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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..

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)..

Synthetic biology open language visual (SBOL Visual) version 2.3. (2021)
Journal Article
Madsen, C., Misirli, G., Palchick, Z., Pocock, M., Roehner, N., Sauro, H., …Bartley Bartley, B. (2021). Synthetic biology open language visual (SBOL Visual) version 2.3

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 2.3..

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)..

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.

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.

Synthetic Biology Open Language (SBOL) Version 2.3. (2019)
Journal Article
Misirli. (2019). Synthetic Biology Open Language (SBOL) Version 2.3. Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2019-0025

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 2.3..

Receiver Design Using Genetic Circuits in Molecular Communication (2019)
Presentation / Conference
Misirli. (2019, April). Receiver Design Using Genetic Circuits in Molecular Communication. Presented at 4th workshop on Molecular Communications, Linz, Austria

Understanding the dynamics of molecular communications between cells and intracellular response is crucial to create predictable cellular applications. When the propagation mechanism is diffusion based, the arrival histogram of molecules becomes heav... Read More about Receiver Design Using Genetic Circuits in Molecular Communication.

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference (2018)
Journal Article
Misirli. (2018). A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS synthetic biology, 2812-2823. https://doi.org/10.1021/acssynbio.8b00201

A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in an... Read More about A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.

Harmonizing semantic annotations for computational models in biology (2018)
Journal Article
Misirli. (2018). Harmonizing semantic annotations for computational models in biology. Briefings in bioinformatics, bby087 - bby087. https://doi.org/10.1093/bib/bby087

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for... Read More about Harmonizing semantic annotations for computational models in biology.

A computational workflow for the automated generation of models of genetic designs (2018)
Journal Article
Misirli. (2018). A computational workflow for the automated generation of models of genetic designs. ACS synthetic biology, 1548-1559. https://doi.org/10.1021/acssynbio.7b00459

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modelling often requires expert knowledge and data to build models. Clearly, manual creation of models is no... Read More about A computational workflow for the automated generation of models of genetic designs.

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., …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

A standard-enabled workflow for synthetic biology. (2017)
Journal Article
Mısırlı, G., Nguyen, T., Oberortner, E., Samineni, M., Wipat, A., Zhang, M., …Kuwahara, H. (2017). A standard-enabled workflow for synthetic biology. Transactions, 793 - 803. https://doi.org/10.1042/BST20160347

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select... Read More about A standard-enabled workflow for synthetic biology..

Constructing Synthetic Biology Workflows in the Cloud (2017)
Journal Article
Misirli. (2017). Constructing Synthetic Biology Workflows in the Cloud. Engineering Biology, 61-65. https://doi.org/10.1049/enb.2017.0001

The synthetic biology design process has traditionally been heavily dependent upon manual searching, acquisition and integration of existing biological data. A large amount of such data is already available from Internet-based resources, but data exc... Read More about Constructing Synthetic Biology Workflows in the Cloud.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. (2016)
Journal Article
Wipat, A., Hallinan, J., Madsen, C., McLaughlin, J., Mısırlı, G., Pocock, M., & Flanagan, K. (2016). The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. ACS synthetic biology, 487 - 497. https://doi.org/10.1021/acssynbio.5b00210

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange design... Read More about The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs..

Data Integration and Mining for Synthetic Biology Design. (2016)
Journal Article
Mısırlı, G., Hallinan, J., Pocock, M., Lord, P., McLaughlin, J., Sauro, H., & Wipat, A. (2016). Data Integration and Mining for Synthetic Biology Design. ACS synthetic biology, 1086 - 1097. https://doi.org/10.1021/acssynbio.5b00295

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existin... Read More about Data Integration and Mining for Synthetic Biology Design..

libSBOLj 2.0: A Java Library to Support SBOL 2.0 (2016)
Journal Article
Misirli. (2016). libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 34 - 37. https://doi.org/10.1109/LLS.2016.2546546

The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic d... Read More about libSBOLj 2.0: A Java Library to Support SBOL 2.0.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. (2015)
Journal Article
Gilfellon, O., Honorato-Zimmer, R., Pocock, M., Madsen, C., Waites, W., Cavaliere, M., …Wipat, A. (2015). Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics, 908 - 917. https://doi.org/10.1093/bioinformatics/btv660

MOTIVATION: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the for... Read More about Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization..

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. (2014)
Journal Article
Röttger, R., Baumbach, J., Wipat, A., Misirli, G., & Hallinan, J. (2014). BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of Integrative Bioinformatics, 244 - ?. https://doi.org/10.2390/biecoll-jib-2014-244

As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organis... Read More about BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species..

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts (2014)
Journal Article
Hallinan, J. S., Gilfellon, O., Misirli, G., & Wipat, A. (2014). Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, https://doi.org/10.1109/cibcb.2014.6845520

Populations of bacteria acting in collaboration can produce complex behaviors which are not achievable by individual cells. There has, consequently, been considerable interest in the engineering of bacterial populations. Here we describe an approach... Read More about Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts.

Model annotation for synthetic biology: automating model to nucleotide sequence conversion. (2011)
Journal Article
Misirli, G., Hallinan, J. S., Yu, T., Lawson, J. R., Wimalaratne, S. M., Cooling, M. T., & Wipat, A. (2011). Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics, 27(7), 973 - 979. https://doi.org/10.1093/bioinformatics/btr048

MOTIVATION: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembl... Read More about Model annotation for synthetic biology: automating model to nucleotide sequence conversion..

SBML Level 3 Package Proposal: Annotation (2011)
Report
Hucka, M., Laibe, C., Juty, N., Liebermeister, W., Keating, S., Lloyd, C., …Hoops, S. (in press). SBML Level 3 Package Proposal: Annotation. Nature Proceedings

The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of soft... Read More about SBML Level 3 Package Proposal: Annotation.

Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits
Journal Article
Misirli. Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits. bioRxiv,

AbstractEngineering 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 where manual analys... Read More about Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits.