Natalie J Stanford

Natalie J Stanford
The University of Manchester · School of Computer Science

Systems Biology PhD

About

11
Publications
2,174
Reads
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341
Citations
Citations since 2016
2 Research Items
222 Citations
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2016201720182019202020212022010203040
2016201720182019202020212022010203040
Introduction
I am a Chemist turned Systems Biologist, specialising in rational design (reverse engineering/modelling) of microorganisms (yeast, E.coli, cyanobacteria) in order to improve biofuel and fine chemical product yield. I am also establishing recommendations for long-term data, model, and other asset management in life sciences, particularly for systems biology. This is part of the data-stewardship work package of ISBE (Infrastructure for Systems Biology Europe).
Additional affiliations
October 2014 - present
The University of Manchester
Position
  • Systems Biology Informatics Manager
Description
  • Establishing research asset (data/models/SOPs/maps) management recommendations for Infrastructure for Systems Biology in Europe (ISBE - http://project.isbe.eu/) and FAIRDOM (http://fair-dom.org/) to support long term research asset management.
April 2013 - September 2014
The University of Manchester
Position
  • Systems Biology Community Consultant
Description
  • Working on Infrastructure for Systems Biology in Europe (ISBE - http://project.isbe.eu/).
December 2012 - March 2013
LifeGlimmer
Position
  • Biotechnology Consultant
Description
  • Advised on a rational design strategy for biofuel and fine chemical production from yeast. This work was in conjunction with companies including Abengoa, and Organobalance. The project was headed by Jan De Bont of BioconsultancyWageningen.
Education
October 2007 - November 2011
October 2004 - July 2007

Publications

Publications (11)
Article
Full-text available
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 on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate...
Article
Cyanobacteria are capable of directly converting sunlight, carbon dioxide and water into hydrocarbon fuel or precursors thereof. Many biological and non-biological factors will influence the ability of such a production system to become economically sustainable. We evaluated two factors in engineerable cyanobacteria which could potentially limit ec...
Article
Full-text available
To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented metabolite transport, lipid metabolism and other pathways, and was no...
Chapter
Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating datasets and integrating them into models involves a wide range of scientific expertise. As a result these datasets are often collected by one set of res...
Article
Full-text available
Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. Results: Our analysis revealed several challenges to representing WC models using the current standards. Conclusion: We, therefore, propose sev...
Article
Full-text available
Sustainable production of target compounds such as biofuels and high-value chemicals for pharmaceutical, agrochemical, and chemical industries is becoming an increasing priority given their current dependency upon diminishing petrochemical resources. Designing these strains is difficult, with current methods focusing primarily on knocking-out genes...
Article
In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway using kinetic data from both experimental measurements and literature review. Our methodology is presented by using the example of serine biosynthesis in E. coli.
Conference Paper
Full-text available
A major result of the various genome programs has been an accumulation of complete genomic sequences and their associated annotation. These resources are extremely valuable to various fields of biology, not least metabolism and metabolic modelling. As these complete sequences have started appearing they have been used to derive lists of metabolic r...
Data
Yeast SBML files. ZIP file containing the latest reconstruction in SBML format. The metabolic network reconstruction is described using MIRIAM-compliant SBML, compatible with many Systems Biology software packages, including the COBRA toolbox. The model is also available in decompartmentalised form, and in an old SBML format (level 2, version 1) fo...
Data
Poorly characterised genes. Excel spreadsheet. The network is built upon intensive literature mining to identify reactions. Many genes still do not have detailed literature describing the functions of their products, yet (by what little is known or through sequence analysis) they appear likely to be involved in metabolism. The attached list describ...
Article
Background: To date several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in their scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented lipid metabolism and other pathways. The recent iIN...

Network

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