At Merck, John was tasked with leading a high-throughput screening automation lab and overseeing an implementation strategy that could 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 to maximize efficiency while providing meaningful data to guide process development. This work also included building appropriate templates and data collection methods to manage large data sets.

Selected publications:

1) 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

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

3) 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 helped to evaluate mechanistic chromatography modeling workflows while at Merck to better understand ways to implement in process development. This entailed evaluating different software options as well as working to mentor other scientists and experts to help build a more comprehensive modeling strategy in combination with other techniques like biophysical homology modeling and quantitative structure-activity relationship (QSAR). Initial work helped the team to better understand scale-down offsets with miniaturized RoboColumns. General modeling discussions ultimately helped stem discussions around how best to potentially use for future regulatory filings. As a thought leader in this field, John has also served as a co-organizer for the Recovery Conference Series sponsored Modeling Workshops and as a participant in a multi-institution project sponsored through NIIMBL.

Selected publications:

1) 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 Chrom A, 2023, 1693:463878. https://doi.org/10.1016/j.chroma.2023.463878

2) Roush D, et al., Toward in silico CMC: An industrial collaborative approach to model-based process development. Biotechnol Bioeng, 2020; 117:3986-4000. https://doi.org/10.1002/bit.27520

3) 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

4) Benner SW, Welsh JP, Rauscher MA, Pollard JM, Prediction of lab and manufacturing scale chromatography performance using mini-columns and mechanistic modeling. J Chrom 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