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NCSTAR - Publications

2025-2026

  1. Spatial transcriptomics and histopathological analyses reveal potential biomarkers and immune features linked to recurrence in head and neck cancer. Nguyen Q, Weeramange CE, Chen Y, Nguyen KM, Zhang X, Hartel G, Causer A, Mulay O, Pavithra P, Lam PY, Gonzalez Cruz J. Frontiers in Immunology.;17:1713732. https://doi.org/10.3389/fimmu.2026.1713732
  2. SpaMTP: integrative statistical analysis and visualization of spatial metabolomics and transcriptomics data. Causer A, Lu T, Kriel J, Moffet JJ, Fitzgerald CC, Newman A, Vu H, Tan X, Vo T, Cui C, Narayana VK. Nature Methods. 2026 Jul 31:1-6. doi: 10.1038/s41592-026-03140-8. PMCID: PMC13441920  PMID: 42538468
  3. Performance of deep learning methods for spatial gene expression prediction from histology images: a comprehensive assessment. Xie J, Tan X, Jiang Y, Nguyen H, Ye N, Nguyen Q. Bioinformatics Advances. 2026 Jul 20:vbag202. DOI: 10.1093/bioadv/vbag202 PMID: 42564865 PMCID: PMC13445978
  4. SpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and time. Loo L, Xia K, Crosetto N, Bienko M, Xu C, Chen J, Reguant AP, Li C, Wang J, Wei X, Liu L. Nature Methods. 2026 Jul 9:1-5. DOI: 10.1038/s41592-026-03150-6. PMID: 42426405 
  5. Unraveling lncRNA diversity at a single cell resolution and in a spatial context across different cancer types. Prakrithi P, Vo T, Xiong Z, Vu H, Nguyen LT, Newman A, Wilhelmey J, Whitehall V, Cruz JL, Wood S, Mallett AJ. Nature Methods. 2026 May 14:1-4. doi: 10.1038/s41592-026-03071-4. PMCID: PMC13259954  PMID: 42135486
  6. Intra-and inter-organ communications in aging and cancer: Local and global spatial perspectives. Mulay O, Benedicto A, Murata Y, Ng MS, Cruz JL, Nguyen Q. . InSeminars in Cell & Developmental Biology 2026 May 1 (Vol. 179, p. 103672). Academic Press. DOI: 10.1016/j.semcdb.2026.103672 PMID: 41794017 
  7. Progressive fibrosis in human MASLD is associated with spatially linked transcriptomic signatures of metabolic reprogramming and senescence. Vu H, Sun Y, Xiong Z, Tan X, Radford-Smith D, Causer A, Dickens AM, Hyötyläinen T, Evstafev I, Oresic M, Nefzger C. JHEP Reports. 2026 Feb 1;8(2):101657. DOI: 10.1016/j.jhepr.2025.101657 PMID: 41541503 PMCID: PMC12800363
  8. Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data. Tan X, Mulay O, Xie J, MacDonald S, Kim T, Zhou C, Xiong Z, Tan SX, Ye N, McCart Reed A, Khosrotehrani K. Nature Communications. 2026 Jan 16;17(1):1781.  doi: 10.1038/s41467-026-68487-0. PMCID: PMC12917206  PMID: 41545411

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Other top publications

2019-2024
  1. Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues. Pham D, Tan X, Balderson B, Xu J, Grice LF, Yoon S, Willis EF, Tran M, Lam PY, Raghubar A, Kalita-de Croft P. Nature communications. 2023 Nov 25;14(1):7739. DOI: 10.1038/s41467-023-43120-6 PMID: 38007580 PMCID: PMC10676408
  2. A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Tran M, Yoon S, Teoh M, Andersen S, Lam PY, Purdue BW, Raghubar A, Hanson SJ, Devitt K, Jones K, Walters S. Frontiers in immunology. 2022 Jul 29;13:911873. DOI: 10.3389/fimmu.2022.911873 PMID: 35967449 PMCID: PMC9373800
  3. A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images. Su A, Lee H, Tan X, Suarez CJ, Andor N, Nguyen Q, Ji HP. NPJ precision oncology. 2022 Mar 2;6(1):14. DOI: 10.1038/s41698-022-00252-0 PMID: 35236916  PMCID: PMC8891271
  4.  SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells. Tan X, Su A, Tran M, Nguyen Q. Bioinformatics. 2020 Apr 1;36(7):2293-4. DOI: 10.1093/bioinformatics/btz914 PMID: 31808789 
Top contributed publications
  1. VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population. Tran TT, Hoang TH, Tran MH, Pham TM, Nguyen NN, Vu GM, Duong VC, Vu QT, Nguyen NT, Vu HQ, Nguyen TM. Nature Communications. 2026 Jul 22;17(1):6679. DOI: 10.1038/s41467-026-75375-0 PMID: 42486871 PMCID: PMC13392358
  2.  CD8+ T cells sustain vaccination-induced immunity against dissemination of contained tuberculosis in immunosuppressed hosts. Miranda-Hernandez S, Kumar M, Henderson A, Graham E, Tan X, Taylor J, Meehan MT, Ceja Z, del Pozo-Ramos L, Pan Y, Tsui E. . Nature Communications. 2026 Mar 24;17(1):4476.DOI: 10.1038/s41467-026-70911-4 PMID: 41876499 PMCID: PMC13187035
  3. Genetic Ablation and Multi‐Omics Profiling Reveal CEP55 as a Key Driver of Tumorigenesis in Diverse Cancer Models. Rashidieh B, Yang Y, Bain AL, Theron P, Vosloo C, Keshvari S, Ahangar P, Bowden B, Tria SM, Wang BB, Isenmann S. Advanced Science. 2025 Nov 28:e76782. DOI: 10.1002/advs.76782 PMID: 42573585  PMCID: PMC13455837
  4. BRRIAR lncRNA alters breast cancer risk by modulating interferon signaling in cis and in trans. Sivakumaran H, Nair S, Bitar M, Lu X, Wang L, Liu J, Karunarathne DS, Prakrithi P, Jacquelin S, Rivera IS, Hillman KM. . Molecular Cancer. 2026 Jan 7;25(1):5. DOI: 10.1186/s12943-025-02510-8
    PMID: 41501810  PMCID: PMC12777463
  5. Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor-associated SPP1+ macrophages and fibroblasts. Sathe A, Mason K, Grimes SM, Zhou Z, Lau BT, Bai X, Su A, Tan X, Lee H, Suarez CJ, Nguyen Q. Clinical Cancer Research. 2023 Jan 4;29(1):244-60. DOI: 10.1158/1078-0432.CCR-22-2041 PMID: 36239989  PMCID: PMC9811165
  6. Understanding heterogeneity in the pathogenesis and drug responses of ulcerative colitis through single-cell and spatial transcriptomics. Phillips J, Tambakis G, Kumar R, Croft A, Brown I, Rosty C, Anderson R, Belz G, Oliver AJ, Xiong A, Nguyen Q. Frontiers in Immunology. 2026 Mar 31;17:1794207. DOI: 10.3389/fimmu.2026.1794207 PMID: 41988199 PMCID: PMC13076525