Modular design: Implementing proven engineering principles in biotechnology
Abstract
Modular design resides at the foundation of contemporary engineering, enabling rapid, efficient, and reproducible construction and maintenance of complex systems across applications. Remarkably, modularity has recently been discovered as a governing principle in natural biological systems from genes to proteins to complex networks within a cell and organism communities. The convergent knowledge of natural and engineered modular systems provides a key to drive modern biotechnology to address emergent challenges associated with health, food, energy, and the environment. Here, we first present the theory and application of modular design in traditional engineering fields. We further discuss the significance and impact of modular architectures on systems biology and biotechnology. Next, we focus on the very recent theoretical and experimental advances in modular cell engineering that seeks to enable rapid and systematic development of microbial catalysts capable of efficiently synthesizing a large space of useful chemicals. We conclude with an outlook towards theoretical and practical opportunities for a more systematic and effective application of modular engineering in biotechnology.
- Authors:
-
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Univ. of Tennessee, Knoxville, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1598476
- Alternate Identifier(s):
- OSTI ID: 1573281
- Grant/Contract Number:
- SC0019412
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biotechnology Advances
- Additional Journal Information:
- Journal Volume: 37; Journal Issue: 7; Journal ID: ISSN 0734-9750
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Modular design; Modularity; Modular cell; Modular cell engineering; ModCell; Systems biology; Metabolic engineering; Synthetic biology; Robustness; Evolvability; Networks; Pareto optimality; Industrialization of biology; Microbial biocatalysis
Citation Formats
Garcia, Sergio, and Trinh, Cong T. Modular design: Implementing proven engineering principles in biotechnology. United States: N. p., 2019.
Web. doi:10.1016/j.biotechadv.2019.06.002.
Garcia, Sergio, & Trinh, Cong T. Modular design: Implementing proven engineering principles in biotechnology. United States. https://doi.org/10.1016/j.biotechadv.2019.06.002
Garcia, Sergio, and Trinh, Cong T. Fri .
"Modular design: Implementing proven engineering principles in biotechnology". United States. https://doi.org/10.1016/j.biotechadv.2019.06.002. https://www.osti.gov/servlets/purl/1598476.
@article{osti_1598476,
title = {Modular design: Implementing proven engineering principles in biotechnology},
author = {Garcia, Sergio and Trinh, Cong T.},
abstractNote = {Modular design resides at the foundation of contemporary engineering, enabling rapid, efficient, and reproducible construction and maintenance of complex systems across applications. Remarkably, modularity has recently been discovered as a governing principle in natural biological systems from genes to proteins to complex networks within a cell and organism communities. The convergent knowledge of natural and engineered modular systems provides a key to drive modern biotechnology to address emergent challenges associated with health, food, energy, and the environment. Here, we first present the theory and application of modular design in traditional engineering fields. We further discuss the significance and impact of modular architectures on systems biology and biotechnology. Next, we focus on the very recent theoretical and experimental advances in modular cell engineering that seeks to enable rapid and systematic development of microbial catalysts capable of efficiently synthesizing a large space of useful chemicals. We conclude with an outlook towards theoretical and practical opportunities for a more systematic and effective application of modular engineering in biotechnology.},
doi = {10.1016/j.biotechadv.2019.06.002},
journal = {Biotechnology Advances},
number = 7,
volume = 37,
place = {United States},
year = {Fri Jun 07 00:00:00 EDT 2019},
month = {Fri Jun 07 00:00:00 EDT 2019}
}
Web of Science
Works referenced in this record:
Metabolic engineering in the host Yarrowia lipolytica
journal, November 2018
- Abdel-Mawgoud, Ahmad M.; Markham, Kelly A.; Palmer, Claire M.
- Metabolic Engineering, Vol. 50
Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli
journal, September 2010
- Ajikumar, P. K.; Xiao, W.-H.; Tyo, K. E. J.
- Science, Vol. 330, Issue 6000, p. 70-74
Biological Networks: The Tinkerer as an Engineer
journal, September 2003
- Alon, U.
- Science, Vol. 301, Issue 5641
Total Synthesis of a Functional Designer Eukaryotic Chromosome
journal, March 2014
- Annaluru, Narayana; Muller, Héloïse; Mitchell, Leslie A.
- Science, Vol. 344, Issue 6179
Modular manufacturing processes: Status, challenges, and opportunities
journal, August 2017
- Baldea, Michael; Edgar, Thomas F.; Stanley, Bill L.
- AIChE Journal, Vol. 63, Issue 10
Applications of CRISPR technologies in research and beyond
journal, September 2016
- Barrangou, Rodolphe; Doudna, Jennifer A.
- Nature Biotechnology, Vol. 34, Issue 9
Multivariate modular metabolic engineering for pathway and strain optimization
journal, October 2014
- Biggs, Bradley Walters; De Paepe, Brecht; Santos, Christine Nicole S.
- Current Opinion in Biotechnology, Vol. 29
USERTM friendly DNA engineering and cloning method by uracil excision
journal, March 2007
- Bitinaite, J.; Rubino, M.; Varma, K. H.
- Nucleic Acids Research, Vol. 35, Issue 6
Pairwise selection assembly for sequence-independent construction of long-length DNA
journal, February 2010
- Blake, William J.; Chapman, Brad A.; Zindal, Anuradha
- Nucleic Acids Research, Vol. 38, Issue 8
A systematic literature review on modular product design
journal, March 2016
- Bonvoisin, Jérémy; Halstenberg, Friedrich; Buchert, Tom
- Journal of Engineering Design, Vol. 27, Issue 7
Principles of genetic circuit design
journal, April 2014
- Brophy, Jennifer A. N.; Voigt, Christopher A.
- Nature Methods, Vol. 11, Issue 5
Design Structure Matrix Extensions and Innovations: A Survey and New Opportunities
journal, February 2016
- Browning, Tyson R.
- IEEE Transactions on Engineering Management, Vol. 63, Issue 1
Metabolic engineering tools in model cyanobacteria
journal, November 2018
- Carroll, Austin L.; Case, Anna E.; Zhang, Angela
- Metabolic Engineering, Vol. 50
Bricks and blueprints: methods and standards for DNA assembly
journal, June 2015
- Casini, Arturo; Storch, Marko; Baldwin, Geoffrey S.
- Nature Reviews Molecular Cell Biology, Vol. 16, Issue 9
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013
- Caspi, Ron; Altman, Tomer; Billington, Richard
- Nucleic Acids Research, Vol. 42, Issue D1
The BioGRID interaction database: 2017 update
journal, December 2016
- Chatr-aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie
- Nucleic Acids Research, Vol. 45, Issue D1
The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly
journal, February 2013
- Chen, Wei-Hua; Qin, Zhong-Jun; Wang, Jin
- Nucleic Acids Research, Vol. 41, Issue 8
Energy- and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions
journal, April 2016
- Cheong, Seokjung; Clomburg, James M.; Gonzalez, Ramon
- Nature Biotechnology, Vol. 34, Issue 5
The evolutionary origins of modularity
journal, March 2013
- Clune, Jeff; Mouret, Jean-Baptiste; Lipson, Hod
- Proceedings of the Royal Society B: Biological Sciences, Vol. 280, Issue 1755
Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
journal, November 2013
- Colloms, Sean D.; Merrick, Christine A.; Olorunniji, Femi J.
- Nucleic Acids Research, Vol. 42, Issue 4
Downstream bioprocessing: recent advances and future promise
journal, October 2011
- Cramer, Steven M.; Holstein, Melissa A.
- Current Opinion in Chemical Engineering, Vol. 1, Issue 1
Modular cell biology: retroactivity and insulation
journal, January 2008
- Del Vecchio, Domitilla; Ninfa, Alexander J.; Sontag, Eduardo D.
- Molecular Systems Biology, Vol. 4, Issue 1
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
journal, October 1997
- DeRisi, J. L.; Iyer, Vishwanath R.; Brown, Patrick O.
- Science, Vol. 278, Issue 5338, p. 680-686
Identification of growth-coupled production strains considering protein costs and kinetic variability
journal, December 2018
- Dinh, Hoang V.; King, Zachary A.; Palsson, Bernhard O.
- Metabolic Engineering Communications, Vol. 7
Relative potential of biosynthetic pathways for biofuels and bio-based products
journal, December 2011
- Dugar, Deepak; Stephanopoulos, Gregory
- Nature Biotechnology, Vol. 29, Issue 12
Multi-omic data integration enables discovery of hidden biological regularities
journal, October 2016
- Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin
- Nature Communications, Vol. 7, Issue 1
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
journal, June 2014
- Farasat, I.; Kushwaha, M.; Collens, J.
- Molecular Systems Biology, Vol. 10, Issue 6, p. 731-731
Fat synthesis in adipose tissue. An examination of stoichiometric constraints
journal, September 1986
- Fell, D. A.; Small, J. R.
- Biochemical Journal, Vol. 238, Issue 3
In silico design and adaptive evolution of Escherichia coli for production of lactic acid
journal, September 2005
- Fong, Stephen S.; Burgard, Anthony P.; Herring, Christopher D.
- Biotechnology and Bioengineering, Vol. 91, Issue 5, p. 643-648
Evolution of Bow-Tie Architectures in Biology
journal, March 2015
- Friedlander, Tamar; Mayo, Avraham E.; Tlusty, Tsvi
- PLOS Computational Biology, Vol. 11, Issue 3
Complete biosynthesis of opioids in yeast
journal, August 2015
- Galanie, S.; Thodey, K.; Trenchard, I. J.
- Science, Vol. 349, Issue 6252
Multiobjective strain design: A framework for modular cell engineering
journal, January 2019
- Garcia, Sergio; Trinh, Cong T.
- Metabolic Engineering, Vol. 51
Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009
- Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
- Nature Methods, Vol. 6, Issue 5, p. 343-345
Effects of network modularity on the spread of perturbation impact in experimental metapopulations
journal, July 2017
- Gilarranz, Luis J.; Rayfield, Bronwyn; Liñán-Cembrano, Gustavo
- Science, Vol. 357, Issue 6347
The human disease network
journal, May 2007
- Goh, K. -I.; Cusick, M. E.; Valle, D.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 21
Coming of age: ten years of next-generation sequencing technologies
journal, May 2016
- Goodwin, Sara; McPherson, John D.; McCombie, W. Richard
- Nature Reviews Genetics, Vol. 17, Issue 6
Modularity and stability in ecological communities
journal, June 2016
- Grilli, Jacopo; Rogers, Tim; Allesina, Stefano
- Nature Communications, Vol. 7, Issue 1
A Protein Complex Network of Drosophila melanogaster
journal, October 2011
- Guruharsha, K. G.; Rual, Jean-François; Zhai, Bo
- Cell, Vol. 147, Issue 3
From molecular to modular cell biology
journal, December 1999
- Hartwell, Leland H.; Hopfield, John J.; Leibler, Stanislas
- Nature, Vol. 402, Issue S6761
A Census of Human Soluble Protein Complexes
journal, August 2012
- Havugimana, Pierre C.; Hart, G. Traver; Nepusz, Tamás
- Cell, Vol. 150, Issue 5
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
journal, December 2018
- Heckmann, David; Lloyd, Colton J.; Mih, Nathan
- Nature Communications, Vol. 9, Issue 1
Systematic module and interface definition using component design structure matrix
journal, December 2010
- Helmer, Robert; Yassine, Ali; Meier, Christoph
- Journal of Engineering Design, Vol. 21, Issue 6
Degree of Modularity in Engineering Systems and Products with Technical and Business Constraints
journal, June 2007
- Hölttä-Otto, Katja; de Weck, Olivier
- Concurrent Engineering, Vol. 15, Issue 2
Polyketide and non-ribosomal peptide synthases: Falling together by coming apart
journal, March 2003
- Hutchinson, C. R.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 6
Design and synthesis of a minimal bacterial genome
journal, March 2016
- Hutchison, C. A.; Chuang, R. -Y.; Noskov, V. N.
- Science, Vol. 351, Issue 6280
Combinatorial pathway optimization for streamlined metabolic engineering
journal, October 2017
- Jeschek, Markus; Gerngross, Daniel; Panke, Sven
- Current Opinion in Biotechnology, Vol. 47
Modular and platform methods for product family design: literature analysis
journal, June 2005
- Jose, Alberto; Tollenaere, Michel
- Journal of Intelligent Manufacturing, Vol. 16, Issue 3
A survey of enabling technologies in synthetic biology
journal, January 2013
- Kahl, Linda J.; Endy, Drew
- Journal of Biological Engineering, Vol. 7, Issue 1
Metabolic engineering in methanotrophic bacteria
journal, May 2015
- Kalyuzhnaya, Marina G.; Puri, Aaron W.; Lidstrom, Mary E.
- Metabolic Engineering, Vol. 29
Life cycle performance of modular buildings: A critical review
journal, September 2016
- Kamali, Mohammad; Hewage, Kasun
- Renewable and Sustainable Energy Reviews, Vol. 62
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000
- Kanehisa, Minoru; Goto, Susumu
- Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
Varying environments can speed up evolution
journal, August 2007
- Kashtan, N.; Noor, E.; Alon, U.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 34
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
journal, December 2016
- Khodayari, Ali; Maranas, Costas D.
- Nature Communications, Vol. 7, Issue 1
Modular enzymes
journal, January 2001
- Khosla, Chaitan; Harbury, Pehr B.
- Nature, Vol. 409, Issue 6817
Modular Chemical Process Intensification: A Review
journal, June 2017
- Kim, Yong-ha; Park, Lydia K.; Yiacoumi, Sotira
- Annual Review of Chemical and Biomolecular Engineering, Vol. 8, Issue 1
Next-generation genome-scale models for metabolic engineering
journal, December 2015
- King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.
- Current Opinion in Biotechnology, Vol. 35
Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion
journal, January 2017
- King, Zachary A.; O'Brien, Edward J.; Feist, Adam M.
- Metabolic Engineering, Vol. 39
Biological robustness
journal, November 2004
- Kitano, Hiroaki
- Nature Reviews Genetics, Vol. 5, Issue 11
On the feasibility of growth-coupled product synthesis in microbial strains
journal, July 2015
- Klamt, Steffen; Mahadevan, Radhakrishnan
- Metabolic Engineering, Vol. 30
When Do Two-Stage Processes Outperform One-Stage Processes?
journal, December 2017
- Klamt, Steffen; Mahadevan, Radhakrishnan; Hädicke, Oliver
- Biotechnology Journal, Vol. 13, Issue 2
Rapid and Reliable DNA Assembly via Ligase Cycling Reaction
journal, September 2013
- Kok, Stefan de; Stanton, Leslie H.; Slaby, Todd
- ACS Synthetic Biology, Vol. 3, Issue 2
Large-scale de novo DNA synthesis: technologies and applications
journal, April 2014
- Kosuri, Sriram; Church, George M.
- Nature Methods, Vol. 11, Issue 5
Pathway design using de novo steps through uncharted biochemical spaces
journal, January 2018
- Kumar, Akhil; Wang, Lin; Ng, Chiam Yu
- Nature Communications, Vol. 9, Issue 1
Engineering modular ester fermentative pathways in Escherichia coli
journal, November 2014
- Layton, Donovan S.; Trinh, Cong T.
- Metabolic Engineering, Vol. 26
A comprehensive metabolic map for production of bio-based chemicals
journal, January 2019
- Lee, Sang Yup; Kim, Hyun Uk; Chae, Tong Un
- Nature Catalysis, Vol. 2, Issue 1
MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules
journal, January 2005
- Li, Mamie Z.; Elledge, Stephen J.
- Nature Genetics, Vol. 37, Issue 3
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
journal, February 2007
- Li, Mamie Z.; Elledge, Stephen J.
- Nature Methods, Vol. 4, Issue 3
Designing customized cell signalling circuits
journal, May 2010
- Lim, Wendell A.
- Nature Reviews Molecular Cell Biology, Vol. 11, Issue 6
Applications and advances of metabolite biosensors for metabolic engineering
journal, September 2015
- Liu, Di; Evans, Trent; Zhang, Fuzhong
- Metabolic Engineering, Vol. 31
Computational methods in metabolic engineering for strain design
journal, August 2015
- Long, Matthew R.; Ong, Wai Kit; Reed, Jennifer L.
- Current Opinion in Biotechnology, Vol. 34
Transcriptomics technologies
journal, May 2017
- Lowe, Rohan; Shirley, Neil; Bleackley, Mark
- PLOS Computational Biology, Vol. 13, Issue 5
Modular Metabolic Engineering for Biobased Chemical Production
journal, February 2019
- Lu, Hongyuan; Villada, Juan C.; Lee, Patrick K. H.
- Trends in Biotechnology, Vol. 37, Issue 2
The connectivity structure, giant strong component and centrality of metabolic networks
journal, July 2003
- Ma, H. -W.; Zeng, A. -P.
- Bioinformatics, Vol. 19, Issue 11
Co-evolution of strain design methods based on flux balance and elementary mode analysis
journal, December 2015
- Machado, Daniel; Herrgård, Markus J.
- Metabolic Engineering Communications, Vol. 2
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
journal, June 2003
- Martin, Vincent J. J.; Pitera, Douglas J.; Withers, Sydnor T.
- Nature Biotechnology, Vol. 21, Issue 7
Quantitative Design of Regulatory Elements Based on High-Precision Strength Prediction Using Artificial Neural Network
journal, April 2013
- Meng, Hailin; Wang, Jianfeng; Xiong, Zhiqiang
- PLoS ONE, Vol. 8, Issue 4
Modular and Hierarchically Modular Organization of Brain Networks
journal, January 2010
- Meunier, David; Lambiotte, Renaud; Bullmore, Edward T.
- Frontiers in Neuroscience, Vol. 4
Integrative approaches for finding modular structure in biological networks
journal, September 2013
- Mitra, Koyel; Carvunis, Anne-Ruxandra; Ramesh, Sanath Kumar
- Nature Reviews Genetics, Vol. 14, Issue 10
Dynamic control of endogenous metabolism with combinatorial logic circuits
journal, November 2018
- Moser, Felix; Espah Borujeni, Amin; Ghodasara, Amar N.
- Molecular Systems Biology, Vol. 14, Issue 11
Advances in de novo strain design using integrated systems and synthetic biology tools
journal, October 2015
- Ng, Chiam Yu; Khodayari, Ali; Chowdhury, Anupam
- Current Opinion in Chemical Biology, Vol. 28
Engineering Cellular Metabolism
journal, March 2016
- Nielsen, Jens; Keasling, Jay D.
- Cell, Vol. 164, Issue 6
Genetic circuit design automation
journal, March 2016
- Nielsen, A. A. K.; Der, B. S.; Shin, J.
- Science, Vol. 352, Issue 6281
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
journal, November 2016
- Noor, Elad; Flamholz, Avi; Bar-Even, Arren
- PLOS Computational Biology, Vol. 12, Issue 11
Recent progress in consolidated bioprocessing
journal, June 2012
- Olson, Daniel G.; McBride, John E.; Joe Shaw, A.
- Current Opinion in Biotechnology, Vol. 23, Issue 3, p. 396-405
Redesigning metabolism based on orthogonality principles
journal, May 2017
- Pandit, Aditya Vikram; Srinivasan, Shyam; Mahadevan, Radhakrishnan
- Nature Communications, Vol. 8, Issue 1
Structural and Functional Brain Networks: From Connections to Cognition
journal, October 2013
- Park, H. -J.; Friston, K.
- Science, Vol. 342, Issue 6158
Metabolomics: the apogee of the omics trilogy
journal, March 2012
- Patti, Gary J.; Yanes, Oscar; Siuzdak, Gary
- Nature Reviews Molecular Cell Biology, Vol. 13, Issue 4
Designing New Cellular Signaling Pathways
journal, March 2009
- Pryciak, Peter M.
- Chemistry & Biology, Vol. 16, Issue 3
The second wave of synthetic biology: from modules to systems
journal, June 2009
- Purnick, Priscilla E. M.; Weiss, Ron
- Nature Reviews Molecular Cell Biology, Vol. 10, Issue 6
Hierarchical Organization of Modularity in Metabolic Networks
journal, August 2002
- Ravasz, E.
- Science, Vol. 297, Issue 5586
Bacterial polymers: biosynthesis, modifications and applications
journal, June 2010
- Rehm, Bernd H. A.
- Nature Reviews Microbiology, Vol. 8, Issue 8
Expanding ester biosynthesis in Escherichia coli
journal, March 2014
- Rodriguez, Gabriel M.; Tashiro, Yohei; Atsumi, Shota
- Nature Chemical Biology, Vol. 10, Issue 4
Automated design of synthetic ribosome binding sites to control protein expression
journal, October 2009
- Salis, Howard M.; Mirsky, Ethan A.; Voigt, Christopher A.
- Nature Biotechnology, Vol. 27, Issue 10, p. 946-950
Toward a Product System Modularity Construct: Literature Review and Reconceptualization
journal, May 2007
- Salvador, Fabrizio
- IEEE Transactions on Engineering Management, Vol. 54, Issue 2
Refactoring the Embden–Meyerhof–Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria
journal, February 2017
- Sánchez-Pascuala, Alberto; de Lorenzo, Víctor; Nikel, Pablo I.
- ACS Synthetic Biology, Vol. 6, Issue 5
Multidimensional Optimality of Microbial Metabolism
journal, May 2012
- Schuetz, R.; Zamboni, N.; Zampieri, M.
- Science, Vol. 336, Issue 6081
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
journal, December 2008
- Shao, Zengyi; Zhao, Hua; Zhao, Huimin
- Nucleic Acids Research, Vol. 37, Issue 2
Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
journal, April 2012
- Shoval, O.; Sheftel, H.; Shinar, G.
- Science, Vol. 336, Issue 6085
A Network Approach to Define Modularity of Components in Complex Products
journal, January 2007
- Sosa, Manuel E.; Eppinger, Steven D.; Rowles, Craig M.
- Journal of Mechanical Design, Vol. 129, Issue 11
Protein complexes and functional modules in molecular networks
journal, September 2003
- Spirin, V.; Mirny, L. A.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 21
Modular Brain Networks
journal, January 2016
- Sporns, Olaf; Betzel, Richard F.
- Annual Review of Psychology, Vol. 67, Issue 1
A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
journal, October 2003
- Stuart, J. M.
- Science, Vol. 302, Issue 5643
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
journal, October 2016
- Szklarczyk, Damian; Morris, John H.; Cook, Helen
- Nucleic Acids Research, Vol. 45, Issue D1
Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria
journal, January 2017
- Tan, Gao-Yi; Liu, Tiangang
- Metabolic Engineering, Vol. 39
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca
journal, April 2012
- Temme, K.; Zhao, D.; Voigt, C. A.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 18
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome"
journal, September 2005
- Tettelin, H.; Masignani, V.; Cieslewicz, M. J.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 39
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome
journal, September 2016
- Thompson, R. Adam; Dahal, Sanjeev; Garcia, Sergio
- Biotechnology for Biofuels, Vol. 9, Issue 1
Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production
journal, June 2012
- Trinh, Cong T.
- Applied Microbiology and Biotechnology, Vol. 95, Issue 4
Modular cell design for rapid, efficient strain engineering toward industrialization of biology
journal, November 2016
- Trinh, Cong T.; Mendoza, Brian
- Current Opinion in Chemical Engineering, Vol. 14
Design, construction and performance of the most efficient biomass producing E. coli bacterium
journal, November 2006
- Trinh, Cong T.; Carlson, Ross; Wlaschin, Aaron
- Metabolic Engineering, Vol. 8, Issue 6
Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses
journal, April 2008
- Trinh, C. T.; Unrean, P.; Srienc, F.
- Applied and Environmental Microbiology, Vol. 74, Issue 12, p. 3634-3643
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism
journal, November 2008
- Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich
- Applied Microbiology and Biotechnology, Vol. 81, Issue 5
Rational design of efficient modular cells
journal, November 2015
- Trinh, Cong T.; Liu, Yan; Conner, David J.
- Metabolic Engineering, Vol. 32
One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid
journal, November 2003
- Tsuge, K.
- Nucleic Acids Research, Vol. 31, Issue 21
The role of product architecture in the manufacturing firm
journal, May 1995
- Ulrich, Karl
- Research Policy, Vol. 24, Issue 3
Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms
journal, June 2017
- von Kamp, Axel; Klamt, Steffen
- Nature Communications, Vol. 8, Issue 1
Small modular reactors: Simpler, safer, cheaper?
journal, September 2012
- Vujić, Jasmina; Bergmann, Ryan M.; Škoda, Radek
- Energy, Vol. 45, Issue 1
The small world inside large metabolic networks
journal, September 2001
- Wagner, Andreas; Fell, David A.
- Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 268, Issue 1478
The road to modularity
journal, December 2007
- Wagner, Günter P.; Pavlicev, Mihaela; Cheverud, James M.
- Nature Reviews Genetics, Vol. 8, Issue 12
MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes
journal, January 2018
- Wang, Lin; Maranas, Costas D.
- ACS Synthetic Biology, Vol. 7, Issue 2
A review of computational tools for design and reconstruction of metabolic pathways
journal, December 2017
- Wang, Lin; Dash, Satyakam; Ng, Chiam Yu
- Synthetic and Systems Biotechnology, Vol. 2, Issue 4
Towards Industry 4.0 - Standardization as the crucial challenge for highly modular, multi-vendor production systems
journal, January 2015
- Weyer, Stephan; Schmitt, Mathias; Ohmer, Moritz
- IFAC-PapersOnLine, Vol. 48, Issue 3
Biological Robustness: Paradigms, Mechanisms, and Systems Principles
journal, January 2012
- Whitacre, James Michael
- Frontiers in Genetics, Vol. 3
A Prototype for Modular Cell Engineering
journal, August 2017
- Wilbanks, Brandon; Layton, Donovan S.; Garcia, Sergio
- ACS Synthetic Biology, Vol. 7, Issue 1
Progress with Proteome Projects: Why all Proteins Expressed by a Genome Should be Identified and How To Do It
journal, December 1996
- Wilkins, Marc R.; Sanchez, Jean-Charles; Gooley, Andrew A.
- Biotechnology and Genetic Engineering Reviews, Vol. 13, Issue 1
The LASER database: Formalizing design rules for metabolic engineering
journal, December 2015
- Winkler, James D.; Halweg-Edwards, Andrea L.; Gill, Ryan T.
- Metabolic Engineering Communications, Vol. 2
Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications
journal, August 2016
- Wu, Gang; Yan, Qiang; Jones, J. Andrew
- Trends in Biotechnology, Vol. 34, Issue 8
The future of metabolic engineering and synthetic biology: Towards a systematic practice
journal, May 2012
- Yadav, Vikramaditya G.; De Mey, Marjan; Giaw Lim, Chin
- Metabolic Engineering, Vol. 14, Issue 3
Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis
journal, August 2018
- Yang, Yaping; Lin, Yuheng; Wang, Jian
- Nature Communications, Vol. 9, Issue 1
Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
journal, March 2012
- Zhang, Fuzhong; Carothers, James M.; Keasling, Jay D.
- Nature Biotechnology, Vol. 30, Issue 4
SLiCE: a novel bacterial cell extract-based DNA cloning method
journal, January 2012
- Zhang, Yongwei; Werling, Uwe; Edelmann, Winfried
- Nucleic Acids Research, Vol. 40, Issue 8
Works referencing / citing this record:
Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures
journal, October 2019
- Seo, Hyeongmin; Lee, Jong-Won; Garcia, Sergio
- Biotechnology for Biofuels, Vol. 12, Issue 1
Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis
journal, June 2019
- Garcia, Sergio; Trinh, Cong T.
- Processes, Vol. 7, Issue 6