Nikolaus Sonnenschein

Associate Professor at DTU Bioengineering, Computer Aided Biotechnology Group

Interests

Biology Metabolism, Cell factories, Metabolic modeling

Automation Lab-automation, Cloud laboratoriers, Biofoundries, Reproducible research

Software Open Source Research Software, CAD for Biology, CI/CD, DevOps, SCRUM

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

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

2007-2010 Advanced Bioinformatics Laboratory Course III: Genomics & Elementary Systems Biology, Jacobs University Bremen, Germany, instructor 2007 – 2010, annually

Oral Conference Presentations

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.

Preprints

[1] R. M. Lennen, K. Jensen, E. T. Mohammed, S. Malla, R. A. Börner, K. Chekina, E. Özdemir, I. Bonde, A. Koza, J. Maury, L. E. Pedersen, L. Y. Schöning, N. Sonnenschein, B. O. Palsson, M. O.A. Sommer, A. M. Feist, A. T. Nielsen, and M. J. Herrgård. Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production. bioRxiv, 2019. doi:10.1101/634105.

Articles (last 6 years)

[1] 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.

[2] 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.

[3] M. M. Jessop-Fabre and N. Sonnenschein. Improving reproducibility in synthetic biology. Front Bioeng Biotechnol, 7:18, February 2019. doi:10.1101/329714.

[4] 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. Feist, G. Fengos, R. M. T. Fleming, B. Garcia-Jimenez, V. Hatzimanikatis, W. van Helvoirt, C. Henry, H. Hermjakob, M. J. Herrgard, H. U. Kim, Z. King, J. J. Koehorst, S. Klamt, E. Klipp, M. Lakshmanan, N. Le Novere, D.-Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, O. Resendis, B. Palsson, J. A. Papin, K. R. Patil, M. Poolman, N. D. Price, A. Richelle, I. Rocha, B. Sanchez, P. Schaap, R. S. Malik Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaca, J. O. Vik, J. A. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, and C. Zhang. Memote: a community-driven effort towards a standardized genome-scale metabolic model test suite. Nature Biotechnology, pages accepted, 8 2019.

[5] 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. 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.

[6] 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.

[7] 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.

[8] 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.

[9] 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.

[10] 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.

[11] 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.

[12] 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.

[13] 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.

[14] 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.

[15] 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.

[16] 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.

[17] 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.

[18] 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.

[19] 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.

[20] 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.

[21] 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.

[22] 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.

[23] 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.

[24] 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.

[25] 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.

[26] 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.