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2026 Journal Article Kinetic sampling shows the effect of medium composition on metabolic control in Saccharomyces cerevisiaeDe Leeuw, Marina and Nielsen, Lars Keld (2026). Kinetic sampling shows the effect of medium composition on metabolic control in Saccharomyces cerevisiae. Microbial Cell Factories, 25 (1) 76, 1-9. doi: 10.1186/s12934-025-02884-w |
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2026 Journal Article Omics-guided engineering of CHO cells reveals host targets to support AAV productionTzimou, Konstantina, López-García, Guillem, Sipahi, Meryem Irem, Nielsen, Lars K. and Lavado-García, Jesús (2026). Omics-guided engineering of CHO cells reveals host targets to support AAV production. Molecular Therapy Advances, 34 (3) 201771, 1-21. doi: 10.1016/j.omta.2026.201771 |
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2026 Journal Article Extracellular vesicle depletion improves transient gene expression performance and alters cellular transcriptional responses in CHO cellRahimi, Marzia, Pérez-Rubio, Pol, Vargas-Gracia, Juliana, Kempen, Paul J., Nielsen, Lars K. and Lavado-García, Jesús (2026). Extracellular vesicle depletion improves transient gene expression performance and alters cellular transcriptional responses in CHO cell. Biomedicine & Pharmacotherapy, 201 119749, 119749. doi: 10.1016/j.biopha.2026.119749 |
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2026 Journal Article Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymesArdalani, Omid, Phaneuf, Patrick V., Krishnan, Kalpathy J., Pride, David, Nielsen, Lars K. and Palsson, Bernhard O. (2026). Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes. Science Advances, 12 (27) eaeb3363, eaeb3363-27. doi: 10.1126/sciadv.aeb3363 |
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2026 Conference Publication Multi-scale Metabolic Modeling and SimulationCarstensen, Peter E., Groves, Teddy, Nielsen, Lars K., Krühne, Ulrich, Gernaey, Krist V. and Jørgensen, John B. (2026). Multi-scale Metabolic Modeling and Simulation. Hamilton, Canada: PSE Press. doi: 10.69997/sct.196453 |
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2026 Journal Article A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cellsDi Giusto, Pablo, Choi, Dong-Hyuk, Antonakoudis, Athanasios, Duraikannan, Vikash Gokul, Craveur, Pierrick, Cowie, Nicholas Luke, Ganapathy, Tejaswini, Ramesh, Kannan, Benavidez-López, Santiago, Orellana, Camila A., Jiménez, Natalia E., Dworkin, Leo Alexander, Morrissey, James, Marin de Mas, Igor, Strain, Benjamin, Valdez-Cruz, Norma A., Trujillo-Roldán, Mauricio A., Marzluf, Jannis, Martínez, Verónica S., Zehetner, Leopold, Altamirano, Claudia, Vega-Letter, Ana Maria, Priem, Bradley, Cao, Haoyu Chris, Hold, Martin, Ma, Junyu, Hong, Yi Fan, Gopalakrishnan, Saratram, Enuh, Blaise Manga ... Lewis, Nathan E. (2026). A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells. Cell Systems, 17 (6) 101574, 101574-6. doi: 10.1016/j.cels.2026.101574 |
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2026 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. (2026). Gas–liquid mass-transfer modeling in industrial-scale bioreactors: a standardized framework and critical assessment. Chemical Engineering Journal Advances, 25 100982, 1-35. doi: 10.1016/j.ceja.2025.100982 |
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2026 Journal Article High-throughput optimization of antibody production in CHO cells by tuning heavy- and light-chain promoter strengthRahimi, Marzia, Adams, Anna Christina, Grav, Lise M., Nielsen, Lars K. and Lavado-García, Jesús (2026). High-throughput optimization of antibody production in CHO cells by tuning heavy- and light-chain promoter strength. Frontiers in Bioengineering and Biotechnology, 13 1747473. doi: 10.3389/fbioe.2025.1747473 |
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2026 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 (2026). Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasets. Molecular and Cellular Proteomics, 25 (1) 101475, 1-14. doi: 10.1016/j.mcpro.2025.101475 |
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2025 Journal Article Systematic evaluation of vector sequence elements in isogenic CHO cells for improved antibody productionRahimi, Marzia, Adams, Anna Christina, Grav, Lise Marie, Nielsen, Lars K. and Lavado-Garcia, Jesus (2025). Systematic evaluation of vector sequence elements in isogenic CHO cells for improved antibody production. ACS Synthetic Biology, 15 (1), 342-352. doi: 10.1021/acssynbio.5c00861 |
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2025 Journal Article Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coliArdalani, 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. doi: 10.1371/journal.ppat.1013775 |
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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, 1-20. 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 Cupriavidus necator 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, 1-1. 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, 33 (1), 48-56. 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) P119, 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 |
