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    •
    Dr Goksel Misirli

    Dr Goksel Misirli

    Title
    Senior Lecturer (Computing)
    Location
    Colin Reeves Building: CR40
    Phone
    +44 (0) 1782 734028
    Email
    g.misirli@keele.ac.uk

    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

    • Yang B, Misirli G, Wipat A, Hallinan J. 2022. Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosystems, 104730, vol. 219. link> doi> full text>
    • Mısırlı G, Yang B, James K, Wipat A. 2021. Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology, Article acssynbio.1c00157. doi> link> full text>
    • Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A. 2019. 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>
    • Wates W, Misirli G, Cavaliere M, Danos V, Wipat A. 2018. A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synthetic Biology. doi> full text>
    • Mısırlı G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones T, Densmore D, Myers CJ, Wipat A. 2018. A computational workflow for the automated generation of models of genetic designs. ACS Synth Biol. link> doi> full text>

    Full Publications Listshow

    Journal Articles

    • Buecherl L, Mitchell T, Scott-Brown J, Vaidyanathan P, Vidal G, Baig H, Bartley B, Beal J, Crowther M, Fontanarrosa P, Gorochowski T, Grünberg R, Kulkarni V, McLaughlin J, Mısırlı G, Oberortner E, Wipat A, Myers C. 2023. Synthetic biology open language (SBOL) version 3.1.0. Journal of Integrative Bioinformatics, vol. 20(1). doi> link> full text>
    • Yang B, Misirli G, Wipat A, Hallinan J. 2022. Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosystems, 104730, vol. 219. link> doi> full text>
    • Mısırlı G, Yang B, James K, Wipat A. 2021. Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology, Article acssynbio.1c00157. doi> link> full text>
    • Gennari JH, König M, Misirli G, Neal ML, Nickerson DP, Waltemath D. 2021. OMEX metadata specification (version 1.2). J Integr Bioinform, vol. 18(3). link> doi> full text>
    • Baig H, Fontanarossa P, McLaughlin J, Scott-Brown J, Vaidyanathan P, Gorochowski T, Misirli G, Beal J, Myers C. 2021. Synthetic biology open language visual (SBOL visual) version 3.0. J Integr Bioinform, vol. 18(3). link> doi> full text>
    • Baig H, Fontanarossa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhakta S, Bhatia S, Bissell M, Clancy K, Cox RS, Goñi Moreno A, Gorochowski T, Grunberg R, Lee J, Luna A, Madsen C, Misirli G, Nguyen T, Le Novere N, Palchick Z, Pocock M, Roehner N, Sauro H, Scott-Brown J, Sexton JT, Stan G-B, Tabor JJ, Terry L, Vazquez Vilar M, Voigt CA, Wipat A, Zong D, Zundel Z, Beal J, Myers C. 2021. Synthetic biology open language visual (SBOL Visual) version 2.3. J Integr Bioinform, vol. 18(3). link> doi> full text>
    • Mısırlı G, Yang B, James K, Wipat A. Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits. doi> full text>
    • McLaughlin JA, Beal J, Mısırlı G, Grünberg R, Bartley BA, Scott-Brown J, Vaidyanathan P, Fontanarrosa P, Oberortner E, Wipat A, Gorochowski TE, Myers CJ. 2020. The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Front Bioeng Biotechnol, 1009, vol. 8. link> doi> full text>
    • Brown B, Bartley B, Beal J, Bird JE, Goñi-Moreno Á, McLaughlin JA, Mısırlı G, Roehner N, Skelton DJ, Poh CL, Ofiteru ID, James K, Wipat A. 2020. Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL). ACS Synth Biol, 2410-2417, vol. 9(9). link> doi>
    • Baig H, Fontanarrosa P, Kulkarni V, McLaughlin JA, Vaidyanathan P, Bartley B, Beal J, Crowther M, Gorochowski TE, Grünberg R, Misirli G, Scott-Brown J, Oberortner E, Wipat A, Myers CJ. 2020. Synthetic biology open language (SBOL) version 3.0.0. J Integr Bioinform, vol. 17(2-3). link> doi> full text>
    • Baig H, Fontanarrosa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Moreno AG, Gorochowski T, Grunberg R, Luna A, Madsen C, Misirli G, Nguyen T, Le Novere N, Palchick Z, Pocock M, Roehner N, Sauro H, Scott-Brown J, Sexton JT, Stan G-B, Tabor JJ, Vilar MV, Voigt CA, Wipat A, Zong D, Zundel Z, Beal J, Myers C. 2020. Synthetic biology open language visual (SBOL visual) version 2.2. J Integr Bioinform, vol. 17(2-3). link> doi> full text>
    • Misirli G, Beal J, Gorochowski TE, Stan G-B, Wipat A, Myers CJ. 2020. SBOL Visual 2 Ontology. ACS Synthetic Biology. doi> link> full text>
    • Misirli G, Beal J, Gorochowski T, Stan G-B, Wipat A, Myers C. 2020. SBOL Visual 2 Ontology. doi>
    • Crowther M, Grozinger L, Pocock M, Taylor CPD, McLaughlin JA, Mısırlı G, Bartley BA, Beal J, Goñi-Moreno A, Wipat A. 2020. 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>
    • Cook AA, Misirli G, Fan Z. 2020. Anomaly Detection for IoT Time-Series Data: A Survey. IEEE INTERNET OF THINGS JOURNAL, 6481-6494, vol. 7(7). link> doi> full text>
    • Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, Pocock M, Samineni M, Scott-Brown J, Tarter Y, Zhang M, Zhang Z, Zundel Z, Beal J, Bissell M, Clancy K, Gennari JH, Misirli G, Myers C, Oberortner E, Sauro H, Wipat A. 2019. Synthetic Biology Open Language (SBOL) Version 2.3. J Integr Bioinform, vol. 16(2). link> doi> full text>
    • Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A. 2019. 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>
    • Neal ML, König M, Nickerson DP, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook SM, Alba MD, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty NS, Myers CJ, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. 2019. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics, 540-550, vol. 20(2). doi> link> full text>
    • Misirli G, Taylor R, Goni-Moreno A, McLaughlin JA, Myers C, Gennari J, Lord P, Wipat A. 2018. SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits. doi>
    • Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. 2019. Harmonizing semantic annotations for computational models in biology. Brief Bioinform, 540-550, vol. 20(2). link> doi> full text>
    • Brown B, Atallah C, McLaughlin JA, Misirli G, Goñi-Moreno Á, Roehner N, Skelton DJ, Bartley B, Beal J, Poh CL, Ofiteru ID, Wipat A. 2018. Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL). doi>
    • Wates W, Misirli G, Cavaliere M, Danos V, Wipat A. 2018. A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synthetic Biology. doi> full text>
    • Mısırlı G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones T, Densmore D, Myers CJ, Wipat A. 2018. A computational workflow for the automated generation of models of genetic designs. ACS Synth Biol. link> doi> full text>
    • Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A. 2018. Synthetic Biology Open Language (SBOL) Version 2.2.0. J Integr Bioinform, vol. 15(1). link> doi> full text>
    • McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A. 2018. SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synth Biol, 682-688, vol. 7(2). link> doi> full text>
    • Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, McLaughlin JA, Mısırlı G, Nguyen T, Oberortner E, Samineni M, Wipat A, Zhang M, Zundel Z. 2017. A standard-enabled workflow for synthetic biology. Biochem Soc Trans, 793-803, vol. 45(3). link> doi> full text>
    • Misirli G, Madsen C, Murieta ISD, Bultelle M, Flanagan K, Pocock M, Hallinan J, Mclaughlin JA, Clark-Casey J, Lyne M, Micklem G, STAN G-B, Kitney R, Wipat A. 2017. Constructing Synthetic Biology Workflows in the Cloud. Engineering Biology. doi> link>
    • Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari J, Myers C, Sauro H, Wipat A. 2016. Synthetic Biology Open Language (SBOL) Version 2.1.0. J Integr Bioinform, 291, vol. 13(3). link> doi>
    • Madsen C, McLaughlin JA, Mısırlı G, Pocock M, Flanagan K, Hallinan J, Wipat A. 2016. 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>
    • Mısırlı G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A. 2016. Data Integration and Mining for Synthetic Biology Design. ACS Synth Biol, 1086-1097, vol. 5(10). link> doi> full text>
    • Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ. 2016. Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synth Biol, 498-506, vol. 5(6). link> doi>
    • Zhang Z, Nguyen T, Roehner N, Misirli G, Pocock M, Oberortner E, Samineni M, Zundel Z, Beal J, Clancy K, Wipat A, Myers CJ. 2016. libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 34-37, vol. 1. doi> link> full text>
    • McLaughlin JA, Pocock M, Mısırlı G, Madsen C, Wipat A. 2016. VisBOL: Web-Based Tools for Synthetic Biology Design Visualization. ACS Synth Biol, 874-876, vol. 5(8). link> doi>
    • Zhang Z, Nguyen T, Roehner N, Misirli G, Pocock M, Oberortner E, Samineni M, Zundel Z, Beal J, Clancy K, Wipat A, Myers CJ. 2016. libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 1. doi>
    • Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O, Honorato-Zimmer R, Zuliani P, Danos V, Wipat A. 2015. 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>
    • Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. 2015. Synthetic Biology Open Language (SBOL) Version 2.0.0. J Integr Bioinform, 272, vol. 12(2). link> doi>
    • Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. 2015. Synthetic Biology Open Language (SBOL) Version 2.0.0. J Integr Bioinform, 902-991, vol. 12(2). link> doi>
    • Misirli G, Hallinan J, Wipat A. 2014. Composable Modular Models for Synthetic Biology. JETC, 22:1, vol. 11. doi> full text>
    • Myers C, Clancy K, Misirli G, Oberortner E, Pocock M, Quinn J, Roehner N, Sauro HM. 2015. The synthetic biology open language. Methods Mol Biol, 323-336, vol. 1244. link> doi>
    • Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A. 2014. BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. J Integr Bioinform, 244, vol. 11(2). link> doi>
    • Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ. 2015. Proposed data model for the next version of the synthetic biology open language. ACS Synth Biol, 57-71, vol. 4(1). link> doi>
    • Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan G-B, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM. 2014. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology, 545-550, vol. 32(6). link> doi>
    • Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM. 2013. Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins. Proteomics, 3298-3308, vol. 13(22). link> doi>
    • Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan JS. 2013. BacillOndex: an integrated data resource for systems and synthetic biology. J Integr Bioinform, 224, vol. 10(2). link> doi>
    • Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A. 2011. Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics, 973-979, vol. 27(7). link> doi> full text>
    • Hucka M, Laibe C, Juty N, Liebermeister W, Keating S, Lloyd C, Knuepfer C, Misirli G, Schulz M, Waltemath D, Taschuk M, Swainston N, Le Novère N, Lister A, Bergmann F, Henkel R, Krause F, Hoops S. SBML Level 3 Package Proposal: Annotation. Nature Precedings. doi>
    • Swainston N, Waltemath D, Swainston N, Lister A, Bergmann F, Henkel R, Hoops S, Hucka M, Juty N, Keating S, Knuepfer C, Krause F, Laibe C, Liebermeister W, Lloyd C, Misirli G, Schulz M, Taschuk M, Le Novère N. SBML Level 3 Package Proposal: Annotation. Nature Precedings. doi>
    • Cooling MT, 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, 925-931, vol. 26(7). link> doi>
    • Hallinan JS, Misirli G, Wipat A. 2010. Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. Annu Int Conf IEEE Eng Med Biol Soc, 768-774, vol. 2010. link> doi>
    • Misirli G. A comparative analysis for SARS-CoV-2. link>
    • Durmaz MG, Tulluk N, Aksoy RD, Yilmaz HB, Yang B, Wipat A, Pusane AE, Mısırlı G, Tugcu T. Engineering genetic circuits in receiver cells for diffusion-based molecular data communications. doi>
    • Mısırlı G. libSBOLj3: A graph-based library for design and data exchange in synthetic biology. doi>

    Other

    • Woolley S, de Quincey E, Flint T, Grandison T, Rugg G, Fleck R, Whittington P, Ortolani M, Misirli G, Collins T. 2022. Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University. Electronic Workshops in Computing. BCS Learning & Development. doi> link> full text>
    • Yang B, Misirli G, Wipat A, Hallinan J, IEEE. 2021. 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>
    • Ajibode JS, Beal J, Scott-Brown J, Gorochowski T, Myers C, Misirli G. 2021. Towards collaborative and automated development of resources for data standards in synthetic biology. https://www.iwbdaconf.org/2021/docs/IWBDA2021Proceedings.pdf. link> full text>
    • Misirli G, Yang B, Wipat A. 2019. Model-driven design of genetic regulatory networks using virtual parts. http://www.iwbdaconf.org/2019/docs/IWBDA19Proceedings.pdf. full text>
    • Mısırlı G, Beal J, Gorochowski TE, Stan G-B, Wipat A, Myers CJ. 2020. SBOL Visual 2 Ontology. ACS Synth Biol (pp. 972-977, vol. 9). link> doi> full text>
    • Mısırlı G, Beal J, Gorochowski TE, Stan G-B, Wipat A, Myers CJ. 2020. SBOL Visual 2 Ontology. ACS Synth Biol (pp. 972-977, vol. 9). link> doi> full text>
    • Aksoy D, Yilmaz B, Kuran S, Wipat A, Pusane AE, Misirli G, Tugcu T. 2019. Receiver Design Using Genetic Circuits in Molecular Communication. full text>
    • Misirli G and Lord P. 2017. Tawny-SBOL: Using ontologies to design and constrain genetic circuits. link> full text>
    • Misirli G, Nguyen T, McLaughlin J, Myers C, Wipat A. Standard Enabled Model Generator for Genetic Circuit Design. http://www.iwbdaconf.org/2017/docs/IWBDA_2017_Proceedings.pdf. full text>
    • Hallinan J, Gilfellon O, Misirli G, Wipat A. 2014. Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. CIBCB (pp. 1-8). IEEE. doi> link>

    School of Computer Science and Mathematics
    Keele University
    Staffordshire
    ST5 5AA