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2019 Journal Article Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic UpdateCruz-Morales, Pablo, Orellana, Camila A., Moutafis, George, Moonen, Glenn, Rincon, Gonzalo, Nielsen, Lars K. and Marcellin, Esteban (2019). Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update. Genome Biology and Evolution, 11 (7), 2035-2044. doi: 10.1093/gbe/evz096 |
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2019 Journal Article Systems-level engineering and characterization of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB)de Souza Pinto Lemgruber, Renato, Valgepea, Kaspar, Tappel, Ryan, Behrendorff, James B., Palfreyman, Robin William, Plan, Manuel, Hodson, Mark P., Simpson, Séan Dennis, Nielsen, Lars K., Köpke, Michael and Marcellin, Esteban (2019). Systems-level engineering and characterization of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB). Metabolic Engineering, 53, 14-23. doi: 10.1016/j.ymben.2019.01.003 |
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2019 Journal Article Shedding light: the importance of reverse transcription efficiency standards in data interpretationSchwaber, Jessica, Andersen, Stacey and Nielsen, Lars (2019). Shedding light: the importance of reverse transcription efficiency standards in data interpretation. Biomolecular Detection and Quantification, 17 100077, 100077. doi: 10.1016/j.bdq.2018.12.002 |
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2018 Journal Article Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generationGrav, Lise Marie, Sergeeva, Daria, Lee, Jae Seong, Marín De Mas, Igor, Lewis, Nathan E., Andersen, Mikael Rørdam, Nielsen, Lars K., Lee, Gyun Min and Kildegaard, Helene Faustrup (2018). Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generation. ACS Synthetic Biology, 7 (9) acssynbio.8b00140, 2148-2159. doi: 10.1021/acssynbio.8b00140 |
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2018 Journal Article Linking genotype and phenotype in an economically viable propionic acid biosynthesis processLuna-Flores, Carlos H., Stowers, Chris C., Cox, Brad M., Nielsen, Lars K. and Marcellin, Esteban (2018). Linking genotype and phenotype in an economically viable propionic acid biosynthesis process. Biotechnology for Biofuels, 11 (1) 224, 224. doi: 10.1186/s13068-018-1222-9 |
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2018 Journal Article Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysisHardwick, Simon A., Chen, Wendy Y., Wong, Ted, Kanakamedala, Bindu S., Deveson, Ira W., Ongley, Sarah E., Santini, Nadia S., Marcellin, Esteban, Smith, Martin A., Nielsen, Lars K., Lovelock, Catherine E., Neilan, Brett A. and Mercer, Tim R. (2018). Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis. Nature Communications, 9 (1) 3096, 3096. doi: 10.1038/s41467-018-05555-0 |
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2018 Journal Article Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiaePeng, Bingyin, Nielsen, Lars K., Kampranis, Sotirios C. and Vickers, Claudia E. (2018). Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae. Metabolic Engineering, 47, 83-93. doi: 10.1016/j.ymben.2018.02.005 |
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2018 Journal Article Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effectBuchsteiner, Maria, Quek, Lake-Ee, Gray, Peter and Nielsen, Lars K. (2018). Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect. Biotechnology and Bioengineering, 115 (9), 2315-2327. doi: 10.1002/bit.26724 |
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2018 Journal Article From reconstruction to C4 metabolic engineering: a case study for overproduction of polyhydroxybutyrate in bioenergy grassesGomes de Oliveira Dal'Molin, Cristiana, Quek, Lake-Ee, Saa, Pedro A., Palfreyman, Robin and Nielsen, Lars Keld (2018). From reconstruction to C4 metabolic engineering: a case study for overproduction of polyhydroxybutyrate in bioenergy grasses. Plant Science, 273, 50-60. doi: 10.1016/j.plantsci.2018.03.027 |
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2018 Journal Article Towards industrial production of isoprenoids in Escherichia coli: lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathwayAlonso-Gutierrez, Jorge, Koma, Daisuke, Hu, Qijun, Yang, Yuchen, Chan, Leanne Jade G., Petzold, Christopher J., Adams, Paul D., Vickers, Claudia E., Nielsen, Lars K., Keasling, Jay D. and Lee, Taek Soon (2018). Towards industrial production of isoprenoids in Escherichia coli: lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnology and Bioengineering, 115 (4), 1000-1013. doi: 10.1002/bit.26530 |
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2018 Journal Article H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenumValgepea, Kaspar, de Souza Pinto Lemgruber, Renato, Abdalla, Tanus, Binos, Steve, Takemori, Nobuaki, Takemori, Ayako, Tanaka, Yuki, Tappel, Ryan, Köpke, Michael, Simpson, Séan Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2018). H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum. Biotechnology for Biofuels, 11 (1) 55, 55. doi: 10.1186/s13068-018-1052-9 |
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2018 Journal Article RNA-seq highlights high clonal variation in monoclonal antibody producing CHO cellsOrellana, Camila A., Marcellin, Esteban, Palfreyman, Robin W., Munro, Trent P., Gray, Peter P. and Nielsen, Lars K. (2018). RNA-seq highlights high clonal variation in monoclonal antibody producing CHO cells. Biotechnology Journal, 13 (3) 1700231, e1700231. doi: 10.1002/biot.201700231 |
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2018 Journal Article Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenumLemgruber, Renato de Souza Pinto, Valgepea, Kaspar, Hodson, Mark P., Tappel, Ryan, Simpson, Sean D., Kopke, Michael, Nielsen, Lars K. and Marcellin, Esteban (2018). Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenum. Metabolomics, 14 (3) 35, 35. doi: 10.1007/s11306-018-1331-2 |
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2018 Journal Article Advances in analytical tools for high throughput strain engineeringMarcellin, Esteban and Nielsen, Lars Keld (2018). Advances in analytical tools for high throughput strain engineering. Current Opinion in Biotechnology, 54, 33-40. doi: 10.1016/j.copbio.2018.01.027 |
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2018 Journal Article Universal Alternative Splicing of Noncoding ExonsDeveson, Ira W., Brunck, Marion E., Blackburn, James, Tseng, Elizabeth, Hon, Ting, Clark, Tyson A., Clark, Michael B., Crawford, Joanna, Dinger, Marcel E., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2018). Universal Alternative Splicing of Noncoding Exons. Cell Systems, 6 (2), 245-255. doi: 10.1016/j.cels.2017.12.005 |
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2018 Journal Article An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiaePeng, Bingyin, Wood, Rebecca J., Nielsen, Lars K. and Vickers, Claudia E. (2018). An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiae. ACS Synthetic Biology, 7 (2), 748-751. doi: 10.1021/acssynbio.7b00355 |
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2017 Journal Article Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic NetworksAveresch, Nils J. H., Martínez, Verónica S., Nielsen, Lars K. and Krömer, Jens O. (2017). Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synthetic Biology, 7 (2), 490-509. doi: 10.1021/acssynbio.7b00304 |
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2017 Journal Article Genome-scale model guided design of Propionibacterium for enhanced propionic acid productionNavone, Laura, McCubbin, Tim, Gonzalez-Garcia, Ricardo A., Nielsen, Lars K. and Marcellin, Esteban (2017). Genome-scale model guided design of Propionibacterium for enhanced propionic acid production. Metabolic Engineering Communications, 6, 1-12. doi: 10.1016/j.meteno.2017.11.001 |
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2017 Journal Article Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrestMills, Richard J., Titmarsh, Drew M., Koenig, Xaver, Parker, Benjamin L., Ryall, James G., Quaife-Ryan, Gregory A., Voges, Holly K., Hodson, Mark P., Ferguson, Charles, Drowley, Lauren, Plowright, Alleyn T., Needham, Elise J., Wang, Qing-Dong, Gregorevic, Paul, Xin, Mei, Thomas, Walter G., Parton, Robert G., Nielsen, Lars K., Launikonis, Bradley S., James, David E., Elliott, David A., Porrello, Enzo R. and Hudson, James E. (2017). Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest. Proceedings of the National Academy of Sciences of the United States of America, 114 (40), E8372-E8381. doi: 10.1073/pnas.1707316114 |
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2017 Journal Article Cell-free pipeline for discovery of thermotolerant xylanases and endo-1,4-β-glucanasesGagoski, Dejan, Shi, Zhenyu, Nielsen, Lars Keld, Vickers, Claudia E., Mahler, Stephen, Speight, Robert, Johnston, Wayne A. and Alexandrov, Kirill (2017). Cell-free pipeline for discovery of thermotolerant xylanases and endo-1,4-β-glucanases. Journal of Biotechnology, 259, 191-198. doi: 10.1016/j.jbiotec.2017.07.014 |
