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2021
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Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Mol, Viviënne ; Bennett, Martyn ; Sánchez, Benjamín J. ; Lisowska, Beata K. ; Herrgård, Markus J. ; Nielsen, Alex Toftgaard ; Leak, David J. ; Sonnenschein, Nikolaus
in: Metabolic Engineering, vol: 65, pages: 123-134

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1016/j.ymben.2021.03.002

2020
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Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism (Nature Communications, (2019), 10, 1, (3586), 10.1038/s41467-019-11581-3)

Lu, Hongzhong ; Li, Feiran ; Sánchez, Benjamín José ; Zhu, Zhengming ; Li, Gang ; Domenzain, Iván ; Marcišauskas, Simonas ; Anton, Petre Mihail ; Lappa, Dimitra ; Lieven, Christian ; Beber, Moritz Emanuel ; Sonnenschein, Nikolaus ; Kerkhoven, Eduard J. ; Nielsen, Jens
in: Nature Communications, vol: 11, issue: 1

Type: Journal article

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41467-020-19358-9

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CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli

Landberg, Jenny Marie ; Wright, Naia Risager ; Wulff, Tune ; Herrgård, Markus J. ; Nielsen, Alex Toftgaard
in: Biotechnology and Bioengineering, vol: 117, issue: 12, pages: 3835-3848

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1002/bit.27536

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Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of S. cerevisiae

Wright, Naia Risager ; Wulff, Tune ; Palmqvist, Eva Akke ; Jørgensen, Thomas Rubæk ; Workman, Christopher T. ; Sonnenschein, Nikolaus ; Rønnest, Nanna Petersen ; Herrgård, Markus J.
in: Biotechnology and Bioengineering, vol: 117, issue: 7, pages: 2074-2088

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1002/bit.27353

 

Genome-Wide CRISPRi-Based Identification of Targets for Decoupling Growth from Production

Li, Songyuan ; Jendresen, Christian Bille ; Landberg, Jenny Marie ; Pedersen, Lasse Ebdrup ; Sonnenschein, Nikolaus ; Ingemann Jensen, Sheila ; Nielsen, Alex Toftgaard
in: ACS Synthetic Biology, vol: 9, issue: 5, pages: 1030–1040

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1021/acssynbio.9b00143

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MEMOTE for standardized genome-scale metabolic model testing

Lieven, Christian ; Beber, Moritz Emanuel ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M. T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; van Helvoirt, Wout ; Henry, Christopher S. ; Hermjakob, Henning ; Herrgard, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong-Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran Raosaheb ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín José ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaca, Paulo ; Vik, Jon Olav ; Wodke, Judith A. H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng
in: Nature Biotechnology, vol: 38, issue: 3, pages: 272-276

Type: Journal article

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41587-020-0446-y

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Single-cell technologies to understand the mechanisms of cellular adaption in chemostats

Wright, Naia Risager ; Rønnest, Nanna P. ; Sonnenschein, Nikolaus
in: Frontiers in Bioengineering and Biotechnology, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.3389/fbioe.2020.579841

2019
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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, Hongzhong ; Li, Feiran ; Sánchez, Benjamín J ; Zhu, Zhengming ; Li, Gang ; Domenzain, Iván ; Marcišauskas, Simonas ; Anton, Petre Mihail ; Lappa, Dimitra ; Lieven, Christian ; Beber, Moritz Emanuel ; Sonnenschein, Nikolaus ; Kerkhoven, Eduard J ; Nielsen, Jens
in: Nature Communications, vol: 10, issue: 1, pages: 3586

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-11581-3

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

D'Arrigo, Isotta ; Cardoso, João G. R. ; Rennig, Maja ; Sonnenschein, Nikolaus ; Herrgård, Markus J. ; Long, Katherine S.
in: Environmental Microbiology Reports, vol: 11, issue: 2, pages: 87-97

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1758-2229.12704