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2027 Journal Article Plug-and-Play or Plug-and-Pray? Impact of random versus targeted integration on the linearity and orthogonality of synthetic gene circuits in CHO cellsLim, Sheryl Li Yan, Nielsen, Lars K., Jiménez del Val, Ioscani and Lavado-García, Jesús (2027). Plug-and-Play or Plug-and-Pray? Impact of random versus targeted integration on the linearity and orthogonality of synthetic gene circuits in CHO cells. Synthetic and Systems Biotechnology, 19, 69-80. doi: 10.1016/j.synbio.2026.10.004 |
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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 Machine-learning surrogates enable rapid prediction of 3-D substrate gradients in industrial bioreactorsPuig-I-Laborda, Víctor, Carrasco Muriel, Jorge, Castañeda Tena, Andrea, Groves, Teddy, le Nepvou de Carfort, Johan, Krühne, Ulrich, Gernaey, Krist V., Haringa, Cees, Puig-de-Dou, Ignasi and Nielsen, Lars Keld (2026). Machine-learning surrogates enable rapid prediction of 3-D substrate gradients in industrial bioreactors. Nature Communications. doi: 10.1038/s41467-026-78273-7 |
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2026 Journal Article Automated mini-bioreactors reveal the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putidaSaavedra, Mariana Arango, Grassi, Sara, Jespersen, Magnus Ganer, Rocha, Catarina, Kandasamy, Viji, Nielsen, Lars Keld, Nikel, Pablo Ivan and Donati, Stefano (2026). Automated mini-bioreactors reveal the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putida. ACS Synthetic Biology, 15 (10), 4023-4038. doi: 10.1021/acssynbio.6c00205 |
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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 PREFER: An Ontology for the PREcision FERmentation CommunityAmigó, Txell, Tan, Shawn Zheng Kai, Phanthanourak, Angel Luu, Schulz, Sebastian, Colaianni, Pasquale D., Maszczyk, Dominik M., Milesi, Ester, Schlembach, Ivan, Semenov Petrov, Mykhaylo, Reventós Montané, Marta, Nielsen, Lars K., Förster, Jochen, Palsson, Bernhard Ø., Sudarsan, Suresh and Santos, Alberto (2026). PREFER: An Ontology for the PREcision FERmentation Community. Scientific Data. doi: 10.1038/s41597-026-08099-x |
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2026 Journal Article A Robust Isotope Ratio LC–MS/MS Workflow for High-Throughput Metabolic Profiling of BacteriaRocha, Catarina, Pinto, Sergi Pujol, Jensen, Sheila Ingemann, Nielsen, Lars Keld and Donati, Stefano (2026). A Robust Isotope Ratio LC–MS/MS Workflow for High-Throughput Metabolic Profiling of Bacteria. Analytical Chemistry, 98 (33), 23989-23997. doi: 10.1021/acs.analchem.5c04931 |
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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 |
