Standard virtual biological parts: a repository of modular modeling components for synthetic biology. - Mike T. Cooling; V. Rouilly; Goksel Misirli; James R. Lawson; Tommy Yu; Jennifer Hallinan; Anil Wipat (Bioinform., 2010)

Model annotation for synthetic biology: automating model to nucleotide sequence conversion. - Goksel Misirli; Jennifer Hallinan; Tommy Yu; James R. Lawson; Sarala M. Wimalaratne; Mike T. Cooling; Anil Wipat (Bioinform., 2011)

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. - Goksel Misirli; Anil Wipat; Joseph Mullen; Katherine James; Matthew R. Pocock; Wendy Smith; Nick Allenby; Jennifer Hallinan (J. Integr. Bioinform., 2013)

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. - Jennifer Hallinan; Owen Gilfellon; Goksel Misirli; Anil Wipat (CIBCB, 2014)

Composable Modular Models for Synthetic Biology. - Goksel Misirli; Jennifer Hallinan; Anil Wipat (ACM J. Emerg. Technol. Comput. Syst., 2014)

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. - Goksel Misirli; Jennifer Hallinan; Richard Röttger; Jan Baumbach; Anil Wipat (J. Integr. Bioinform., 2014)

Synthetic Biology Open Language (SBOL) Version 2.0.0. - Bryan Bartley; Jacob Beal; Kevin Clancy; Goksel Misirli; Nicholas Roehner; Ernst Oberortner; Matthew R. Pocock; Michael Bissell; Curtis Madsen; Tramy Nguyen; Zhen Zhang 006; John H. Gennari; et al. (J. Integr. Bioinform., 2015)

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. - Goksel Misirli; Matteo Cavaliere; William Waites; Matthew R. Pocock; Curtis Madsen; Owen Gilfellon; Ricardo Honorato-Zimmer; Paolo Zuliani; Vincent Danos; Anil Wipat (Bioinform., 2016)

Synthetic Biology Open Language (SBOL) Version 2.1.0. - Jacob Beal; Robert Sidney Cox III; Raik Grünberg; James Alastair McLaughlin; Tramy Nguyen; Bryan Bartley; Michael Bissell; Kiri Choi; Kevin Clancy; Chris Macklin; Curtis Madsen; Goksel Misirli; et al. (J. Integr. Bioinform., 2016)

Tawny-SBOL: Using Ontologies to Design and Constrain Genetic Circuits. - Goksel Misirli; Phillip Lord (ICBO, 2017)

Compiling Combinatorial Genetic Circuits with Semantic Inference. - William Waites; Goksel Misirli; Matteo Cavaliere; Vincent Danos; Anil Wipat (CoRR, 2018)

Synthetic Biology Open Language (SBOL) Version 2.2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Jacob Beal; Michael Bissell; Kiri Choi; Kevin Clancy; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2018)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

Synthetic Biology Open Language (SBOL) Version 2.3. - Curtis Madsen; Ángel Goñi-Moreno; Umesh P; Zachary Palchick; Nicholas Roehner; Christian Atallah; Bryan Bartley; Kiri Choi; Robert Sidney Cox III; Thomas E. Gorochowski; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2019)

Anomaly Detection for IoT Time-Series Data: A Survey. - Andrew A. Cook; Goksel Misirli; Zhong Fan (IEEE Internet Things J., 2020)

Synthetic biology open language visual (SBOL visual) version 2.2. - Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Michael Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2020)

Synthetic biology open language (SBOL) version 3.0.0. - Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Jacob Beal; Matthew Crowther; Thomas E. Gorochowski; Raik Grünberg; Goksel Misirli; James Scott-Brown; et al. (J. Integr. Bioinform., 2020)

Synthetic biology open language visual (SBOL Visual) version 2.3. - Hasan Baig; Pedro Fontanarossa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Shyam Bhakta; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2021)

Synthetic biology open language visual (SBOL visual) version 3.0. - Hasan Baig; Pedro Fontanarossa; James Alastair McLaughlin; James Scott-Brown; Prashant Vaidyanathan; Thomas E. Gorochowski; Goksel Misirli; Jacob Beal; Chris J. Myers (J. Integr. Bioinform., 2021)

OMEX metadata specification (version 1.2). - John H. Gennari; Matthias König 003; Goksel Misirli; Maxwell Lewis Neal; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2021)

Modelling the fitness landscapes of a SCRaMbLEd yeast genome. - Bill Yang; Goksel Misirli; Anil Wipat; Jennifer Hallinan (Biosyst., 2022)

Synthetic biology open language (SBOL) version 3.1.0. - Lukas Buecherl; Thomas Mitchell; James Scott-Brown; Prashant Vaidyanathan; Gonzalo Vidal; Hasan Baig; Bryan Bartley; Jacob Beal; Matthew Crowther; Pedro Fontanarrosa; Thomas E. Gorochowski; Raik Grünberg; et al. (J. Integr. Bioinform., 2023)

libSBOLj3: a graph-based library for design and data exchange in synthetic biology. - Göksel Misirli (Bioinform., 2023)