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Research

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Publications

Full list of publications at Google Scholar.

  1. Honkala, A. (2025). Python Encoders for Archetypal Convex Hulls (PEACH): PyTorch-Based Archetypal Analysis. bioRxiv, 2025-12.
  2. Honkala, A. (2025). Connecting Preclinical Models to Patient Outcomes: A Machine Learning Dataset for Predictive Validity in Drug Development. NeurIPS 2025 AI4Science Workshop (Abstract).
  3. Stefan, K., Gordon, R., Rolig, A., Honkala, A., Tailor, D., Davis, L. E., Modi, R. I., Joshipura, M., Khamar, B., & Malhotra, S. V. (2024). Mycobacterium w—a promising immunotherapeutic intervention for diseases. Frontiers in Immunology, 15, 1450118.
  4. Dheeraj, A., Garcia-Marques, F. J., Tailor, D., Bermudez, A., Resendez, A., Pandrala, M., Grau, B., Kumar, P., Haley, C. B., Honkala, A., ... & Malhotra, S. V. (2024). Inhibition of protein translational machinery in triple-negative breast cancer as a promising therapeutic strategy. Cell Reports Medicine, 5(5).
  5. Zhou, X., Shen, X., Johnson, J. S., Spakowicz, D. J., Agnello, M., Zhou, W., Avina, M., Honkala, A., Chleilat, F., Chen, S. J., ... & Snyder, M. P. (2024). Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host & Microbe, 32(4), 506–526.
  6. Tailor, D., Tsai, C. F., Honkala, A., Li, W., Liu, T., Pejovic, T., & Malhotra, S. V. (2022). Targeting mRNA processing pathways in ovarian cancer with a small molecule inhibitor. Cancer Research, 82(12_Supplement), 2645–2645.
  7. Honkala, A., Malhotra, S. V., Kummar, S., & Junttila, M. R. (2022). Harnessing the predictive power of preclinical models for oncology drug development. Nature Reviews Drug Discovery, 21(2), 99–114.
  8. Honkala, A., & Snyder, M. (2022). Monitoring Health Through Wearables and Connected Devices. Journal of The Society of Instrument and Control Engineers, 61(8), 572–577.
  9. Honkala, A., Smith, B., Margulis, K., & Zare, R. (2022). Myeloid cell-targeted nanoparticles and related compositions and methods. US Patent App. 17/783,939.
  10. Alavi, A., Bogu, G. K., Wang, M., Rangan, E. S., Brooks, A. W., Wang, Q., Honkala, A., ... & Snyder, M. P. (2022). Real-time alerting system for COVID-19 and other stress events using wearable data. Nature Medicine, 28(1), 175–184.
  11. Tailor, D., Resendez, A., Garcia-Marques, F. J., Pandrala, M., Going, C. C., Bermudez, A., Honkala, A., ... & Malhotra, S. V. (2021). Y box binding protein 1 inhibition as a targeted therapy for ovarian cancer. Cell Chemical Biology, 28(8), 1206–1220.
  12. Keating, B. J., Mukhtar, E. H., Elftmann, E. D., Eweje, F. R., Gao, H., Ibrahim, L. I., Honkala, A., ... & Snyder, M. P. (2021). Early detection of SARS-CoV-2 and other infections in solid organ transplant recipients and household members using wearable devices. Transplant International, 34(6), 1019–1031.
  13. Li-Pook-Than, J., Banuelos, S., Honkala, A., Sahoo, M. K., Pinsky, B. A., & Snyder, M. P. (2021). Long-read sequencing of SARS-CoV-2 reveals novel transcripts and a diverse complex transcriptome landscape. bioRxiv.
  14. Si, P., Honkala, A., de la Zerda, A., & Smith, B. R. (2020). Optical Microscopy and Coherence Tomography of Cancer in Living Subjects. Trends in Cancer, 6(3), 205–222.
  15. Margulis, K., Honkala, A., Kalashnikova, I., Noll, S. E., Hill, M., Zare, R. N., & Smith, B. R. (2020). Nanoparticles decorated with granulocyte-colony stimulating factor for targeting myeloid cells. Nanoscale, 12(4), 2752–2763.
  16. Honkala, A. T., Tailor, D., & Malhotra, S. V. (2020). Guanylate-Binding Protein 1: An Emerging Target in Inflammation and Cancer. Frontiers in Immunology, 10, 3139.
  17. Owyong, M., Hosseini-Nassab, N., Efe, G., Honkala, A., van den Bijgaart, R. J. E., Plaks, V., & Smith, B. R. (2017). Cancer immunotherapy getting brainy: visualizing the distinctive CNS metastatic niche to illuminate therapeutic resistance. Drug Resistance Updates, 33, 23–35.
  18. Eaton, K. A., Honkala, A., Auchtung, T. A., & Britton, R. A. (2011). Probiotic Lactobacillus reuteri ameliorates disease due to enterohemorrhagic Escherichia coli in germfree mice. Infection and Immunity, 79(1), 185–191.