DTU Bioengineering
DTU Biosustain
Nikolaus Sonnenschein

Nikolaus Sonnenschein

Associate Professor

Department of Biotechnology and Biomedicine

SB-Computer-Aided-Biotechnology

Technical University of Denmark

Søltofts Plads

Building 223, room 224

2800 Kgs. Lyngby

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2020
 

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

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

  PDF

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

Jensen, Pernille Rose ; Matos, Marta ; Sonnenschein, Nikolaus ; Meier, Sebastian
in: Analytical Chemistry, vol: 91, issue: 8, pages: 5395-5402

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acs.analchem.9b00660

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Improving Reproducibility in Synthetic Biology

Jessop-Fabre, Mathew M. ; Sonnenschein, Nikolaus
in: Frontiers in Bioengineering and Biotechnology, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3389/fbioe.2019.00018

  PDF

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, Ilaria ; Pasotti, Lorenzo ; Sonnenschein, Nikolaus ; Rama, Erlinda ; Cavaletti, Matteo ; Magni, Paolo ; Calvio, Cinzia ; Herrgård, Markus J.
in: Microbial Cell Factories, vol: 18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-018-1052-2

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

Jensen, Kristian ; Broeken, Valentijn ; Hansen, Anne Sofie Lærke ; Sonnenschein, Nikolaus ; Herrgård, Markus J.
in: Metabolic Engineering Communications, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.mec.2019.e00087

2018
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MARSI: metabolite analogues for rational strain improvement

Cardoso, João G. R. ; Zeidan, Ahmad A ; Jensen, Kristian ; Sonnenschein, Nikolaus ; Neves, Ana Rute ; Herrgård, Markus J
in: Bioinformatics, vol: 34, issue: 13, pages: 2319-2321

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1093/bioinformatics/bty108

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

Lieven, Christian ; Herrgård, Markus J. ; Sonnenschein, Nikolaus
in: Biotechnology Journal, vol: 13, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/biot.201800011

2017
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DD-DeCaF: Data-Driven Design of Cell Factories and Communities

Beber, Moritz Emanuel ; Dannaher, Danny ; Fodor, Matyas ; Galkina, Svetlana ; Redestig, Nils Henning ; Sonnenschein, Nikolaus ; Herrgard, Markus
part of: Book of Abstracts, Sustain 2017, 2017
Presented at:
Sustain 2017

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2017

  PDF

Memote - The genome-scale metabolic model test suite

Lieven, Christian ; Beber, Moritz Emanuel ; Sonnenschein, Nikolaus
part of: Book of Abstracts, Sustain 2017, 2017
Presented at:
Sustain 2017

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2017

  PDF

Systems biology solutions for biochemical production challenges

Hansen, Anne Sofie Lærke ; Lennen, Rebecca M ; Sonnenschein, Nikolaus ; Herrgard, Markus
in: Current Opinion in Biotechnology, vol: 45, pages: 85-91

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.copbio.2016.11.018

2016
 

Engineering an NADPH/NADPRedox Biosensor in Yeast

Zhang, Jie ; Sonnenschein, Nikolaus ; Pihl, Thomas Peter Boye ; Pedersen, Kasper Rud ; Jensen, Michael Krogh ; Keasling, Jay
in: A C S Synthetic Biology, vol: 5, issue: 12, pages: 1546–1556

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1021/acssynbio.6b00135

 

Genome-Scale Models

Bergdahl, Basti ; Sonnenschein, Nikolaus ; Machado, Daniel ; Herrgard, Markus ; Förster, Jochen
part of: Fundamental Bioengineering, pages: 143-182, 2015, Weinheim, Germany

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1002/9783527697441.ch06

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Optlang: An algebraic modeling language for mathematical optimization

Jensen, Kristian ; Cardoso, Joao ; Sonnenschein, Nikolaus
in: The Journal of Open Source Software

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.21105/joss.00139

2015
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Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Cardoso, Joao ; Andersen, Mikael Rørdam ; Herrgard, Markus ; Sonnenschein, Nikolaus
in: Frontiers in Bioengineering and Biotechnology, vol: 3, issue: 13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.3389/fbioe.2015.00013

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Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A. ; Almaas, E. ; Bauer, E. ; Bordbar, A. ; Burgard, A. P. ; Chang, R. L. ; Drager, A. ; Famili, I. ; Feist, A. M. ; Fleming, R. M. ; Fong, S. S. ; Hatzimanikatis, V. ; Herrgard, M. J. ; Holder, A. ; Hucka, M. ; Hyduke, D. ; Jamshidi, N. ; Lee, Sang Yup ; Le Novere, N. ; Lerman, J. A. ; Lewis, Nathan ; Ma, D. ; Mahadevan, R. ; Maranas, C. ; Nagarajan, H. ; Navid, A. ; Nielsen, Jens ; Nielsen, L. K. ; Nogales, J. ; Noronha, A. ; Pal, C. ; Palsson, Bernhard ; Papin, J. A. ; Patil, Kiran R. ; Price, N. D. ; Reed, J. L. ; Saunders, M. ; Senger, R. S. ; Sonnenschein, Nikolaus ; Sun, Yuekai ; Thiele, I.
in: Molecular Systems Biology, vol: 11, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.15252/msb.20156157

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Editorial: Current Challenges in Modeling Cellular Metabolism

Machado, Daniel ; Zhuang, Kai ; Sonnenschein, Nikolaus ; Herrgard, Markus
in: Frontiers in Bioengineering and Biotechnology, vol: 3

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.3389/fbioe.2015.00193

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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

King, Zachary A. ; Draeger, Andreas ; Ebrahim, Ali ; Sonnenschein, Nikolaus ; Lewis, Nathan ; Palsson, Bernhard O.
in: PLoS Computational Biology, vol: 11, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1371/journal.pcbi.1004321

 

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

Bordbar, Aarash ; McCloskey, Douglas ; Zielinski, Daniel C ; Sonnenschein, Nikolaus ; Jamshidi, Neema ; Palsson, Bernhard
in: Cell Systems, vol: 1, issue: 4, pages: 283-292

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.cels.2015.10.003

2014
 

A compendium of genetic variant data

Cardoso, Joao ; Schöning, Lars Yannik ; Herrgard, Markus ; Sonnenschein, Nikolaus
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

 

A kinetic model of thiamine biosynthesis in Escherichia coli

Matos, Marta ; Herrgard, Markus ; Andersen, Mikael Rørdam ; Sonnenschein, Nikolaus
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

 

Evolution Reveals A Glutathione-dependent Mechanism Of 3-hydroxypropionic Acid Detoxification

Kildegaard, Kanchana Rueksomtawin ; Hallström, Björn M. ; Blicher, Thomas H. ; Sonnenschein, Nikolaus ; Jensen, Niels Bjerg ; Sherstyk, Svetlana ; Harrison, Scott James ; Maury, Jerome ; Herrgard, Markus ; Juncker, Agnieszka ; Förster, Jochen ; Nielsen, Jens ; Borodina, Irina
Presented at:
Metabolic Engineering X

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2014

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Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

Kildegaard, Kanchana Rueksomtawin ; Hallström, Björn M. ; Blicher, Thomas H. ; Sonnenschein, Nikolaus ; Jensen, Niels Bjerg ; Sherstyk, Svetlana ; Harrison, Scott James ; Maury, Jerome ; Herrgard, Markus ; Juncker, Agnieszka ; Förster, Jochen ; Nielsen, Jens ; Borodina, Irina
in: Metabolic Engineering, vol: 26, pages: 57-66

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.ymben.2014.09.004

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Putting computational modeling at the fingertips of bench biologists

Sonnenschein, Nikolaus ; Herrgard, Markus
Presented at:
2nd EMBO Conference on Visualizing Biological Data

Type: Poster (Peer reviewed)

Status: Published     |    Year: 2014