Dr. Katharina Nöh

Head of Modeling of Biochemical Networks and Cells

Vice head of Modeling and Simulation

Contact

+49 2461/61-9294

+49 2461/61-3870

E-Mail

ORCID

Address

Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße
52428 Jülich

Institute of Bio- and Geosciences (IBG)

Biotechnology (IBG-1)

Building 15.7 / Room R 205

CURRENT RESEARCH INTERESTS

Development of computational methods to analyze complex biochemical networks and cellular processes, with focus on systems‐scale and quantitativeness. For this, we are working at the intersection of applied mathematics, statistics, data science and computational science and engineering. Having a strong background in metabolic flux analysis with isotopic tracers, our group is continuously advancing and enriching the computational toolchains, which we apply to analyze a broad range of bacterial systems, ranging from biotechnological production hosts to human threads such as Mycobacterium tuberculosis and Salmonella typhimurium. Recently, we got interested in the spatio‐temporal analysis of single microbial cells and their heterogeneity, unlocked by microfluidic lab-on-chip systems and time‐lapse imaging. Aiming at unbiased insights into developing cell populations, we use traditional and modern deep learning approaches for feature extraction and Bayesian learning for model aggregation from heterogeneous data sets.

Vita

2011 ‐ present Head of Modeling of Biochemical Networks and Cells,
Institute of Bio- and Geosciences, IBG-1: Biotechnology,
Forschungszentrum Jülich, Germany

2009 ‐ present Vice Head of Modeling and Simulation, Institute of Bio- and Geosciences,
IBG‐1: Biotechnology, Forschungszentrum Jülich, Germany

2006 ‐ 2009 Postdoctoral fellow in Fermentation Technology Group,
Institute of Biotechnology, IBT‐2, Forschungszentrum Jülich, Germany

2006 PhD in Mathematics, Siegen University, Germany

1999 Diploma in Mathematics, Siegen University, Germany

Publications

Pre-Prints

Borah, K., Beyß, M., Ye, X., Barber, J., Costa, C., Newcombe, J., Theorell, A., Bailey, M.J., Beste, D.J., McFadden, J. & Nöh, K. (2022) Bayesian multi-model-based ¹³C¹⁵N-metabolic flux analysis quantifies carbon-nitrogen metabolism in mycobacteria. bioRvix 2022.03.08.483448. (OA)

Sachs, C.C., Ruzaeva, K., Seiffarth, J., Wiechert, W., Berkels, B. & Nöh K (2022) CellSium – Versatile cell simulator for microcolony ground truth generation. bioRxiv 2022.03.24.485611 (OA)

Journal Articles

1. Feierabend, M, Renz, A, Zelle, E, Nöh, K, Wiechert, W, & Dräger, A (2021). High-quality genome-scale reconstruction of Corynebacterium glutamicum ATCC 13032. Frontiers in Microbiology 12. (OA)

2. Theorell, A, Jadebeck, JF, Nöh, K, & Stelling, J (2021). PolyRound: Polytope rounding for random sampling in metabolic networks. Bioinformatics btab552. (OA)

3. Beyß, M, Parra-Peña, VD, Ramirez-Malule, H, Nöh, K (2021). Robustifying experimental tracer design for ¹³C-metabolic flux analysis. Frontiers in Bioengineering and Biotechnology 9. (OA)

4. Zelle, E, Pfelzer, N, Oldiges, M, Koch-Koerfges, A, Bott, M, Nöh, K, & Wiechert, W. (2021). An energetic profile of Corynebacterium glutamicum underpinned by measured biomass yield on ATP. Metabolic Engineering 65, 66–78.

5. Jadebeck JF, Theorell A, Leweke S, Nöh K (2020) HOPS: High-performance library for (non‑)uniform sampling of convex-constrained models. Bioinformatics 37(12):1776-1777.

6. Graf M, Haas T, T eleki A, Feith A, Cerff M, Wiechert W, Nöh K, Busche T, Kalinowski J, Takors R (2020) Revisiting the growth modulon of Corynebacterium glutamicum under glucose limited chemostat conditions. Frontiers in Bioengineering and Biotechnology 8. (OA)

7. Theorell A, Nöh K (2020). Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis. Bioinformatics 36(1):232-240.

8. Borah K, Beyß M, Theorell A, Wu H, Basu P, Mendum TA, Nӧh K, Beste DJV, McFadden J (2019). Intracellular Mycobacterium tuberculosis exploits multiple host nitrogen sources during growth in human macrophages. Cell Reports 29(11):3580-3591.e4. (OA)

9. Sachs CC., Koepff J, Wiechert W, Grünberger A, Nöh K (2019). mycelyso – high-throughput analysis of Streptomyces mycelium live cell imaging data. BMC Bioinformatics 20(1):452. (OA)

10. Kappelmann J, Beyß M, Nöh K, Noack S (2019). Separation of ¹³C- and ¹⁵N-isotopologues of amino acids with a primary amine without mass resolution by means of O-phthalaldehyde derivatization and collision induced dissociation. Analytical Chemistry 91(21):13407-13417.

11. Leygeber M, Lindemann D, Sachs CC, Kaganovitch E, Wiechert W, Nöh K, Kohlheyer D (2019). Analyzing microbial population heterogeneity — Expanding the toolbox of microfluidic single-cell cultivations. Journal of Molecular Biology 431(23):4569-4588.

12. Beyß M, Azzouzi S, Weitzel M, Wiechert W, Nöh K (2019). The design of FluxML: A universal modeling language for ¹³C metabolic flux analysis. Frontiers in Microbiology 10. (OA)

13. Theorell A, Seiffarth J, Grünberger A, Nöh K (2019). When a single lineage is not enough: Uncertainty-Aware Tracking for spatio-temporal live-cell image analysis. Bioinformatics 35(7):1221-1228.

14. Koepff J, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Oldiges M, Grünberger A (2018). Germination and growth analysis of Streptomyces lividans at the single-cell level under varying medium compositions. Frontiers in Microbiology 9:1-10. (OA)

15. Nöh K, Niedenführ S, Beyß M, Wiechert W (2018). A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments. PLOS Computational Biology 14(10), e1006533. (OA)

16. Delp J, Gutbier S, Cerff M, Zasada C, Niedenführ S, Zhao L, Smirnova L, Hartung T, Borlinghaus H, Schreiber F, Bergemann J, Gätgens J, Beyß M, Azzouzi S, Waldmann T, Kempa S, Nöh K, Leist M (2018). Stage-specific metabolic features of differentiating neurons: implications for toxicant sensitivity. Toxicology and Applied Pharmacology 354:64-80.

17. Baierl A, Theorell A, Mackfeld U, Marquardt P, Hoffmann F, Moers S, Nöh K, Buchholz PCF, Pleiss J, Pohl M (2018). Towards a mechanistic understanding of factors controlling the stereoselectivity of transketolase. ChemCatChem 10(12):2601-2611.

18. Theorell A, Leweke S, Wiechert W, Nöh K (2017). To be certain about the uncertainty: Bayesian statistics for ¹³C metabolic flux analysis. Biotechnology and Bioengineering 114(11):2668-2684.

19. Vasilakou E, Machado D, Theorell A, Rocha I, Nöh K, Oldiges M, Wahl SA (2016) Current state and challenges for dynamic metabolic modeling. Current Opinion in Microbiology 33:97-104.

20. Sachs CC, Grünberger A, Helfrich S, Probst C, Wiechert W, Kohlheyer D, Nöh K (2016) Image-based single cell profiling: High-throughput processing of Mother Machine experiments. PLOS ONE 11(9):e0163453. (OA)

21. Dalman T, Wiechert W, Nöh K (2016) A scientific workflow framework for ¹³C metabolic flux analysis. Journal of Biotechnology 232:12-24.

22. Niedenführ S, ten Pierick A, van Dam PTN, Suarez-Mendez CA, Nöh K, Wahl SA (2016) Natural isotope correction of MS/MS measurements for metabolomics and ¹³C fluxomics. Biotechnology and Bioengineering 113:1137-1147.

23. Grünberger A, Probst C, Helfrich S, Nanda A, Stute B, Wiechert W, von Lieres E, Nöh K, Frunzke J (2015) Spatiotemporal microbial single-cell analysis using a high-throughput microfluidics cultivation platform. Cytometry A 87(12):1101-1115.

24. Helfrich S, Azzouzi CE, Probst C, Seiffarth J, Grünberger A, Wiechert W, Kohlheyer D, Nöh K (2015) Vizardous: Interactive analysis of microbial populations with single cell resolution. Bioinformatics 31(23):3875-3877.

25. Helfrich S, Pfeifer E, Krämer C, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Frunzke J (2015) Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations. Molecular Microbiology 98(4):636-650.

26. Krämer CEM, Singh A, Helfrich S, Grünberger A, Wiechert W, Nöh K, Kohlheyer D (2015) Non invasive microbial metabolic activity sensing at single cell level by perfusion of calcein acetoxymethyl ester. PLOS ONE 10(10):e0141768. (OA)

27. Niedenführ S, Wiechert W, Nöh K (2015) How to measure metabolic fluxes: A taxonomic guide for ¹³C fluxomics. Current Opinion in Biotechnology 34:82-90.

28. Buescher JM, et al. (2015) A roadmap for interpreting ¹³C metabolite labeling patterns from cells. Current Opinion in Biotechnology 34:189-201.

29. Lien SK, Niedenführ S, Sletta H, Nöh K, Bruheim P (2015) Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA. BMC Systems Biology 9(1):6. (OA)

30. Witthoff S, Schmitz K, Niedenführ S, Nöh K, Noack S, Bott M, Marienhagen J (2015) Metabolic engineering of Corynebacterium glutamicum for methanol metabolism. Applied and Environmental Microbiology 81(6):2215-2225.

31. Nöh K, Droste P, Wiechert W (2015) Visual workflows for ¹³C-metabolic flux analysis. Bioinformatics 31(3):346-354.

32. Probst C, Grünberger A, Braun N, Helfrich S, Nöh K, Wiechert W, Kohlheyer D (2015) Rapid inoculation of single bacteria into parallel picoliter fermentation chambers. Analytical Methods 7(1):91-98.

33. Wiechert W, Nöh K (2013) Isotopically non-stationary metabolic flux analysis: Complex yet highly informative. Current Opinion in Biotechnology 24:979-986.

34. Mustafi N, Grünberger A, Mahr R, Helfrich S, Nöh K, Blombach B, Kohlheyer D, Frunzke J (2014) Application of a genetically encoded biosensor for live cell imaging of L-valine production in pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum strains. PLOS ONE 9(1):e85731.

35. Beste DJV, Nöh K, Niedenführ S, Mendum TA, Hawkins ND, Ward JL, Beale MH, McFadden J (2013) ¹³C-flux spectral analysis of host-pathogen metabolism reveals a mixed diet for intracellular Mycobacterium tuberculosis. Chemistry & Biology 20(8):1012-1021.

36. Wiechert W, Nöh K, Weitzel M (2013) Metabolic isotopomer labeling systems. Part III: Path tracing. Mathematical Biosciences 244:1-12.

37. Droste P, Nöh K, Wiechert W (2013) Omix - A visualization tool for metabolic networks with highest usability and customizability in focus. Chemie - Ingenieur - Technik 85:849-862.

38. Hanke T, Nöh K, Noack S, Polen T, Bringer-Meyer S, Sahm H, Wiechert W, Bott M (2013) Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H. Applied and Environmental Microbiology 79:2336-2348.

39. Dalman T, Dörnemann T, Juhnke E, Weitzel M, Wiechert W, Nöh K, Freisleben B (2013) Cloud MapReduce for Monte Carlo bootstrap applied to metabolic flux analysis. Future Generation Computer Systems 29:582-590.

40. Weitzel M, Nöh K, Dalman T, Niedenführ S, Stute B, Wiechert W (2013). 13CFLUX2 – High performance software suite for ¹³C-metabolic flux analysis. Bioinformatics 29(1):143-145.

41. Droste P, Wiechert W, Nöh K (2012) Semi-automatic drawing of metabolic networks. Information Visualization 11:171-187.

42. Tillack J, Paczia N, Nöh K, Wiechert W, Noack S (2012). Error propagation analysis for quantitative intracellular metabolomics. Metabolites
2(4):1012-1030.

43. Rühl M, Rupp B, Nöh K, Wiechert W, Sauer U, Zamboni N (2012) Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of ¹³C metabolic flux analysis. Biotechnology and Bioengineering 109:763-771.

44. Droste P, Miebach S, Niedenführ S, Wiechert W, Nöh K (2011) Visualizing multi-omics data in metabolic networks with the software Omix – a case study. Biosystems 105(2):154-161.

45. Hadlich F, Nöh K, Wiechert W (2011). Determination of flux directions by thermodynamic network analysis: computing informative metabolite pools. Mathematics and Computers in Simulation 82(3):460-470.

46. Bartek T, Blombach B, Lang S, Eikmanns BJ, Wiechert W, Oldiges M, Nöh K, Noack S (2011) Comparative ¹³C metabolic flux analysis of pyruvate dehydrogenase complex-deficient, L-valine producing Corynebacterium glutamicum. Applied and Environmental Microbiology 77(18):6644-6652.

47. Nöh K, Wiechert W (2011) The benefits of being transient: Isotope-based metabolic flux analysis at the short time scale. Applied and Environmental Microbiology 91(5):1247-1265.

48. Noack S, Nöh K, Moch M, Oldiges M, Wiechert W (2011) Stationary versus non-stationary ¹³C MFA: A comparison using a consistent dataset. Journal of Biotechnology 154(2-3):179-190.

49. Dalman T, Weitzel M, Wiechert W, Freisleben B, Nöh K (2011). An online provenance service for distributed metabolic flux analysis workflows. IEEE 9th European Conference on Web Services, pp. 91–98.

50. Beste DJV, Bonde B, Hawkins N, Ward JL, Beale MH, Noack S, Nöh K, Kruger NJ, Ratcliffe RG, McFadden J (2011) ¹³C Metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLOS Pathogens 7(7):e1002091. (OA)

51. Dalman T, Doernemann T, Juhnke E, Weitzel M, Smith M, Wiechert W, Nöh K, Freisleben B (2010). Metabolic Flux Analysis in the Cloud. IEEE 6th International Conference on e-Science, pp. 57–64.

52. Wahl SA, Nöh K, Wiechert W (2008) ¹³C labeling experiments at metabolic nonstationary conditions: An exploratory study. BMC Bioinformatics 9:152. (OA)

53. von Lieres E, Frauen C, Nöh K (2008) Fast solution of chromatographic particle and column models on parallel computers. International Journal of Pure and Applied Mathematics 42(3).

54. Weitzel M, Wiechert W, Nöh K (2007) The topology of metabolic isotope labeling networks. BMC Bioinformatics 8:315. (OA)

55. Nöh K, Grönke K, Luo B, Takors R, Oldiges M, Wiechert W (2007) Metabolic flux analysis at ultra short time scale: Isotopically non-stationary ¹³C labeling experiments. Journal of Biotechnology 129(2):249-267.

56. Adam S, Nöh K, Wiechert W (2007) Modeling and simulation of falling dominoes: a fertile example for simulation education. Simulation News Europe 17(1):41-44.

57. Nöh K, Wahl SA, Wiechert W (2006) Computational tools for isotopically instationary ¹³C labeling experiments under metabolic steady state conditions. Metabolic Engineering 8(6):554-577.

58. Nöh K, Wiechert W (2006) Experimental design principles for isotopically instationary ¹³C labeling experiments. Biotechnology and Bioengineering 94(2):234-251.

59. Wiechert W, Nöh K (2005). From stationary to instationary metabolic flux analysis. Advances in Biochemical Engineering/Biotechnology 92:145–172.

Book Chapters

1. Wiechert W, Nöh K (2021) Quantitative Metabolic Flux Analysis based on Isotope Labeling. In J. Nielsen, G. Stephanopoulos, S. Lee (eds), Metabolic Engineering: Concepts and Applications (Vol. 13a, pp. 73-136). Weinheim, Germany: Wiley-VCH Verlag GmbH.

2. Wiechert W, Niedenführ S, Nöh K (2015) A Primer to ¹³C Metabolic Flux Analysis. In J. Villadsen (ed), Fundamental Bioengineering (pp. 97–142). Weinheim, Germany: Wiley-VCH Verlag GmbH.

3. Zelle E, Nöh K, Wiechert W (2015) Growth and Production Capabilities of Corynebacterium glutamicum: Interrogating a Genome-scale Metabolic Network Model. In Burkovski A (ed), Corynebacterium glutamicum: From Systems Biology to Biotechnological Applications (p. 190). Caister Academic Press.

4. Wiechert W, Haunschild M, Weitzel M, Nöh K, von Lieres E, Wahl SA, Qeli E, Freisleben B (2006) Grid Computing for Systems Biology. In: Barth T, Schüll A (eds) Grid Computing. Vieweg.

Last Modified: 12.10.2023