Application of combinatorial optimization strategies in synthetic biology

Nature Communications
Gita Naseri, Mattheos A G Koffas


In the first wave of synthetic biology, genetic elements, combined into simple circuits, are used to control individual cellular functions. In the second wave of synthetic biology, the simple circuits, combined into complex circuits, form systems-level functions. However, efforts to construct complex circuits are often impeded by our limited knowledge of the optimal combination of individual circuits. For example, a fundamental question in most metabolic engineering projects is the optimal level of enzymes for maximizing the output. To address this point, combinatorial optimization approaches have been established, allowing automatic optimization without prior knowledge of the best combination of expression levels of individual genes. This review focuses on current combinatorial optimization methods and emerging technologies facilitating their applications.


Oct 8, 2005·Expert Review of Proteomics·Leonardo Mariño-RamírezDavid Landsman
Jul 18, 2006·Nature Biotechnology·Brian F PflegerJay D Keasling
Feb 13, 2007·Metabolic Engineering·Hal Alper, Gregory Stephanopoulos
Feb 16, 2008·FEBS Letters·Rafael Silva-Rocha, Víctor de Lorenzo
Sep 23, 2008·Cell·Joel R Neilson, Phillip A Sharp
Jul 28, 2009·Nature·Harris H WangGeorge M Church
Oct 6, 2009·Nature Biotechnology·Howard M SalisChristopher A Voigt
Jul 20, 2010·Nature Biotechnology·Joseph R WarnerRyan T Gill
May 24, 2011·Methods in Enzymology·Howard M Salis
Jun 28, 2011·Methods in Cell Biology·Kiryl D Piatkevich, Vladislav V Verkhusha
Nov 30, 2011·PLoS Computational Biology·Rutger HermsenTerence Hwa
Sep 12, 2012·Journal of the American Chemical Society·Lauren R Polstein, Charles A Gersbach
Nov 20, 2012·Biology of the Cell·Gopal P PathakChandra L Tucker
Apr 25, 2013·Molecular Therapy. Nucleic Acids·Kimberly A WilsonMatthew H Porteus
Jan 7, 2014·Applied and Environmental Microbiology·Tao XuJizhong Zhou
Jan 15, 2014·Metabolic Engineering·John W K OliverShota Atsumi
Jan 29, 2014·Molecular BioSystems·Konrad MüllerMatias D Zurbriggen
Mar 7, 2014·Metabolic Engineering·Pieter CoussementMarjan De Mey
Aug 26, 2014·Nature Chemical Biology·Kate ThodeyChristina D Smolke
Nov 8, 2014·Computational and Structural Biotechnology Journal·Amanda K FisherRyan S Senger
Nov 25, 2014·Nature Biotechnology·Michael J SmanskiChristopher A Voigt
Dec 30, 2014·Current Opinion in Chemical Biology·Jared C Lewis
Jan 27, 2015·Chemistry & Biology·Yuta NihongakiMoritoshi Sato
Feb 11, 2015·Nature Chemical Biology·Lauren R Polstein, Charles A Gersbach
Feb 13, 2015·Proceedings of the National Academy of Sciences of the United States of America·Stephanie BrownSarah E O'Connor
Feb 17, 2015·ACS Synthetic Biology·Kathleen A CurranHal S Alper
May 10, 2015·Nucleic Acids Research·Leslie A MitchellJef D Boeke
Jun 10, 2015·Current Opinion in Chemical Biology·Jie ZhangJay D Keasling
Jun 13, 2015·Scientific Reports·J Andrew JonesMattheos A G Koffas
Jul 15, 2015·Nucleic Acids Research·Jameson K RogersGeorge M Church
Aug 8, 2015·Biotechnology and Bioengineering·Todd S Freestone, Huimin Zhao
Dec 25, 2015·Journal of Biological Engineering·Shasha ZhangChunbo Lou

❮ Previous
Next ❯


Oct 14, 2020·Protein Science : a Publication of the Protein Society·Jamie A Davies
Dec 1, 2020·Critical Reviews in Food Science and Nutrition·Prasoon KumarPratyoosh Shukla
Dec 11, 2020·Metabolic Engineering·Rosanna YoungPaul S Freemont
Nov 25, 2020·Trends in Microbiology·Amit SrivastavaPratyoosh Shukla
Mar 10, 2021·Nature Communications·Xiao-Ran JiangGuo-Qiang Chen
Oct 3, 2020·Current Opinion in Biotechnology·Jeffrey J CzajkaYinjie J Tang
May 18, 2021·Biotechnology Advances·Andrew CurrinRainer Breitling
May 31, 2021·Metabolic Engineering·Anna K WronskaJean-Marc Daran
Jun 29, 2021·Critical Reviews in Biochemistry and Molecular Biology·Matthew WongMattheos Koffas
May 18, 2021·The New Phytologist·Constantine GaragounisKalliope K Papadopoulou

❮ Previous
Next ❯

Methods Mentioned

flow cytometry
genetic modifications
enzymatic assay
RNA seq

Related Concepts

Related Feeds

Biomaterial Engineering

Advances in biomaterial engineering have permitted the development of sophisticated drug-releasing materials with a biomimetic 3D support that allow a better control of the microenvironment of transplanted cells. Here is the latest research.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Yuval HartUri Alon
Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Jacob D. FealaGiovanni Paternostro
© 2021 Meta ULC. All rights reserved