Biography
I am a senior lecturer at the School of Computer Science and Mathematics. Before joining Keele University, I worked as a postdoctoral researcher at Newcastle University, where I also obtained my PhD from the School of Computing Science. My PhD thesis title was “Data integration strategies for informing computational design in synthetic biology”. Previously, I worked in different companies including Ericsson and Reed Business Information as a software engineer, and I have a BSc in Control and Computer Engineering. I particularly enjoy doing research at the boundaries of computing and biology.
Research and scholarship
My research includes the development of novel algorithms, computational design paradigms and frameworks, utilising large, heterogeneous and complex datasets. Semantic Web, ontologies, biological networks, data integration and mining, visualisation, computational workflows, data and model-driven design approaches are some of the areas that I explore. Particularly, I demonstrated the utility of these approaches in synthetic and systems biology, to computationally design biological systems, and to gain biological insights.
Developing model-driven design approaches is a major part of my research to facilitate genetic design automation, and thus, to scale up biological designs in order to achieve novel and complex systems. I apply data integration techniques to mine biological design information, and research in the use of formal semantics to capture this information for machine interoperability.
I am part of the data standard communities in systems and synthetic biology, and have been particularly involved in the development of the Synthetic Biology Open Language to standardise the computational exchange of synthetic biology designs between different tools.
I also use Cloud computing to develop useful applications such as distributed computational workflows.
Google Scholar: https://scholar.google.co.uk/citations?user=o54loSkAAAAJ
- Data Integration & Mining
- Distributed Systems
- Synthetic & Systems Biology
- Semantic Web & Ontologies
- Data Visualisation
- Computational Modelling & Simulation
- Data Standards
Please see my personal page for more details.
Teaching
- CSC-20021 Web Technologies
- CSC-30012 Communications and Networks
- CSC-40039 Cloud Computing
Further information
Google Scholar: https://scholar.google.co.uk/citations?user=o54loSkAAAAJ
Twitter: https://twitter.com/gokselmisirli
Google Plus: https://plus.google.com/112541210718015518924
Selected Publications
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Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosystems, 104730, vol. 219. link> doi> full text>2022.
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Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology, Article acssynbio.1c00157. doi> link> full text>2021.
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SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information. ACS Synth Biol, 1498-1514, vol. 8(7). link> doi> full text>2019.
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A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synthetic Biology. doi> full text>2018.
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A computational workflow for the automated generation of models of genetic designs. ACS Synth Biol. link> doi> full text>2018.
Full Publications Listshow
Journal Articles
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Synthetic biology open language (SBOL) version 3.1.0. Journal of Integrative Bioinformatics, vol. 20(1). doi> link> full text>2023.
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Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosystems, 104730, vol. 219. link> doi> full text>2022.
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Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology, Article acssynbio.1c00157. doi> link> full text>2021.
- 2021.
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Synthetic biology open language visual (SBOL visual) version 3.0. J Integr Bioinform, vol. 18(3). link> doi> full text>2021.
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Synthetic biology open language visual (SBOL Visual) version 2.3. J Integr Bioinform, vol. 18(3). link> doi> full text>2021.
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The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Front Bioeng Biotechnol, 1009, vol. 8. link> doi> full text>2020.
- 2020.
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Synthetic biology open language (SBOL) version 3.0.0. J Integr Bioinform, vol. 17(2-3). link> doi> full text>2020.
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Synthetic biology open language visual (SBOL visual) version 2.2. J Integr Bioinform, vol. 17(2-3). link> doi> full text>2020.
- 2020.
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SBOL Visual 2 Ontology. doi>2020.
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ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL). ACS Synth Biol, 962-966, vol. 9(4). link> doi> full text>2020.
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Anomaly Detection for IoT Time-Series Data: A Survey. IEEE INTERNET OF THINGS JOURNAL, 6481-6494, vol. 7(7). link> doi> full text>2020.
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Synthetic Biology Open Language (SBOL) Version 2.3. J Integr Bioinform, vol. 16(2). link> doi> full text>2019.
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SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information. ACS Synth Biol, 1498-1514, vol. 8(7). link> doi> full text>2019.
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Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics, 540-550, vol. 20(2). doi> link> full text>2019.
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SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits. doi>2018.
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Harmonizing semantic annotations for computational models in biology. Brief Bioinform, 540-550, vol. 20(2). link> doi> full text>2019.
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Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL). doi>2018.
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A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synthetic Biology. doi> full text>2018.
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A computational workflow for the automated generation of models of genetic designs. ACS Synth Biol. link> doi> full text>2018.
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Synthetic Biology Open Language (SBOL) Version 2.2.0. J Integr Bioinform, vol. 15(1). link> doi> full text>2018.
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SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synth Biol, 682-688, vol. 7(2). link> doi> full text>2018.
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A standard-enabled workflow for synthetic biology. Biochem Soc Trans, 793-803, vol. 45(3). link> doi> full text>2017.
- 2017.
- 2016.
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The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. ACS Synth Biol, 487-497, vol. 5(6). link> doi> full text>2016.
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Data Integration and Mining for Synthetic Biology Design. ACS Synth Biol, 1086-1097, vol. 5(10). link> doi> full text>2016.
- 2016.
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libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 34-37, vol. 1. doi> link> full text>2016.
- 2016.
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libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 1. doi>2016.
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Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics, 908-917, vol. 32(6). link> doi> full text>2015.
- 2015.
- 2015.
- 2014.
- 2015.
- 2014.
- 2015.
- 2014.
- 2013.
- 2013.
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Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics, 973-979, vol. 27(7). link> doi> full text>2011.
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SBML Level 3 Package Proposal: Annotation. Nature Precedings. doi>
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SBML Level 3 Package Proposal: Annotation. Nature Precedings. doi>
- 2010.
- 2010.
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A comparative analysis for SARS-CoV-2. link>
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Engineering genetic circuits in receiver cells for diffusion-based molecular data communications. doi>
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libSBOLj3: A graph-based library for design and data exchange in synthetic biology. doi>
Other
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Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University. Electronic Workshops in Computing. BCS Learning & Development. doi> link> full text>2022.
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Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome. 2021 IEEE CONFERENCE ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (CIBCB) (pp. 103-111). link> doi> full text>2021.
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Towards collaborative and automated development of resources for data standards in synthetic biology. https://www.iwbdaconf.org/2021/docs/IWBDA2021Proceedings.pdf. link> full text>2021.
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Model-driven design of genetic regulatory networks using virtual parts. http://www.iwbdaconf.org/2019/docs/IWBDA19Proceedings.pdf. full text>2019.
- 2020.
- 2020.
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Receiver Design Using Genetic Circuits in Molecular Communication. full text>2019.
- 2017.
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Standard Enabled Model Generator for Genetic Circuit Design. http://www.iwbdaconf.org/2017/docs/IWBDA_2017_Proceedings.pdf. full text>
- 2014.
School of Computer Science and Mathematics
Keele University
Staffordshire
ST5 5AA
Email: scm.admin@keele.ac.uk
Tel:+44 (0) 1782 731830