Literature DB >> 16934450

Systems biology as a foundation for genome-scale synthetic biology.

Christian L Barrett1, Tae Yong Kim, Hyun Uk Kim, Bernhard Ø Palsson, Sang Yup Lee.   

Abstract

As the ambitions of synthetic biology approach genome-scale engineering, comprehensive characterization of cellular systems is required, as well as a means to accurately model cell-scale molecular interactions. These requirements are coincident with the goals of systems biology and, thus, systems biology will become the foundation for genome-scale synthetic biology. Systems biology will form this foundation through its efforts to reconstruct and integrate cellular systems, develop the mathematics, theory and software tools for the accurate modeling of these integrated systems, and through evolutionary mechanisms. As genome-scale synthetic biology is so enabled, it will prove to be a positive feedback driver of systems biology by exposing and forcing researchers to confront those aspects of systems biology which are inadequately understood.

Mesh:

Year:  2006        PMID: 16934450     DOI: 10.1016/j.copbio.2006.08.001

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  27 in total

Review 1.  Advantages and limitations of current network inference methods.

Authors:  Riet De Smet; Kathleen Marchal
Journal:  Nat Rev Microbiol       Date:  2010-08-31       Impact factor: 60.633

2.  Calculating life? A sociological perspective on systems biology.

Authors:  Jane Calvert; Joan H Fujimura
Journal:  EMBO Rep       Date:  2009-08       Impact factor: 8.807

Review 3.  The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms.

Authors:  Gil Alterovitz; Taro Muso; Marco F Ramoni
Journal:  Brief Bioinform       Date:  2009-11-11       Impact factor: 11.622

4.  New approach for phylogenetic tree recovery based on genome-scale metabolic networks.

Authors:  Daniel Gamermann; Arnaud Montagud; J Alberto Conejero; Javier F Urchueguía; Pedro Fernández de Córdoba
Journal:  J Comput Biol       Date:  2014-03-10       Impact factor: 1.479

5.  Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.

Authors:  André B Canelas; Nicola Harrison; Alessandro Fazio; Jie Zhang; Juha-Pekka Pitkänen; Joost van den Brink; Barbara M Bakker; Lara Bogner; Jildau Bouwman; Juan I Castrillo; Ayca Cankorur; Pramote Chumnanpuen; Pascale Daran-Lapujade; Duygu Dikicioglu; Karen van Eunen; Jennifer C Ewald; Joseph J Heijnen; Betul Kirdar; Ismo Mattila; Femke I C Mensonides; Anja Niebel; Merja Penttilä; Jack T Pronk; Matthias Reuss; Laura Salusjärvi; Uwe Sauer; David Sherman; Martin Siemann-Herzberg; Hans Westerhoff; Johannes de Winde; Dina Petranovic; Stephen G Oliver; Christopher T Workman; Nicola Zamboni; Jens Nielsen
Journal:  Nat Commun       Date:  2010       Impact factor: 14.919

6.  A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis.

Authors:  Xin Fang; Anders Wallqvist; Jaques Reifman
Journal:  BMC Syst Biol       Date:  2009-09-15

7.  Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.

Authors:  Adam M Feist; Daniel C Zielinski; Jeffrey D Orth; Jan Schellenberger; Markus J Herrgard; Bernhard Ø Palsson
Journal:  Metab Eng       Date:  2009-10-17       Impact factor: 9.783

Review 8.  Toward engineering synthetic microbial metabolism.

Authors:  George H McArthur; Stephen S Fong
Journal:  J Biomed Biotechnol       Date:  2009-12-14

9.  Comparison of evolutionary algorithms in gene regulatory network model inference.

Authors:  Alina Sîrbu; Heather J Ruskin; Martin Crane
Journal:  BMC Bioinformatics       Date:  2010-01-27       Impact factor: 3.169

Review 10.  Bacteria as computers making computers.

Authors:  Antoine Danchin
Journal:  FEMS Microbiol Rev       Date:  2008-11-07       Impact factor: 16.408

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