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2020 Journal Article Publisher Correction: MEMOTE for standardized genome-scale metabolic model testingLieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda ... Zhang, Cheng (2020). Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38 (4), 504-504. doi: 10.1038/s41587-020-0477-4 |
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2020 Journal Article Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid productionBongers, Mareike, Perez-Gil, Jordi, Hodson, Mark P., Schrübbers, Lars, Wulff, Tune, Sommer, Morten Oa, Nielsen, Lars K. and Vickers, Claudia E. (2020). Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production. eLife, 9 e48685, e48685. doi: 10.7554/eLife.48685 |
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2020 Journal Article MEMOTE for standardized genome-scale metabolic model testingLieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda ... Zhang, Cheng (2020). MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38 (3), 272-276. doi: 10.1038/s41587-020-0446-y |
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2020 Other Outputs Enhancing CO2-valorization using Clostridium autoethanogenum for sustainable fuel and chemicals productionHeffernan, James K., Valgepea, Kaspar, de Souza Pinto Lemgruber, Renato, Casini, Isabella, Plan, Manuel, Tappel, Ryan, Simpson, Sean D., Köpke, Michael, Nielsen, Lars K. and Marcellin, Esteban (2020). Enhancing CO2-valorization using Clostridium autoethanogenum for sustainable fuel and chemicals production. doi: 10.1101/2020.01.23.917666 |
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2020 Journal Article Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical productionHenry, Matthew N., MacDonald, Michael A., Orellana, Camila A., Gray, Peter P., Gillard, Marianne, Baker, Kym, Nielsen, Lars K., Marcellin, Esteban, Mahler, Stephen and Martinez, Veronica S. (2020). Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production. Biotechnology and Bioengineering, 117 (4) bit.27269, 1187-1203. doi: 10.1002/bit.27269 |
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2020 Journal Article Engineering Escherichia coli for propionic acid production through the Wood‐Werkman cycleGonzalez‐Garcia, R. A., McCubbin, T., Turner, M. S., Nielsen, L. K. and Marcellin, E. (2020). Engineering Escherichia coli for propionic acid production through the Wood‐Werkman cycle. Biotechnology and Bioengineering, 117 (1), 167-183. doi: 10.1002/bit.27182 |
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2019 Journal Article A TetR-family protein (CAETHG_0459) activates transcription from a new promoter motif associated with essential genes for autotrophic growth in acetogensLemgruber, Renato de Souza Pinto, Valgepea, Kaspar, Garcia, Ricardo Axayacatl Gonzalez, de Bakker, Christopher, Palfreyman, Robin William, Tappel, Ryan, Kopke, Michael, Simpson, Sean Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2019). A TetR-family protein (CAETHG_0459) activates transcription from a new promoter motif associated with essential genes for autotrophic growth in acetogens. Frontiers in Microbiology, 10 2549, 2549. doi: 10.3389/fmicb.2019.02549 |
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2019 Journal Article Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: metabolic response to chronic exposure to Aldrin in prostate cancerde Mas, Igor Marin, Torrents, Laura, Bedia, Carmen, Nielsen, Lars K., Cascante, Marta and Tauler, Roma (2019). Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: metabolic response to chronic exposure to Aldrin in prostate cancer. BMC Genomics, 20 (1) 652. doi: 10.1186/s12864-019-5979-4 |
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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 |
