Synthetic biology

Section edited by Sang Yup Lee

This section covers the application of systems biology, biotechnology and an engineering approach to the design and construction of novel biological functions, and in particular those with industrial or biomedical importance.

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  1. Research Article

    Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

    Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high capacity to produce polyunsaturated fatty acids and tr...

    Nicolás Loira, Sebastian Mendoza, María Paz Cortés, Natalia Rojas, Dante Travisany, Alex Di Genova, Natalia Gajardo, Nicole Ehrenfeld and Alejandro Maass

    BMC Systems Biology 2017 11:66

    Published on: 4 July 2017

  2. Research Article

    Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

    The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clost...

    Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas and Dolly Montoya

    BMC Systems Biology 2017 11:58

    Published on: 1 June 2017

  3. Research Article

    Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case

    Model based design plays a fundamental role in synthetic biology. Exploiting modularity, i.e. using biological parts and interconnecting them to build new and more complex biological circuits is one of the key...

    Yadira Boada, Gilberto Reynoso-Meza, Jesús Picó and Alejandro Vignoni

    BMC Systems Biology 2016 10:27

    Published on: 11 March 2016

  4. Research article

    A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication

    Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to enginee...

    Katja Kolar, Hanna M. Wischhusen, Konrad Müller, Maria Karlsson, Wilfried Weber and Matias D. Zurbriggen

    BMC Systems Biology 2015 9:97

    Published on: 30 December 2015

  5. Research article

    Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae

    The gene expression and secretion of fungal lignocellulolytic enzymes are tightly controlled at the transcription level using independent mechanisms to respond to distinct inducers from plant biomass. An advan...

    D.B.R.K. Gupta Udatha, Evangelos Topakas, Margarita Salazar, Lisbeth Olsson, Mikael R. Andersen and Gianni Panagiotou

    BMC Systems Biology 2015 9:77

    Published on: 14 November 2015

  6. Research article

    Hierarchy of non-glucose sugars in Escherichia coli

    Understanding how cells make decisions, and why they make the decisions they make, is of fundamental interest in systems biology. To address this, we study the decisions made by E. coli on which genes to express ...

    Guy Aidelberg, Benjamin D Towbin, Daphna Rothschild, Erez Dekel, Anat Bren and Uri Alon

    BMC Systems Biology 2014 8:133

    Published on: 24 December 2014

  7. Research article

    Photo-sensitive degron variants for tuning protein stability by light

    Regulated proteolysis by the proteasome is one of the fundamental mechanisms used in eukaryotic cells to control cellular behavior. Efficient tools to regulate protein stability offer synthetic influence on mo...

    Svetlana Usherenko, Hilke Stibbe, Massimiliano Muscó, Lars-Oliver Essen, Ekaterina A Kostina and Christof Taxis

    BMC Systems Biology 2014 8:128

    Published on: 18 November 2014

  8. Methodology Article

    Multicriteria global optimization for biocircuit design

    One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple...

    Irene Otero-Muras and Julio R Banga

    BMC Systems Biology 2014 8:113

    Published on: 24 September 2014

  9. Research article

    Modeling the dependence of respiration and photosynthesis upon light, acetate, carbon dioxide, nitrate and ammonium in Chlamydomonas reinhardtiiusing design of experiments and multiple regression

    In photosynthetic organisms, the influence of light, carbon and inorganic nitrogen sources on the cellular bioenergetics has extensively been studied independently, but little information is available on the c...

    Stéphanie Gérin, Grégory Mathy and Fabrice Franck

    BMC Systems Biology 2014 8:96

    Published on: 16 August 2014

  10. Research article

    Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

    Thermobifida fusca is a cellulolytic bacterium with potential to be used as a platform organism for sustainable industrial production of biofuels, pharmaceutical ingredients and other bioprocesses due to its cap...

    Niti Vanee, J Paul Brooks, Victor Spicer, Dmitriy Shamshurin, Oleg Krokhin, John A Wilkins, Yu Deng and Stephen S Fong

    BMC Systems Biology 2014 8:86

    Published on: 13 August 2014

  11. Research article

    Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

    The gut microbiota plays an important role in human health and disease by acting as a metabolic organ. Metagenomic sequencing has shown how dysbiosis in the gut microbiota is associated with human metabolic di...

    Ibrahim E El-Semman, Fredrik H Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir H Soliman and Jens Nielsen

    BMC Systems Biology 2014 8:41

    Published on: 3 April 2014

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