Publications

Preprints

  1. Wright, N. R., Wulff, T., Workman, C. T., Rønnest, N. P. & Sonnenschein, N. Emergence of phenotypically distinct subpopulations is a factor in adaptation of recombinant Saccharomyces cerevisiae under glucose-limited conditions. bioRxiv (2021). doi:10.1101/2021.01.18.427050
  2. Lennen, R. M., Jensen, K., Mohammed, E. T., Malla, S., Börner, R. A., Chekina, K., Özdemir, E., Bonde, I., Koza, A., Maury, J., Pedersen, L. E., Schöning, L. Y., Sonnenschein, N., Palsson, B. O., Sommer, M. O. A., Feist, A. M., Nielsen, A. T. & Herrgård, M. J. Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production. bioRxiv (2019). doi:10.1101/634105

Peer reviewed publications

  1. Mol, V., Bennett, M., Sánchez, B. J., Lisowska, B. K., Herrgård, M. J., Nielsen, A. T., Leak, D. J. & Sonnenschein, N. Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism. Metabolic Engineering 65, 123–134 (2021).
  2. Wright, N. R., Wulff, T., Palmqvist, E. A., Jørgensen, T. R., Workman, C. T., Sonnenschein, N., Rønnest, N. P. & Herrgård, M. J. Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of Saccharomyces cerevisiae. Biotechnol. Bioeng. 117, 2074–2088 (2020).
  3. Li, S., Jendresen, C. B., Landberg, J., Pedersen, L. E., Sonnenschein, N., Jensen, S. I. & Nielsen, A. T. Genome-Wide CRISPRi-Based Identification of Targets for Decoupling Growth from Production. ACS Synth. Biol. 9, 1030–1040 (2020).
  4. Lu, H., Li, F., Sánchez Benjamı́n 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. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat. Commun. 10, 3586 (2019).
  5. Jensen, P. R., Matos, M. R. A., Sonnenschein, N. & Meier, S. Combined In-Cell NMR and Simulation Approach to Probe Redox-Dependent Pathway Control. Anal. Chem. 91, 5395–5402 (2019).
  6. Massaiu, I., Pasotti, L., Sonnenschein, N., Rama, E., Cavaletti, M., Magni, P., Calvio, C. & Herrgård, M. J. 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, 3 (2019).
  7. Lieven, C., Petersen, L. A. H., Jørgensen, S. B., Gernaey, K. V., Herrgard, M. J. & Sonnenschein, N. A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. Front. Microbiol. 9, 2947 (2018).
  8. Jensen, K., Broeken, V., Lærke Hansen, A. S., Sonnenschein, N. & Herrgård, M. J. OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs. Metabolic Engineering Communications e00087 (2019). doi:10.1016/j.mec.2019.e00087
  9. Jessop-Fabre, M. M. & Sonnenschein, N. Improving Reproducibility in Synthetic Biology. Front Bioeng Biotechnol 7, 18 (2019).
  10. Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., Garcı́a-Jiménez Beatriz, Hatzimanikatis, V., Helvoirt, W. van, Henry, C. S., Hermjakob, H., Herrgård, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., König, M., Lakshmanan, M., Lee, D.-Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez Benjamı́n J, Schaap, P. J., Malik Sheriff, R. S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M. & Zhang, C. MEMOTE for standardized genome-scale metabolic model testing. Nat. Biotechnol. 38, 272–276 (2020).
  11. Lieven, C., Herrgård, M. J. & Sonnenschein, N. Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts And Their Applications In Industrial Biotechnology. Biotechnol. J. 1800011 (2018). doi:10.1002/biot.201800011
  12. Cardoso, J. G. R., Zeidan, A. A., Jensen, K., Sonnenschein, N., Neves, A. R. & Herrgård, M. J. MARSI: metabolite analogues for rational strain improvement. Bioinformatics (2018). doi:10.1093/bioinformatics/bty108
  13. Hansen, A. S. L., Lennen, R. M., Sonnenschein, N. & Herrgård, M. J. Systems biology solutions for biochemical production challenges. Curr. Opin. Biotechnol. 45, 85–91 (2017).
  14. Cardoso, J. G. R., Jensen, K., Lieven, C., Lærke Hansen, A. S., Galkina, S., Beber, M., Özdemir, E., Herrgård, M. J., Redestig, H. & Sonnenschein, N. Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories. ACS Synth. Biol. (2018). doi:10.1021/acssynbio.7b00423
  15. Jensen, K., Cardoso, J. G. R. & Sonnenschein, N. Optlang: An algebraic modeling language for mathematical optimization. The Journal of Open Source Software 2, (2017).
  16. Zhang, J., Sonnenschein, N., Pihl, T. P. B., Pedersen, K. R., Jensen, M. K. & Keasling, J. D. Engineering an NADPH/NADP+ redox biosensor in yeast. ACS Synth. Biol. acssynbio.6b00135 (2016). doi:10.1021/acssynbio.6b00135
  17. Beber, M. E., Fretter, C., Jain, S., Sonnenschein, N., Müller-Hannemann, M. & Hütt, M.-T. Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks. Journal of the Royal Society, Interface / the Royal Society 9, 3426–3435 (2012).
  18. Bergdahl, B., Sonnenschein, N., Machado, D., Herrgård, M. & Forster, J. in Fundamental Bioengineering 143–182 (Wiley-VCH Verlag GmbH & Co. KGaA, 2015). doi:10.1002/9783527697441.ch06
  19. Bordbar, A., McCloskey, D., Zielinski, D. C., Sonnenschein, N., Jamshidi, N. & Palsson, B. Ø. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems 1, 283–292 (2015).
  20. Cardoso, J. G. R., Andersen, M. R., Herrgard, M. J. & Sonnenschein, N. Analysis of genetic variation and potential applications in genome-scale metabolic modeling. Frontiers in bioengineering and biotechnology 3, 13 (2015).
  21. Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, 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, S. Y., Le Novere, N., Lerman, J. A., Lewis, N. E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L. K., Nogales, J., Noronha, A., Pal, C., Palsson, B. Ø., Papin, J. A., Patil, K. R., Price, N. D., Reed, J. L., Saunders, M., Senger, R. S., Sonnenschein, N., Sun, Y. & Thiele, I. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology 11, 831–831 (2015).
  22. Kildegaard, K. R., Hallström, B. M., Blicher, T. H., Sonnenschein, N., Jensen, N. B., Sherstyk, S., Harrison, S. J., Maury, J., Herrgard, M. J., Juncker, A. S., Forster, J., Nielsen, J. & Borodina, I. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metabolic engineering 26C, 57–66 (2014).
  23. King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E. & Palsson, B. Ø. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS computational biology 11, e1004321 (2015).
  24. Machado, D., Zhuang, K. H., Sonnenschein, N. & Herrgard, M. J. Editorial: Current Challenges in Modeling Cellular Metabolism. Frontiers in bioengineering and biotechnology 3, 107 (2015).
  25. Sonnenschein, N., Geertz, M., Muskhelishvili, G. & Hütt, M.-T. Analog regulation of metabolic demand. BMC Systems Biology 5, 40 (2011).
  26. Sonnenschein, N., Golib Dzib, J. F., Lesne, A., Eilebrecht, S., Boulkroun, S., Zennaro, M.-C., Benecke, A. & Hütt, M.-T. A Network Perspective on Metabolic Inconsistency. BMC systems biology 6, 41 (2012).
  27. Sonnenschein, N., Hütt, M.-T., Stoyan, H. & Stoyan, D. Ranges of control in the transcriptional regulation of Escherichia coli. BMC systems biology 3, 119 (2009).
  28. Sonnenschein, N., Marr, C. & Hütt, M.-T. A topological characterization of medium-dependent essential metabolic reactions. Metabolites 2, 632–647 (2012).
  29. Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., Hucka, M., Hull, D., Jameson, D., Jamshidi, N., Jonsson, J. J., Juty, N., Keating, S., Nookaew, I., Le Novère, N., Malys, N., Mazein, A., Papin, J. A., Price, N. D., Selkov, E., Sigurdsson, M. I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., Beek, J. H. G. M. van, Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H. V., Kell, D. B., Mendes, P. & Palsson, B. Ø. A community-driven global reconstruction of human metabolism. Nature biotechnology 31, 419–425 (2013).