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2017 Journal Article Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeastPeng, Bingyin, Plan, Manuel R., Carpenter, Alexander, Nielsen, Lars K. and Vickers, Claudia E. (2017). Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast. Biotechnology for Biofuels, 10 (1) 43, 43. doi: 10.1186/s13068-017-0728-x |
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2017 Journal Article Improved production of propionic acid using genome shufflingLuna-Flores, Carlos H., Palfreyman, Robin W., Kromer, Jens O., Nielsen, Lars K. and Marcellin, Esteban (2017). Improved production of propionic acid using genome shuffling. Biotechnology Journal, 12 (2) 1600120, 1600120. doi: 10.1002/biot.201600120 |
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2017 Conference Publication Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrestHudson, J., Mills, R., Titmarsh, D., Koenig, X., Parker, B., Ryall, J., Quaife-Ryan, G., Voges, H., Hodson, M., Ferguson, C., Drowley, L., Plowright, A., Wang, Q., Gregorevic, P., Xin, M., Thomas, W., Parton, R., Nielsen, L., Launikonis, B., James, D., Elliott, D. and Porrello, E. (2017). Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest. Abstracts for the 65th Cardiac Society of Australia and New Zealand Annual Scientific Meeting and the International Society for Heart Research Australasian Section Annual Scientific Meeting, Perth, Australia, 10 - 13 August 2017. Chatswood, NSW, Australia: Elsevier. doi: 10.1016/j.hlc.2017.06.375 |
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2017 Journal Article A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiaePeng, Bingyin, Plan, Manuel R., Chrysanthopoulos, Panagiotis, Hodson, Mark P., Nielsen, Lars K. and Vickers, Claudia E. (2017). A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metabolic Engineering, 39, 209-219. doi: 10.1016/j.ymben.2016.12.003 |
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2016 Journal Article The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-productionWilliams, Thomas C., Peng, Bingyin, Vickers, Claudia E. and Nielsen, Lars K. (2016). The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production. Metabolic Engineering Communications, 3, 142-152. doi: 10.1016/j.meteno.2016.05.001 |
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2016 Journal Article A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolismHefzi, Hooman, Ang, Kok Siong, Hanscho, Michael, Bordbar, Aarash, Ruckerbauer, David, Lakshmanan, Meiyappan, Orellana, Camila A., Baycin-Hizal, Deniz, Huang, Yingxiang, Ley, Daniel, Martinez, Veronica S., Kyriakopoulos, Sarantos, Jimenez, Natalia E., Zielinski, Daniel C., Quek, Lake-Ee, Wulff, Tune, Arnsdorf, Johnny, Li, Shangzhong, Lee, Jae Seong, Paglia, Giuseppe, Loira, Nicolas, Spahn, Philipp N., Pedersen, Lasse E., Gutierrez, Jahir M., King, Zachary A., Lund, Anne Mathilde, Nagarajan, Harish, Thomas, Alex, Abdel-Haleem, Alyaa M. ... Lewis, Nathan E. (2016). A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism. Cell Systems, 3 (5), 434-443.e8. doi: 10.1016/j.cels.2016.10.020 |
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2016 Journal Article Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin productionTierrafría, Víctor H. , Licona-Cassani, Cuauhtemoc, Maldonado-Carmona, Nidia, Romero-Rodríguez, Alba, Centeno-Leija, Sara, Marcellin, Esteban, Rodríguez-Sanoja, Romina, Ruiz-Villafan, Beatriz, Nielsen, Lars K. and Sánchez, Sergio (2016). Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production. Applied Microbiology and Biotechnology, 100 (21), 9229-9237. doi: 10.1007/s00253-016-7811-2 |
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2016 Journal Article Tetanus toxin production is triggered by the transition from amino acid consumption to peptidesLicona-Cassani, Cuauhtemoc, Steen, Jennifer A., Zaragoza, Nicolas E., Moonen, Glenn, Moutafis, George, Hodson, Mark P., Power, John, Nielsen, Lars K. and Marcellin, Esteban (2016). Tetanus toxin production is triggered by the transition from amino acid consumption to peptides. Anaerobe, 41, 113-124. doi: 10.1016/j.anaerobe.2016.07.006 |
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2016 Journal Article In vitro production of baculoviruses: identifying host and virus genes associated with high productivityNguyen, Quan, Tran, Trinh Tb, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2016). In vitro production of baculoviruses: identifying host and virus genes associated with high productivity. Applied Microbiology and Biotechnology, 100 (21), 1-15. doi: 10.1007/s00253-016-7774-3 |
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2016 Journal Article Spliced synthetic genes as internal controls in RNA sequencing experimentsHardwick, Simon A., Chen, Wendy Y., Wong, Ted, Deveson, Ira W., Blackburn, James, Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Spliced synthetic genes as internal controls in RNA sequencing experiments. Nature Methods, 13 (9), 792-798. doi: 10.1038/nmeth.3958 |
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2016 Journal Article Representing genetic variation with synthetic DNA standardsDeveson, Ira W., Chen, Wendy Y., Wong, Ted, Hardwick, Simon A., Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Representing genetic variation with synthetic DNA standards. Nature Methods, 13 (9), 784-791. doi: 10.1038/nmeth.3957 |
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2016 Journal Article Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic modelsHiguera, Pedro Saa and Nielsen, Lars K. (2016). Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. Bioinformatics, 32 (24), 3807-3814. doi: 10.1093/bioinformatics/btw555 |
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2016 Journal Article Metabolic reconstruction of Setaria italica: a systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grassesde Oliveira Dal'Molin, Cristiana Gomes, Orellana, Camila, Gebbie, Leigh, Steen, Jennifer, Hodson, Mark, Plan, Manuel, Chrysanthopoulos, Panagiotis, Macqualter, Richard, Palfreyman, Robin W. and Nielsen, Lars K. (2016). Metabolic reconstruction of Setaria italica: a systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses. Frontiers in Plant Science, 7 (1138) 1138, 1-18. doi: 10.3389/fpls.2016.01138 |
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2016 Journal Article II-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networksSaa, Pedro A. and Nielsen, Lars K. (2016). II-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks. Bioinformatics, 32 (15), 2330-2337. doi: 10.1093/bioinformatics/btw132 |
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2016 Journal Article Construction of feasible and accurate kinetic models of metabolism: a Bayesian approachSaa, Pedro A. and Nielsen, Lars K. (2016). Construction of feasible and accurate kinetic models of metabolism: a Bayesian approach. Scientific Reports, 6 (1) 29635, 29635. doi: 10.1038/srep29635 |
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2016 Journal Article Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animalsOrmerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016). Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) 36, 36.1-36.17. doi: 10.1186/s40168-016-0181-2 |
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2016 Journal Article Recon 2.2: from reconstruction to model of human metabolismSwainston, Neil, Smallbone, Kieran, Hefzi, Hooman, Dobson, Paul D., Brewer, Judy, Hanscho, Michael, Zielinski, Daniel C., Ang, Kok Siong, Gardiner, Natalie J., Gutierrez, Jahir M., Kyriakopoulos, Sarantos, Lakshmanan, Meiyappan, Li, Shangzhong, Liu, Joanne K., Martinez, Veronica S., Orellana, Camila A., Quek, Lake-Ee, Thomas, Alex, Zanghellini, Juergen, Borth, Nicole, Lee, Dong-Yup, Nielsen, Lars K., Kell, Douglas B., Lewis, Nathan E. and Mendes, Pedro (2016). Recon 2.2: from reconstruction to model of human metabolism. Metabolomics, 12 (7) 109, 109. doi: 10.1007/s11306-016-1051-4 |
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2016 Journal Article Low carbon fuels and commodity chemicals from waste gases-systematic approach to understand energy metabolism in a model acetogenMarcellin, Esteban, Behrendorff, James B., Nagaraju, Shilpa, DeTissera, Sashini, Segovia, Simon, Palfreyman, Robin W., Daniell, James, Licona-Cassani, Cuauhtemoc, Quek, Lake-ee, Speight, Robert, Hodson, Mark P., Simpson, Sean D., Mitchell, Wayne P., Kopke, Michael and Nielsen, Lars K. (2016). Low carbon fuels and commodity chemicals from waste gases-systematic approach to understand energy metabolism in a model acetogen. Green Chemistry, 18 (10), 3020-3028. doi: 10.1039/c5gc02708j |
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2016 Journal Article Genetic and biochemical characterization of genes involved in hyaluronic acid synthesis in Streptococcus zooepidemicusZhang, Yali, Luo, Kailai, Zhao, Qiushuang, Qi, Zhengliang, Nielsen, Lars Keld and Liu, Hao (2016). Genetic and biochemical characterization of genes involved in hyaluronic acid synthesis in Streptococcus zooepidemicus. Applied Microbiology and Biotechnology, 100 (8), 3611-3620. doi: 10.1007/s00253-016-7286-1 |
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2016 Journal Article A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysisSaa, Pedro A. and Nielsen, Lars K. (2016). A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis. Biochimica et Biophysica Acta - General Subjects, 1860 (3), 576-587. doi: 10.1016/j.bbagen.2015.12.015 |
