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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 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 |
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2022 Journal Article Analytical tools for unravelling the metabolism of gas-fermenting ClostridiaHeffernan, James K., Mahamkali, Vishnu, Valgepea, Kaspar, Marcellin, Esteban and Nielsen, Lars K. (2022). Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Current Opinion in Biotechnology, 75 102700, 102700. doi: 10.1016/j.copbio.2022.102700 |
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2022 Journal Article Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventionsGhaffari, Pouyan, Shoaie, Saeed and Nielsen, Lars K. (2022). Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions. Journal of Translational Medicine, 20 (1) 173, 173. doi: 10.1186/s12967-022-03365-z |
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2022 Journal Article Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenumValgepea, Kaspar, Talbo, Gert, Takemori, Nobuaki, Takemori, Ayako, Ludwig, Christina, Mahamkali, Vishnuvardhan, Mueller, Alexander P., Tappel, Ryan, Köpke, Michael, Simpson, Séan Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2022). Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum. mSystems, 7 (2), 1. doi: 10.1128/msystems.00026-22 |
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2022 Journal Article Modelling apoptosis resistance in CHO cells with CRISPR‐mediated knock‐outs of Bak1, Bax, and BokMacDonald, Michael A., Barry, Craig, Groves, Teddy, Martínez, Verónica S., Gray, Peter P., Baker, Kym, Shave, Evan, Mahler, Stephen, Munro, Trent, Marcellin, Esteban and Nielsen, Lars K. (2022). Modelling apoptosis resistance in CHO cells with CRISPR‐mediated knock‐outs of Bak1, Bax, and Bok. Biotechnology and Bioengineering, 119 (6), 1380-1391. doi: 10.1002/bit.28062 |
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2022 Journal Article Soft‐sensors application for automated feeding control in high‐throughput mammalian cell culturesMartínez‐Monge, I., Martínez, C., Decker, M., Udugama, I. A., Marín de Mas, I., Gernaey, K. V. and Nielsen, L.K. (2022). Soft‐sensors application for automated feeding control in high‐throughput mammalian cell cultures. Biotechnology and Bioengineering, 119 (4), 1077-1090. doi: 10.1002/bit.28032 |
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2022 Journal Article Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potentialBarry, Craig P., Gillane, Rosemary, Talbo, Gert H., Plan, Manual, Palfreyman, Robin, Haber-Stuk, Andrea K., Power, John, Nielsen, Lars K. and Marcellin, Esteban (2022). Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Molecular Omics, 18 (3), 226-236. doi: 10.1039/d1mo00150g |
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2021 Journal Article Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networkGrapotte, 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 (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7 |
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2021 Journal Article Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putidaKozaeva, Ekaterina, Volkova, Svetlana, Matos, Marta R.A., Mezzina, Mariela P., Wulff, Tune, Volke, Daniel C., Nielsen, Lars K. and Nikel, Pablo I. (2021). Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida. Metabolic Engineering, 67, 373-386. doi: 10.1016/j.ymben.2021.07.014 |
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2021 Journal Article Towards sustainable bioinoculants: a fermentation strategy for high cell density cultivation of Paraburkholderia sp. SOS3, a plant growth-promoting bacterium isolated in Queensland, AustraliaPetersen, Ian, Paungfoo-Lonhienne, Chanyarat, Marcellin, Esteban, Nielsen, Lars Keld and Gonzalez, Axayacatl (2021). Towards sustainable bioinoculants: a fermentation strategy for high cell density cultivation of Paraburkholderia sp. SOS3, a plant growth-promoting bacterium isolated in Queensland, Australia. Fermentation, 7 (2) 58, 1-17. doi: 10.3390/fermentation7020058 |
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2021 Journal Article multiTFA: a Python package for multi-variate thermodynamics-based flux analysisMahamkali, Vishnuvardhan, McCubbin, Tim, Beber, Moritz Emanuel, Noor, Elad, Marcellin, Esteban and Nielsen, Lars Keld (2021). multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. Bioinformatics, 37 (18), 3064-3066. doi: 10.1093/bioinformatics/btab151 |
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2021 Journal Article Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationshipsSchwaber, Jessica L., Korbie, Darren, Andersen, Stacey, Lin, Erica, Chrysanthopoulos, Panagiotis K., Trau, Matt and Nielsen, Lars K. (2021). Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PLoS ONE, 16 (2 ) e0246107, e0246107. doi: 10.1371/journal.pone.0246107 |
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2021 Journal Article Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applicationsMacDonald, Michael A., Nöbel, Matthias, Roche Recinos, Dinora, Martínez, Verónica S., Schulz, Benjamin L., Howard, Christopher B., Baker, Kym, Shave, Evan, Lee, Yih Yean, Marcellin, Esteban, Mahler, Stephen, Nielsen, Lars Keld and Munro, Trent (2021). Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applications. Critical Reviews in Biotechnology, 42 (7), 1-17. doi: 10.1080/07388551.2021.1998821 |
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2020 Journal Article SmartPeak automates targeted and quantitative metabolomics data processingKutuzova, Svetlana, Colaianni, Pasquale, Röst, Hannes, Sachsenberg, Timo, Alka, Oliver, Kohlbacher, Oliver, Burla, Bo, Torta, Federico, Schrübbers, Lars, Kristensen, Mette, Nielsen, Lars, Herrgård, Markus J. and McCloskey, Douglas (2020). SmartPeak automates targeted and quantitative metabolomics data processing. Analytical Chemistry, 92 (24), 15968-15974. doi: 10.1021/acs.analchem.0c03421 |
