A5019729791- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Complex Network Analysis Techniques
- Enzyme Catalysis and Immobilization
- thermodynamics and calorimetric analyses
- Gastrointestinal motility and disorders
- Diet and metabolism studies
- Gut microbiota and health
- Process Optimization and Integration
- Metabolomics and Mass Spectrometry Studies
- Sensor Technology and Measurement Systems
- Environmental DNA in Biodiversity Studies
- Data Visualization and Analytics
- Traffic control and management
- Fermentation and Sensory Analysis
- Helicobacter pylori-related gastroenterology studies
- Chemical and Physical Properties in Aqueous Solutions
- Cell Image Analysis Techniques
- Complex Systems and Time Series Analysis
- Species Distribution and Climate Change
- Conferences and Exhibitions Management
- Advanced Control Systems Optimization
- Bacterial Genetics and Biotechnology
Institute for Globally Distributed Open Research and Education
2023
Novo Nordisk Foundation
2017-2021
Technical University of Denmark
2017-2021
Foundation Center
2017
Constructor University
2011-2016
Max Planck Institute for Molecular Genetics
2014-2016
Abstract Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 an associated ecosystem comprehensive computational resource performing the metabolism Saccharomyces cerevisiae ––an important organism widely used cell-factory. tracks community development with version control, setting standard how GEMs can be continuously updated in simple reproducible way. We...
Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, biochemistry database serves as foundation biochemical data underlying and KBase. The embodies several properties that, taken together, distinguish it from other published resources by: (i) including compartmentalization, transport reactions, charged molecules proton balancing reactions; (ii)...
Abstract eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as web-based interface. While the website now counts around 1,000 distinct monthly users, its design could not accommodate larger compound databases it lacked scalable Application Programming Interface (API) for integration into other tools developed by systems biology community. Here, we report on recent updates to well addition new Python-based...
Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering cells for production valuable chemicals proteins. Unfortunately, majority these methods' implementations are either not published, rely proprietary software, or do provide documented interfaces, which has precluded their mainstream adoption in field. In this work we present cameo, platform-independent software that enables silico targets both experienced...
Abstract Several studies have shown that neither the formal representation nor functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability across groups software tools cannot be guaranteed. Here, we present memote ( https://github.com/opencobra/memote ) an open-source containing community-maintained, standardized set me tabolic mo del te sts. The tests cover range aspects from...
Commentary26 August 2020Open Access Community standards to facilitate development and address challenges in metabolic modeling Maureen A Carey orcid.org/0000-0003-2890-5445 Division of Infectious Diseases International Health, Department Medicine, University Virginia, Charlottesville, VA, USA Search for more papers by this author Andreas Dräger orcid.org/0000-0002-1240-5553 Computational Systems Biology Infection Antimicrobial-Resistant Pathogens, Institute Biomedical Informatics (IBMI),...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...
Background The long-term management of irritable bowel syndrome (IBS) poses many challenges. In short-term studies, eHealth interventions have been demonstrated to be safe and practical for at-home monitoring the effects probiotic treatments a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, polyols (FODMAPs). IBS has linked alterations microbiota. Objective aim this study was determine whether web-based low-FODMAP (LFD) intervention treatment were equally good at...
Few-node subgraphs are the smallest collective units in a network that can be investigated. They beyond scale of individual nodes but more local than, for example, communities. When statistically over- or under-represented, they called motifs. Network motifs have been interpreted as building blocks shape dynamic behaviour networks. It is this promise potentially explaining emergent properties complex systems with relatively simple structures led to an interest ever-growing number studies and...
Genome scale metabolic models (GEMs) and other constraint-based (CBMs) play a pivotal role in understanding biological phenotypes advancing research areas like engineering, human disease modelling, drug discovery, personalized medicine. Despite their growing application, significant challenge remains ensuring the reproducibility of GEMs, primarily due to inconsistent reporting inadequate model documentation results. Addressing this gap, we introduce FROG analysis, community driven initiative...
Metabolic systems need to show high performance under typical environmental conditions and, at the same time, maintain certain functions a broad range of perturbations and varying conditions. It is precisely this robustness with respect large changes that makes metabolic networks potentially very interesting role model for technical production distribution systems. Here we develop formalism compare these optimization strategies from one domain can also be successfully applied other domains.
Extensive drug treatment gene expression data have been generated in order to identify biomarkers that are predictive for toxicity or classify compounds. However, such patterns often highly variable across compounds and lack robustness. We others previously shown supervised based on pathway concepts rather than unsupervised more robust can be used assess entire classes of drugs reliably.We developed a database, ToxDB, the analysis functional consequences at level. collected 2694 computed...
Manufacturing systems can be modeled as networked work connected by material flow. Characteristics such performance and robustness are influenced the manufacturing network's static structure, i.e. topology, its dynamic behavior, The statistical analysis of topological features networks has been used in many disciplines to predict however, meaningfulness each individual measure differ between network types. Therefore, it is necessary determine which measures evaluate compare networks. This...
Measuring the agreement between a gene expression profile and known transcriptional regulatory network is an important step in functional interpretation of bacterial physiological state. In this way, general design principles can be explored. One such interpretive framework relationship digital control, that is, impact sequence-specific interactions, analog i.e., extent influence chromosomal structure. Here, we present time-resolved profiles Escherichia coli's growth cycle as measured by...
ABSTRACT For over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, biochemistry database serves as foundation biochemical data underlying and KBase. The embodies several properties that, taken together, distinguish it from other published resources by: (i) including compartmentalization, transport reactions, charged molecules proton balancing reactions;; (ii)...
We achieve a significant improvement in thermodynamic-based flux analysis (TFA) by introducing multivariate treatment of thermodynamic variables and leveraging component contribution, the state-of-the-art implementation group contribution methodology. Overall, method greatly reduces uncertainty variables.We present multiTFA, Python our framework. evaluated application using core Escherichia coli model achieved median reduction 6.8 kJ/mol reaction Gibbs free energy ranges, while three out 12...
Metagenomic analysis is largely concerned with untargeted genetic characterisation of the taxonomic and functional composition whole communities organisms.Researchers ask questions from metagenomic sequencing such as 'who present' (what organisms are present), 'what they doing' (which functions performing)?The nature this field that it intersects ecology, medicine, statistics, bioinformatics.Facilitated by development Next-Generation Sequencing (NGS), often generates large datasets...
RegulonDB is a database storing the biological information behind transcriptional regulatory network (TRN) of bacterium Escherichia coli. It one key bioinformatics resources for Systems Biology investigations bacterial gene regulation. Like most databases, content drifts with time, both due to accumulation new and refinements in underlying concepts. Conclusions based on previous versions may no longer hold. Here, we study change some topological properties TRN E. coli, as provided by across...
ABSTRACT Computational systems biology methods enable rational design of cell factories on a genomescale and thus accelerate the engineering cells for production valuable chemicals proteins. Unfortunately, majority these methods’ implementations are either not published, rely proprietary software, or do provide documented interfaces, which has precluded their mainstream adoption in field. In this work we present cameo, platform-independent software that enables silico targets both...
An amendment to this paper has been published and can be accessed via a link at the top of paper.