All Outputs (55)

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. (2015)
Journal Article
Gilfellon, O., Honorato-Zimmer, R., Pocock, M., Madsen, C., Waites, W., Cavaliere, M., …Wipat, A. (2015). Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics, 908 - 917. https://doi.org/10.1093/bioinformatics/btv660

MOTIVATION: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the for... Read More about Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization..

Synthetic Biology Open Language (SBOL) Version 2.0.0 (2015)
Journal Article
Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., Oberortner, E., …Sauro, H. (2015). Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics, 12(2), 902-991. https://doi.org/10.1515/jib-2015-272

Composable Modular Models for Synthetic Biology. (2014)
Journal Article
Misirli. (2014). Composable Modular Models for Synthetic Biology. https://doi.org/10.1145/2631921

Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo. To support automated, model-driven design it is desira... Read More about Composable Modular Models for Synthetic Biology..

The Synthetic Biology Open Language (2014)
Book Chapter
Myers, C., Clancy, K., Misirli, G., Oberortner, E., Pocock, M., Quinn, J., …Sauro, H. M. (2015). The Synthetic Biology Open Language. . Springer New York. https://doi.org/10.1007/978-1-4939-1878-2_16

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. (2014)
Journal Article
Röttger, R., Baumbach, J., Wipat, A., Misirli, G., & Hallinan, J. (2014). BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of Integrative Bioinformatics, 244 - ?. https://doi.org/10.2390/biecoll-jib-2014-244

As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organis... Read More about BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species..

Proposed Data Model for the Next Version of the Synthetic Biology Open Language (2014)
Journal Article
Roehner, N., Oberortner, E., Pocock, M., Beal, J., Clancy, K., Madsen, C., …Myers, C. J. (2015). Proposed Data Model for the Next Version of the Synthetic Biology Open Language. ACS synthetic biology, 4(1), 57-71. https://doi.org/10.1021/sb500176h

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology (2014)
Journal Article
Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., …Sauro, H. M. (2014). The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology, 32(6), 545-550. https://doi.org/10.1038/nbt.2891

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts (2014)
Journal Article
Hallinan, J. S., Gilfellon, O., Misirli, G., & Wipat, A. (2014). Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, https://doi.org/10.1109/cibcb.2014.6845520

Populations of bacteria acting in collaboration can produce complex behaviors which are not achievable by individual cells. There has, consequently, been considerable interest in the engineering of bacterial populations. Here we describe an approach... Read More about Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts.

Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins (2013)
Journal Article
Pohl, S., Bhavsar, G., Hulme, J., Bloor, A. E., Misirli, G., Leckenby, M. W., …Cranenburgh, R. M. (2013). Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins. Proteomics, 13(22), 3298-3308. https://doi.org/10.1002/pmic.201300183

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology (2013)
Journal Article
Misirli, G., Wipat, A., Mullen, J., James, K., Pocock, M., Smith, W., …Hallinan, J. S. (2013). BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Journal of Integrative Bioinformatics, 10(2), 103-116. https://doi.org/10.1515/jib-2013-224

Model annotation for synthetic biology: automating model to nucleotide sequence conversion. (2011)
Journal Article
Misirli, G., Hallinan, J. S., Yu, T., Lawson, J. R., Wimalaratne, S. M., Cooling, M. T., & Wipat, A. (2011). Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics, 27(7), 973 - 979. https://doi.org/10.1093/bioinformatics/btr048

MOTIVATION: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembl... Read More about Model annotation for synthetic biology: automating model to nucleotide sequence conversion..

SBML Level 3 Package Proposal: Annotation (2011)
Report
Hucka, M., Laibe, C., Juty, N., Liebermeister, W., Keating, S., Lloyd, C., …Hoops, S. (in press). SBML Level 3 Package Proposal: Annotation. Nature Proceedings

The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of soft... Read More about SBML Level 3 Package Proposal: Annotation.

Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits (2010)
Journal Article
Misirli, G. (2010). Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 768-774

Standard virtual biological parts: a repository of modular modeling components for synthetic biology (2010)
Journal Article
Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., & Wipat, A. (2010). Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics, 26(7), 925-931. https://doi.org/10.1093/bioinformatics/btq063

Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits
Journal Article
Misirli. Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits. bioRxiv,

<jats:title>Abstract</jats:title><jats:p>Engineering genetic regulatory circuits is key to the creation of biological applications that are responsive to environmental changes. Computational models can assist in understanding especially large and com... Read More about Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits.