Publications

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  1. Liu, Z., Couetil, J., Sudha, P., Becker, N., Walker, B.A., Huang, K., Zhang, J., Johnson, T.S. (2025). Optimal transport enabled deep transfer learning reveals subtypes of myeloma cells that are associated with short term sham treatment response and high-risk of progression. In preparation
  2. Lazaro, O.*, Li, S.*, Carter, W., Robertson, S., Hickey, B.E., Angus, S.P., House, A., Clapp, W., Qadir, A.S.#, Johnson, T.S.#, Rhodes, S.D.# (2025). A novel induced pluripotent stem cell model of schwann cell differentiation reveals NF2-related gene regulatory networks of the extracellular matrix. Frontiers in Cellular Neuroscience. Under Review
  3. Couetil, J.L., Liu, Z., Alomari, A.K., Zhang, J., Huang, K., Johnson, T.S. (2025). Diagnostic Evidence Gauge of Spatial Transcriptomics (DEGAS): Using transfer learning to map clinical data to spatial transcriptomics in prostate cancer. Genomics Proteomics and Bioinformatics. In Revision (R1)
  4. Li, S., Liu, J., Peyton, M., Lazaro, O., Huang, X., Shi, Z., Zhang, Z., Walker, B.A., Johnson, T.S. (2025) Multiple Myeloma Insights from Single-Cell Analysis: Clonal Evolution, the Microenvironment, Therapy Evasion, and Clinical Implications. Cancers.
  5. Huang, X., Jannu, A.J., Song, Z., Jury-Garfe, N., Lasagna-Reeves, C.A., Alzheimer’s Disease Neuroimaging Initiative, Johnson, T.S., Huang, K., Zhang, J. (2025). Predicting Alzheimer’s disease subtypes and understanding their molecular characteristics in living patients with transcriptomic trajectory profiling. Alzheimer’s and Dementia. 2024;e14241
  6. Roy, G., Syed, R., Lazaro, O., Robertson, S., McCabe, S.D., Rodriguez, D., Mawla, A.M., Johnson, T.S.*, Kalwat, M.A.* (2024) Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learning. eLife. Reviewed Preprint
  7. Yang, X.*, Chatterjee, D.*, Couetil, J., Ardon, V., Zhang, J., Huang, K., Johnson, T. (2024). Gradient boosting reveals spatially diverse cholesterol gene signatures in colon cancer. Frontiers in Genetics.
  8. Jury-Garfe, N., Redding-Ochoa, J., You, Y., Martínez, P., Karahan, H., Chimal-Juárez, E., Johnson, T.S., Zhang, J., Resnick, S., Kim, J., Troncoso, J., Lasagna-Reeves, C. A. (2024). Enhanced microglial dynamics and a paucity of tau seeding in the amyloid plaque microenvironment contribute to cognitive resilience in Alzheimer’s disease. Acta Neuropathologica, 148(1), 15.
  9. Johnson, T.S., Sudha, P., Liu, E., Becker, N., Robertson, S., Blaney, P., Morgan, G., Chopra, V., Dos Santos, C., Nixon, M., Huang, K., Suvannasankha, A., Abu Zaid, M., Abonour, R., Walker, B. (2024). 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma. Nature Communications, 15(1), 4144.
  10. Basu, R., Elmendorf, A. J., Lorentz, B., Mahler, C. A., Lazzaro, O., App, B., Zhou, S., Yamamoto, Y., Suber, M., Wann, J.C., Cheol Roh, H., Sheets, P.L., Johnson, T.S., Flak, J. N. (2024). Ventromedial hypothalamic nucleus subset stimulates tissue thermogenesis via preoptic area outputs.Molecular Metabolism, 84, 101951.
  11.  Obarorakpor, N., Patel, D., Boyarov, R., Amarsaikhan, N., Cepeda, J.R., Eastes, D., Robertson, S., Johnson, T., Yang, K., Tang, Q. and Zhang, L. (2023). Regulatory T cells targeting a pathogenic MHC class II: Insulin peptide epitope postpone spontaneous autoimmune diabetes.Frontiers in Immunology, 14, p.1207108.
  12. Lin, L., Basu, R., Chatterjee, D., Templin, A.T., Flak, J., Johnson, T.S. (2023). Disease Associated Astrocyte and Microglia Markers are Dysregulated in Mice Fed High Fat Diet. Scientific Reports. 13, 12919
  13. Johnson, T., Steere, B., Zhang, P., Zang, Y., Higgs, R., Milch, C., Reinisch, W., Panés, J., Huang, K., D’Haens, G., Krishnan, V. (2023). Mirikizumab-induced transcriptome changes in ulcerative colitis patient biopsies at week 12 are maintained through week 52. Clinical and Translational Gastroenterology (CTG).
  14. Jafari, E., Johnson, T., Wang, Y., Liu, Y., Huang, K. and Wang, Y. (2022). AIscEA: Unsupervised Integration of Single-cell Gene Expression and Chromatin Accessibility via Their Biological Consistency. Bioinformatics. 38(23), 5236-5244.
  15. Alsaleh, L., Li, C., Couetil, J., Ye, Z., Huang, K., Zhang, J., Chen, C., Johnson, T.S. (2022). Spatial Transcriptomic Analysis Reveals Transcriptomic and Cellular Topology Associations in Breast and Prostate Cancers. 14(19), 4856.
  16. Liu, Y., Wang, T., Duggan, B., Huang, K., Zhang, J., Ye, X., Johnson, T.S. (2022). SPCS: A Spatial and Pattern Combined Smoothing Method for Spatial Transcriptomics Expression. Briefings in Bioinformatics.
  17. Sharpnack, M. F.*, Johnson, T. S.*, Chalkley, R., Han, Z., Carbone, D., Huang, K., He, K. (2022). TSAFinder: Exhaustive Tumor Specific Antigen Detection with RNAseq. Bioinformatics.
  18. Johnson, T. S., Christina, Y. Y., Huang, Z., Xu, S., Wang, T., Dong, C., … & Zhang, Y. (2022). Diagnostic Evidence GAuge of Single cells (DEGAS): A flexible deep-transfer learning framework for prioritizing cells in relation to disease. Genome Medicine, 14(1), 1-23.
  19. Lu, Z., Johnson, T.S., Shao, W., Zhang, M., Zhang, J., Huang, K. (2021). Optimal transport- and kernel-based early detection of mild cognitive impairment patients based on magnetic resonance and positron emission tomography images. Alzheimer’s Research & Therapy, 14(1), 1-12.
  20. Huang, X., Huang, K., Johnson, T., Radovich, M., Zhang, J., Ma, J., & Wang, Y. (2021). ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways. NAR Genomics and Bioinformatics, 3(4), lqab097.
  21. Xu, C., Sun, S., Johnson, T., Qi, R., Zhang, S., Zhang, J., & Yang, K. (2021). The glutathione peroxidase Gpx4 prevents lipid peroxidation and ferroptosis to sustain Treg cell activation and suppression of antitumor immunity. Cell Reports, 35(11), 109235.
  22. Awasthi, A., Tan, S., Johnson, T. S., Mo, X. M., Fan, K., Zhang, Y. (2021). PgenePapers: a novel database and search tools of reported regulatory pseudogenes. International Journal of Computational Biology and Drug Design, 13(5-6), 504-519.
  23. Johnson, T.*, Xiang, S.*, Dong, T., Huang, Z., Cheng, M., Wang, T., … & Zhang, J. (2020). Combinatorial analyses reveal that cellular composition changes have different impact on transcriptomic changes of cell type specific genes in Alzheimer’s Disease brains. Scientific Reports.
  24. Johnson, T. S., Xiang, S., Helm, B. R., Abrams, Z. B., Neidecker, P., Machiraju, R., Zhang, Y., … & Zhang, J. (2020). Spatial Cell Type Composition in Normal and Alzheimers Human Brains is Revealed Using Integrated Mouse and Human Single Cell RNA Sequencing. Scientific Reports. 10(1), 1-14.
  25. Sharpnack, M. F., Cho, J. H., Johnson, T. S., Otterson, G. A., Shields, P. G., Huang, K., … & He, K. (2020). Clinical and Molecular Correlates of Tumor Mutation Burden in Non-Small Cell Lung Cancer. Lung Cancer. 146, 36-41.
  26. Huang, Z., Johnson, T., Han, Z., Helm, B., Cao, S., Zhang, C., … Huang, K. (2020) Deep Learning-based Cancer Survival Prognosis from RNA-seq Data: Approaches and Evaluations. BMC Medical Genomics, 13(5), 1-12.
  27. Smerekanych, S.*, Johnson, T. S.*, Huang, K., Zhang, Y. (2020). Pseudogene-gene functional networks are prognostic of patient survival in breast cancer. BMC Medical Genomics. 13(5), 1-13.
  28. Mason, M. J., Schinke, C., Eng, C. L., Towfic, F., Gruber, F., Dervan, A., Multiple Myeloma DREAM Consortium, … & Cui, Y. (2020). Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Leukemia, 34(7), 1866-1874.
  29. Abrams, Z. B., Johnson, T. S., Huang, K., Payne, P. R., & Coombes, K. (2019). A protocol to evaluate RNA sequencing normalization methods. BMC bioinformatics, 20(24), 1-7.
  30. Wang, T., Johnson, T. S., Shao, W., Lu, Z., Helm, B. R., Zhang, J., & Huang, K. (2019). BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes. Genome biology, 20(1), 1-15.
  31. Johnson, T.S., Wang, T., Huang, Z., Yu, C.Y., Wu, Y., Han, Y., Zhang, Y., Huang, K., Zhang, J. (2019). LAmbDA: Label Ambiguous Domain Adaptation Dataset Integration Reduces Batch Effects and Improves Subtype Detection. Bioinformatics, 35(22), 4696-4706.
  32. Johnson, T.S., Li, S., Franz, E., Huang, Z., Li, S.D., Campbell, M.J., Huang, K., Zhang, Y. (2019). PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers. Gigascience, 8(5), giz046.
  33. Yu, C.Y., Xiang, S., Huang, Z., Johnson, T.S., Zhan, X., Han, Z., Huang, K. (2019). Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated with Multiple Myeloma Progression. Frontiers in genetics, 10,
  34. Huang, Z., Zhan, X., Xiang, S., Johnson, T.S., Helm, B., Yu, C.Y., Zhang, J., Salama, P., Rizkalla, M., Han, Z. and Huang, K. (2019). SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer. Frontiers in genetics, 10, 16.
  35. Wang, T., Johnson, T., Zhang, J., & Huang, K. (2018). Topological methods for visualization and analysis of high dimensional single-cell RNA sequencing data. In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2019: Proceedings of the Pacific Symposium(pp. 350-361).
  36. Johnson, T. S., Li, S., Kho, J. R., Huang, K., & Zhang, Y. (2018). Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials. In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018: Proceedings of the Pacific Symposium(pp. 536-547).
  37. Han, Z., Johnson, T., Zhang, J., Zhang, X., & Huang, K. (2017). Functional virtual flow cytometry: a visual analytic approach for characterizing single-cell gene expression patterns. BioMed research international, 2017.
  38. Johnson, T. S., Abrams, Z. B., Mo, X., Zhang, Y., & Huang, K. (2017). Lack of human cytomegalovirus expression in single cells from glioblastoma tumors and cell lines. Journal of neurovirology, 23(5), 671-678.
  39. Johnson, T., Liebner, D., & Chen, J. L. (2017). Opportunities for patient matching algorithms to improve patient care in oncology. JCO Clinical Cancer Informatics, 1.
  40. Johnson, T., Abrams, Z., Zhang, Y., & Huang, K. (2017). Mapping neuronal cell types using integrative multi-species modeling of human and mouse single cell RNA sequencing. In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017(pp. 599-610).