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2025 Journal Article Gas–liquid mass-transfer modeling in industrial-scale bioreactors: a standardized framework and critical assessmentLaborda, Víctor Puig I., Le Nepvou De Carfort, Johan, Krühne, Ulrich, Gernaey, Krist V., Kavanagh, John M., Fletcher, David F. and Nielsen, Lars K. (2025). Gas–liquid mass-transfer modeling in industrial-scale bioreactors: a standardized framework and critical assessment. Chemical Engineering Journal Advances 100982. doi: 10.1016/j.ceja.2025.100982 |
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2025 Journal Article Rare metabolic gene essentiality is a determinant of microniche adaptation in <i>Eschherichia coli</i>Ardalani, Omid, Phaneuf, Patrick V., Krishnan, Jayanth, Chauhan, Siddharth M., Pride, David, Zielinski, Daniel C., Monk, Jonathan M., Nielsen, Lars K. and Palsson, Bernhard O. (2025). Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coli. Plos Pathogens, 21 (12) e1013775, e1013775. doi: 10.1371/journal.ppat.1013775 |
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2025 Journal Article Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasetsBarry, Craig P., Talbo, Gert H., Beauglehole, Aiden, Ovchinnikov, Dmitry, Munro, Trent, Mahler, Stephen, Baker, Kym, Nielsen, Lars K., Mercer, Tim R. and Marcellin, Esteban (2025). Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasets. Molecular and Cellular Proteomics, 25 (1) 101475. doi: 10.1016/j.mcpro.2025.101475 |
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2025 Journal Article Targeted UDP-glucose ceramide glucosyltransferase stable overexpression induces a metabolic switch improving cell performance at high cell densityRahimi, Marzia, Nielsen, Lars K. and Lavado-Garcia, Jesus (2025). Targeted UDP-glucose ceramide glucosyltransferase stable overexpression induces a metabolic switch improving cell performance at high cell density. Frontiers in Bioengineering and Biotechnology, 13 1690203, 1690203. doi: 10.3389/fbioe.2025.1690203 |
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2025 Journal Article Flow-informed Clustering of Bioreactor Volumes to Build CFD-based Compartment ModelsLe Nepvou De Carfort, Johan, Puig I Laborda, Víctor, Nielsen, Lars Keld, Gernaey, Krist V. and Krühne, Ulrich (2025). Flow-informed Clustering of Bioreactor Volumes to Build CFD-based Compartment Models. Chemical Engineering Science, 320 122539, 122539. doi: 10.1016/j.ces.2025.122539 |
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2025 Journal Article Comparative Genomic Assessment of the <scp><i>Cupriavidus necator</i></scp> Species for One‐Carbon Based BiomanufacturingJespersen, Magnus G., Vangsgaard, Emil Funk, Saavedra, Mariana Arango, Donati, Stefano and Nielsen, Lars K. (2025). Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing. Microbial Biotechnology, 18 (7) e70201, e70201. doi: 10.1111/1751-7915.70201 |
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2025 Journal Article Mixture design as a tool for improving full-to-empty particle ratios across various GOIs in rAAV productionTzimou, Konstantina, Hulsbus-Andreu, Pol, Yildirim, Ece Bahar, Nielsen, Lars K. and Lavado-García, Jesús (2025). Mixture design as a tool for improving full-to-empty particle ratios across various GOIs in rAAV production. Gene Therapy. doi: 10.1038/s41434-025-00546-5 |
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2025 Conference Publication CO(2)-metabolism: quantifying mixed carbon oxide and hydrogen gas fermentation by Clostridium autoethanogenumHeffernan, James K., Nielsen, Lars K. and Marcellin, Esteban (2025). CO(2)-metabolism: quantifying mixed carbon oxide and hydrogen gas fermentation by Clostridium autoethanogenum. Inaugural UQ Biosustainability Hub Conference, Tangalooma, QLD, Australia, 7-9 May 2025. |
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2025 Journal Article Evaluating apoptotic gene efficiency for CHO culture performance using targeted integrationCatalán-Tatjer, David, Kumar Ganesan, Saravana, Martínez-Monje, Iván, Grav, Lise M., Lavado-García, Jesús and Nielsen, Lars K. (2025). Evaluating apoptotic gene efficiency for CHO culture performance using targeted integration. ACS Synthetic Biology, 14 (5), 1414-1424. doi: 10.1021/acssynbio.4c00382 |
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2025 Conference Publication CO(2)-Metabolism: Quantifying Mixed Carbon Oxide And Hydrogen Gas Fermentation By Clostridium Autoethanogenum.Heffernan, James K., Gonzalez Garcia, R. Axayactl, McCubbin, Timothy, Kopke, Michael, Valgepea, Kaspar, Nielsen, Lars and Marcellin, Esteban (2025). CO(2)-Metabolism: Quantifying Mixed Carbon Oxide And Hydrogen Gas Fermentation By Clostridium Autoethanogenum.. The Carbon Recycling Network Conference 5, Cheshire, United Kingdom, 9-12 March 2025. |
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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), 212-227. 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 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). Systematic insights into cell density-dependent transcriptional responses upon medium replacements. Biomedicine and Pharmacotherapy, 181 117640, 1-17. 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, 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), e0015624. 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 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 |
