The executable pathway to biological networks.

Briefings in Functional Genomics
Jasmin Fisher, Nir Piterman

Abstract

As time goes by, it becomes more and more apparent that the puzzles of life involve more and more molecular pieces that fit together in increasingly complex ways. Genomics and Proteomics technologies nowadays, produce reliable and quantitative data that could potentially reveal all the molecular pieces of a particular puzzle. However, this is akin to the opening of Pandora's box; and we are now facing the problem of integrating this vast amount of data with its incredible complexity into some coherent whole. With the aid of engineering methods designed to build and analyze computerized man-made systems, a new emerging field called 'Executable Biology' aims to create computer programmes that put together the pieces in ways that allows capturing their dynamicity and ultimately elucidating how molecular function generates cellular function. This review aspires to highlight the main features characterizing these kinds of executable models and what makes them uniquely qualified to reason about and analyze biological networks.

References

Mar 1, 1969·Journal of Theoretical Biology·S A Kauffman
Feb 3, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jasmin FisherDavid Harel
Feb 8, 2006·Genome Génome / Conseil National De Recherches Canada·Ricardo LopesMaria Lucia Carneiro Vieira
Jan 30, 2007·PLoS Computational Biology·Sol EfroniIrun R Cohen
Apr 6, 2007·BMC Systems Biology·Marc A SchaubJasmin Fisher
May 22, 2007·PLoS Computational Biology·Jasmin FisherThomas A Henzinger
Nov 9, 2007·Nature Biotechnology·Jasmin Fisher, Thomas A Henzinger
Feb 5, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Federica CiocchettaPaola Quaglia
Dec 19, 2008·Proceedings of the National Academy of Sciences of the United States of America·Yaki SettyDavid Harel
Aug 7, 2009·Journal of Cell Science·Marta Z Kwiatkowska, John K Heath

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Citations

Apr 25, 2012·Immunologic Research·Vipin NarangAlexandre Gouaillard
Sep 24, 2010·Environmental Microbiology·Ramiro Vilchez-VargasDietmar H Pieper
Oct 13, 2011·Molecular Systems Biology·Marco A Mendoza-ParraHinrich Gronemeyer
Jul 23, 2015·Biophysical Journal·Benjamin A HallJasmin Fisher
Sep 15, 2012·Progress in Biophysics and Molecular Biology·Tom Melham
Jan 23, 2016·PLoS Computational Biology·Ezio Bartocci, Pietro Lió
Mar 9, 2018·Royal Society Open Science·Arnaud Poret, Carito Guziolowski

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