• John has assisted several clients with automation strategies. This has included identifying appropriate methods for specific challenges, implementing experimental set-up and analysis workbook templates, and supporting method development and scripting.

    At Merck, John was tasked with leading a high-throughput screening automation lab to support a diverse pipeline. This entailed identifying different chromatographic screening techniques (resin plates, resin pipette tips, and RoboColumns), using engineering principles to understand benefits and limitations of these techniques, and strategically implementing these techniques at different stages of development. This work also included building appropriate templates and data collection methods to manage large data sets.

    Selected publications:

    1) Welsh J, Altern SH, Lyall JY, Burgess S, Rauscher MA, Lenhoff AM, Cramer SA, Williams C, Coupling high-throughput and modeling approaches to streamline early-stage process development for biologics. Biotechnol Prog. 2025: e3523. https://doi.org/10.1002/btpr.3523

    2) Petroff M, Bao H, Welsh JP, van Beuningen – de Vaan M, Pollard JM, Roush DJ, Kandula S, Machielsen P, Tugcu N, Linden TO, High throughput chromatography strategies for potential use in the formal process characterization of a monoclonal antibody. Biotechnol Bioeng. 2016; 113(6):1273-83. https://doi.org/10.1002/bit.25901

    3) Welsh JP, Pushing the limits of high throughput process development: current state and future directions. Pharm Bioprocess. 2015; 3(1):1-3.

    4) Welsh JP, Petroff MG, Rowicki P, Bao H, Linden T, Roush DJ, Pollard JM, A practical strategy for using miniature chromatography columns in a standardized high throughput workflow for purification development of monoclonal antibodies. Biotechnol Prog. 2014; 30(3):626-35. https://doi.org/10.1002/btpr.1905

  • John is a co-organizer for the Recovery Conference Series sponsored Modeling Workshops and a thought leader in the field. He helped to evaluate mechanistic chromatography modeling workflows while at Merck to better understand ways to utilize in process development. This entailed evaluating different software options as well as building group expertise to implement a more comprehensive modeling strategy in combination with other techniques like biophysical homology modeling and quantitative structure-activity relationship (QSAR). John also previously served as a participant in a multi-institution modeling project sponsored through NIIMBL.

    Selected publications:

    1) Hartmann M, Rauscher M, Robinson J, Welsh J, Roush D, Integration of QSAR models with high-throughput screening to accelerate the development of polishing chromatography unit operations. J Chromatogr A. 2025; 1747:465818. https://doi.org/10.1016/j.chroma.2025.465818

    2) Liu P, Hartmann M, Shankaran A, Li H, Welsh J, Combining descriptive and predictive modeling to systematically design depth filtration-based harvest processes for biologics. Biotechnol Bioeng. 2024; 121(9):2924-35. https://doi.org/10.1002/bit.28765.

    3) Wittkopp F, et al. Current state of implementation of in silico tools in the biopharmaceutical industry – Proceedings of the 5th modeling workshop. Biotechnol Bioeng. 2024; 121(9):2952-73. https://doi.org/10.1002/bit.28768.

    4) Altern SH, Welsh JP, Lyall JY, Kocot AJ, Burgess S, Kumar V, Williams C, Lenhoff AM, Cramer SM, Isotherm model discrimination for multimodal chromatography using mechanistic models derived from high-throughput batch isotherm data. J Chromatogr A. 2023; 1693:463878. https://doi.org/10.1016/j.chroma.2023.463878

    5) Coffman J, et al., Highland games: A benchmarking exercise in predicting biophysical and drug properties of monoclonal antibodies from amino acid sequences. Biotechnol Bioeng. 2020; 117:2100-2115. https://doi.org/10.1002/bit.27349

    6) Benner SW, Welsh JP, Rauscher MA, Pollard JM, Prediction of lab and manufacturing scale chromatography performance using mini-columns and mechanistic modeling. J Chromatogr A. 2019; 1593:54-62. https://doi.org/10.1016/j.chroma.2019.01.063

  • As a graduate student working in James Swartz’s lab, John became an expert in cell-free protein synthesis and understanding when best to apply this powerful tool (toxic proteins, small proteins containing disulfide bonds, and non-natural amino acid incorporations allowing for bioconjugations). Manipulating the folding environment to more closely mimic the in vivo endoplasmic reticulum allowed for better production of mammalian proteins, and protein engineering approaches led to the creation of novel enzymes and conjugate vaccines.

    Selected publications:

    1) Lu Y, Welsh JP, Swartz JR, Production and stabilization of the trimeric influenza hemagglutinin stem domain for potentially broadly protective influenza vaccines. Proc Natl Acad Sci U S A. 2013;111(1):125-30. https://doi.org/10.1073/pnas.1308701110

    2) Welsh JP, Lu Y, He XS, Greenberg HB, Swartz JR, Cell-free production of trimeric influenza hemagglutinin head domain proteins as vaccine antigens. Biotechnol Bioeng. 2012;109(12):2962-9. https://doi.org/10.1002/bit.24581

    3) Welsh JP, Bonomo J, Swartz JR, Localization of BiP to translating ribosomes increases soluble accumulation of secreted eukaryotic proteins in an E. coli cell-free system. Biotechnol Bioeng. 2011;108(8):1739-48. https://doi.org/10.1002/bit.23111

    4) Welsh JP, Patel KP, Manthiram K, Swartz JR, Multiply mutated Gaussia luciferases provide prolonged and intense bioluminescence. Biochem Biophys Res Commun. 2009;389(4):563-8. https://doi.org/10.1016/j.bbrc.2009.09.006