McSweeney, M. A., Patterson, A. T., Loeffler, K., Cuellar Lelo de Larrea, R., McNerney, M. P., Kane, R. S., & Styczynski, M. P. (2025). A modular cell-free protein biosensor platform using split T7 RNA polymerase. Science Advances, 11(8), eado6280.Link
Han, Y., & Styczynski, M. P. (2024). Assessing structural uncertainty of biochemical regulatory networks in metabolic pathways under varying data quality. NPJ Systems Biology and Applications, 10(1), 94.Link
VA Montgomery, AJ Wood‐Yang, MP Styczynski, MR Prausnitz (2024). Feasibility of engineered Bacillus subtilis for use as a microbiome‐based topical drug delivery platform. Bioengineering & Translational MedicineLink
Montgomery, V.A., Cain, E., Styczynski, M.P., Prausnitz M.R. (2023). Bacillus subtilis engineered for topical delivery of an antifungal agent. Plos one 18 (11) Link
Piorino, F., Patterson, A. T., Han, Y., Styczynski, M.P. (2023). Plasmid Crosstalk in Cell-Free Expression Systems. ACS Synthetic Biology. Link
Piorino, F., Styczynski, M.P. (2023). Complex Dependence of Escherichia coli-based Cell-Free Expression on Sonication Energy During Lysis. ACS Synthetic Biology. Link
Piorino, F., Styczynski, M.P. (2023). A Cell-Free Biosensor for Assessment of Hyperhomocysteinemia. ACS Synthetic Biology, 12(8), 2487-2492 Link
Patterson, A. T., Styczynski, M.P. (2023). Rapid and Finely-Tuned Expression for Deployable Sensing Applications. Advances in Biochemical Engineering/Biotechnology. Link
McSweeney, M. A., Zhang, Y., Styczynski, M.P. (2023). Short Activators and Repressors for RNA Toehold Switches. ACS Synthetic Biology, 12(3), 681-688. Link
Lee, J. Y., Han, Y., Styczynski, M.P. (2023). Towards inferring absolute concentrations from relative abundance in time-course GC-MS metabolomics data. Molecular Omics, 19, 126-136. Link
Piorino, F., Styczynski, M.P. (2022). Harnessing Escherichia coli’s Native Machinery for Detection of Vitamin C (Ascorbate) Deficiency. ACS Synthetic Biology, 11(11), 3592-3600. Link
Piorino, F., Patterson, A. T. & Styczynski M.P. (2022). Low-cost, point-of-care biomarker quantification. Current Opinion in Biotechnology, 76, 102738. Link
Sridharan, H., Piorino, F., & Styczynski, M. P. (2022). Systems biology-based analysis of cell-free systems. Current Opinion in Biotechnology, 75, 102703. Link
Ahmed, T., Zhang, Y., Lee, J.H., Styczynski, M.P., Takayama, S. (2022). Nucleic Acid Partitioning in PEG-Ficoll Protocells. Chem. Eng. Data 2022, 67, 8, 1964–1971. Link
Miguez A.M., Zhang Y., Styczynski M.P. (2022) Metabolomics Analysis of Cell-Free Expression Systems Using Gas Chromatography-Mass Spectrometry. In: Karim A.S., Jewett M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Link
Lee, J.Y., Styczynski, M.P. Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework. Sci Rep 12, 762 (2022). Link
Miguez, A.M., Zhang, Y., Piorino, F., Styczynski, M.P. (2021). Metabolic dynamics in Escherichia coli-based cell-free systems. ACS Synthetic Biology, 10(9), 2252-2265. Link
Lee, J.Y., Nguyen, B., Orosco, C., Styczynski, M.P. (2021). SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions. BMC Bioinformatics 22, 365. Link
Zhang, Y., Steppe, P.L., Kazman, M.W., Styczynski, M.P. (2021). Point-of-Care Analyte Quantification and Digital Readout via Lysate-Based Cell-Free Biosensors Interfaced with Personal Glucose Monitors. ACS Synthetic Biology, 10, 11, 2862-2869. Link
Zhang, Y., Kojima, T., Kim, G.A., McNerney, M.P., Takayama, S., Styczynski, M.P. Protocell arrays for simultaneous detection of diverse analytes. Nat Commun 12, 5724 (2021). Link
McSweeney, M.A., Styczynski, M.P. (2021). Effective use of linear DNA in cell-free expression systems. Frontiers in Bioengineering and Biotechnology, 9:715328. Link
Dromms, R.A., Lee, J.Y., Styczynski, M.P. (2020). LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. BMC Bioinformatics, 21(1), 1-14. Link
McNerney, M.P., Piorino, F., Michel, C.L., Styczynski, M.P. (2020). Active analyte import improves dynamic range and sensitivity of a Vitamin B12 biosensor. ACS Synthetic Biology, 9(2), 402-411. Link
Novais, F. J., Pires, P. R. L., Alexandre, P. A., Dromms, R. A., Iglesias, A. H., Ferraz, J. B. S., … & Fukumasu, H. (2019). Identification of a metabolomic signature associated with feed efficiency in beef cattle. BMC Genomics, 20(1), 8. Link
McNerney, M., Michel, C., Kishore, K., Standeven, J., & Styczynski, M. P. (2019). Dynamic and tunable metabolite control for robust minimal-equipment assessment of serum zinc. Nature Communications, 10. Link
Joyner, C. J., Brito, C. F., Saney, C. L., Joice Cordy, R., Smith, M. L., Lapp, S. A., … & DeBarry, J. D. (2019). Humoral immunity prevents clinical malaria during Plasmodium relapses without eliminating gametocytes. PLoS Pathogens, 15(9), e1007974. Link
Miguez, A., McNerney, M., & Styczynski, M. (2019). Metabolic Profiling of Escherichia coli-based Cell-Free Expression Systems for Process Optimization. Industrial & Engineering Chemistry Research. Link
McNerney, M. P., Zhang, Y., Steppe, P., Silverman, A. D., Jewett, M. C., & Styczynski, M. P. (2019). Point-of-care biomarker quantification enabled by sample-specific calibration. Science Advances, 5(9), eaax4473. Link
Zanetti, K. A., Hall, R. D., Griffin, J. L., Putri, S., Salek, R. M., Styczynski, M. P., … & van der Hooft, J. J. (2019). The Metabolomics Society—Current State of the Membership and Future Directions. Metabolites, 9(5), 89. Link
Tang, Y., Joyner, C. J., Cordy, R. J., Center, M. H. P. I., Galinski, M. R., Lamb, T. J., & Styczynski, M. P. (2019). Multi-omics Integrative Analysis of Acute and Relapsing Malaria in a Non-Human Primate Model of P. vivax infection. BioRxiv, 564195. Link
Smith, M. L., Miguez, A. M., & Styczynski, M. P. (2019). Gas Chromatography–Mass Spectrometry Microbial Metabolomics for Applications in Strain Optimization. In Microbial Metabolic Engineering (pp. 179-189). Humana Press, New York, NY. Link
Lee, J. Y., & Styczynski, M. P. (2018). NS-kNN: a modified k-nearest neighbors approach for imputing metabolomics data. Metabolomics, 14(12), 153. Link
Tang, Y., Gupta, A., Garimalla, S., Galinski, M. R., Styczynski, M. P., Fonseca, L. L., … & MaHPIC Consortium. (2018). Metabolic modeling helps interpret transcriptomic changes during malaria. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 1864(6), 2329-2340. Link
Smith, M. L., & Styczynski, M. P. (2018). Systems Biology-Based Investigation of Host–Plasmodium Interactions. Trends in Parasitology. Link
McNerney, M. P., & Styczynski, M. P. (2018). Small molecule signaling, regulation, and potential applications in cellular therapeutics. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 10(2), e1405. Link
Miguez, A. M., McNerney, M. P., & Styczynski, M. P. (2018). Metabolomics analysis of the toxic effects of the production of lycopene and its precursors. Frontiers in Microbiology, 9, 760. Link
Watstein, D. M., & Styczynski, M. P. (2017). Development of a pigment-based whole-cell zinc biosensor for human serum. ACS Synthetic Biology, 7(1), 267-275. Link
McNerney, M. P., & Styczynski, M. P. (2017). Precise control of lycopene production to enable a fast-responding, minimal-equipment biosensor. Metabolic Engineering, 43, 46-53. Link
Zia, M., Chi, T., Park, J. S., Su, A., Gonzalez, J. L., Jo, P. K., … & Bakir, M. S. (2016). 3-D integrated electronic microplate platform for low-cost repeatable biosensing applications. IEEE Transactions on Components, Packaging and Manufacturing Technology, 6(12), 1827-1833. Link
Styczynski, M. P., & Theis, F. J. (2016). Editorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology. Current opinion in biotechnology, 39, iv. Link
Chi, T., Park, J. S., Butts, J. C., Hookway, T. A., Su, A., Zhu, C., … Wang, H. (2015). A Multi-Modality CMOS Sensor Array for Cell-Based Assay and Drug Screening. IEEE Transactions on Biomedical Circuits and Systems, 9 (6), 801–814. Link
Yin, W., Garimalla, S., Moreno, A., Galinski, M. R., & Styczynski, M. P. (2015). A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems. BMC Systems Biology, 9, 49. Link
Su, A., Styczynski, M.P. (2015), Manipulation of complex metabolism in complex eukaryotic systems to control cell state. Current Opinion in Chemical Engineering, 10, 63-69. Link
McNerney, M., Watstein, D. M., & Styczynski, M. P. (2015). Precision metabolic engineering: The design of responsive, selective, and controllable metabolic Systems. Metabolic Engineering, 31, 123–131. Link
Dhakshinamoorthy, S., Dinh, N.-T., Skolnick, J., & Styczynski, M. P. (2015). Metabolomics identifies the intersection of phosphoethanolamine with menaquinone-triggered apoptosis in an in vitro model of leukemia. Molecular Biosystems, 11 (9), 2406–2416. Link
Dromms, R. A., & Styczynski, M. P. (2015). Improved metabolite profile smoothing for flux estimation. Molecular Biosystems, 11 (9), 2394–2405. Link
Watstein, D. M., McNerney, M. P., & Styczynski, M. P. (2015). Precise metabolic engineering of carotenoid biosynthesis in Escherichia coli towards a low-cost biosensor. Metabolic Engineering, 31, 171–180. Link
Yin, W., Kissinger, J. C., Moreno, A., Galinski, M. R., & Styczynski, M. P. (2015). From genome-scale data to models of infectious disease: A Bayesian network-based strategy to drive model development. Mathematical Biosciences, 270 (Pt B), 156–168. Link
Vermeersch, K. A., Wang, L., Mezencev, R., McDonald, J. F., & Styczynski, M. P. (2015). OVCAR-3 spheroid-derived cells display distinct metabolic profiles. PloS One, 10 (2), e0118262. Link
Cipriano, R. C., Smith, M. L., Vermeersch, K. A., Dove, A. D. M., & Styczynski, M. P. (2015). Differential metabolite levels in response to spawning-induced inappetence in Atlantic salmon Salmo salar. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, 13, 52–59. Link
Vermeersch, K. A., Wang, L., McDonald, J. F., & Styczynski, M. P. (2014). Distinct metabolic responses of an ovarian cancer stem cell line. BMC Systems Biology, 8, 134. Link
Lee, K. J., Yin, W., Arafat, D., Tang, Y., Uppal, K., Tran, V., … Gibson, G. (2014). Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. Frontiers in Cell and Developmental Biology, 2, 54. Link
Vermeersch, K. A., & Styczynski, M. P. (2013). Applications of metabolomics in cancer research. Journal of Carcinogenesis, 12, 9. Link
Thompson, D. A.; Roy, S.; Chan, M.; Styczynski, M. P.; Pfiffner, J.; French, C.; Socha, A.; Thielke, A.; Napolitano, S.; Muller, P.; Kellis, M.; Konieczka, J.H.; Wapinski, I.; Regev, A. (2013). Evolutionary principles of modular gene regulation in yeasts. eLife, 2 e00603. Link
Dromms, R. A., & Styczynski, M. P. (2012). Systematic applications of metabolomics in metabolic engineering. Metabolites, 2 (4), 1090–1122. Link
Meyer, M.; Wong, B.; Styczynski, M.; Munzner, T.; Pfister, H. (2010). Pathline: A Tool For Comparative Functional Genomics. Computer Graphics Forum, 29 (3), 1043-1052. Link
Styczynski, M. P., Jensen, K. L., Rigoutsos, I., & Stephanopoulos, G. (2008, March). BLOSUM62 miscalculations improve search performance. Nature Biotechnology. United States. Link
Styczynski, M. P., Moxley, J. F., Tong, L. V, Walther, J. L., Jensen, K. L., & Stephanopoulos, G. N. (2007). Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery. Analytical Chemistry, 79 (3), 966–973. Link
Styczynski, M. P., Fischer, C. R., & Stephanopoulos, G. N. (2006). The intelligent design of evolution. Molecular Systems Biology. England. Link
Jensen, K. L., Styczynski, M. P., Rigoutsos, I., & Stephanopoulos, G. N. (2006). A generic motif discovery algorithm for sequential data. Bioinformatics (Oxford, England), 22 (1), 21–28. Link
Styczynski, M. P.; Stephanopoulos, G. (2005). Overview of computational methods for the inference of gene regulatory networks. Computers & Chemical Engineering, 29 (3), 519-534. Link
Styczynski, M. P., Jensen, K. L., Rigoutsos, I., & Stephanopoulos, G. N. (2004). An extension and novel solution to the (l,d)-motif challenge problem. Genome Informatics. International Conference on Genome Informatics, 15 (2), 63–71. Link
Gwaltney, C. R.; Styczynski, M. P.; Stadtherr, M. A. (2004). Reliable computation of equilibrium states and bifurcations in food chain models. Computers & Chemical Engineering, 28 (10), 1981-1996. Link