Nikolaus Sonnenschein
Associate Professor at DTU Bioengineering, Computer Aided Biotechnology Group
Professional Experience
Nov2019 - now
Associate Professor, DTU Bioengineering, Technical University of Denmark
Jul2016 - Sep2019
Senior Researcher, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
Aug2013 - Jun2016
Research Scientist, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
Mar2011 - Jul2013
Postdoctoral Researcher, University of California, San Diego, USA
Sep2007 - Jan2011
PhD Student, Jacobs University Bremen, Germany
Oct2005 - Jul2006
Research Assistant, Technical University of Darmstadt, Germany
Feb2005 - Jun2006
Student Assistant, Berlin-Brandenburgische Akademie der Wissenschaften, Germany
Education
Jan2011
PhD in Bioinformatics, Jacobs University Bremen, Germany
Jul2007
Diplom in Biology (equivalent to M.Sc.), Technical University of Darmstadt, Germany
May2004
Vordiplom in Biology (equivalent to B.Sc.), Technical University of Darmstadt, Germany
Teaching Experience
Lectures and Course
2020
27410 Computer-aided cell factory design, Technical University of Denmark, Lyngby, lecturer, annually
2016-2019
29901 Scientific Computing for Life Scientists and Metabolic Modeling for Cell Factory Design, Technical University of Denmark, Lyngby, lecturer, annually
2016, 2018
27750 Advanced Experimental Synthetic Biology for Cell Factories, Technical University of Denmark, Lyngby, lecturer
2012-2013
BENG 123. Systems Biology and Bioengineering, University of California, San Diego, USA, instructor,annually
2010
Bioinformatics and Computational Biology I, Jacobs University Bremen, Germany, substitute lecturer 2010, occasionally
Oral Conference Presentations
Oct2020
Invited speaker, KIChE Fall Meeting International Symposium, Korean Institute of Chemical Engineers, e-conference
Sep2020
Invited speaker, 1st VH Online Yeast conference, Versuchsanstalt der Hefeindustrie e.BV., e-conference
Apr2020
Invited speaker, BioProcess International Europe, e-conference
Nov2019
Invited speaker, European Summit of Industrial Biotechnology (ESIB 2019), Graz, Austria
Oct2018
Invited speaker, 5th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018), Seattle, WA, USA
June2018
Invited speaker, Metabolic Engineering X, Munich, Germany
Apr2018
Invited speaker, “Advancing Synthetic Biology” (mini-symposium), Beijing University of Chemical Technology, Beijing, China
Dec2017
Invited speaker, 4th Synthetic Biology & Gene Editing Congress, London, UK
Aug2017
Selected talk, 18th International Conference on Systems Biology (ICSB 2017), Blacksburg, VA, USA
May2014
Invited speaker, 3rd Conference on Constraint-Based Reconstruction and Analysis (COBRA 2014), Charlottesville, VA, USA
Conference Organization
Mar2019
Organizer of Copenhagen Bioscience Cluster conference on “Software in the lifesciences: Development, Usability, Sustainability”
2019
Member of the International Programme Committee of the Foundation of Systems Biology in Engineering conference (FOSBE), Valencia, Spain
2016
Organization committee member and chairman, 11th Copenhagen Bioscience Conference, Favrholm, Denmark, “Data-driven Biotechnology – bench, bioreactor and bedside”.
Editorial and Peer Review Activities
Among others, peer reviewer for PLoS Computational Biology, Bioinformatics, Genome Biology, BMC Systems Biology, BMC Evolutionary Biology, Biotechnology and Bioengineering. Verified Peer Review record at https://publons.com/researcher/643329/nikolaus-sonnenschein. Guest editor for Frontiers in Bioengineering research topic “Current challenges in modeling cellular metabolism”.
Publications
A list is also available here https://goo.gl/DzH3My. My name underlined indicates corresponding authorship.
Articles
[1] V. Mol, M. Bennett, B. J. Sánchez, B. K. Lisowska, M. J. Herrgård, A. T. Nielsen, D. J. Leak, and N. Sonnenschein. Genome-scale metabolic modeling of p. thermoglucosidasius ncimb 11955 reveals metabolic bottlenecks in anaerobic metabolism. Metabolic Engineering, 65:123–134, 2021. doi:https://doi.org/10.1016/j.ymben.2021.03.002.
[2] S. Li, C. B. Jendresen, J. Landberg, L. E. Pedersen, N. Sonnenschein, S. I. Jensen, and A. T. Nielsen. Genome-Wide CRISPRi-Based identification of targets for decoupling growth from production. ACS Synth. Biol., 9(5):1030–1040, May 2020.
[3] C. Lieven, M. E. Beber, B. G. Olivier, F. T. Bergmann, M. Ataman, P. Babaei, J. A. Bartell, L. M. Blank, S. Chauhan, K. Correia, C. Diener, A. Dräger, B. E. Ebert, J. N. Edirisinghe, J. P. Faria, A. M. Feist, G. Fengos, R. M. T. Fleming, B. García-Jiménez, V. Hatzimanikatis, W. van Helvoirt, C. S. Henry, H. Hermjakob, M. J. Herrgård, A. Kaafarani, H. U. Kim, Z. King, S. Klamt, E. Klipp, J. J. Koehorst, M. König, M. Lakshmanan, D.-Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, F. Liu, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. M. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, B. O. Palsson, J. A. Papin, K. R. Patil, M. Poolman, N. D. Price, O. Resendis-Antonio, A. Richelle, I. Rocha, B. J. Sánchez, P. J. Schaap, R. S. Malik Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaça, J. O. Vik, J. A. H. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, and C. Zhang. MEMOTE for standardized genome-scale metabolic model testing. Nat. Biotechnol., 38(3):272–276, March 2020.
[4] N. R. Wright, T. Wulff, E. A. Palmqvist, T. R. Jørgensen, C. T. Workman, N. Sonnenschein, N. P. Rønnest, and M. J. Herrgård. Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of saccharomyces cerevisiae. Biotechnol. Bioeng., 117(7):2074–2088, July 2020.
[5] K. Jensen, V. Broeken, A. S. Lærke Hansen, N. Sonnenschein, and M. J. Herrgård. OptCouple: joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs. Metabolic Engineering Communications, pages e00087, March 2019. doi:10.1016/j.mec.2019.e00087.
[6] P. R. Jensen, M. R. A. Matos, N. Sonnenschein, and S. Meier. Combined In-Cell NMR and simulation approach to probe Redox-Dependent pathway control. Anal. Chem., 91(8):5395–5402, April 2019. doi:10.1021/acs.analchem.9b00660.
[7] M. M. Jessop-Fabre and N. Sonnenschein. Improving reproducibility in synthetic biology. Front Bioeng Biotechnol, 7:18, February 2019. doi:10.1101/329714.
[8] H. Lu, F. Li, B. J. Sánchez, Z. Zhu, G. Li, I. Domenzain, S. Marcišauskas, P. M. Anton, D. Lappa, C. Lieven, M. E. Beber, N. Sonnenschein, E. J. Kerkhoven, and J. Nielsen. A consensus s. cerevisiae metabolic model yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat. Commun., 10(1):3586, August 2019. doi:10.1038/s41467-019-11581-3.
[9] I. Massaiu, L. Pasotti, N. Sonnenschein, E. Rama, M. Cavaletti, P. Magni, C. Calvio, and M. J. Herrgård. 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. Microb. Cell Fact., 18(1):3, January 2019. doi:10.1186/s12934-018-1052-2.
[10] J. G. R. Cardoso, K. Jensen, C. Lieven, A. S. Lærke Hansen, S. Galkina, M. Beber, E. Özdemir, M. J. Herrgård, H. Redestig, and N. Sonnenschein. Cameo: a python library for computer aided metabolic engineering and optimization of cell factories. ACS Synth. Biol., April 2018. doi:10.1021/acssynbio.7b00423.
[11] J. G. R. Cardoso, A. A. Zeidan, K. Jensen, N. Sonnenschein, A. R. Neves, and M. J. Herrgård. MARSI: metabolite analogues for rational strain improvement. Bioinformatics, February 2018. doi:10.1093/bioinformatics/bty108.
[12] C. Lieven, M. J. Herrgård, and N. Sonnenschein. Microbial methylotrophic metabolism: recent metabolic modeling efforts and their applications in industrial biotechnology. Biotechnol. J., pages 1800011, June 2018. doi:10.1002/biot.201800011.
[13] C. Lieven, L. A. H. Petersen, S. B. Jørgensen, K. V. Gernaey, M. J. Herrgard, and N. Sonnenschein. A Genome-Scale metabolic model for methylococcus capsulatus (bath) suggests reduced efficiency electron transfer to the particulate methane monooxygenase. Front. Microbiol., 9:2947, December 2018. doi:10.3389/fmicb.2018.02947.
[14] A. S. L. Hansen, R. M. Lennen, N. Sonnenschein, and M. J. Herrgård. Systems biology solutions for biochemical production challenges. Curr. Opin. Biotechnol., 45:85–91, June 2017. doi:10.1016/j.copbio.2016.11.018.
[15] K. Jensen, J. G.R. Cardoso, and N. Sonnenschein. Optlang: an algebraic modeling language for mathematical optimization. The Journal of Open Source Software, jan 2017. doi:10.21105/joss.00139.
[16] J. Zhang, N. Sonnenschein, T. P. B. Pihl, K. R. Pedersen, M. K. Jensen, and J. D. Keasling. Engineering an NADPH/NADP+ redox biosensor in yeast. ACS Synth. Biol., pages acssynbio.6b00135, 2016. doi:10.1021/acssynbio.6b00135.
[17] B. Bergdahl, N. Sonnenschein, D. Machado, M. Herrgård, and J. Forster. Genome-Scale Models - Fundamental Bioengineering. In Fundamental Bioengineering, pages 143–182. Wiley-VCH Verlag GmbH & Co. KGaA, 2015. doi:10.1002/9783527697441.ch06.
[18] A. Bordbar, D. McCloskey, D. C. Zielinski, N. Sonnenschein, N. Jamshidi, and B. Ø. Palsson. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems, 1(4):283–292, oct 2015. doi:10.1016/j.cels.2015.10.003.
[19] J. G. R. Cardoso, M. R. Andersen, M. J. Herrgard, and N. Sonnenschein. Analysis of genetic variation and potential applications in genome-scale metabolic modeling. Frontiers in bioengineering and biotechnology, 3:13, 2015. doi:10.3389/fbioe.2015.00013.
[20] A. Ebrahim, E. Almaas, E. Bauer, A. Bordbar, A. P. Burgard, R. L. Chang, A. Dräger, I. Famili, A. M. Feist, R. M. Fleming, S. S. Fong, V. Hatzimanikatis, M. J. Herrgard, A. Holder, M. Hucka, D. Hyduke, N. Jamshidi, S. Y. Lee, N. Le Novere, J. A. Lerman, N. E. Lewis, D. Ma, R. Mahadevan, C. Maranas, H. Nagarajan, A. Navid, J. Nielsen, L. K. Nielsen, J. Nogales, A. Noronha, C. Pal, B. Ø. Palsson, J. A. Papin, K. R. Patil, N. D. Price, J. L. Reed, M. Saunders, R. S. Senger, N. Sonnenschein, Y. Sun, and I. Thiele. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology, 11(10):831–831, oct 2015. doi:10.15252/msb.20156157.
[21] Z. A. King, A. Dräger, A. Ebrahim, N. Sonnenschein, N. E. Lewis, and B. Ø. Palsson. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS computational biology, 11(8):e1004321, 2015. doi:10.1371/journal.pcbi.1004321.
[22] D. Machado, K. H. Zhuang, N. Sonnenschein, and M. J. Herrgard. Editorial: Current Challenges in Modeling Cellular Metabolism. Frontiers in bioengineering and biotechnology, 3:107, 2015. doi:10.3389/fcell.2015.00017.
[23] K. R. Kildegaard, B. M. Hallström, T. H. Blicher, N. Sonnenschein, N. B. Jensen, S. Sherstyk, S. J. Harrison, J. Maury, M. J. Herrgard, A. S. Juncker, J. Forster, J. Nielsen, and I. Borodina. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metabolic engineering, 26C:57–66, 2014. doi:10.1016/j.ymben.2014.09.004.
[24] I. Thiele, N. Swainston, R. M. T. Fleming, A. Hoppe, S. Sahoo, M. K. Aurich, H. Haraldsdottir, M. L. Mo, O. Rolfsson, M. D. Stobbe, S. G. Thorleifsson, R. Agren, C. Bölling, S. Bordel, A. K. Chavali, P. Dobson, W. B. Dunn, L. Endler, D. Hala, M. Hucka, D. Hull, D. Jameson, N. Jamshidi, J. J. Jonsson, N. Juty, S. Keating, I. Nookaew, N. Le Novère, N. Malys, A. Mazein, J. A. Papin, N. D. Price, E. Selkov, M. I. Sigurdsson, E. Simeonidis, N. Sonnenschein, K. Smallbone, A. Sorokin, J. H. G. M. van Beek, D. Weichart, I. Goryanin, J. Nielsen, H. V. Westerhoff, D. B. Kell, P. Mendes, and B. Ø. Palsson. A community-driven global reconstruction of human metabolism. Nature biotechnology, 31(5):419–425, 2013. doi:10.1038/nbt.2488.
[25] N. Sonnenschein, C. Marr, and M.-T. Hütt. A topological characterization of medium-dependent essential metabolic reactions. Metabolites, 2(3):632–647, 2012. doi:10.3390/metabo2030632.
[26] N. Sonnenschein, J. F. Golib Dzib, A. Lesne, S. Eilebrecht, S. Boulkroun, M.-C. Zennaro, A. Benecke, and M.-T. Hütt. A Network Perspective on Metabolic Inconsistency. BMC systems biology, 6(1):41, 2012. doi:10.1186/1752-0509-6-41.
[27] M. E. Beber, C. Fretter, S. Jain, N. Sonnenschein, M. Müller-Hannemann, and M.-T. Hütt. Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks. Journal of the Royal Society, Interface / the Royal Society, 9(77):3426–3435, 2012. doi:10.1098/rsif.2012.0490.
[28] N. Sonnenschein, M. Geertz, G. Muskhelishvili, and M.-T. Hütt. Analog regulation of metabolic demand. BMC Systems Biology, 5(1):40, 2011. doi:10.1186/1752-0509-5-40.
[29] N. Sonnenschein, M.-T. Hütt, H. Stoyan, and D. Stoyan. Ranges of control in the transcriptional regulation of Escherichia coli. BMC systems biology, 3:119, 2009. doi:10.1186/1752-0509-3-119.