A5072794019- Scientific Computing and Data Management
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Biomedical Text Mining and Ontologies
- Gene Regulatory Network Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Business Process Modeling and Analysis
- Semantic Web and Ontologies
- Simulation Techniques and Applications
- Enzyme Catalysis and Immobilization
- Biofuel production and bioconversion
- Advanced Control Systems Optimization
- Model-Driven Software Engineering Techniques
- Algal biology and biofuel production
- Big Data Technologies and Applications
- Data Quality and Management
- Enzyme Structure and Function
- Evolution and Genetic Dynamics
- Corporate Law and Human Rights
- Photosynthetic Processes and Mechanisms
- Innovation Policy and R&D
- Insurance and Financial Risk Management
- Fungal and yeast genetics research
- Technology Assessment and Management
University of Manchester
2010-2019
Health Information Management
2016-2018
Humboldt-Universität zu Berlin
2012
The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful growing catalog natural products and high-value chemicals. However, development at industrial levels been hindered by large resource investments required. Here we present an integrated Design-Build-Test-Learn (DBTL) pipeline for discovery optimization biosynthetic pathways, which is designed be compound agnostic automated throughout. We initially applied...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures Models (https://fairdomhub.org/) the Systems Biology community. It web-accessible storing sharing systems biology research assets. enables researchers to organize, share publish data, models protocols, interlink them in context of investigations that produced them, interrogate via API interfaces. By using FAIRDOMHub, can achieve more effective exchange with...
The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based logical layering data such as reaction fluxes, metabolite concentrations, constants. resulting models contain realistic standard rate laws plausible parameters, adhere to the thermodynamics, reproduce predefined steady state. These features have not been simultaneously achieved by previous workflows....
Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model predict biological processes. Researchers therefore require tools resources facilitate sharing data, for linking systems models. There are a large number public repositories storing particular type, example transcriptomics or proteomics, there several repositories. However, this silo-type storage models is not conducive investigations. Interdependencies between multiple...
To date, several genome-scale network reconstructions have been used to describe the metabolism of yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced well annotated, under-represented metabolite transport, lipid other pathways, was not amenable constraint-based analyses because lack pathway connectivity.We expanded reconstruction incorporate many new reactions from literature represented these a...
Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.We organized the 2015 Whole-Cell Modeling Summer School teach WC evaluate need new standards software by recoding recently published model in Systems Biology Markup Language.Our analysis revealed several challenges representing using current standards.We, therefore, propose standards, software,...
Commentary28 December 2015Open Access The evolution of standards and data management practices in systems biology Natalie J Stanford Corresponding Author Manchester Institute Biotechnology, University Manchester, UK School Computer Science, Search for more papers by this author Katherine Wolstencroft Leiden Advanced University, Leiden, Netherlands Martin Golebiewski Heidelberg Theoretical Studies, Heidelberg, Germany Renate Kania Nick Juty European Molecular Biology Laboratory,...
Sustainable production of target compounds such as biofuels and high-value chemicals for pharmaceutical, agrochemical chemical industries is becoming an increasing priority given their current dependency upon diminishing petrochemical resources. Designing these strains difficult, with methods focussing primarily on knocking-out genes, dismissing other vital steps strain design including the overexpression dampening genes. The predictions from also do not translate well into successful in...
Abstract In many disciplines, data is highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers are a core component this infrastructure. Drawing our experience work by other groups, we outline ten lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose...
A major result of the various genome programs has been an accumulation complete genomic sequences and their associated annotation. These resources are extremely valuable to fields biology, not least metabolism metabolic modelling. As these have started appearing they used derive lists reactions that catalysed by enzymes whose genes identified in sequence. "reconstructions" further interpreted as networks several analyses can be derived from them. In case popular model organism Saccharomyces...