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Neil Swainston
Researcher at University of Liverpool
Publications - 90
Citations - 6780
Neil Swainston is an academic researcher from University of Liverpool. The author has contributed to research in topics: SBML & Synthetic biology. The author has an hindex of 32, co-authored 86 publications receiving 5690 citations. Previous affiliations of Neil Swainston include University of Manchester & European Bioinformatics Institute.
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Journal ArticleDOI
A community-driven global reconstruction of human metabolism
Ines Thiele,Neil Swainston,Ronan M. T. Fleming,Andreas Hoppe,Swagatika Sahoo,Maike K. Aurich,Hulda S. Haraldsdóttir,Monica L. Mo,Ottar Rolfsson,Miranda D. Stobbe,Miranda D. Stobbe,Stefan Gretar Thorleifsson,Rasmus Agren,Christian Bölling,Sergio Bordel,Arvind K. Chavali,Paul D. Dobson,Warwick B. Dunn,Warwick B. Dunn,Lukas Endler,David Hala,Michael Hucka,Duncan Hull,Daniel Jameson,Neema Jamshidi,Jon J. Jonsson,Nick Juty,Sarah M. Keating,Intawat Nookaew,Nicolas Le Novère,Nicolas Le Novère,Naglis Malys,Naglis Malys,Alexander Mazein,Jason A. Papin,Nathan D. Price,Evgeni Selkov,Martin I. Sigurdsson,Evangelos Simeonidis,Evangelos Simeonidis,Nikolaus Sonnenschein,Kieran Smallbone,Anatoly Sorokin,Anatoly Sorokin,Johannes H. G. M. van Beek,Dieter Weichart,Igor Goryanin,Jens Nielsen,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes,Bernhard O. Palsson,Bernhard O. Palsson +53 more
TL;DR: Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.
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ChEBI in 2016: Improved services and an expanding collection of metabolites.
Janna Hastings,Gareth Owen,Adriano Dekker,Marcus Ennis,Namrata Kale,Venkatesh Muthukrishnan,Steve Turner,Neil Swainston,Pedro Mendes,Christoph Steinbeck +9 more
TL;DR: This update paper has substantially extended the collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast and added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.
Journal ArticleDOI
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Markus J. Herrgård,Neil Swainston,Paul D. Dobson,Warwick B. Dunn,K.Yalçın Arga,Mikko Arvas,Nils Blüthgen,Simon Borger,Roeland Costenoble,Matthias Heinemann,Michael Hucka,Nicolas Le Novère,Peter Li,Wolfram Liebermeister,Monica L. Mo,Ana Paula Oliveira,Dina Petranovic,Stephen Pettifer,Evangelos Simeonidis,Kieran Smallbone,Irena Spasic,Dieter Weichart,Roger Brent,David S. Broomhead,Hans V. Westerhoff,Betul Kirdar,Merja Penttilä,Edda Klipp,Bernhard O. Palsson,Uwe Sauer,Stephen G. Oliver,Pedro Mendes,Jens Nielsen,Douglas B. Kell +33 more
TL;DR: This work describes how it has produced a consensus metabolic network reconstruction for S. cerevisiae, and places special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning.
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Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
TL;DR: Improving enzymes by directed evolution requires the navigation of very large search spaces; this work surveys how to do this intelligently.
Journal ArticleDOI
Growth control of the eukaryote cell: a systems biology study in yeast
Juan I. Castrillo,Leo A. H. Zeef,David C. Hoyle,Nianshu Zhang,Andrew Hayes,David C. J. Gardner,Michael Cornell,June Petty,Luke Hakes,Leanne Wardleworth,Bharat M. Rash,Marie Brown,Warwick B. Dunn,David Broadhurst,Kerry O'Donoghue,Svenja Hester,Tom Dunkley,Sarah R. Hart,Neil Swainston,Peter Li,Simon J. Gaskell,Norman W. Paton,Kathryn S. Lilley,Douglas B. Kell,Stephen G. Oliver +24 more
TL;DR: This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell and has direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eUKaryoticcell.