Nikolaus Sonnenschein

Publications

• A topological characterization of medium-dependent essential metabolic reactions.
• Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks.
• Genome-Scale Models
• Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of Saccharomyces cerevisiae
• Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks
• Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
• A genome-scale metabolic model for Methylococcus capsulatus predicts reduced efficiency uphill electron transfer to pMMO
• Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modelling
• 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
• Do genome-scale models need exact solvers or clearer standards?
• A network perspective on metabolic inconsistency.
• Putting computational modeling at the fingertips of bench biologists
• Systems biology solutions for biochemical production challenges
• Evolution Reveals A Glutathione-dependent Mechanism Of 3-hydroxypropionic Acid Detoxification
• Engineering an NADPH/NADP+ Redox Biosensor in Yeast
• Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
• MARSI: metabolite analogues for rational strain improvement
• Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling
• Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology
• Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells
• Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
• Ranges of control in the transcriptional regulation of Escherichia coli.
• Analysis of genetic variation and potential applications in genome-scale metabolic modeling.
• Analog regulation of metabolic demand.
• A community-driven global reconstruction of human metabolism.
• Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance.
• Editorial: Current Challenges in Modeling Cellular Metabolism.
• OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs
• 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
• A kinetic model of thiamine biosynthesis in Escherichia coli
• DD-DeCaF: Data-Driven Design of Cell Factories and Communities
• A compendium of genetic variant data
• Optlang: An algebraic modeling language for mathematical optimization
• Memote - The genome-scale metabolic model test suite
• A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
• Improving Reproducibility in Synthetic Biology
• Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism (Nature Communications, (2019), 10, 1, (3586), 10.1038/s41467-019-11581-3)
• Emergence of phenotypically distinct subpopulations is a factor in adaptation of recombinant Saccharomyces cerevisiae under glucose-limited conditions
• Genome-scale metabolic modelling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism.
• Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
• Single-cell technologies to understand the mechanisms of cellular adaption in chemostats
• MEMOTE for standardized genome-scale metabolic model testing
• Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism
• Genome-Wide CRISPRi-Based Identification of Targets for Decoupling Growth from Production
• A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase
• Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies
• Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics
• Engineering precursor supply for the high-level production of ergothioneine in Saccharomyces cerevisiae
• Emergence of Phenotypically Distinct Subpopulations Is a Factor in Adaptation of Recombinant Saccharomyces cerevisiae under Glucose-Limited Conditions
• A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility
• Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model
• CRI-SPA, a mating based CRISPR-Cas9 assisted method for high-throughput genetic modification of yeast strain libraries
• Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals
• Geckopy 3.0: enzyme constraints, thermodynamics constraints and omics integration in python
• Probing efficient microbial CO2 utilization through metabolic and process modeling
• CRI-SPA: a high-throughput method for systematic genetic editing of yeast libraries
• Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO
• Probing efficient microbial CO2 utilisation through metabolic and process modelling
• teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering