Outputs (43)

MicroMaps: Ontology-driven Semantic Geospatial Data Fusion Approach for IoT Integration and Decision Making in Smart Cities (2025)
Presentation / Conference Contribution
Rayis, A., Ortolani, M., David, R.-M., Hirschi, R., & Misirli, G. (2025, August). MicroMaps: Ontology-driven Semantic Geospatial Data Fusion Approach for IoT Integration and Decision Making in Smart Cities. Presented at 2025 the 9th International Conference on Cloud, Big Data and Communication Systems (ICCBDCS 2025), Manchester

Smart cities generate large amounts of Internet of
Things data from diverse sources, often presented in varying
formats and with inconsistent quality, complicating effective data
management and interoperability. Despite recent advancements
relate... Read More about MicroMaps: Ontology-driven Semantic Geospatial Data Fusion Approach for IoT Integration and Decision Making in Smart Cities.

BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications (2024)
Journal Article
Durmaz, M. G., Tulluk, N., Aksoy, R. D., Yilmaz, H. B., Yang, B., Wipat, A., Pusane, A. E., Mısırlı, G., & Tugcu, T. (in press). BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications. Synthetic Biology, https://doi.org/10.1093/synbio/ysae015

Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules an... Read More about BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications.

libSBOLj3: a graph-based library for design and data exchange in synthetic biology. (2023)
Journal Article
Mısırlı, G. (2023). libSBOLj3: a graph-based library for design and data exchange in synthetic biology. Bioinformatics, 39(8), 3. https://doi.org/10.1093/bioinformatics/btad525

The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBO... Read More about libSBOLj3: a graph-based library for design and data exchange in synthetic biology..

Not to be sniffed at: repurposing existing RNA-seq data to examine changes to human nasal microbiome composition in COVID-19 infection, compared to influenza and healthy controls (2023)
Journal Article
Wainwright, F., Misirli, G., & Andras, P. (2023). Not to be sniffed at: repurposing existing RNA-seq data to examine changes to human nasal microbiome composition in COVID-19 infection, compared to influenza and healthy controls. Microbiota in Health and Disease, 5(2), Article e845. https://doi.org/10.26355/mhd_20236_845

Objective: The human microbiome is essential in maintaining healthy physiology; compositional changes have been implicated in numerous physical and mental diseases. Thus far, COVID-19 microbiome research has focused primarily upon gut and lung bacter... Read More about Not to be sniffed at: repurposing existing RNA-seq data to examine changes to human nasal microbiome composition in COVID-19 infection, compared to influenza and healthy controls.

Synthetic biology open language (SBOL) version 3.1.0 (2023)
Journal Article
Buecherl, L., Mitchell, T., Scott-Brown, J., Vaidyanathan, P., Vidal, G., Baig, H., Bartley, B., Crowther, M., Fontanarrosa, P., Gorochowski, T., Grünberg, R., Kulkarni, V., McLaughlin, J., Misirli, G., Oberortner, E., Wipat, A., Myers, C., & Beal, J. (2023). Synthetic biology open language (SBOL) version 3.1.0. Journal of Integrative Bioinformatics, 20(1), 20220058. https://doi.org/10.1515/jib-2022-0058

Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about mu... Read More about Synthetic biology open language (SBOL) version 3.1.0.

Proceedings of the 35th International BCS Human Computer Interaction Conference (HCI 2022) - Index (2022)
Presentation / Conference Contribution
de Quincey, E., Woolley, S. I., Ortolani, M., Misirli, G., Mandal, B., Kanwal, N., Mitchell, J., & Rooney, J. (2022, July). Proceedings of the 35th International BCS Human Computer Interaction Conference (HCI 2022) - Index. Presented at 35th International BCS Human-Computer Interaction Conference (HCI2022), Keele, Staffordshire, England, UK

Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University (2022)
Presentation / Conference Contribution
Woolley, S., de Quincey, E., Flint, T., Grandison, T., Rugg, G., Fleck, R., Whittington, P., Ortolani, M., Misirli, G., & Collins, T. (2022, July). Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University. Presented at 35th International BCS Human-Computer Interaction Conference, Keele, Staffordshire, UK

Modelling the fitness landscapes of a SCRaMbLEd yeast genome. (2022)
Journal Article
Yang, B., Misirli, G., Wipat, A., & Hallinan, J. (2022). Modelling the fitness landscapes of a SCRaMbLEd yeast genome. BioSystems, https://doi.org/10.1016/j.biosystems.2022.104730

The use of microorganisms for the production of industrially important compounds and enzymes is becoming increasingly important. Eukaryotes have been less widely used than prokaryotes in biotechnology, because of the complexity of their genomic struc... Read More about Modelling the fitness landscapes of a SCRaMbLEd yeast genome..

Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits (2021)
Journal Article
Yang, B., James, K., Wipat, A., & Misirli, G. (2021). Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS synthetic biology, 10(12), 3304-3315. https://doi.org/10.1021/acssynbio.1c00157

Engineering genetic regulatory circuits is key to the creation of biological applications that are responsive to environmental changes. Computational models can assist in understanding especially large and complex circuits for which manual analysis i... Read More about Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits.

OMEX metadata specification (version 1.2). (2021)
Journal Article
Nickerson, D., Waltemath, D., Gennari, J., König, M., Misirli, G., & Neal, M. (2021). OMEX metadata specification (version 1.2). Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2021-0020

A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons be... Read More about OMEX metadata specification (version 1.2)..