About

I am a senior postdoctoral researcher at the School of Computing Science, and a member of the Interdisciplinary Computing and Complex BioSystems (ICOS) research group. I have a PhD in synthetic biology from Newcastle University. My PhD supervisors were Prof. Anil Wipat and Dr Jennifer Hallinan. My PhD thesis title was "Data Integration to inform computational design in synthetic biology" and the thesis outlined the early applications, if not the first, of data integration in the field. I have a BSc in Control and Computer Engineering from Istanbul Technical University.

Research

I am involved in research activities exploring the idea of design automation for biological systems, in the area of synthetic biology. I focus upon biological design automation, with the aim of scaling up biological system designs, in order to achieve novel and complex designs. I am interested in model-driven design approaches that have already been used to synthesize complex electronic systems, computer software and so on. Moreover, I explore the use of formal semantics to capture design information for machine interoperability. I am part of the data standard communities in synthetic biology, particularly SBOL, to standardise the computational exchange of synthetic biology designs between different tools. Data standards are especially important in the nascent field of synthetic biology, in order to combine the power of many useful tools that are still under development, and to execute complex computational workflows using these tools.

I was a local organiser in different conferences and workshops including IWBDA 2016 and ICB2014, and I was involved in national and international collaborations. My publishing records include papers in high-quality journals, including Nature Biotechnology, Bioinformatics and ACS Synthetic Biology.

Specialties: Synthetic biology, data integration, systems biology, biological networks, genetic circuit design, modelling of biological systems, SBML, rule-based models, Semantic Web and biological ontologies

Principal Investigator

Prof. Anil Wipat
Dr. Jennifer Hallinan

Publications

  • Misirli, G., Hallinan, J., Pocock, M., Lord, P., McLaughlin, J. A., Sauro, H., andWipat, A. (2016). Data integration and mining for synthetic biology design. ACS Synthetic Biology.
  • Misirli, G., Cavaliere, M., Waites, W., Pocock, M., Madsen, C., Gilfellon, O., Honorato-Zimmer, R., Zuliani, P., Danos, V., and Wipat, A. (2016). Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation. Bioinformatics, 32(6), 908–917.
  • Madsen, C., McLaughlin, J. A., Misirli, G., Pocock, M., Flanagan, K., Hallinan, J., and Wipat, A. (2016). The sbol stack: A platform for storing, publishing, and sharing synthetic biology designs. ACS Synthetic Biology, 5(6), 487–497.
  • Roehner, N., Beal, J., Clancy, K., Bartley, B., Misirli, G., Gruenberg, R., Oberortner, E., Pocock, M., Bissell, M., Madsen, C., NGUYEN, T., Zhang, M., Zhang, Z., Zundel, Z., Densmore, D., Gennari, J., Wipat, A., Sauro, H., and Myers, C. J. (2016). Sharing structure and function in biological design with sbol 2.0. ACS Synthetic Biology. – 4 citations
  • McLaughlin, J. A., Pocock, M., Misirli, G., Madsen, C., and Wipat, A. (2016). Visbol: Web-based tools for synthetic biology design visualization. ACS Synthetic Biology.
  • Zhang, Z., Nguyen, T., Roehner, N., Misirli, G., Pocock, M., Oberortner, E., Samineni, M., Zundel, Z., Beal, J., Clancy, K., Wipat, A., and Myers, C. J. (2016). libsbolj 2.0: A java library to support sbol 2.0. IEEE Life Sciences Letters, 1(4), 34–37.
  • Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, Z., Gennari, J. H., Myers, C., Wipat, A., and Sauro, H. (2015). Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics, 12(2), 272.
  • Roehner, N., Oberortner, E., Pocock, M., Beal, J., Clancy, K., Madsen, C., Misirli, G., Wipat, A., Sauro, H., and Myers, C. J. (2015). Proposed data model for the next version of the synthetic biology open language. ACS Synthetic Biology, 4(1), 57–71.
  • McLaughlin, J., Misirli, G., Pocock, M., and Wipat, A. (2016). An environment for augmented biodesign using integrated data resources. In 8th InternationalWorkshop on Bio-Design Automation.
  • Pocock, M., Taylor, C., McLaughlin, J., Misirli, G., and Wipat, A. (2016). An environment for augmented biodesign using integrated data resources. In 8th International Workshop on Bio-Design Automation.
  • Madsen, C., Misirli, G., Pocock, M., Hallinan, J., and Wipat, A. (2015). Sbol stack: The one-stop-shop for storing and publishing synthetic biology designs. In 7th International Workshop on Bio-Design Automation.
  • Gilfellon, O., Misirli, G., Madsen, C., Hallinan, J., Zuliani, P., and Wipat, A. (2015). Synbad: An svp design framework. In 7th International Workshop on Bio-Design Automation.
  • Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., and Pocock, M. (2015). The synthetic biology open language 2.0. In 7th International Workshop on Bio-Design Automation.
  • Zhang, Z., Nguyen, T., Roehner, N., Misirli, G., Pocock, M., Oberortner, E., Beal, J., Clancy, K., Wipat, A., and Myers, C. (2015). libsbolj 2.0: A java library to support sbol 2.0. In IEEE SY-Bio Workshop to Address Topics in Systems and Synthetic Biology, Dallas, US.
  • G. Misirli, J. S. Hallinan, and A. Wipat, “Composable modular models for synthetic biology,” Acm journal on emerging technologies in computing systems, accepted, 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • G. Misirli, “Data integration strategies for informing computational design in synthetic biology,” PhD Thesis, 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.
  • 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.
  • 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] 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.
  • 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.
  • 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.
  • J. S. Hallinan, G. Misirli, and A. Wipat, Evolutionary computation for the design of a stochastic switch for synthetic genetic circuitsIEEE, 2010.

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Last update: 15 July 2014 by Dr. Goksel Misirli  |  All rights reserved