E
Evangelos Simeonidis
Researcher at Institute for Systems Biology
Publications - 35
Citations - 2877
Evangelos Simeonidis is an academic researcher from Institute for Systems Biology. The author has contributed to research in topics: Metabolic network & Systems biology. The author has an hindex of 19, co-authored 34 publications receiving 2643 citations. Previous affiliations of Evangelos Simeonidis include University of Luxembourg & University College London.
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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.
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.
Journal ArticleDOI
Towards a genome-scale kinetic model of cellular metabolism
TL;DR: A method for building a parameterized genome-scale kinetic model of a metabolic network and, whilst approximative, has considerably broader remit than any existing models of its type.
Journal ArticleDOI
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.
Kieran Smallbone,Hanan L. Messiha,Kathleen M. Carroll,Catherine L. Winder,Naglis Malys,Naglis Malys,Warwick B. Dunn,Warwick B. Dunn,Ettore Murabito,Neil Swainston,Joseph O. Dada,Farid Khan,Pınar Pir,Evangelos Simeonidis,Irena Spasic,Irena Spasic,Jill A. Wishart,Dieter Weichart,Neil W. Hayes,Neil W. Hayes,Daniel Jameson,David S. Broomhead,Stephen G. Oliver,Stephen G. Oliver,Simon J. Gaskell,Simon J. Gaskell,John E.G. McCarthy,Norman W. Paton,Hans V. Westerhoff,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes +32 more
TL;DR: This bottom‐up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought.
Journal ArticleDOI
Further developments towards a genome-scale metabolic model of yeast
Paul D. Dobson,Kieran Smallbone,Daniel Jameson,Evangelos Simeonidis,Karin Lanthaler,Pınar Pir,Chuan-Zhen Lu,Neil Swainston,Warwick B. Dunn,Paul R. Fisher,Duncan Hull,Marie Brown,Olusegun Oshota,Natalie J. Stanford,Douglas B. Kell,Ross D. King,Stephen G. Oliver,Robert Stevens,Pedro Mendes,Pedro Mendes +19 more
TL;DR: The development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature evidence and richly annotated according to MIRIAM standards is reported.