All Outputs (41)

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., …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.

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..

Proceedings of the 35th International BCS Human Computer Interaction Conference (HCI 2022) - Index (2022)
Conference Proceeding
de Quincey, E., Woolley, S. I., Ortolani, M., Misirli, G., Mandal, B., Kanwal, N., …Rooney, J. (2022). Proceedings of the 35th International BCS Human Computer Interaction Conference (HCI 2022) - Index. . https://doi.org/10.14236/ewic/HCI2022.0

Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University (2022)
Conference Proceeding
Woolley, S., de Quincey, E., Flint, T., Grandison, T., Rugg, G., Fleck, R., …Collins, T. (2022). Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University. . https://doi.org/10.14236/ewic/hci2022.1

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, 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.

Synthetic biology open language visual (SBOL visual) version 3.0. (2021)
Journal Article
Baig, H., Myers, C., McLaughlin, J., Scott-Brown, J., Vaidyanathan, P., Gorochowski, T., …Fontanarossa, P. (2021). Synthetic biology open language visual (SBOL visual) version 3.0. Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2021-0013

People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other mol... Read More about Synthetic biology open language visual (SBOL visual) version 3.0..

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)..

Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome (2021)
Presentation / Conference
Misirli. (2021, October). Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome. Presented at 2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)

Towards collaborative and automated development of resources for data standards in synthetic biology (2021)
Journal Article
Gorochowski, T., Myers, C., Misirli, G., Ajibode, J., Beal, J., & Scott-Brown, J. (2021). Towards collaborative and automated development of resources for data standards in synthetic biology

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering (2020)
Journal Article
Grünberg, R., Bartley, B., Scott-Brown, J., Vaidyanathan, P., Fontanarrosa, P., Oberortner, E., …Misirli, G. (2020). The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Frontiers in Bioengineering and Biotechnology, https://doi.org/10.3389/fbioe.2020.01009

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. W... Read More about The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.

Synthetic biology open language (SBOL) version 3.0.0. (2020)
Journal Article
Bartley, B., Beal, J., McLaughlin, J., Vaidyanathan, P., Baig, H., Fontanarrosa, P., …Myers, C. (2020). Synthetic biology open language (SBOL) version 3.0.0. Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2020-0017

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 3.0.0..

Synthetic biology open language visual (SBOL visual) version 2.2 (2020)
Journal Article
Baig, H., Fontanarrosa, P., Kulkarni, V., McLaughlin, J., Vaidyanathan, P., Bartley, B., …Myers, C. (2020). Synthetic biology open language visual (SBOL visual) version 2.2. Journal of Integrative Bioinformatics, 17(2-3), Article 20200014. https://doi.org/10.1515/jib-2020-0014

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and oth... Read More about Synthetic biology open language visual (SBOL visual) version 2.2.

ShortBOL: A language for scripting designs for engineered biological systems using SyntheticBiology Open Language (SBOL). (2020)
Journal Article
Misirli. (2020). ShortBOL: A language for scripting designs for engineered biological systems using SyntheticBiology Open Language (SBOL). ACS synthetic biology, 962-966. https://doi.org/10.1021/acssynbio.9b00470

The Synthetic Biology Open Language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine-to-machine communication. However, manual editing of SBOL is generally difficult for non-triv... Read More about ShortBOL: A language for scripting designs for engineered biological systems using SyntheticBiology Open Language (SBOL)..

SBOL Visual 2 Ontology (2020)
Journal Article
Misirli. (2020). SBOL Visual 2 Ontology. ACS synthetic biology, 972-977. https://doi.org/10.1021/acssynbio.0c00046

Standardizing the visual representation of genetic parts and circuits is essential for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Ope... Read More about SBOL Visual 2 Ontology.

Anomaly Detection for IoT Time-Series Data: A Survey (2019)
Journal Article
Misirli, & Fan. (2019). Anomaly Detection for IoT Time-Series Data: A Survey. IEEE Internet of Things, https://doi.org/10.1109/JIOT.2019.2958185

Abstract—Anomaly detection is a problem with applications for a wide variety of domains, it involves the identification of novel or unexpected observations or sequences within the data being captured. The majority of current anomaly detection method... Read More about Anomaly Detection for IoT Time-Series Data: A Survey.

Model-driven design of genetic regulatory networks using virtual parts (2019)
Presentation / Conference
Misirli. (2019, July). Model-driven design of genetic regulatory networks using virtual parts. Presented at 11th International Workshop on Bio-Design Automation (IWBDA 2019), Cambridge

Conference paper.

SBOL Visual 2 Ontology (2019)
Presentation / Conference
Misirli, G. (2019, July). SBOL Visual 2 Ontology. Presented at 11th International Workshop on Bio-Design Automation (IWBDA 2019), Cambridge

Conference paper.

SBOL-OWL: An ontological approach for formal and semantic representation of synthetic biology information (2019)
Journal Article
Misirli. (2019). SBOL-OWL: An ontological approach for formal and semantic representation of synthetic biology information. ACS synthetic biology, 1498-1514. https://doi.org/10.1021/acssynbio.8b00532

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on capt... Read More about SBOL-OWL: An ontological approach for formal and semantic representation of synthetic biology information.