Literature DB >> 11356281

Whole-cell simulation: a grand challenge of the 21st century.

M Tomita1.   

Abstract

Study of the cell will never be complete unless its dynamic behavior is understood. The complex behavior of the cell cannot be determined or predicted unless a computer model of the cell is constructed and computer simulation is undertaken. Rapid accumulation of biological data from genome, proteome, transcriptome and metabolome projects can bring us to the point where it is no longer purely speculative to discuss how to construct virtual cells in silico. This article describes attempts to construct whole cell models. The E-CELL project has completed a couple of virtual cell models, and computer simulations have revealed some biological surprises.

Mesh:

Year:  2001        PMID: 11356281     DOI: 10.1016/s0167-7799(01)01636-5

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN: 0167-7799            Impact factor:   19.536


  51 in total

1.  Plant proteomics: BLASTing out of a MudPIT.

Authors:  Julian P Whitelegge
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-23       Impact factor: 11.205

Review 2.  Contribution of structural genomics to understanding the biology of Escherichia coli.

Authors:  Allan Matte; J Sivaraman; Irena Ekiel; Kalle Gehring; Zongchao Jia; Miroslaw Cygler
Journal:  J Bacteriol       Date:  2003-07       Impact factor: 3.490

3.  Toward rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic T-cell maturation.

Authors:  Sol Efroni; David Harel; Irun R Cohen
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

4.  Prospects of a computational origin of life endeavor.

Authors:  Barak Shenhav; Doron Lancet
Journal:  Orig Life Evol Biosph       Date:  2004-02       Impact factor: 1.950

5.  The two-regime method for optimizing stochastic reaction-diffusion simulations.

Authors:  Mark B Flegg; S Jonathan Chapman; Radek Erban
Journal:  J R Soc Interface       Date:  2011-10-19       Impact factor: 4.118

6.  Modelling ecological systems in a changing world.

Authors:  Matthew R Evans
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-01-19       Impact factor: 6.237

7.  Reaction diffusion modeling of calcium dynamics with realistic ER geometry.

Authors:  Shawn Means; Alexander J Smith; Jason Shepherd; John Shadid; John Fowler; Richard J H Wojcikiewicz; Tomas Mazel; Gregory D Smith; Bridget S Wilson
Journal:  Biophys J       Date:  2006-04-14       Impact factor: 4.033

8.  Metabolomics and machine learning: explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules.

Authors:  Douglas B Kell
Journal:  Mol Biol Rep       Date:  2002       Impact factor: 2.316

9.  Computational reasoning across multiple models.

Authors:  Guy Tsafnat; Enrico W Coiera
Journal:  J Am Med Inform Assoc       Date:  2009-08-28       Impact factor: 4.497

10.  A multiformalism and multiresolution modelling environment: application to the cardiovascular system and its regulation.

Authors:  Alfredo I Hernández; Virginie Le Rolle; Antoine Defontaine; Guy Carrault
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2009-12-13       Impact factor: 4.226

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