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2025 Journal Article Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cellsHefzi, Hooman, Martínez-Monge, Iván, Marin de Mas, Igor, Cowie, Nicholas Luke, Toledo, Alejandro Gomez, Noh, Soo Min, Karottki, Karen Julie la Cour, Decker, Marianne, Arnsdorf, Johnny, Camacho-Zaragoza, Jose Manuel, Kol, Stefan, Schoffelen, Sanne, Pristovšek, Nuša, Hansen, Anders Holmgaard, Miguez, Antonio A., Bjørn, Sara Petersen, Brøndum, Karen Kathrine, Javidi, Elham Maria, Jensen, Kristian Lund, Stangl, Laura, Kreidl, Emanuel, Kallehauge, Thomas Beuchert, Ley, Daniel, Ménard, Patrice, Petersen, Helle Munck, Sukhova, Zulfiya, Bauer, Anton, Casanova, Emilio, Barron, Niall ... Lewis, Nathan E. (2025). Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells. Nature Metabolism, 7 (1) P119, 1-16. doi: 10.1038/s42255-024-01193-7 |
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2024 Journal Article Unlocking DOE potential by selecting the most appropriate design for rAAV optimizationTzimou, Konstantina, Catalán-Tatjer, David, Nielsen, Lars K. and Lavado-García, Jesús (2024). Unlocking DOE potential by selecting the most appropriate design for rAAV optimization. Molecular Therapy - Methods and Clinical Development, 32 (4) 101329, 1-16. doi: 10.1016/j.omtm.2024.101329 |
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2024 Journal Article Title: Systematic insights into cell density-dependent transcriptional responses upon medium replacementsPérez-Rubio, Pol, Romero, Elianet Lorenzo, Cervera, Laura, Gòdia, Francesc, Nielsen, Lars Keld and Lavado-García, Jesús (2024). Title: Systematic insights into cell density-dependent transcriptional responses upon medium replacements. Biomedicine and Pharmacotherapy, 181 117640, 117640. doi: 10.1016/j.biopha.2024.117640 |
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2024 Journal Article Unsupervised Learning Bioreactor RegimesLaborda, Víctor Puig I., Puiman, Lars, Groves, Teddy, Haringa, Cees and Nielsen, Lars Keld (2024). Unsupervised Learning Bioreactor Regimes. Computers & Chemical Engineering, 194 108891, 1-17. doi: 10.1016/j.compchemeng.2024.108891 |
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2024 Journal Article Single‐Batch Expression of an Experimental Recombinant Snakebite Antivenom Based on an Oligoclonal Mixture of Human Monoclonal AntibodiesAdams, Anna C., Grav, Lise M., Ahmadi, Shirin, Holst Dahl, Camilla, Ljungars, Anne, Laustsen, Andreas H. and Nielsen, Lars K. (2024). Single‐Batch Expression of an Experimental Recombinant Snakebite Antivenom Based on an Oligoclonal Mixture of Human Monoclonal Antibodies. Biotechnology Journal, 19 (10) e202400348, e202400348. doi: 10.1002/biot.202400348 |
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2024 Journal Article Unravelling the essential elements for recombinant adeno-associated virus (rAAV) production in animal cell-based platformsCatalán-Tatjer, David, Tzimou, Konstantina, Nielsen, Lars K. and Lavado-García, Jesús (2024). Unravelling the essential elements for recombinant adeno-associated virus (rAAV) production in animal cell-based platforms. Biotechnology Advances, 73 108370. doi: 10.1016/j.biotechadv.2024.108370 |
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2024 Journal Article Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traitsArdalani, O., Phaneuf, P. V., Mohite, O. S., Nielsen, L. K. and Palsson, B. O. (2024). Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems, 9 (7). doi: 10.1128/msystems.00156-24 |
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2024 Journal Article Integrating genome-scale metabolic models with patient plasma metabolome to study endothelial metabolism in situSilva-Lance, Fernando, Montejano-Montelongo, Isabel, Bautista, Eric, Nielsen, Lars K., Johansson, Pär I. and Marin de Mas, Igor (2024). Integrating genome-scale metabolic models with patient plasma metabolome to study endothelial metabolism in situ. International Journal of Molecular Sciences, 25 (10) 5406, 1-22. doi: 10.3390/ijms25105406 |
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2024 Journal Article Bayesian regression facilitates quantitative modeling of cell metabolismGroves, Teddy, Cowie, Nicholas Luke and Nielsen, Lars Keld (2024). Bayesian regression facilitates quantitative modeling of cell metabolism. ACS Synthetic Biology, 13 (4), 1205-1214. doi: 10.1021/acssynbio.3c00662 |
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2024 Journal Article Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterationsHeffernan, James, Garcia Gonzalez, R. Axayactl, Mahamkali, Vishnu, McCubbin, Tim, Daygon, Dara, Liu, Lian, Palfreyman, Robin, Harris, Audrey, Koepke, Michael, Valgepea, Kaspar, Nielsen, Lars Keld and Marcellin, Esteban (2024). Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microbial Biotechnology, 17 (4) e14452, e14452. doi: 10.1111/1751-7915.14452 |
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2024 Journal Article Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivationNöbel, Matthias, Barry, Craig, MacDonald, Michael A., Baker, Kym, Shave, Evan, Mahler, Stephen, Munro, Trent, Martínez, Verónica S., Nielsen, Lars K. and Marcellin, Esteban (2024). Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation. Biotechnology and Bioengineering, 121 (4), 1371-1383. doi: 10.1002/bit.28613 |
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2024 Journal Article Shu: Visualization of high dimensional biological pathwaysCarrasco Muriel, Jorge, Cowie, Nicholas, Taylor Parkins, Shannara, Mansouvar, Marjan, Groves, Teddy and Nielsen, Lars Keld (2024). Shu: Visualization of high dimensional biological pathways. Bioinformatics, 40 (3) btae140, 1-4. doi: 10.1093/bioinformatics/btae140 |
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2024 Journal Article LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic modelsSaa, Pedro A., Zapararte, Sebastian, Drovandi, Christopher C. and Nielsen, Lars K. (2024). LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models. BMC Bioinformatics, 25 (1) 3, 1-8. doi: 10.1186/s12859-023-05616-2 |
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2023 Journal Article CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cellsVlassis, Arsenios, Jensen, Tanja L., Mohr, Marina, Jedrzejczyk, Dominika J., Meng, Xiangyou, Kovacs, Gergo, Morera-Gómez, Martí, Barghetti, Andrea, Muyo Abad, Sergi, Baumgartner, Roland F., Natarajan, Kedar N., Nielsen, Lars K., Warnecke, Tanya and Gill, Ryan T. (2023). CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells. iScience, 26 (12) 108287, 1-30. doi: 10.1016/j.isci.2023.108287 |
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2023 Journal Article Comparative constraint‐based modelling of fruit development across species highlights nitrogen metabolism in the growth‐defence trade‐offColombié, Sophie, Prigent, Sylvain, Cassan, Cédric, Hilbert‐Masson, Ghislaine, Renaud, Christel, Dell'Aversana, Emilia, Carillo, Petronia, Moing, Annick, Beaumont, Chloé, Beauvoit, Bertrand, McCubbin, Tim, Nielsen, Lars Keld and Gibon, Yves (2023). Comparative constraint‐based modelling of fruit development across species highlights nitrogen metabolism in the growth‐defence trade‐off. The Plant Journal, 116 (3), 786-803. doi: 10.1111/tpj.16409 |
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2023 Journal Article Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economyOrsi, Enrico, Nikel, Pablo Ivan, Nielsen, Lars Keld and Donati, Stefano (2023). Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy. Nature Communications, 14 (1) 6673, 1-9. doi: 10.1038/s41467-023-42166-w |
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2023 Journal Article Omics data for sampling thermodynamically feasible kinetic modelsde Leeuw, Marina, Matos, Marta R.A. and Nielsen, Lars Keld (2023). Omics data for sampling thermodynamically feasible kinetic models. Metabolic Engineering, 78, 41-47. doi: 10.1016/j.ymben.2023.05.002 |
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2023 Journal Article An automated workflow for multi-omics screening of microbial model organismsDonati, Stefano, Mattanovich, Matthias, Hjort, Pernille, Jacobsen, Simo Abdessamad Baallal, Blomquist, Sarah Dina, Mangaard, Drude, Gurdo, Nicolas, Pastor, Felix Pacheco, Maury, Jérôme, Hanke, Rene, Herrgård, Markus J., Wulff, Tune, Jakočiūnas, Tadas, Nielsen, Lars Keld and McCloskey, Douglas (2023). An automated workflow for multi-omics screening of microbial model organisms. npj Systems Biology and Applications, 9 (1) 14, 1-12. doi: 10.1038/s41540-023-00277-6 |
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2023 Journal Article A protocol for the automatic construction of highly curated genome-scale models of human metabolismMarin de Mas, Igor, Herand, Helena, Carrasco, Jorge, Nielsen, Lars K. and Johansson, Pär I. (2023). A protocol for the automatic construction of highly curated genome-scale models of human metabolism. Bioengineering, 10 (5) 576. doi: 10.3390/bioengineering10050576 |
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2023 Journal Article Enhancing CHO cell productivity through a dual selection system using Aspg and Gs in glutamine free mediumHa, Tae Kwang, Òdena, Andreu, Karottki, Karen Julie la Cour, Kim, Che Lin, Hefzi, Hooman, Lee, Gyun Min, Faustrup Kildegaard, Helene, Nielsen, Lars K., Grav, Lise Marie and Lewis, Nathan E. (2023). Enhancing CHO cell productivity through a dual selection system using Aspg and Gs in glutamine free medium. Biotechnology and Bioengineering, 120 (4), 1159-1166. doi: 10.1002/bit.28318 |
