Dr Goksel Misirli

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

I am a lecturer at the School of Computing and Mathematics. Before joining to 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.

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.

Selected Publications

  • Neal ML, König M, Nickerson D, Misirli 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. 2018. Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 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>
  • McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A. SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synth Biol, vol. 7(2), 682-688. 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>

Full Publications List show

Journal Articles

  • Neal ML, König M, Nickerson D, Misirli 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. 2018. Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 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>
  • Waites W, Mısırlı G, Cavaliere M, Danos V, Wipat A. 2018. A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synth Biol. link> doi>
  • 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. SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synth Biol, vol. 7(2), 682-688. 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. A standard-enabled workflow for synthetic biology. Biochem Soc Trans, vol. 45(3), 793-803. 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, vol. 13(3), 291. link> doi>
  • McLaughlin JA, Pocock M, Mısırlı G, Madsen C, Wipat A. VisBOL: Web-Based Tools for Synthetic Biology Design Visualization. ACS Synth Biol, vol. 5(8), 874-876. 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, vol. 5(6), 487-497. 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, vol. 5(10), 1086-1097. 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, vol. 5(6), 498-506. 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, vol. 1, 34-37. doi> link> full text>
  • 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, vol. 32(6), 908-917. 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, vol. 12(2), 902-991. 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, vol. 4(1), 57-71. 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, vol. 12(2), 272. link> doi>
  • 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, vol. 1244, 323-336. link> doi>
  • Misirli G, Hallinan J, Wipat A. 2014. Composable Modular Models for Synthetic Biology. JETC, vol. 11, 22:1. doi> full text>
  • 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, vol. 32(6), 545-550. 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, vol. 11(2), 244. 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, vol. 13(22), 3298-3308. 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, vol. 10(2), 224. 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, vol. 27(7), 973-979. link> doi> full text>
  • Hallinan JS, Misirli G, Wipat A. 2010. Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. Conf Proc IEEE Eng Med Biol Soc, vol. 2010, 768-774. link> 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, vol. 26(7), 925-931. link> doi>

Other

  • 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>
  • Misirli G and Lord P. Tawny-SBOL: Using ontologies to design and constrain genetic circuits. full text>

CSC-20021 Web Technologies
CSC-30012 Communications and Networks
CSC-40039 Cloud Computing

Latest Keele research news
Book an open day
About Keele University