Dr. Goksel Misirli

Research Associate

I’m an RA at School of Computing Science, Newcastle University, UK. I have done my PhD in synthetic biology under the supervision of Prof. Anil Wipat and Dr. Jennifer Hallinan. I have a BSc in Control and Computer Engineering from Istanbul Technical University, Turkey.

My principle research interests are synthetic biology, systems biology as a foundation for synthetic biology, design of synthetic genetic circuits, and data integration. During the course of my PhD, I have developed data integration strategies to inform computational design in synthetic biology. The techniques developed will be used to guide the design of genetic regulatory networks in Bacillus subtilis, a model organism.

I aim to automate parts of the synthetic biology life cycle, by integrating existing biological data to create a semantically enriched knowledge base that can be used to inform the design of synthetic genetic circuits, creating dynamic models of basic synthetic biological parts, and automating the conversion of models of genetic circuits to synthesisable DNA sequences.

Research Interests

  • Synthetic Biology
  • Systems Biology
  • Data Integration
  • Semantic Web

Publications

  • G. Misirli, J. S. Hallinan, and A. Wipat, “Composable modular models for synthetic biology,” Acm journal on emerging technologies in computing systems, accepted, 2014.
    [Bibtex]
    @article{12,
    author = {Misirli, Goksel and Hallinan, Jennifer S. and Wipat, Anil},
    title = {Composable Modular Models for Synthetic Biology},
    journal = {ACM Journal on Emerging Technologies in Computing Systems, accepted},
    year = {2014}
    }
  • G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, and A. Wipat, “Bacillusregnet: a transcriptional regulation database and analysis platform for bacillus species,” Journal of integrative bioinformatics, 2014.
    [Bibtex]
    @article{14,
    author = {Misirli, G. and Hallinan, J. and Röttger, Richard and Baumbach, Jan and Wipat, A.},
    title = {BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species },
    journal = {Journal of Integrative Bioinformatics},
    year = {2014}
    }
  • N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, and C. J. Myers, “Proposed data model for the next version of the synthetic biology open language,” Acs synthetic biology, 2014.
    [Bibtex]
    @article{13,
    author = {Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Beal, Jacob and Clancy, Kevin and Madsen, Curtis and Misirli, Goksel and Wipat, Anil and Sauro, Herbert and Myers, Chris J.},
    title = {Proposed Data Model for the Next Version of the Synthetic Biology Open Language},
    journal = {ACS Synthetic Biology},
    year = {2014}
    }
  • J. Hallinan, O. Gilfellon, G. Misirli, and A. Wipat, “Tuning receiver characteristics in bacterial quorum communication: an evolutionary approach using standard virtual biological parts,” in 2014 ieee conference on computational intelligence in bioinformatics and computational biology, 2014.
    [Bibtex]
    @inproceedings{11,
    author = {Hallinan, Jennifer and Gilfellon, Owen and Misirli, Goksel and Wipat, Anil},
    title = {Tuning Receiver Characteristics in Bacterial Quorum Communication: An Evolutionary Approach Using Standard Virtual Biological Parts},
    booktitle = {2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology},
    year = {2014}
    }
  • M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, C. J. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grunberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro, “The synthetic biology open language (sbol) provides a community standard for communicating designs in synthetic biology,” Nature biotechnology, vol. 32, iss. 6, pp. 545-550, 2014.
    [Bibtex]
    @article{10,
    author = {Galdzicki, Michal and Clancy, Kevin P. and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y. and Rodriguez, Cesar A. and Roehner, Nicholas and Wilson, Mandy L. and Adam, Laura and Anderson, J. Christopher and Bartley, Bryan A. and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Grunberg, Raik and Hallinan, Jennifer and Hillson, Nathan J. and Johnson, Jeffrey D. and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A. and Sirin, Evren and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Gennari, John H. and Myers, Chris J. and Sauro, Herbert M.},
    title = {The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology},
    journal = {Nature Biotechnology},
    volume = {32},
    number = {6},
    pages = {545-550},
    abstract = {The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.},
    year = {2014}
    }
  • S. Pohl, G. Bhavsar, J. Hulme, A. E. Bloor, G. Misirli, M. W. Leckenby, D. S. Radford, W. Smith, A. Wipat, D. E. Williamson, C. R. Harwood, and R. M. Cranenburgh, “Proteomic analysis of bacillus subtilis strains engineered for improved production of heterologous proteins,” Proteomics, vol. 13, iss. 22, pp. 3298-3308, 2013.
    [Bibtex]
    @article{9,
    author = {Pohl, Susanne and Bhavsar, Gaurav and Hulme, Joanne and Bloor, Alexandra E. and Misirli, Goksel and Leckenby, Matthew W. and Radford, David S. and Smith, Wendy and Wipat, Anil and Williamson, E. Diane and Harwood, Colin R. and Cranenburgh, Rocky M.},
    title = {Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins},
    journal = {PROTEOMICS},
    volume = {13},
    number = {22},
    pages = {3298-3308},
    keywords = {Anthrax protective antigen
    Biomedicine
    Gene deletion
    Proteases
    Recombinant protein
    Secretion},
    year = {2013}
    }
  • M. Galdzicki, E. Oberortner, M. Pocock, J. Quinn, M. L. Wilson, E. Appleton, B. Bartley, J. Beal, S. Bhatia, R. Cox, R. Grunberg, G. Misirli, H. Plahar, N. Roehner, L. Soldotova, G. Stan, D. Densmore, C. Myers, H. Sauro, and A. Wipat, “Recent advances in the synthetic biology open language,” , 2013.
    [Bibtex]
    @article{8,
    author = {Galdzicki, Michal and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline and Wilson, Mandy L. and Appleton, Evan and Bartley, Bryan and Beal, Jacob and Bhatia, Swapnil and Cox, Robert and Grunberg, Raik and Misirli, Goksel and Plahar, Hector and Roehner, Nicholas and Soldotova, Larisa and Stan, Guy-Bart and Densmore, Doug and Myers, Chris and Sauro, Herbert and Wipat, Anil },
    title = { Recent Advances in the Synthetic Biology Open Language},
    month = {July 12-13},
    year = {2013}
    }
  • G. Misirli, “Data integration strategies for informing computational design in synthetic biology,” PhD Thesis, 2013.
    [Bibtex]
    @phdthesis{7,
    author = {Misirli, Goksel},
    title = {Data integration strategies for informing computational design in synthetic biology},
    university = {Newcastle University},
    year = {2013}
    }
  • G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, and J. Hallinan, “Bacillondex: an integrated data resource for systems and synthetic biology,” Journal of integrative bioinformatics, 2013.
    [Bibtex]
    @article{6,
    Author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J.},
    Title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
    Journal = {Journal of Integrative Bioinformatics},
    Year = {2013} }
  • G. Misirli, J. S. Hallinan, T. Yu, J. R. Lawson, S. M. Wimalaratne, M. T. Cooling, and A. Wipat, “Model annotation for synthetic biology: automating model to nucleotide sequence conversion,” Bioinformatics, vol. 27, iss. 7, pp. 973-979, 2011.
    [Bibtex]
    @article{5,
    Author = {Misirli, Goksel and Hallinan, Jennifer S. and Yu, Tommy and Lawson, James R. and Wimalaratne, Sarala M. and Cooling, Michael T. and Wipat, Anil},
    Title = {Model annotation for synthetic biology: automating model to nucleotide sequence conversion},
    Journal = {Bioinformatics},
    Volume = {27},
    Number = {7},
    Pages = {973-979},
    Abstract = {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 assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models.Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC.Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html.Contact: anil.wipat@ncl.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.},
    Year = {2011} }
  • G. Misirli, J. Hallinan, J. Weile, S. Cockell, and A. Wipat, “Bacillondex: data integration and visualisation for bacillus subtilis,” School of Computing Science, University of Newcastle upon Tyne. 2011.
    [Bibtex]
    @techreport{4,
    Author = {Misirli, G. and Hallinan, J. and Weile, J. and Cockell, S. and Wipat, A.},
    Title = {BacillOndex: Data integration and visualisation for Bacillus subtilis},
    Institution = {School of Computing Science, University of Newcastle upon Tyne.},
    Year = {2011} }
  • M. Galdzicki, M. L. Wilson, C. A. Rodriguez, L. Adam, A. Adler, C. J. Anderson, J. Beal, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grünberg, T. S. Ham, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, J. Peccoud, H. Plahar, M. R. Pocock, N. Roehner, T. F. Smith, G. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, “Synthetic biology open language (sbol) version 1.0.0,” 2011.
    [Bibtex]
    @techreport{2,
    Author = {Galdzicki, Michal and Wilson, Mandy L. and Rodriguez, Cesar A. and Adam, Laura and Adler, Aaron and Anderson, J. Christopher and Beal, Jacob and Chandran, Deepak and Densmore, Douglas and Drory, Omri A. and Endy, Drew and Gennari, John H. and Grünberg, Raik and Ham, Timothy S. and Kuchinsky, Allan and Lux, Matthew W. and Madsen, Curtis and Misirli, Goksel and Myers, Chris J. and Peccoud, Jean and Plahar, Hector and Pocock, Matthew R. and Roehner, Nicholas and Smith, Trevor F. and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Sauro, Herbert M.},
    Title = {Synthetic Biology Open Language (SBOL) Version 1.0.0},
    Keywords = {SBOL},
    Year = {2011} }
  • N. Swainston, D. Waltemath, A. Lister, F. Bergmann, R. Henkel, S. Hoops, M. Hucka, N. Juty, S. Keating, C. Knuepfer, F. Krause, C. Laibe, W. Liebermeister, C. Lloyd, G. Misirli, M. Schulz, M. Taschuk, and N. Le Novère, “Sbml level 3 package proposal: annotation,” Nature precedings, 2011.
    [Bibtex]
    @article{7,
    Author = {Swainston, Neil and Waltemath, Dagmar and Lister, Allyson and Bergmann, Frank and Henkel, Ron and Hoops, Stefan and Hucka, Michael and Juty, Nick and Keating, Sarah and Knuepfer, Christian and Krause, Falko and Laibe, Camille and Liebermeister, Wolfram and Lloyd, Catherine and Misirli, Goksel and Schulz, Marvin and Taschuk, Morgan and Le Novère, Nicolas},
    Title = {SBML Level 3 Package Proposal: Annotation},
    Journal = {Nature Precedings},
    Abstract = {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 software tools supporting and encouraging their use and development.With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such extension is described here, with an initial proposal of an Annotation package.This proposal extends the current Core annotation specification to provide support for a richer set of semantic annotations while adhering more closely to the existing specification of Resource Description Framework (RDF).},
    Keywords = {sbml},
    Year = {2011} }
  • M. T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu, J. Hallinan, and A. Wipat, “Standard virtual biological parts: a repository of modular modeling components for synthetic biology,” Bioinformatics, vol. 26, iss. 7, pp. 925-931, 2010.
    [Bibtex]
    @article{1,
    Author = {Cooling, M. T. and Rouilly, V. and Misirli, G. and Lawson, J. and Yu, T. and Hallinan, J. and Wipat, A.},
    Title = {Standard virtual biological parts: a repository of modular modeling components for synthetic biology},
    Journal = {Bioinformatics},
    Volume = {26},
    Number = {7},
    Pages = {925-931},
    Abstract = {Motivation: Fabrication of synthetic biological systems is greatly enhanced by incorporating engineering design principles and techniques such as computer-aided design. To this end, the ongoing standardization of biological parts presents an opportunity to develop libraries of standard virtual parts in the form of mathematical models that can be combined to inform system design. Results: We present an online Repository, populated with a collection of standardized models that can readily be recombined to model different biological systems using the inherent modularity support of the CellML 1.1 model exchange format. The applicability of this approach is demonstrated by modeling gold-medal winning iGEM machines. Availability and Implementation: The Repository is available online as part of http://models.cellml.org. We hope to stimulate the worldwide community to reuse and extend the models therein, and contribute to the Repository of Standard Virtual Parts thus founded. Systems Model architecture information for the Systems Model described here, along with an additional example and a tutorial, is also available as Supplementary information. The example Systems Model from this manuscript can be found at http://models.cellml.org/workspace/bugbuster. The Template models used in the example can be found at http://models.cellml.org/workspace/SVP_Templates200906. Contact: m.cooling@auckland.ac.nz Supplementary information: Supplementary data are available at Bioinformatics online.},
    Year = {2010} }
  • J. S. Hallinan, G. Misirli, and A. Wipat, Evolutionary computation for the design of a stochastic switch for synthetic genetic circuitsIEEE, 2010.
    [Bibtex]
    @misc{3,
    Author = {Hallinan, J. S. and Misirli, G. and Wipat, A.},
    Title = {Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits},
    Publisher = {IEEE},
    Pages = {768-774},
    Month = {Aug. 31 2010-Sept. 4 2010},
    Abstract = {Biological systems are inherently stochastic, a fact which is often ignored when simulating genetic circuits. Synthetic biology aims to design genetic circuits de novo, and cannot therefore afford to ignore the effects of stochastic behavior. Since computational design tools will be essential for large-scale synthetic biology, it is important to develop an understanding of the role of stochasticity in molecular biology, and incorporate this understanding into computational tools for genetic circuit design. We report upon an investigation into the combination of evolutionary algorithms and stochastic simulation for genetic circuit design, to design regulatory systems based on the Bacillus subtilis sin operon.},
    Keywords = {biology computing
    evolutionary computation
    genetic engineering
    genetics
    microorganisms
    stochastic processes
    Bacillus subtilis sin operon
    computational design tools
    evolutionary algorithms
    genetic circuit design
    large-scale synthetic biology
    molecular biology
    stochastic switch
    synthetic genetic circuits},
    ISBN = {1557-170X},
    Year = {2010} }

Publications

Contact

Address: School of Computing Science, Claremont Tower, Newcastle University, Newcastle upon Tyne, NE1 7RU