Skip to main content


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.

Page 1 of 2

  1. Content type: Research article

    Classic metabolic engineering strategies often induce significant flux imbalances to microbial metabolism, causing undesirable outcomes such as suboptimal conversion of substrates to products. Several mathemat...

    Authors: Juan A. Martínez, Alberto Rodriguez, Fabian Moreno, Noemí Flores, Alvaro R. Lara, Octavio T. Ramírez, Guillermo Gosset and Francisco Bolivar

    Citation: BMC Systems Biology 2018 12:102

    Published on:

  2. Content type: Research article

    Mounting evidence from genome-wide studies of cancer shows that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent ce...

    Authors: Kimberly C. Olney, David B. Nyer, Daniel A. Vargas, Melissa A. Wilson Sayres and Karmella A. Haynes

    Citation: BMC Systems Biology 2018 12:83

    Published on:

  3. Content type: Research article

    Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess ...

    Authors: Bruno Pereira, Joana Miguel, Paulo Vilaça, Simão Soares, Isabel Rocha and Sónia Carneiro

    Citation: BMC Systems Biology 2018 12:61

    Published on:

  4. Content type: Methodology Article

    State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell...

    Authors: Roland Prielhofer, Juan J. Barrero, Stefanie Steuer, Thomas Gassler, Richard Zahrl, Kristin Baumann, Michael Sauer, Diethard Mattanovich, Brigitte Gasser and Hans Marx

    Citation: BMC Systems Biology 2017 11:123

    Published on:

  5. Content type: Research Article

    In favorable conditions bacterial doubling time is less than 20 min, shorter than DNA replication time. In E. coli a single round of genome replication lasts about 40 min and it must be accomplished about 20 min ...

    Authors: Joanna Jaruszewicz-Błońska and Tomasz Lipniacki

    Citation: BMC Systems Biology 2017 11:117

    Published on:

  6. Content type: Research Article

    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...

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

    Citation: BMC Systems Biology 2017 11:66

    Published on:

  7. Content type: Research Article

    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...

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

    Citation: BMC Systems Biology 2017 11:58

    Published on:

  8. Content type: Research Article

    Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic swit...

    Authors: Miriam Leon, Mae L. Woods, Alex J. H. Fedorec and Chris P. Barnes

    Citation: BMC Systems Biology 2016 10:130

    Published on:

  9. Content type: Research article

    A complex network of gene interactions controls gene regulation throughout development and the life of the organisms. Insights can be made into these processes by studying the functional interactions (or “moti...

    Authors: Ashley A. Jermusyk, Nicholas P. Murphy and Gregory T. Reeves

    Citation: BMC Systems Biology 2016 10:85

    Published on:

  10. Content type: Research Article

    Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. In the realm of synthetic biology, it is of great interest to engineer geneti...

    Authors: Nikolay Martyushenko, Sigurd Hagen Johansen, Cheol-Min Ghim and Eivind Almaas

    Citation: BMC Systems Biology 2016 10:39

    Published on:

  11. Content type: Research Article

    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...

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

    Citation: BMC Systems Biology 2016 10:27

    Published on:

  12. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2015 9:97

    Published on:

  13. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2015 9:77

    Published on:

  14. Content type: Research article

    Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and tr...

    Authors: Mohammad Tajparast and Dominic Frigon

    Citation: BMC Systems Biology 2015 9:43

    Published on:

  15. Content type: Research article

    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 ...

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

    Citation: BMC Systems Biology 2014 8:133

    Published on:

  16. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2014 8:128

    Published on:

  17. Content type: Methodology Article

    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...

    Authors: Irene Otero-Muras and Julio R Banga

    Citation: BMC Systems Biology 2014 8:113

    Published on:

  18. Content type: Research article

    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...

    Authors: Stéphanie Gérin, Grégory Mathy and Fabrice Franck

    Citation: BMC Systems Biology 2014 8:96

    Published on:

  19. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2014 8:86

    Published on:

  20. Content type: Research article

    The koji mold, Aspergillus oryzae is widely used for the production of industrial enzymes due to its particularly high protein secretion capacity and ability to perform post-translational modifications. However, ...

    Authors: Lifang Liu, Amir Feizi, Tobias Österlund, Carsten Hjort and Jens Nielsen

    Citation: BMC Systems Biology 2014 8:73

    Published on:

  21. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2014 8:41

    Published on:

  22. Content type: Methodology article

    Heterologous gene expression is an important tool for synthetic biology that enables metabolic engineering and the production of non-natural biologics in a variety of host organisms. The translational efficien...

    Authors: Amanda M Lanza, Kathleen A Curran, Lindsey G Rey and Hal S Alper

    Citation: BMC Systems Biology 2014 8:33

    Published on:

  23. Content type: Research article

    Contact-dependent inhibition (CDI) has been recently revealed as an intriguing but ubiquitous mechanism for bacterial competition in which a species injects toxins into its competitors through direct physical ...

    Authors: Andrew E Blanchard, Venhar Celik and Ting Lu

    Citation: BMC Systems Biology 2014 8:23

    Published on:

  24. Content type: Research article

    Cyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements. They can use solar energy to convert CO2 and other reduced c...

    Authors: Thomas J Mueller, Bertram M Berla, Himadri B Pakrasi and Costas D Maranas

    Citation: BMC Systems Biology 2013 7:142

    Published on:

  25. Content type: Methodology article

    Metabolic control analysis (MCA) and supply–demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic regulation. Supply–dema...

    Authors: Fei He, Vincent Fromion and Hans V Westerhoff

    Citation: BMC Systems Biology 2013 7:131

    Published on:

  26. Content type: Research article

    Synthetic genetic transistors are vital for signal amplification and switching in genetic circuits. However, it is still problematic to efficiently select the adequate promoters, Ribosome Binding Sides (RBSs) ...

    Authors: Yi-Ying Lee, Chih-Yuan Hsu, Ling-Jiun Lin, Chih-Chun Chang, Hsiao-Chun Cheng, Tsung-Hsien Yeh, Rei-Hsing Hu, Che Lin, Zhen Xie and Bor-Sen Chen

    Citation: BMC Systems Biology 2013 7:109

    Published on:

  27. Content type: Research article

    Organisms have evolved ways of regulating transcription to better adapt to varying environments. Could the current functional genomics data and models support the possibility of engineering a genome with compl...

    Authors: Javier Carrera and Alfonso Jaramillo

    Citation: BMC Systems Biology 2013 7:108

    Published on:

  28. Content type: Methodology article

    The modular design of synthetic gene circuits via composable parts (DNA segments) and pools of signal carriers (molecules such as RNA polymerases and ribosomes) has been successfully applied to bacterial syste...

    Authors: Mario Andrea Marchisio, Moreno Colaiacovo, Ellis Whitehead and Jörg Stelling

    Citation: BMC Systems Biology 2013 7:42

    Published on:

  29. Content type: Research article

    An important step in strain optimization is to identify reactions whose activities should be modified to achieve the desired cellular objective. Preferably, these reactions are identified systematically, as th...

    Authors: Mona Yousofshahi, Michael Orshansky, Kyongbum Lee and Soha Hassoun

    Citation: BMC Systems Biology 2013 7:29

    Published on:

  30. Content type: Research article

    Alginate is an industrially important polysaccharide, currently produced commercially by harvesting of marine brown sea-weeds. The polymer is also synthesized as an exo-polysaccharide by bacteria belonging to ...

    Authors: Sven EF Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind Jakobsen, Per Bruheim, Trond E Ellingsen, Jens Nielsen and Svein Valla

    Citation: BMC Systems Biology 2013 7:19

    Published on:

  31. Content type: Research article

    Several studies have shown that the utilization of mixed carbon feeds instead of methanol as sole carbon source is beneficial for protein production with the methylotrophic yeast Pichia pastoris. In particular, g...

    Authors: Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol and Aljoscha Wahl

    Citation: BMC Systems Biology 2013 7:17

    Published on:

  32. Content type: Research article

    MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad ran...

    Authors: Carla Bosia, Matteo Osella, Mariama El Baroudi, Davide Corà and Michele Caselle

    Citation: BMC Systems Biology 2012 6:131

    Published on:

  33. Content type: Research article

    Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mim...

    Authors: Angel Goñi-Moreno and Martyn Amos

    Citation: BMC Systems Biology 2012 6:126

    Published on:

  34. Content type: Methodology article

    Elementary mode (EM) analysis is ideally suited for metabolic engineering as it allows for an unbiased decomposition of metabolic networks in biologically meaningful pathways. Recently, constrained minimal cut...

    Authors: Christian Jungreuthmayer and Jürgen Zanghellini

    Citation: BMC Systems Biology 2012 6:103

    Published on:

  35. Content type: Research article

    Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential...

    Authors: Michael J McAnulty, Jiun Y Yen, Benjamin G Freedman and Ryan S Senger

    Citation: BMC Systems Biology 2012 6:42

    Published on:

  36. Content type: Research article

    Pichia stipitis and Pichia pastoris have long been investigated due to their native abilities to metabolize every sugar from lignocellulose and to modulate methanol consumption, respectively. The latter has been ...

    Authors: Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew and Jens Nielsen

    Citation: BMC Systems Biology 2012 6:24

    Published on:

  37. Content type: Research article

    We consider the possibility of engineering metabolic pathways in a chassis organism in order to synthesize novel target compounds that are heterologous to the chassis. For this purpose, we model metabolic netw...

    Authors: Pablo Carbonell, Davide Fichera, Shashi B Pandit and Jean-Loup Faulon

    Citation: BMC Systems Biology 2012 6:10

    Published on:

  38. Content type: Research article

    Carbon-13 (13C) analysis is a commonly used method for estimating reaction rates in biochemical networks. The choice of carbon labeling pattern is an important consideration when designing these experiments. We p...

    Authors: Jan Schellenberger, Daniel C Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A Scott, Jennifer L Reed, Andrei L Osterman and Bernhard ∅ Palsson

    Citation: BMC Systems Biology 2012 6:9

    Published on:

  39. Content type: Research article

    Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many ...

    Authors: David J Baumler, Roman G Peplinski, Jennifer L Reed, Jeremy D Glasner and Nicole T Perna

    Citation: BMC Systems Biology 2011 5:182

    Published on:

  40. Content type: Research article

    Identifying cellular subsystems that are involved in the expression of a target phenotype has been a very active research area for the past several years. In this paper, cellular subsystem refers to a group of ge...

    Authors: Willam Hendrix, Andrea M Rocha, Kanchana Padmanabhan, Alok Choudhary, Kathleen Scott, James R Mihelcic and Nagiza F Samatova

    Citation: BMC Systems Biology 2011 5:172

    Published on:

  41. Content type: Research article

    Improving the synthesis rate of desired metabolites in metabolic systems is one of the main tasks in metabolic engineering. In the last decade, metabolic engineering approaches based on the mathematical optimi...

    Authors: Wu-Hsiung Wu, Feng-Sheng Wang and Maw-Shang Chang

    Citation: BMC Systems Biology 2011 5:145

    Published on:

2017 Journal Metrics

  • Citation Impact
    2.05 - 2-year Impact Factor
    2.505 - 5-year Impact Factor
    0.689 - Source Normalized Impact per Paper (SNIP)
    1.109 - SCImago Journal Rank (SJR)


    Social Media Impact
    523 mentions