article • Trends in Biotechnology, September 2020, Elsevier

    Anjun Ma

  78. 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

  79. 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

  80. 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

  81. 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

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

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

    Anjun Ma

  83. 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

  84. 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

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

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

    Anjun Ma

  86. 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

  87. 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

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

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

    Anjun Ma

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

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

    Anjun Ma

  90. 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

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

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

    Anjun Ma

  92. 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

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

    Article • Genes, May 2018, MDPI AG

    Anjun Ma

  94. 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

  95. 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