Publications
Godar, A.G., Kamoku, C., Gonzalez-Ochoa, P., Cristobal, F., Taquillo, L., Wang, X., Nielsen, D.R. (2026), Engineering de novo monoethanolamine production from glucose in Escherichia coli, Biotechnol. Bioeng., 123(3): 785-791.
Godar, A.G., Cristobal, F., Taquillo, L., Wang, X., Nielsen, D.R.* (2026), Native carbonic anhydrase activity provides a critical and sufficient CO2 concentrating mechanism for Escherichia coli succinate fermentation, Fermentation, 12(2): 101.
Zhang, R., Yang, W., Zhang, R., Godar, A.G., Rijal, S., Youssef, A., Nielsen, D.R., Zheng, W., Tian, X. (2025), Phase Separation to Buffer Growth-Mediated Dilution in Synthetic Circuits, Cell, 188(26): 7413-7427.E15.
Telenar, T., Godar, A., Lee, J.S., Zhang, J., Nielsen, D.R., Green, M. (2025), Tuning the surface properties and biofouling resistance of fluorinated siloxane copolymers. Langmuir, 41(20):12587-12596.
Kamoku, C., Bhavaraju, P., Travis, C., Taquillo, L., Nielsen, D.R. (2025), Photosynthetic sorbitol production in Synechococcus sp. PCC 7002 is enhanced by addressing phosphatase promiscuity, nutrient availability and Calvin cycle bottlenecks. Metab. Eng., 91: 181-191.
Jones, C.M., Innes, S., Holland, S., Burch, T., Parrish, S., Nielsen, D.R. (2025), In situ, High-Resolution Quantification of CO2 Uptake Rates via Automated Off-Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures. Biotechnol. Bioeng., 122(3):594-605.
Kamoku, C., Nielsen, D.R. (2025), Highly Iterated Palindrome 1 (HIP1) sequence improves Synechococcus sp. PCC 7002 transformation efficiencies in a homology- and methylation-dependent manner. Biotechnol. Prog., e3518.
Ravindran, S., Hajinajaf, N., Kundu, P., Comes, J., Nielsen, D.R., Varman, A.M., Ghosh, A. (2024), Genome-scale metabolic model reconstruction and investigation into the fluxome of the fast-growing cyanobacterium Synechococcus sp. PCC 11901, ACS Synth. Biol., Accepted.
Kamoku, C., Cooper, C., Straub, A., Miller, N., Nielsen, D.R. (2024), Delivery of novel replicating vectors to Synechococcus sp. PCC 7002 via natural transformation of plasmid multimers, Synth. Biol. Eng, sbe00428.
Liu, A., Ellis, D., Mhatre, A., Brahmankar, S., Seto, J., Nielsen, D.R., Varman, A.M. (2024), Biomanufacturing of value-added chemicals from lignin, Curr. Opin. Biotechnol., 89:103178.
Godar, A.G., Chase, T., Conway, D., Ravichandran, D., Woodson, I., Lai, Y.J., Song, K., Rittmann, B.E., Wang, X., Nielsen, D.R. (2024), ‘Dark’ CO2 fixation in succinate fermentations enabled by direct CO2 delivery via hollow fiber membrane carbonation. Bioprocess Biosyst Eng. 47: 223-233.
Liu, A., Machas, M., Mhatre, A., Hajinajaf, N., Sarnaik, A., Nichols, N., Frazer, S., Wang, X., Varman, A.M., Nielsen, D.R. (2024), Synergistic Co-Utilization of Biomass-Derived Sugars Enhances Aromatic Amino Acid Production by Engineered Escherichia coli. Biotechnol. Bioeng., 121(2): 784-794.
Park, J.O., Nielsen, D.R. (2023), Editorial overview: Energy biotechnology as an integral solution to global challenges, Curr. Opin. Biotechnol., 84: 103006
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., 195: 108916.
Mhatre, 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, 193:288-298
Webb, 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., 72:133-149
Dookeran, 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): 3561–3575
Godar, 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: 1147–1158
Bu, 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.
