Literature DB >> 19758796

Computational design tools for synthetic biology.

Mario A Marchisio1, Jörg Stelling.   

Abstract

Computer-aided design, pervasive in other engineering disciplines, is currently developing in synthetic biology. Concepts for standardization and hierarchies of parts, devices and systems provide a basis for efficient engineering in biology. Recently developed computational tools, for instance, enable rational (and graphical) composition of genetic circuits from standard parts, and subsequent simulation for testing the predicted functions in silico. The computational design of DNA and proteins with predetermined quantitative functions has made similar advances. The biggest challenge, however, is the integration of tools and methods into powerful and intuitively usable workflows-and the field is only starting to address it.

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Year:  2009        PMID: 19758796     DOI: 10.1016/j.copbio.2009.08.007

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


  32 in total

Review 1.  Computational tools for the synthetic design of biochemical pathways.

Authors:  Marnix H Medema; Renske van Raaphorst; Eriko Takano; Rainer Breitling
Journal:  Nat Rev Microbiol       Date:  2012-01-23       Impact factor: 60.633

Review 2.  Genetic design automation: engineering fantasy or scientific renewal?

Authors:  Matthew W Lux; Brian W Bramlett; David A Ball; Jean Peccoud
Journal:  Trends Biotechnol       Date:  2011-10-14       Impact factor: 19.536

3.  Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down.

Authors:  Peter Neubauer; Emmanuel Anane; Stefan Junne; Mariano Nicolas Cruz Bournazou
Journal:  Adv Biochem Eng Biotechnol       Date:  2021       Impact factor: 2.635

4.  Automated Biocircuit Design with SYNBADm.

Authors:  Irene Otero-Muras; Julio R Banga
Journal:  Methods Mol Biol       Date:  2021

5.  GeneGenie: optimized oligomer design for directed evolution.

Authors:  Neil Swainston; Andrew Currin; Philip J Day; Douglas B Kell
Journal:  Nucleic Acids Res       Date:  2014-04-29       Impact factor: 16.971

6.  Programming languages for synthetic biology.

Authors:  P Umesh; F Naveen; Chanchala Uma Maheswara Rao; Achuthsankar S Nair
Journal:  Syst Synth Biol       Date:  2011-02-20

7.  GeneDesign 3.0 is an updated synthetic biology toolkit.

Authors:  Sarah M Richardson; Paul W Nunley; Robert M Yarrington; Jef D Boeke; Joel S Bader
Journal:  Nucleic Acids Res       Date:  2010-03-08       Impact factor: 16.971

8.  GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs.

Authors:  Yizhi Cai; Mandy L Wilson; Jean Peccoud
Journal:  Nucleic Acids Res       Date:  2010-02-18       Impact factor: 16.971

Review 9.  Synthetic biology approaches in drug discovery and pharmaceutical biotechnology.

Authors:  Heinz Neumann; Petra Neumann-Staubitz
Journal:  Appl Microbiol Biotechnol       Date:  2010-04-16       Impact factor: 4.813

Review 10.  Engineering cell-based therapies to interface robustly with host physiology.

Authors:  Kelly A Schwarz; Joshua N Leonard
Journal:  Adv Drug Deliv Rev       Date:  2016-06-03       Impact factor: 15.470

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