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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 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 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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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 Journal Article Do genome-scale models need exact solvers or clearer standards?Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P., Chang, Roger L., Draeger, Andreas, Famili, Iman, Feist, Adam M., Fleming, Ronan M. T., Fong, Stephen S., Hatzimanikatis, Vassily, Herrgard, Markus J., Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novere, Nicolas, Lerman, Joshua A., Lewis, Nathan E., Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K., Nogales, Juan ... Thiele, Ines (2015). Do genome-scale models need exact solvers or clearer standards?. Molecular Systems Biology, 11 (10) 831, 831. doi: 10.15252/msb.20156157 |
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2015 Journal Article A liquid chromatography-tandem mass spectrometry-based investigation of the lamellar interstitial metabolome in healthy horses and during experimental laminitis inductionMedina-Torres, C. E., van Eps, A. W., Nielsen, L. K. and Hodson, M. P. (2015). A liquid chromatography-tandem mass spectrometry-based investigation of the lamellar interstitial metabolome in healthy horses and during experimental laminitis induction. Veterinary Journal, 206 (2), 161-169. doi: 10.1016/j.tvjl.2015.07.031 |
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2015 Journal Article Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditionsLim, SooA, Marcellin, Esteban, Jacob, Shana and Nielsen, Lars K. (2015). Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. Journal of Proteomics, 126, 24-33. doi: 10.1016/j.jprot.2015.05.021 |
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2015 Journal Article Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activitiesPeng, Bingyin, Williams, Thomas C., Henry, Matthew, Nielsen, Lars K. and Vickers, Claudia E. (2015). Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microbial Cell Factories, 14 (1) 91, 1-11. doi: 10.1186/s12934-015-0278-5 |
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2015 Journal Article Intracellular trafficking of baculovirus particles: A quantitative study of the hearNPV/HzAm1 cell and AcMNPV/sf9 cell systemsMatindoost, Leila, Nielsen, Lars K and Reid, Steve (2015). Intracellular trafficking of baculovirus particles: A quantitative study of the hearNPV/HzAm1 cell and AcMNPV/sf9 cell systems. Viruses, 7 (5), 2288-2307. doi: 10.3390/v7052288 |
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2015 Journal Article Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiaeWilliams, T. C., Averesch, N. J. H., Winter, G., Plan, M. R., Vickers, C. E., Nielsen, L. K. and Kromer, J. O. (2015). Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metabolic Engineering, 29, 124-134. doi: 10.1016/j.ymben.2015.03.008 |
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2015 Journal Article Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiaeBrennan, Timothy C. R., Williams, Thomas C., Schulz, Benjamin L., Palfreyman, Robin W., Kroemer, Jens O. and Nielsen, Lars K. (2015). Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 81 (10), 3316-3325. doi: 10.1128/AEM.04144-14 |
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2015 Journal Article A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactionsSaa, Pedro and Nielsen, Lars K. (2015). A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions. PLoS Computational Biology, 11 (4) e1004195, 1-25. doi: 10.1371/journal.pcbi.1004195 |
