1. Bryan Wang, Bharat Kanwar, Annie C. Bowles-Welch, Walker Byrnes, Paloma Casteleiro Costa, Caroline Filan, Reginald Tran, Theresa Kotanchek, Francisco Robles, Krishnendu Roy, Stephen Balakirsky, Automated Vertical Wheel Bioreactor Integrated with Process Analytics for T Cell Manufacturing, Cytotherapy, 2025, doi: 10.1016/j.jcyt.2025.08.007.
  2. Rebecca S. Schneider, Elisa B. Nieves, Bhavay Aggarwal, Annie C. Bowles-Welch, Hazel Y. Stevens, Linda E. Kippner, Scott D. Boden, Kenneth Mautner, Hicham Drissi, Krishnendu Roy, Wilbur A. Lam, Saurabh Sinha, Andrés J. García On-chip 3D potency assay for improved prediction of clinical outcomes for cell therapy candidates for osteoarthritis. Nat. Comm. 2025  
  3. Chatterjee P, Stevens HY, Kippner LE, Bowles-Welch AC, Drissi H, Mautner K, Yeago C, Gibson G, Roy K. Single-cell Transcriptome and Crosstalk Analysis Reveals Immune Alterations and Key Pathways in the Bone Marrow of Knee Osteoarthritis Patients. iScience 2024 110827
  4. Wang B, Chen RQ, Roy K. Interfacing data science with cell therapy manufacturing; where we are and where we need to be. Cytotherapy 2024
  5. Liu Z, Wang B, Kanwar B, Wang K, Bowles-Welch A, Balakirsky S, Roy K, ZhangC. An in-situ localized cell density monitoring method for adherent cells in hollow fiber bioreactors. Sensors and Actuators B: Chemical, Volume 407, 2024, 135467, ISSN 0925-4005,
  6. Stevens, H. Y., Jimenez, A. C., Wang, B., Li, Y., Selvam, S. and Bowles-Welch, A. C. (2024). Mesenchymal Stromal Cell (MSC) Functional Analysis—Macrophage Activation and Polarization Assays. Bio-protocol 14(6): e4957. DOI: 10.21769/BioProtoc.4957.
  7. Li Y, Stevens HY, Sivaraman S, Porter LN, Hoffman AR, Gibb SL, Selvam S, Bowles-Welch AC. Streamlined Methods for Processing and Cryopreservation of Cell Therapy Products Using Automated Systems. Bio-protocol 2023 Dec 20;13(24):e4900. doi: 10.21769/BioProtoc.4900. PMID: 38156031; PMCID: PMC10751237.
  8. Chen RQ, Joffe B, Casteleiro Costa P, Filan C, Wang B, Balakirsky S, Robles F, Roy K, Li J. Real-time semantic segmentation and anomaly detection of functional images for cell therapy manufacturing. Cytotherapy, Volume 25, Issue 12, 2023, Pages 1361-1369, ISSN 1465-3249,
  9. Mautner K, Gottschalk M, Boden SD, Akard A, Bae WC, Black L, Boggess B, Chatterjee P, Chung CB, Easley KA, Gibson G, Hackel J, Jensen K, Kippner L, Kurtenbach C, Kurtzberg J, Mason RA, Noonan B, Roy K, Valentine V, Yeago C, Drissi H. Cell-based versus corticosteroid injections for knee pain in osteoarthritis: a randomized phase 3 trial. Nat Med (2023).
  10. Van Grouw A, Colonna MB, Maughon TS, Shen X, Larey AM, Moore SG, Yeago C, Fernandez FM, Edison AS, Stice SL, Marklein RA, Bowles-Welch AC. Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency. Stem Cells, 2023, 41(8):792-808. doi: 10.1093/stmcls/sxad039 PMID: 37279550
  11. Culberson AL, Bowles-Welch AC, Wang B, Kottke PA, Jimenez AC, Roy K, Fedorov AG. Early detection and metabolic pathway identification of T cell activation by in-process intracellular mass spectrometry. Cytotherapy. 2023 Sep;25(9):1006-1015. doi: 10.1016/j.jcyt.2023.03.010.
  12. 1016/j.bonr.2023.101656. https://doi.org/10.1016/j.bonr.2023.101656 10. Keenum MC, Chatterjee P, Atalis A, Pandey B, Jimenez A, Roy K. Single-cell epitope-transcriptomics reveal lung stromal and immune cell response kinetics to nanoparticle-delivered RIG-I and TLR4 agonists. Biomaterials. 2023 Jun;297:122097. doi: 10.1016/j.biomaterials.2023.122097.
  13. Bowles-Welch AC, Jimenez AC, Stevens HY, Frey Rubio DA, Kippner LE, Yeago C, Roy K. Mesenchymal stromal cells for bone trauma, defects, and disease: Considerations for manufacturing, clinical translation, and effective treatments. Bone Rep. 2023 Jan 20;18:101656. doi:
  14. Vantucci CE, Guyer T, Leguineche K, Chatterjee P, Lin A, Nash KE, Hastings MA, Fulton T, Smith CT, Maniar D, Frey Rubio DA, Peterson K, Andraca Harrer J, Willett NJ, Roy K, Guldberg RE. Systemic Immune Modulation Alters Local Bone Regeneration in a Delayed Treatment Composite Model of Non-Union Extremity Trauma. Front. Surg., 2022 07 July, Sec. Reconstructive and Plastic Surgery. Doi: 10.3389/fsurg.2022.934773
  15. Casteleiro Costa P, Wang B, Filan C, Bowles-Welch A, Yeago C, Roy K, Robles FE. Functional imaging with dynamic quantitative oblique back-illumination microscopy. J Biomed Opt. 2022 Jun;27(6):066502. doi: 10.1117/1.JBO.27.6.066502.
  16. Jimenez AC, Heist CA, Navaei M, Yeago C, Roy K. Longitudinal two-dimensional gas chromatography mass spectrometry as a non-destructive at-line monitoring tool during cell manufacturing identifies volatile features correlative to cell product quality. Cytotherapy. 2022 Nov;24(11):1136-1147. doi: 10.1016/j.jcyt.2022.06.001.
  17. Culberson AL, Chilmonczyk MA, Kottke PA, Bowles-Welch AC, Ghoshal D, Federov AG. Sample-to-Analysis Platform for Rapid Intracellular Mass Spectrometry. Lab on a Chip, 2021 21(23):4696-4706. doi: 10.1039/d1lc00884f PMID: 34751694
  18. Medrano-Trochez, C., Chatterjee, P., Pradhan, P. et al. Single-cell RNA-seq of out-of-thaw mesenchymal stromal cells shows tissue-of-origin differences and inter-donor cell-cycle variations. Stem Cell Res Ther 12, 565 (2021).  
  19. Wang, B., Bowles-Welch, A. C., Yeago, C., Roy, K., Process analytical technologies in cell therapy manufacturing: State-of-the-art and future directions. J. Adv. Manuf. Process. 2021 4(1), e10106.  
  20. Doron G, Klontzas ME, Mantalaris A, Guldberg RE, Temenoff JS. Multiomics characterization of mesenchymal stromal cells cultured in monolayer and as aggregates. Biotechnol Bioeng 2020 Jun;117(6):1761-1778. doi: 10.1002/bit.27317.
  21. Stevens HY, Bowles AC, Yeago C, and Roy K. Molecular Crosstalk Between Macrophages and Mesenchymal Stromal Cells. Front. Cell Dev. Biol. 2020 8:600160. doi: 10.3389/fcell.2020.600160