Publications Publications from ASU Swain, K., Sharon, I., Blackson, W., Parrish, S., Tekel, S., Schmeing, T.M., Nielsen, D.R., Nannenga, B.L. (2023), Soluble and stable cyanophycin synthetase expression enhances heterologous cyanophycin production in Escherichia coli, Biochem. Eng. J., AcceptedMhatre, A., Kalscheur, B., Bhakta, K., Sarnaik, A.P., Flores, A., Nielsen, D.R., Wang, X., Soundappan, T., Varman, A.M. (2022), Consolidated Bioprocessing of Hemicellulose to Fuels and chemicals through an Engineered Bacillus subtilis-Escherichia coli Consortium, Renew. Energy, 193:288-298Webb, J.P., Paiva, A.C., Rossoni, L., Alstrom-Moore, A., Springthorpe, V., Vaud, S., Yeh, V., Minde, D.-P., Langer, S., Walker, H., Hounslow, A., Nielsen, D.R., Larson, T., Lilley, K., Stephens, G., Thomas, G.H., Bonev, B.B., Kelly, D.J., Conradie, A., Green, J. (2022), Multi-omic based production strain improvement (MOBpsi) for bio-manufacturing of toxic chemicals. Metab. Eng., 72:133-149Dookeran, Z., Nielsen, D.R.* (2021), Systematic engineering of Synechococcus elongatus UTEX 2973 for photosynthetic production of L-lysine, cadaverine, and glutarate, ACS Synth. Biol. 10(12): 3561–3575Godar, A., Kamoku, C., Nielsen, D.R., Wang, X.* (2021), Synthetic biology strategies to address waste CO2 loss during biofuel production, (2021) Curr. Opin. Environ. Sci. Health, 24:100305.Thompson, B.+, Machas, M.+, Abed, O., Nielsen, D.R.* (2021), Applying a ‘Metabolic Funnel’ for Phenol Production in Escherichia coli, Fermentation, 7:216.Flores, A., Holland, S., Mhatre, A., Sarnaik, A., Godar, A., Onyeabor, M., Varman, A., Wang, X.*, Nielsen, D.R.* (2021), A Coculture-Coproduction System Designed for Enhanced Carbon Conservation through Inter-Strain Metabolic Cooperation, Metab. Eng., 67:387-395..Jones, C.M., Parrish, S., Nielsen, D.R.* (2021), Exploiting Polyploidy for Markerless and Plasmid-free Genome Engineering in Cyanobacteria. ACS Synth. Biol., 10(9):2371-2382..Beattie, A., Vermaas, W., Darzins, A., Holland, S.C., Li, S., McGowen, J., Nielsen, D.R., Quinn, J.C.* (2021), A probabilistic economic and environmental impact assessment of a cyanobacteria-based biorefinery. Algal Res., 59:102454.Machas, M., Kurgan, G., Abed, O., Shapiro, A., Wang, X., Nielsen, D.R.* (2021), Escherichia coli’s Transcriptional Response to Different Styrene Exposure Modes Reveals Novel Toxicity and Tolerance Insights, J. Ind. Microbiol. Biotechnol., 48(1-2):kuab019..Jones, C.M., Korosh, T.C., Nielsen, D.R., Pfleger, B.F.* (2021), Optimization of a T7-RNA Polymerase System in Synechococcus sp. PCC 7002 Mirrors the Protein Overproduction Phenotype from E. coli BL21(DE3), Appl. Microbiol. Biotechnol., 105: 1147–1158Bu, G., Simmons, C., Nielsen, D.R., Nannenga, B.* (2020), Tetragonal crystal form of the cyanobacterial bicarbonate transporter regulator SbtB from Synechocystis sp. PCC 6803, Acta Crystallogr. F, 76(9).Bu, G., Parrish, S., Gleason, P., Nielsen, D.R., Nannenga, B.* (2020), Heterologous expression and purification of the bicarbonate transporter BicA from Synechocystis sp. PCC 6803, Protein Expr. Purif., 175:105716.Flores, A.D., Choi, H.G., Martinez, R.M., Onyeabor, M., Ayla, E.Z., Godar, A., Machas, M.S., Nielsen, D.R.*, Wang, X.* (2020) Catabolic Division of Labor Enhances Production of D-Lactate and Succinate from Glucose-Xylose Mixtures in Engineered Escherichia coli Coculture Systems, Front. Bioeng. Biotechnol., doi: 10.3389/fbioe.2020.00329.Sarnaik, A.P., Liu, A., Nielsen, D.R., Varman, A.M.* (2020) High-Throughput Screening for Efficient Microbial Biotechnology, Curr. Opin. Biotechnol., 64: 131-150.Flores, A.D., Ayla, E.Z., Nielsen, D.R., Wang, X., (2019) Engineering a Synthetic, Catabolically-Orthogonal Co-Culture System for Enhanced Conversion of Lignocellulose-Derived Sugars to Ethanol, ACS Synth. Biol., 8(5):1089-1099.Flores, A.D., Wang, X., Nielsen, D.R.*, (2019) Recent Trends in Integrated Bioprocesses: Aiding and Expanding Microbial Biofuel/Biochemical Production, Curr. Opin. Biotechnol., 57:82-87.Kurgan, G., Panyon, L., Rodriguez-Sanchez, Y., Pacheco, E., Nieves, L., Mann, R., Nielsen, D.R., Wang, X. (2019), Bioprospecting of native efflux pumps to enhance furfural tolerance in ethanologenic Escherichia coli, Appl. Environ. Microbiol., 85(6): e02985-18.Machas, M., Kurgan, G., Jha, A., Flores, A., Schneider, A., Coyle, S., Varman, A., Wang, X., Nielsen, D.R.*, (2018) Emerging Tools, Enabling Technologies, and Future Opportunities for the Bioproduction of Aromatic Chemicals, J. Chem. Technol. Biotechnol., 94(1):38-52.Schulz, T.C., Thompson, S.T., Oelschlager, M., Nielsen, D.R., Vermaas, W., Lamb, H.H.*, (2018) Catalytic Conversion of Cyanobacteria-Derived Fatty Acids to Alkanes for Biorenewable Synthetic Paraffinic Kerosene, Sus. Energy Fuels, 2:882-893.Thompson, B., Pugh, S., Machas, M., and Nielsen, D.R.*, (2018) Muconic Acid Production via Alternative Pathways and a Synthetic “Metabolic Funnel”, ACS Synth. Biol., 7(2):565-575.Machas, M., Thompson, B., McKenna, R., and Nielsen, D.R.*, (2017) Expanding Upon Styrene Biosynthesis to Engineer a Novel Route to 2-Phenylethanol, Biotechnol. J., DOI: 10.1002/biot.201700310.Staggs, K.W., Qiang, Z., Madathil, K., Gregson, C.T., Xia, Y., Vogt, B.D., Nielsen, D.R.*, (2016) High Efficiency and Facile Butanol Recovery with Magnetically Responsive Micro/Mesoporous Carbon Adsorbents, ACS Sustainable Chem. Eng., 5(1):885-894.Thompson, B., Machas, M., Nielsen, D.R.*, (2016) Engineering and Comparison of Non-Natural Pathways for Microbial Phenol Production, Biotechnol. Bioeng., DOI: 10.1002/bit.25942.Godeshala, S., Nitiyanandan, R., Thompson, B., Goklany, S., Nielsen, D.R., Rege, K.* (2016), Folate receptor-targeted aminoglycoside-derived polymers for transgene expression in cancer cells, Bioeng. Translate. Med., 1(2):220–231.Tan, Z., Yoon, J.M., Nielsen, D.R., Shanks, J.V., Jarboe, L.R.* (2016), Membrane Engineering via Trans Unsaturated Fatty Acids Production Improves Escherichia coli Robustness and Production of Biorenewables, Metab. Eng., 35:105-113.Lian, J., McKenna, R., Nielsen, D.R., Brown, R., Wen, Z., Jarboe, L.* (2016), Production of Biorenewable Styrene: Utilization of Biomass-Derived Sugars and Insights into Toxicity, J. Ind. Microbiol. Biotechnol., 43(5):595-604.Thompson, B., Machas, M., and Nielsen, D.R.*, (2015) Creating Pathways Towards Aromatic Building Blocks and Fine Chemicals, Curr. Opin. Biotechnol., 36:1-7.Halloum, I., Thompson, B., Pugh, S., and Nielsen, D.R.*, (2015) Activity of Lactobacillus brevis alcohol dehydrogenase on primary and secondary alcohol biofuel precursors, Fermentation, 1(1), 24-37.Pugh, S., McKenna, R., Halloum, I., and Nielsen, D.R.*, (2015) Engineering Escherichia coli for renewable benzyl alcohol production, Metab. Eng. Comm., Accepted.Staggs, K. and Nielsen, D.R.*, (2015) Improving n-Butanol Production in Batch and Semi-Continuous Processes through Integrated Product Recovery, Proc. Biochem., 50(1):1487–1498.McKenna, R., Moya, L., McDaniel, M., and Nielsen, D.R., (2015) Comparing In Situ Removal Strategies for Improving Styrene Bioproduction, Bioproc. Biosys. Eng., 38(1):165-174.Pugh, S., McKenna, R., Osman, M., Thompson, B., and Nielsen, D.R., (2014) Rational engineering of a novel pathway for producing the aromatic compounds p-hydroxybenzoate, protocatechuate, and catechol in Escherichia coli, Proc. Biochem., 49:1843-1850.McKenna, R., Thompson, B., Pugh, S., and Nielsen, D.R., (2014) Rational and Combinatorial Approaches to Engineering Styrene Production by Saccharomyces cerevisiae, Microb. Cell Fact., 13:123.Zhang, W. and Nielsen, D.R. (2014), Synthetic Biology Applications in Industrial Microbiology, Front. Microbio., 5: 451.Claypool, J., Raman, D.R., Jarboe, L.J., Nielsen, D.R., (2014) Technoeconomic Evaluation of Bio-Based Styrene Production by Engineered Escherichia coli, J. Ind. Microbiol. Biotechnol., 41(8):1211-1216.Thompson, B., Moon, T.S., and Nielsen, D.R., (2014) 'Hybrid' Processing Strategies for Expanding and Improving the Synthesis of Renewable Bioproducts, Curr. Opin. Biotechnol., 30: 17-23.Wiehn, M., Staggs, K., Wang, Y., and Nielsen, D.R., (2014) In Situ Butanol Recovery from Clostridium acetobutylicum Fermentations by Expanded Bed Adsorption, Biotechnol. Progr., 30(1):68-78.Wiehn, M., Levario, T., Staggs, K., Linneen, N., Wang, Y., Pfeffer, R., Lin, J., and Nielsen, D.R., (2013) Adsorption of Short-Chain Alcohols by Hydrophobic Silica Aerogels, Ind. Eng. Chem. Res., 52(51):18379-18385.Nielsen, D.R. and Moon, T.S., (2013) From Promise to Practice. The Role of Synthetic Biology in Green Chemistry, EMBO Reports, 14(12):1034-1038.McKenna, R., Pugh, S., Thompson, B., and Nielsen, D.R., (2013) Microbial Production of the Aromatic Building-Blocks (S)-Styrene Oxide and (R)-1,2-Phenylethanediol from Renewable Resources, Biotechnol. J, 8(12):1465-1475.Wang, B., Pugh, S., Nielsen, D.R., Zhang, W., and Meldrum, D., (2013) Engineering Cyanobacteria for Continuous Production of 3-Hydroxybutyrate Directly from CO2, Metab. Eng., 16:68-77.Adkins, J., Jordan, J., and Nielsen, D.R., (2013) Engineering Escherichia coli for Renewable Production of the 5-Carbon Polyamide Building-Blocks 5-Aminovalerate and Glutarate, Biotechnol. Bioeng., 110(6):1726-1734.Yuan, W., Wiehn, M., Wang, Y., Kim, H.W., Rittmann, B.E., and Nielsen, D.R., (2013) Solid-Phase Extraction of Long-Chain Fatty Acids from Aqueous Solution, Sep. Purif. Technol., 106:1-7.Adkins, J., Pugh, S., McKenna, R., and Nielsen, D.R., (2012), Engineering Microbial Chemical Factories to Produce Renewable 'Biomonomers', Front. Microbio., 3: 313.McKenna, R. and Nielsen, D.R., (2011) Styrene biosynthesis from glucose by engineered E. coli, Metab. Eng., 13(5): 544-554.Levario, T.J., Dai, M., Yuan, W., Vogt, B.D., and Nielsen, D.R., (2011) Rapid Adsorption of Alcohol Biofuels by High Surface Area Mesoporous Carbons, Micropor Mesopor Mat, 148(1): 107-114.Pugh, S., McKenna, R., Moolick, R., and Nielsen, D.R., (2010) Advances and Opportunities at the Interface between Microbial Bioenergy and Nanotechnology, Can. J. Chem. Eng., 89(1): 2-12. Prior to ASU Moon, T.S., Nielsen, D.R., and Prather, K.J., (2011) Sensitivity Analysis of a Proposed Model Mechanism for Newly Created Glucose-6-Oxidases, AIChE J, 58(8): 2303-2308.Nielsen, D.R., Yoon S.H., Yuan, C.J., and Prather, K.J., (2010) Engineering Acetoin and meso-2,3 Butanediol Biosynthesis in E. coli., Biotechnol. J., 5: 274-284.Nielsen, D.R., Amarasiriwardena, G.S., and Prather, K.J., (2010) Predicting the Adsorption of Second Generation Biofuels by Polymeric Resins with Applications for In Situ Product Recovery (ISPR), Biores. Technol., 101(8): 2762-2769.Yeom, S.H., Daugulis, A.J., and Nielsen, D.R., (2010) Estimating the cellular maintenance coefficient and its use in the design of two-phase partitioning bioscrubbers, Bioproc. Biosyst. Eng.,, 33(6): 731-739.Yeom, S.H., Daugulis, A.J., and Nielsen, D.R., (2010) A Strategic Approach for the Design and Operation of Two-phase Partitioning Bioscrubbers for the Treatment of Volatile Organic Compounds, Biotechnol. Progr., 26(6): 1777-1786.Nielsen, D.R., Leonard, E., Yoon S.H., Tseng, H.C., Yuan, C.J., and Prather, K.J., (2009). Engineering Alternative Butanol Production Platforms in Heterologous Bacteria. Metab. Eng., 11(4-5): 262-273.Nielsen, D.R. and Prather, K.J., (2009). In Situ Product Recovery of n-Butanol Using Polymeric Resins, Biotechnol. Bioeng., 102(3): 811-821.Tseng, H.C., Martin, C.H., Nielsen, D.R., and Prather, K.J., (2009). Metabolic engineering of Escherichia coli for the enhanced production of (R)- and (S)-3-hydroxybutyrate. Appl. Environ. Microb., 75(10): 3137-3145.Martin, C.H., Nielsen, D.R., Solomon, K.V., and Prather, K.J., (2009). Synthetic Metabolism: Engineering Biology at the Protein and Pathway Scales, Chem. Biol., 16: 277-286.Leonard, E., Nielsen, D., Solomon, K., and Prather, K.J., (2008). Engineering Microbes with Synthetic Biology Frameworks, Trends Biotechnol., 26(12): 674-681Nielsen, D.R., Daugulis, A.J., and McLellan, P.J., (2007), Dynamic Simulation of Benzene Vapor Treatment by a Two-Phase Partitioning Bioscrubber. Part II: Model Calibration, Validation, and Predictions, Biochem. Eng. J., 36(3): 250-261.Nielsen, D.R., Daugulis, A.J., and McLellan, P.J., (2007), Dynamic Simulation of Benzene Vapor Treatment by a Two-Phase Partitioning Bioscrubber. Part I: Model Development, Parameter Estimation, and Parametric Sensitivity, Biochem. Eng. J., 36(3): 239-249.Nielsen, D.R., Sask, K.N., McLellan, P.J., and Daugulis, A.J. (2006), Benzene Vapor Treatment using a Two-Phase Partitioning Bioscrubber: An Improved Steady-State Protocol to Enhance Long-Term Operation, Bioproc. Biosyst. Eng., 29(4): 229-240.Nielsen, D.R., McLellan, P.J., and Daugulis, A.J. (2006), Direct Estimation of the Oxygen Requirements of Achromobacter xylosoxidans for Aerobic Degradation of Monoaromatic Hydrocarbons (BTEX) in a Bioscrubber, Biotechnol. Lett., 28(16): 1293-1298.Nielsen, D.R., Daugulis, A.J., and McLellan, P.J. (2005), Transient Performance of a Two-Phase Partitioning Bioscrubber Treating a Benzene-Contaminated Gas Stream, Environ. Sci. Technol., 39(22): 8971-8977.Nielsen, D.R., Daugulis, A.J., and McLellan, P.J. (2005), A Restructured Framework for Modeling Oxygen Transfer in Two-Phase Partitioning Bioreactors, Biotechnol. Bioeng., 91(6): 773-777.Nielsen, D.R., Daugulis, A.J., and McLellan, P.J. (2005), Quantifying Maintenance Energy Requirements from the Steady-State Operation of a Two-Phase Partitioning Bioscrubber, Biotechnol. Bioeng., 90(2): 248-257.Nielsen, D.R., Daugulis, A.J., and McLellan, P.J. (2003), A Novel Method of Simulating Oxygen Transfer in Two-Phase partitioning Bioreactors, Biotechnol. Bioeng, 83(6): 735-741.Ma, H., Nielsen, D.R., Bowman, C.N., and Davis, R.H.*, (2001) Membrane Surface Modification and Backpulsing for Wastewater Treatment, Sep. Sci. Tech., 36: 1553-1569. From ASU Prior to ASU Total Book Chapters Immethun, C., Henson, R., Wang, X., Nielsen, D.R., and Moon, T.S.*, (2016) Engineering Central Metabolism for Production of Higher Alcohol-Based Biofuels, In: Biotechnologies for Biofuel Production and Optimization (Elsevier), Eckert, C., and Trinh, C.T. (Eds). Elsevier. Intellectual Property ‘Microorganisms Engineered to Produce Phenol and its Derivatives’ (2019), Nielsen, D.R., Pugh, S., Thompson, B., U.S. Patent 10,174,346‘Enzymes and Microorganisms for the Production of 1,3-Butadiene and other Dienes’ (2018), Nielsen, D.R., Pugh, S., McKenna, R., U.S. Patent 10,125,377‘Photosynthetic Production of 3-Hydroxybutyrate from Carbon Dioxide’ (2018), Wang, B., Zhang, W., Meldrum, D., Nielsen, D.R., U.S. Patent 9,944,955‘Microbial Conversion of Glucose to Styrene and its Derivatives’ (2015), Nielsen, D.R., McKenna, R., U.S. Patent 9,150,884
