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.

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)..

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)

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., Bhatia, S., Bhakta, S., Bissell, M., Clancy, K., Cox, R. S., Moreno, A. G., Gorochowski, T., Grunberg, R., Luna, A., Madsen, C., Misirli, G., Nguyen, T., Le Novere, N., Palchick, Z., …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.

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.

Synthetic Biology Open Language (SBOL) Version 2.2.0. (2018)
Journal Article
Misirli. (2018). Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2018-0001

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long... Read More about Synthetic Biology Open Language (SBOL) Version 2.2.0..

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. (2018)
Journal Article
McLaughlin, J., Ofiteru, I., Goñi Moreno, A., Zundel, Z., Misirli, G., Zhang, M., Wipat, A., & Myers, C. (2018). SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS synthetic biology, 682-688. https://doi.org/10.1021/acssynbio.7b00403

The SynBioHub repository (synbiohub.org) is an open-source software project which facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical u... Read More about SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology..

Standard Enabled Model Generator for Genetic Circuit Design (2017)
Presentation / Conference
Myers, C., Wipat, A., Misirli, G., Nguyen, T., & McLaughlin, J. (2017, August). Standard Enabled Model Generator for Genetic Circuit Design. Presented at 9th International Workshop on Bio-Design Automation, Pittsburgh