Publications

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