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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 |
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2016 Journal Article Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactisZhu, Yan, Pham, Thi Huong, Nhiep, Thi Hanh Nguyen, Vu, Ngoc Minh Thu, Marcellin, Esteban, Chakrabortti, Alolika, Wang, Yuanliang, Waanders, Jennifer, Lo, Raquel, Huston, Wilhelmina M., Bansal, Nidhi, Nielsen, Lars K., Liang, Zhao-Xun and Turner, Mark S. (2016). Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis. Molecular Microbiology, 99 (6), 1015-1027. doi: 10.1111/mmi.13281 |
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2016 Book Chapter Metabolic pathway engineering for hyaluronic acid productionMarcellin, Esteban, Chen, Wendy Y. and Nielsen, Lars K. (2016). Metabolic pathway engineering for hyaluronic acid production. Handbook of carbohydrate-modifying biocatalysts. (pp. 683-696) edited by Peter Grunwald. Singapore: Pan Stanford Publishing. doi: 10.1201/9781315185392-21 |
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2016 Book Chapter Algae genome-scale reconstruction, modelling and applicationsDal'Molin, Cristiana G. O. and Nielsen, Lars K. (2016). Algae genome-scale reconstruction, modelling and applications. The Physiology of Microalgae. (pp. 591-598) edited by Michael A. Borowitzka, John Beardall and John A. Raven. Switzerland: Springer International Publishing. doi: 10.1007/978-3-319-24945-2_22 |
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2015 Journal Article Systems biology approaches to understand natural products biosynthesisLicona-Cassani, Cuauhtemoc, Cruz-Morales, Pablo, Manteca, Angel, Barona-Gomez, Francisco, Nielsen, Lars K. and Marcellin, Esteban (2015). Systems biology approaches to understand natural products biosynthesis. Frontiers in Bioengineering and Biotechnology, 3 199, 199.1-199.8. doi: 10.3389/fbioe.2015.00199 |
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2015 Journal Article Dynamic metabolic flux analysis using B-splines to study the effects of temperature shift on CHO cell metabolismMartinez, Verónica S., Buchsteiner, Maria, Gray, Peter, Nielsen, Lars K. and Quek, Lake-Ee (2015). Dynamic metabolic flux analysis using B-splines to study the effects of temperature shift on CHO cell metabolism. Metabolic Engineering Communications, 2, 46-57. doi: 10.1016/j.meteno.2015.06.001 |
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2015 Journal Article Systems analysis of methylerythritol-phosphate pathway flux in E. coli: Insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metaboliteBongers, Mareike, Chrysanthopoulos, Panagiotis K., Behrendorff, James B.Y.H., Hodson, Mark P., Vickers, Claudia E. and Nielsen, Lars K. (2015). Systems analysis of methylerythritol-phosphate pathway flux in E. coli: Insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite. Microbial Cell Factories, 14 (1) 193, 193. doi: 10.1186/s12934-015-0381-7 |
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2015 Journal Article Filling the void: allogeneic myeloid cells for transplantationSchwaber, Jessica L., Brunck, Marion E., Levesque, Jean-Pierre and Nielsen, Lars K. (2015). Filling the void: allogeneic myeloid cells for transplantation. Current Opinion in Hematology, 23 (1), 72-77. doi: 10.1097/MOH.0000000000000205 |
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2015 Other Outputs A unique model platform for C4 plant systems and synthetic biologyNielsen, Lars (2015). A unique model platform for C4 plant systems and synthetic biology. Alexandria, Virginia, United States: Defense Technical Information Center. |
