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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 Conference Publication Quantifying Co-Metabolism of CO/CO2 By Clostridium autoethanogenum in ChemostatsHeffernan, James, Gonzalez-Garcia, R. Axayacatl, McCubbin, Timothy, Köpke, Michael, Valgepea, Kaspar, Nielsen, Lars and Marcellin, Esteban (2023). Quantifying Co-Metabolism of CO/CO2 By Clostridium autoethanogenum in Chemostats. Metabolic Engineering 15, Singapore, 11-15 June 2023. |
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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, 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 |
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2023 Journal Article A multi-level systems biology analysis of Aldrin’s metabolic effects on prostate cancer cellsBedia, Carmen, Dalmau, Nuria, Nielsen, Lars K., Tauler, Romà and Marín de Mas, Igor (2023). A multi-level systems biology analysis of Aldrin’s metabolic effects on prostate cancer cells. Proteomes, 11 (2) 11, 1-19. doi: 10.3390/proteomes11020011 |
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2023 Journal Article Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptidesGurdo, Nicolás, Taylor Parkins, Shannara Kayleigh, Fricano, Martina, Wulff, Tune, Nielsen, Lars Keld and Nikel, Pablo Iván (2023). Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptides. STAR Protocols, 4 (1) 102060, 1-2. doi: 10.1016/j.xpro.2023.102060 |
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2023 Journal Article Endothelial cell phenotypes demonstrate different metabolic patterns and predict mortality in trauma patientsHenriksen, Hanne H., Marín de Mas, Igor, Nielsen, Lars K., Krocker, Joseph, Stensballe, Jakob, Karvelsson, Sigurður T., Secher, Niels H., Rolfsson, Óttar, Wade, Charles E. and Johansson, Pär I. (2023). Endothelial cell phenotypes demonstrate different metabolic patterns and predict mortality in trauma patients. International Journal of Molecular Sciences, 24 (3) 2257, 1-14. doi: 10.3390/ijms24032257 |
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2023 Journal Article Biogas upgrading using Clostridium autoethanogenum for value-added productsHeffernan, James K., Lai, Chun-Yu, Gonzalez-Garcia, R. Axayacatl, Nielsen, Lars Keld, Guo, Jianhua and Marcellin, Esteban (2023). Biogas upgrading using Clostridium autoethanogenum for value-added products. Chemical Engineering Journal, 452 (Part 1) 138950, 1-7. doi: 10.1016/j.cej.2022.138950 |
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2022 Journal Article Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications, 13 (1) 1200. doi: 10.1038/s41467-022-28758-y |
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2022 Journal Article Elucidating dynamics and mechanism of cyclic bioreaction networks using topologically-equivalent electrical circuitsNath, Sarang S., Nielsen, Lars K. and Villadsen, John (2022). Elucidating dynamics and mechanism of cyclic bioreaction networks using topologically-equivalent electrical circuits. Chemical Engineering Science, 262 118015, 1-11. doi: 10.1016/j.ces.2022.118015 |
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2022 Journal Article GRASP: a computational platform for building kinetic models of cellular metabolismMatos, Marta R. A., Saa, Pedro A, Cowie, Nicholas, Volkova, Svetlana, de Leeuw, Marina and Nielsen, Lars K. (2022). GRASP: a computational platform for building kinetic models of cellular metabolism. Bioinformatics Advances, 2 (1) vbac066, 1-3. doi: 10.1093/bioadv/vbac066 |
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2022 Journal Article RNA-seq sample preparation kits strongly affect transcriptome profiles of a gas-fermenting bacteriumde Lima, Lorena Azevedo, Reinmets, Kristina, Nielsen, Lars Keld, Marcellin, Esteban, Harris, Audrey, Köpke, Michael and Valgepea, Kaspar (2022). RNA-seq sample preparation kits strongly affect transcriptome profiles of a gas-fermenting bacterium. Microbiology Spectrum, 10 (4), 1-7. doi: 10.1128/spectrum.02303-22 |
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2022 Journal Article Recycling carbon for sustainable protein production using gas fermentationMarcellin, Esteban, Angenent, Largus T., Nielsen, Lars K. and Molitor, Bastian (2022). Recycling carbon for sustainable protein production using gas fermentation. Current Opinion in Biotechnology, 76 102723, 102723. doi: 10.1016/j.copbio.2022.102723 |
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2022 Journal Article The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibilityMartínez, Verónica S., Saa, Pedro A., Jooste, Jason, Tiwari, Kanupriya, Quek, Lake-Ee and Nielsen, Lars K. (2022). The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility. PLoS Computational Biology, 18 (6) e1010203, e1010203. doi: 10.1371/journal.pcbi.1010203 |
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2022 Conference Publication Adaptive laboratory evolution of Clostridium autoethanogenum to enhance CO2 valorizationHeffernan, James, Gonzalez Garcia, Ricardo A., McCubbin, Timothy, Daygon, Dara, Plan, Manuel, Talbo, Gert, Liu, Lian, Palfreyman, Robin, Köpke, Michael, Nielsen, Lars K. and Marcellin, Esteban (2022). Adaptive laboratory evolution of Clostridium autoethanogenum to enhance CO2 valorization. Biochemical and Molecular Engineering XXII, Cancun, Mexico, 26-30 June 2022. |
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2022 Journal Article Engineering death resistance in CHO cells for improved perfusion cultureMacDonald, Michael A., Nöbel, Matthias, Martínez, Verónica S., Baker, Kym, Shave, Evan, Gray, Peter P., Mahler, Stephen, Munro, Trent, Nielsen, Lars K. and Marcellin, Esteban (2022). Engineering death resistance in CHO cells for improved perfusion culture. mAbs, 14 (1) e2083465, 1-13. doi: 10.1080/19420862.2022.2083465 |
