Research Output 2012 2020

2020

Addressing environmental sustainability of biochemicals

Ögmundarson, Ó., Herrgård, M. J., Forster, J., Hauschild, M. Z. & Fantke, P., 2020, (Accepted/In press) In : Nature Sustainability.

Research output: Contribution to journalJournal articleResearchpeer-review

Awakening dormant glycosyltransferases in CHO cells with CRISPRa

Julie la Cour Karottki, K., Hefzi, H., Xiong, K., Shamie, I., Hansen, A. H., Li, S., Pedersen, L. E., Li, S., Lee, J. S., Min Lee, G., Kildegaard, H. F. & Lewis, N. E., 2020, In : Biotechnology and Bioengineering. 117, 2, p. 593-598

Research output: Contribution to journalJournal articleResearchpeer-review

52 Downloads (Pure)

Environmental hotspots of lactic acid production systems

Ögmundarson, Ó., Sukumara, S., Laurent, A. & Fantke, P., 2020, In : GCB Bioenergy. 12, 1, p. 19-38 20 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2019
83 Downloads (Pure)

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, H., Li, F., Sánchez, B. J., Zhu, Z., Li, G., Domenzain, I., Marcišauskas, S., Anton, P. M., Lappa, D., Lieven, C., Beber, M. E., Sonnenschein, N., Kerkhoven, E. J. & Nielsen, J., 2019, In : Nature Communications. 10, 1, p. 3586 13 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Pereira, R., Wei, Y., Mohamed, E. T. T., Radi, M., Malina, C., Herrgård, M. J., Feist, A. M., Nielsen, J. & Chen, Y., 2019, In : Metabolic Engineering. 56, p. 130-141 12 p.

Research output: Contribution to journalJournal articleResearchpeer-review

10 Downloads (Pure)

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, T., Bosma, E. F., Branco Dos Santos, F., Özdemir, E., Herrgård, M. J., França, L., Ferreira, B., Toftgaard Nielsen, A. & Gudmundsson, S., 2019, In : Microbial Cell Factories. 18, 1, 19 p., 186.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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74 Downloads (Pure)

Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling

D'Arrigo, I., Cardoso, J. G. R., Rennig, M., Sonnenschein, N., Herrgård, M. J. & Long, K. S., 2019, In : Environmental Microbiology Reports. 11, 2, p. 87-97 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

Yang, J. H., Wright, S. N., Hamblin, M., McCloskey, D., Alcantar, M. A., Schrübbers, L., Lopatkin, A. J., Satish, S., Nili, A., Palsson, B. O., Walker, G. C. & Collins, J. J., 2019, In : CELL. 177, 6, p. 1649-1661.e9

Research output: Contribution to journalJournal articleResearchpeer-review

103 Downloads (Pure)

Building a global alliance of biofoundries

Hillson, N., Caddick, M., Cai, Y., Carrasco, J. A., Chang, M. W., Curach, N. C., Bell, D. J., Le Feuvre, R., Friedman, D. C., Fu, X., Gold, N. D., Herrgård, M. J., Holowko, M. B., Johnson, J. R., Johnson, R. A., Keasling, J. D., Kitney, R. I., Kondo, A., Liu, C., Martin, V. J. J. & 16 others, Menolascina, F., Ogino, C., Patron, N. J., Pavan, M., Poh, C. L., Pretorius, I. S., Rosser, S. J., Scrutton, N. S., Storch, M., Tekotte, H., Travnik, E., Vickers, C. E., Yew, W. S., Yuan, Y., Zhao, H. & Freemont, P. S., 2019, In : Nature Communications. 10, 2040.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells

Jensen, P. R., Matos, M., Sonnenschein, N. & Meier, S., 2019, In : Analytical Chemistry. 91, 8, p. 5395-5402 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

256 Downloads (Pure)

Computational methods for microbial cell factory engineering aided by evolution

Jensen, K., 2019, 146 p.

Research output: Book/ReportPh.D. thesisResearch

Open Access
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197 Downloads (Pure)

Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

Luo, H., Hansen, A. S. L., Yang, L., Schneider, K., Kristensen, M., Christensen, U., Christensen, H. B., Du, B., Özdemir, E., Feist, A. M., Keasling, J. D., Jensen, M. K., Herrgård, M. J. & Palsson, B. O., 2019, In : PLOS Biology. 17, 3, e2007050.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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107 Downloads (Pure)

Engineered Reversal of Function in Glycolytic Yeast Promoters

Rajkumar, A. S., Özdemir, E., Lis, A. V., Schneider, K., Qin, J., Jensen, M. K. & Keasling, J. D., 2019, In : ACS Synthetic Biology. 8, 6, p. 1462-1468 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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87 Downloads (Pure)

Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Mohamed, E. T. T., Mundhada, H., Landberg, J. M., Cann, I., Mackie, R. I., Nielsen, A. T., Herrgard, M. J. & Feist, A. M., 2019, In : Microbial Cell Factories. 18, 116.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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363 Downloads (Pure)

Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech

Börner, R. A., Kandasamy, V., Axelsen, A. M., Nielsen, A. T. & Bosma, E. F., 2019, In : F E M S Microbiology Letters. 366, 1, 12 p., fny291.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
87 Downloads (Pure)

Genome-wide systematic identification of methyltransferase recognition and modification patterns

Jensen, T. Ø., Tellgren-Roth, C., Redl, S. M. A., Maury, J., Baallal Jacobsen, S. A., Pedersen, L. E. & Nielsen, A. T., 2019, In : Nature Communications. 10, 1, 3311.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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47 Downloads (Pure)
Open Access
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187 Downloads (Pure)

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Massaiu, I., Pasotti, L., Sonnenschein, N., Rama, E., Cavaletti, M., Magni, P., Calvio, C. & Herrgård, M. J., 2019, In : Microbial Cell Factories. 18, 21 p., 3.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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293 Downloads (Pure)

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Cheng, C., O'Brien, E. J., McCloskey, D., Utrilla, J., Olson, C., LaCroix, R. A., Sandberg, T. E., Feist, A. M., Palsson, B. O. & King, Z. A., 2019, In : PLOS Computational Biology. 15, 6, e1007066.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
112 Downloads (Pure)

Life Cycle Assessment of chosen Biochemicals and Bio-based polymers

Ögmundarson, Ó., 2019, 200 p.

Research output: Book/ReportPh.D. thesisResearch

Open Access
File
4 Downloads (Pure)

Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Ferreira, R., Skrekas, C., Hedin, A., Sánchez, B. J., Siewers, V., Nielsen, J. & David, F., 2019, In : ACS Synthetic Biology. 8, p. 2457-2463

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
14 Downloads (Pure)

Multi-omics analysis of fatty alcohol production in engineered yeasts saccharomyces cerevisiae and yarrowia lipolytica

Dahlin, J., Holkenbrink, C., Marella, E. R., Wang, G., Liebal, U., Lieven, C., Weber, D., McCloskey, D., Ebert, B. E., Herrgård, M. J., Blank, L. M. & Borodina, I., 2019, In : Frontiers in Genetics. 10, 747.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
73 Downloads (Pure)

OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Jensen, K., Broeken, V., Hansen, A. S. L., Sonnenschein, N. & Herrgård, M. J., 2019, In : Metabolic Engineering Communications. 8, 8 p., e00087.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Reprogramming AA catabolism in CHO cells with CRISPR/Cas9 genome editing improves cell growth and reduces byproduct secretion

Ley, D., Pereira, S., Pedersen, L. E., Arnsdorf, J., Hefzi, H., Davy, A. M., Kwang Ha, T., Wulff, T., Kildegaard, H. F. & Andersen, M. R., 2019, In : Metabolic Engineering. 56, p. 120-129 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2018
102 Downloads (Pure)

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Metabolic Engineering. 48, p. 82-93

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
102 Downloads (Pure)

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Metabolic Engineering. 48, p. 233-242

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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189 Downloads (Pure)

A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Lieven, C., Petersen, L. A. H., Jørgensen, S. B., Gernaey, K. V., Herrgard, M. J. & Sonnenschein, N., 2018, In : Frontiers in Microbiology. 9, 15 p., 2947.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
5 Downloads (Pure)

An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast

Snoek, T., Romero-Suarez, D., Zhang, J., Ambri, F., Skjoedt, M. L., Sudarsan, S., Jensen, M. K. & Keasling, J. D., 2018, In : A C S Synthetic Biology. 7, 4, p. 995-1003

Research output: Contribution to journalLetterResearchpeer-review

Open Access
File
69 Downloads (Pure)

Arylalkylamine n-acetyltransferase and uses thereof

Luo, H., 2018, IPC No. C12N9/10; C12N15/00; C12N5/00, Patent No. WO2018108966 , 21 Jun 2018, Priority date 13 Dec 2016, Priority No. EP20160203711

Research output: Patent

Open Access
File
179 Downloads (Pure)

Bacterial cells with improved tolerance to diacids

Lennen, R., Nielsen, A. T., Herrgard, M., Sommer, M. O. A., Feist, A. & Tharwat Tolba Mohamed, E., 2018, IPC No. C12N1/20; C12P7/44; C12P7/46, Patent No. WO2018091525 , 24 May 2018, Priority date 15 Nov 2016, Priority No. US201662422457P

Research output: Patent

Open Access
File
263 Downloads (Pure)

Baicalein reduces oxidative stress in CHO cell cultures and improves recombinant antibody productivity

Kwang Ha, T., Hansen, A. H., Kol, S., Kildegaard, H. F. & Min Lee, G., 2018, In : Biotechnology Journal. 13, 3, 10 p., 1700425.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
254 Downloads (Pure)

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories

Cardoso, J. G. R., Jensen, K., Lieven, C., Hansen, A. S. L., Galkina, S., Beber, M., Özdemir, E., Herrgård, M. J., Redestig, H. & Sonnenschein, N., 2018, In : A C S Synthetic Biology. 7, 4, p. 1163-1166

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
371 Downloads (Pure)

CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

Jakočiūnas, T., Pedersen, L. E., Lis, A. V., Jensen, M. K. & Keasling, J. D., 2018, In : Metabolic Engineering. 48, p. 288-296

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Computational Methods to Assess the Production Potential of Bio-Based Chemicals

Campodonico, M. A., Sukumara, S., Feist, A. M. & Herrgård, M. J., 2018, Synthetic Metabolic Pathways. Vol. 1671. p. 97-116 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

80 Downloads (Pure)

CRISPR/Cas9-multiplexed editing of Chinese hamster ovary B4Gal-T1, 2, 3 and 4 Tailors N-Glycan Profiles of Therapeutics and Secreted Host Cell Proteins

Amann, T., Hansen, A. H., Kol, S., Min Lee, G., Andersen, M. R. & Kildegaard, H. F., 2018, In : Biotechnology Journal. 13, 10, 9 p., 1800111 .

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
142 Downloads (Pure)

Dietary Creatine Supplementation in Gilthead Seabream (Sparus aurata): Comparative Proteomics Analysis on Fish Allergens, Muscle Quality, and Liver

Schrama, D., Cerqueira, M., Raposo, C. S., Rosa da Costa, A. M., Wulff, T., Goncalves, A., Camacho, C., Colen, R., Fonseca, F. & Rodrigues, P. M., 2018, In : Frontiers in Physiology. 9, 17 p., 1844.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
167 Downloads (Pure)

Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections

Imamovic, L., Ellabaan, M. M. H., Dantas Machado, A. M., Citterio, L., Wulff, T., Molin, S., Johansen, H. K. & Sommer, M. O. A., 2018, In : CELL. 172, 1-2, p. 121-134

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Enhancing Metabolic Models with Genome-Scale Experimental Data

Jensen, K., Gudmundsson, S. & Herrgård, M., 2018, Systems Biology. Rajewsky, N., Jurga, S. & Barciszewski, J. (eds.). 2018 ed. Springer, p. 337-350 (RNA Technologies).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Escherichia coli modular coculture system for resveratrol glucosides production

Thuan, N. H., Trung, N. T., Cuong, N. X., Van Cuong, D., Van Quyen, D. & Malla, S., 2018, In : World Journal of Microbiology and Biotechnology. 34, 6, 13 p., 75.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
172 Downloads (Pure)

Evolution of gene knockout strains of E-coli reveal regulatory architectures governed by metabolism

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Nature Communications. 9, 15 p., 3796.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
358 Downloads (Pure)

Genome-wide identification of tolerance mechanisms towards p-coumaric acid in Pseudomonas putida

Calero, P., Jensen, S. I., Bojanovič, K., Lennen, R., Koza, A. & Nielsen, A. T., 2018, In : Biotechnology and Bioengineering. 115, 3, p. 762-774

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
184 Downloads (Pure)

Glucose-dependent promoters for dynamic regulation of metabolic pathways

Maury, J., Kannan, S., Jensen, N. B., Öberg, F. K., Kildegaard, K. R., Forster, J., Nielsen, J., Workman, C. T. & Borodina, I., 2018, In : Frontiers in Bioengineering and Biotechnology. 6, 63.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
175 Downloads (Pure)

Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Frontiers in Microbiology. 9, 16 p., 1793.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
555 Downloads (Pure)

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

Strucko, T., Zirngibl, K., Pereira, F., Kafkia, E., Mohamed, E. T., Rettel, M., Stein, F., Feist, A. M., Jouhten, P., Patil, K. R. & Forster, J., 2018, In : Metabolic Engineering. 47, p. 73-82 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
166 Downloads (Pure)

MARSI: metabolite analogues for rational strain improvement

Cardoso, J. G. R., Zeidan, A. A., Jensen, K., Sonnenschein, N., Neves, A. R. & Herrgård, M. J., 2018, In : Bioinformatics. 34, 13, p. 2319-2321

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
257 Downloads (Pure)

Mass Action Stoichiometric. Simulation for Cell Factory Design

Matos, M. R. A., 2018, Kgs. Lyngby: Technical University of Denmark. 215 p.

Research output: Book/ReportPh.D. thesisResearch

Open Access
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Metabolic engineering of Saccharomyces cerevisiae for cyclic triterpenoid production

Ebert, B. E., Walter, K., Maury, J., Lang, C., Förster, J., Bank, L. M., Czarnotta, E., Knuf, C., Jacobsen, S. A., Guo, H. & Lewandowski, A., 2018, In : Chemie-Ingenieur-Technik. 90, 9, p. 1255-1256

Research output: Contribution to journalConference abstract in journalResearchpeer-review

222 Downloads (Pure)

Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology

Lieven, C., Herrgård, M. J. & Sonnenschein, N., 2018, In : Biotechnology Journal. 13, 8, 8 p., 1800011.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
89 Downloads (Pure)

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Applied and Environmental Microbiology. 84, 19, 17 p., e00823-18.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
323 Downloads (Pure)

RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli

McCloskey, D., Xu, J., Schrübbers, L., Christensen, H. B. & Herrgård, M. J., 2018, In : Metabolic Engineering. 47, p. 383-392

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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