2010 Cooney, M. J., and C. K. H. Guay. Heterotrophic Algal-biodiesel Production: Challenges and Opportunities. In (S. K. Khanal, Editor) Biofuel and bioenergy from biowastes and lignocellulosic biomass. American Society of Civil Engineers. In Press.
2010 Lau, C., Minteer, S. D., and M. J., Cooney. Development of a chitosan scaffold electrode. Electroanalysis. In Press.
2010 Martin, G. L., Minteer, S. D., and M. J. Cooney. Fluorescence characterization of chemical microenvironments in immobilization matrices: Polarity. The Analyst. In Press.
2010 Cooney, M. J. Kinetic Measurements for Enzyme Immobilization. In (S. Minteer, Editor) Enzyme Stabilization: Methods and Protocols. Humana Press. In Press.
2010 Mojica, K. and M. J. Cooney. Uronic acids assay as a relative measure of Anti-Biofilm EPS Activity. Biofouling. In Press.
2010 Young, G. L., and M. J. Cooney. Extraction of Biomass using an Ionic Liquid co-solvent system. Separation and Purification Techniques. In Press.
2009 Cooney, M. J., Young, G. L., and N. Nagle. Extraction of Bio-oils from Microalgae: A Review. Separation and Purification Reviews. 38(4):291-325.
2009 Martin, G. L., Ross, J. A., Minteer, S. D., Jameson, D. M., and M. J. Cooney. Fluorescence characterization of chemical microenvironments in hydrophobically modified chitosan. Carbohydrate Polymers. 77(4):695 – 702.
2009 Sjoholm, K. H., Cooney, M. J., and S. D. Minteer. Effects of degree of deacetylation on enzyme immobilization in hydrophobically modified chitosan. Carbohydrate Polymers. 77(2):420-424.
2009 Martin, G., Minteer, S. D., and M. J. Cooney. Spatial distribution of malate dehydrogenase in chitosan scaffolds. Applied Materials & Interfaces. 1(2):367–372
2009 Cooney, M. J., Petermann, J., Lau, C., and S. D. Minteer. Characterization and evaluation of hydrophobically modified chitosan scaffolds: Towards design of enzyme immobilized flow-through electrodes. Carbohydrate Polymers, 75(3):428-435.
2009 VanderLugt, K., Cooney, M. J., Lechner, A., and P. Lenz. Population dynamics of Bestiolina similis in batch cultures with maintained food levels: Why calanoid copepod populations crash. Journal of the World Aquaculture Society 40(5): 616-628.
2008 Cooney, M. J., Lau, C., Martin, G., Svoboda, V., and. S. D. Minteer. Enzyme catalyzed biofuel cells. Energy and Enviromental Science, 1:320 - 337.
2008 Lau, C., Cooney, M. J., and P. Atanassov. Conductive macroporous composite chitosan-carbon nanotube scaffolds. Langmuir. 24(13):7004-7010.
2008 Scott, D., Cooney, M. J., Liaw, B. Y. Sustainable current generation from the ammonia-polypyrrole interaction. Journal of Materials Chemistry. 27:3216-3222.
2008 Sun, D., Cooney, M. J., and B. Y. Liaw. A promising reconstitution platform for PQQ-dependent apo-enzymes in chitosan-carbon nanotube matrices. Electrochemical Solid State Letters. 11(6) B101-B104.
2008 Svoboda, V., Cooney, M. J., Liaw, B. Y., Minteer, S., Piles, E., , Lehnert, D. Barton, S. C., Dmitri Ivnitski, D., and P. Atanassov. Standardized characterization of electrocatalytic elctrodes. Electroanalysis, 20(10):1099 – 1109.
2008 Cooney, M. J., Windmesier, M, Lau, C., Liaw, B. Y., Klotzbach, T. and S. Minteer. Design of Chitosan Gel Pore Structure: Towards Enzyme Catalyzed Flow-Through Electrodes. Journal of Materials Chemistry. 6:667 – 674.
2008 Cooney, M.J., and B. Y. Liaw. In situ characterization techniques for design and evaluation of micro and nano enzyme-catalyzed power sources. In ( P.S Wang and J. B. Kim Editors) Biomolecular Catalysis: Nanoscale Science and Technology. ACS Symposium Series 986, Oxford University Press.
2007 Atanassov, P., Apblett, C., Banta, S., Brozik, S., Barton, S. C., Cooney, M. J., Liaw, B. Y., Mukerjee, S. and S. Minteer. Enzymatic Biofuel Cells. The Electrochemical Society Interface.
2007 Mojica, K., Elsey, D., and M. J., Cooney. Quantitative analysis of biofilm EPS uronic acid content. Journal of Microbial Methods. Volume 71, Issue 1, Pages 61-65.
2007 Minteer, S., Liaw, B. Y., and M. J. Cooney. Enzyme-Based Biofuel Cells. Current Opinions in Biotechnology. 18: 228 - 234.
2007 Svoboda, V., Rippolz, C., Cooney, M. J., and Bor Yann Liaw In situ characterization of electrochemical polymerization of methylene green on platinum electrodes. The Journal of Electrochemical Society. 154(3): D113 – D116.
2007 Elsey, D., Jameson, D., Raleigh, B., and M. J. Cooney. Flourescent measurement of microalgal neutral lipids. .The Journal of Microbiological Methods. 68(3), 639 – 642.
2007 Cooney, M. J., Maynard,, N., Benemann J., and C. Cannizzaro. Two-phase anaerobic digestion for production of hydrogen-methane mixtures. Bioresource Technology. 98 (14), p.2641-2651.
2006 Konash, A., Cooney, M. J., Liaw, B. Y., Bor Yann Liaw, and D. M. Jameson. Characterization of enzyme-polymer interactions using fluorescence. Journal of Materials Chemistry, 42:4107-4109.
2006 Cooney, M. J., Maynard, N., Cannizzaro, C., and David Harris. On-line measurement of gas production rates. Biotechnology Progress, 22:1456 – 1460.
2006 Denery, J. R., Cooney, M. J., and Q. Li. Metabolic profiling reflecting gene expression in Streptomyces tenjimariensis. Journal of Industrial Biotechnology. 2(1): 51 – 54.
2006 Cooney, M. J., Johnston, W. J., Pohl, S., and R. R. Bidgare. Influence of photoperiod on the pigmentation and metabolic efficiency of the marine aerobic anoxygenic photosynthetic bacterium Erythrobacter longus (strain NJ3Y). Aquatic Microbial Ecology 43:303 – 309.
2006 Johnston, W. J, Cooney, M. J., and B. Y. Liaw. In situ measurement of activity and mass transfer effects in enzyme immobilized electrodes. Enzyme and Microbial Technology. 39(1):131 – 140.
2005 M. J. Cooney, Sweeny, J.; Cesar, R; Alvarez, A.;and Biengfang, P. Effect of triadine treatment on litopenaeus vannamei larvae in a commercial hatchery setting. Journal of the World Aquaculture Society. December, 36(4): 546 – 553.
2005 Johnston, W. A., Cooney, M. J., Schorlemmer, A., Pohl, S., Karl, D. M., and R. Bidigare. Carbon mass balance methodology to characterize the growth of pigmented marine bacteria under conditions of light cycling. Bioprocess and Biosystems Engineering. 27(3):163 – 174.
2005 Johnston, W. J., Liaw, B. Y., Sapra, R., Adams, M. W. W., and M. J. Cooney. Design and characterization of redox enzyme electrodes: new perspectives on established techniques with application to an extremeophilic hydrogenase. Journal of Enzyme and Microbial Technology. 36(4): 540 – 549.
2004 Whiffen, V., Cooney, M. J., Cord-Ruwisch, R. On-line detection of feed demand in high cell density cultures of Escherichia coli by measurement of changes in dissolved oxygen transients in complex media. Biotechnology and Bioengineering. 85(4):423 – 433.
2003 Johnston, W. A., Stewart, M., Lee, P., and M. J. Cooney. Tracking the acetate threshold using DO transient control in medium and high cell density cultivation of recombinant E.coli in complex media. Biotechnology and Bioengineering, November 5, 84(3): 314 – 323.
2003 Johnston, W. and M. J. Cooney. Broth recycling to reduce process noise resulting from concentrated substrate addition in fed-batch cultivation of E. coli. Biotechnology Progress. Mar – Apr 19(2): 659-61
2002 Johnston, W. and M. J. Cooney. Industrial control of recombinant E. coli fed batch culture: new perspectives on traditional controlled variables. Bioprocess and Biosystems Engineering. 25:111-120.
1999 Cooney, M. J., Goh, L. T., Lee, P. L., and M. R. Johns. Structured Model-based analysis and control of the Hyaluronic Acid Fermentation by Streptococcus zooepidemicus: Physiological implications of glucose and complex-nitrogen limited growth. Biotechnology Progress, 15(5): 898-910.
1997 Armstrong, D.L., M.J. Cooney, and M.R. Johns. Growth and amino acid requirements of hyaluronic acid-producing Streptococcus zooepidemicus. Journal of Applied and Environmental. Microbiology, 63(7):309-312.
1996 Cooney, M. J., Roschi, E., Marison, I. W., Comninellis, Ch., and Urs von Stockar. Physiological studies with the sulfate-reducing bacterium Desulfibrio desulfuricans: Evaluation for use in a bio-fuel cell. Enzyme and Microbial Technology, 18:358-365.
1996 Cooney, M. J., Marison, I. W., van Gulik, W., and Urs von Stockar. Calorimetric and Stoichiometric Analysis of Growth of K. fragilis in Continuous Culture: Nitrogen Limitation Imposed Upon Carbon Limited Growth. Journal of Applied Microbiology and Biotechnology, 44: 643-653.
1995 von Stockar, U., Larsson, Ch., Marison, I. W., and M. J. Cooney. Calorimetry of Dual limitations in Yeast Cultures. Thermochim Acta, 250:247-258.
1995 Cooney, M. J., and K. McDonald. Optimal Dynamic Experiments for Bioreactor Model Discrimination: Multivariable Dynamic Model Development for Pure, Continuous Cultures of E. coli and C. utilis. Journal of Applied Microbiology and Biotechnology, 43:826-837.
1993 Cooney, M. J., Rosenberg, M., and C. F. Shoemaker. Rheological properties of whey protein concentrate gels. J. Texture Studies, 24: 325-334.
1993 Cooney, M. J., and K. McDonald. The Monod Constant for Growth for Candida utilis on Ammonium in Continuous and Batch Cultures. Biotechnology Progress, 9:93-96.
1988 Cooney, M. J., and K. McDonald. On-line Analysis of a Fermentation Process. Anthology of Computer Interfaced Experiments for the Undergraduate Laboratory, CACHE Corp. June 1988.