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Number of items: 33.

Article

Buecherl, L, Mitchell, T, Scott-Brown, J, Vaidyanathan, P, Vidal, G, Baig, H, Bartley, B, Beal, J, Crowther, M, Fontanarrosa, P, Gorochowski, T, Grünberg, R, Kulkarni, V, McLaughlin, J, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Oberortner, E, Wipat, A and Myers, C (2023) Synthetic biology open language (SBOL) version 3.1.0. Journal of integrative bioinformatics, 20 (1).

Yang, B, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Wipat, A and Hallinan, J (2022) Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosystems, 219 (104730).

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Yang, B, James, K and Wipat, A (2021) Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology, 10 (12). pp. 3304-3315.

Baig, H, Fontanarossa, P, Kulkarni, V, McLaughlin, J, Vaidyanathan, P, Bartley, B, Bhakta, S, Bhatia, S, Bissell, M, Clancy, K, Cox, RS, Goñi Moreno, A, Gorochowski, T, Grunberg, R, Lee, J, Luna, A, Madsen, C, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Nguyen, T, Le Novere, N, Palchick, Z, Pocock, M, Roehner, N, Sauro, H, Scott-Brown, J, Sexton, JT, Stan, G-B, Tabor, JJ, Terry, L, Vazquez Vilar, M, Voigt, CA, Wipat, A, Zong, D, Zundel, Z, Beal, J and Myers, C (2021) Synthetic biology open language visual (SBOL Visual) version 2.3. J Integr Bioinform.

McLaughlin, JA, Beal, J, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Grünberg, R, Bartley, BA, Scott-Brown, J, Vaidyanathan, P, Fontanarrosa, P, Oberortner, E, Wipat, A, Gorochowski, TE and Myers, CJ (2020) The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Frontiers in Bioengineering and Biotechnology, 8.

Baig, H, Fontanarrosa, P, Kulkarni, V, McLaughlin, JA, Vaidyanathan, P, Bartley, B, Beal, J, Crowther, M, Gorochowski, TE, Grünberg, R, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Scott-Brown, J, Oberortner, E, Wipat, A and Myers, CJ (2020) Synthetic biology open language (SBOL) version 3.0.0. Journal of integrative bioinformatics, 17 (2-3).

Baig, H, Fontanarrosa, P, Kulkarni, V, McLaughlin, J, Vaidyanathan, P, Bartley, B, Bhatia, S, Bhakta, S, Bissell, M, Clancy, K, Cox, RS, Moreno, AG, Gorochowski, T, Grunberg, R, Luna, A, Madsen, C, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Nguyen, T, Le Novere, N, Palchick, Z, Pocock, M, Roehner, N, Sauro, H, Scott-Brown, J, Sexton, JT, Stan, G-B, Tabor, JJ, Vilar, MV, Voigt, CA, Wipat, A, Zong, D, Zundel, Z, Beal, J and Myers, C (2020) Synthetic biology open language visual (SBOL visual) version 2.2. Journal of integrative bioinformatics, 17 (2-3).

Crowther, M, Grozinger, L, Pocock, M, Taylor, CPD, McLaughlin, JA, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Bartley, B, Beal, J, Goni-Moreno, A and Wipat, A (2020) ShortBOL: A language for scripting designs for engineered biological systems using SyntheticBiology Open Language (SBOL). ACS Synthetic Biology, 9 (4). pp. 962-966.

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Beal, J, Gorochowski, TE, Stan, G-B, Wipat, A and Myers, CJ (2020) SBOL Visual 2 Ontology. ACS Synthetic Biology, 9 (4). pp. 972-977.

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Taylor, R, Goni-Moreno, A, McLaughlin, J, Myers, C, Gennari, J, Lord, P and Wipat, A (2019) SBOL-OWL: An ontological approach for formal and semantic representation of synthetic biology information. ACS Synthetic Biology, 8 (7). pp. 1498-1514.

Madsen, C, Goñi Moreno, A, P, U, Palchick, Z, Roehner, N, Atallah, C, Bartley, B, Choi, K, Cox, RS, Gorochowski, T, Grünberg, R, Macklin, C, McLaughlin, J, Meng, X, Nguyen, T, Pocock, M, Samineni, M, Scott-Brown, J, Tarter, Y, Zhang, M, Zhang, Z, Zundel, Z, Beal, J, Bissell, M, Clancy, K, Gennari, JH, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Myers, C, Oberortner, E, Sauro, H and Wipat, A (2019) Synthetic Biology Open Language (SBOL) Version 2.3. Journal of Integrative Bioinformatics, 16 (2).

Neal, ML, König, M, Nickerson, DP, Misirli, G, Kalbasi, R, Dräger, A, Atalag, K, Chelliah, V, Cooling, MT, Cook, DL, Crook, SM, Alba, MD, Friedman, SH, Garny, A, Gennari, JH, Gleeson, P, Golebiewski, M, Hucka, M, Juty, NS, Myers, CJ, Olivier, BG, Sauro, HM, Scharm, M, Snoep, JL, Touré, V, Wipat, A, Wolkenhauer, O and Waltemath, D (2019) Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics, 20 (2). 540 -550.

Neal, ML, König, M, Nickerson, D, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Kalbasi, R, Dräger, A, Atalag, K, Chelliah, V, Cooling, MT, Cook, DL, Crook, S, de Alba, M, Friedman, SH, Garny, A, Gennari, JH, Gleeson, P, Golebiewski, M, Hucka, M, Juty, N, Myers, C, Olivier, BG, Sauro, HM, Scharm, M, Snoep, JL, Touré, V, Wipat, A, Wolkenhauer, O and Waltemath, D (2018) Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. bby087 - bby087.

Misirli, G, Nguyen, T, McLaughlin, JA, Vaidyanathan, P, Jones, T, Densmore, D, Myers, CJ and Wipat, A (2018) A computational workflow for the automated generation of models of genetic designs. ACS Synthetic Biology, 8 (7). pp. 1548-1559.

Cox, RS, Madsen, C, McLaughlin, JA, Nguyen, T, Roehner, N, Bartley, B, Beal, J, Bissell, M, Choi, K, Clancy, K, Grünberg, R, Macklin, C, Misirli, G, Oberortner, E, Pocock, M, Samineni, M, Zhang, M, Zhang, Z, Zundel, Z, Gennari, JH, Myers, C, Sauro, H and Wipat, A (2018) Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of integrative bioinformatics, 15 (1).

McLaughlin, JA, Myers, CJ, Zundel, Z, Misirli, G, Zhang, M, Ofiteru, ID, Goñi Moreno, A and Wipat, A (2018) SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synthetic Biology, 7 (2). pp. 682-688.

Myers, CJ, Beal, J, Gorochowski, TE, Kuwahara, H, Madsen, C, McLaughlin, JA, Mısırlı, G, Nguyen, T, Oberortner, E, Samineni, M, Wipat, A, Zhang, M and Zundel, Z (2017) A standard-enabled workflow for synthetic biology. Biochemical Society Transactions, 45 (3). 793 - 803.

Misirli, G, Madsen, C, Murieta, ISD, Bultelle, M, Flanagan, K, Pocock, M, Hallinan, J, Mclaughlin, JA, Clark-Casey, J, Lyne, M, Micklem, G, STAN, G-B, Kitney, R and Wipat, A (2017) Constructing Synthetic Biology Workflows in the Cloud. Engineering Biology, 1 (1). pp. 61-65.

Beal, J, Cox, RS, Grünberg, R, McLaughlin, J, Nguyen, T, Bartley, B, Bissell, M, Choi, K, Clancy, K, Macklin, C, Madsen, C, Misirli, G, Oberortner, E, Pocock, M, Roehner, N, Samineni, M, Zhang, M, Zhang, Z, Zundel, Z, Gennari, J, Myers, C, Sauro, H and Wipat, A (2016) Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of integrative bioinformatics, 13 (3). 291 - ?.

Madsen, C, McLaughlin, JA, Mısırlı, G, Pocock, M, Flanagan, K, Hallinan, J and Wipat, A (2016) The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. ACS Synthetic Biology, 5 (6). 487 - 497.

Mısırlı, G, Hallinan, J, Pocock, M, Lord, P, McLaughlin, JA, Sauro, H and Wipat, A (2016) Data Integration and Mining for Synthetic Biology Design. ACS Synthetic Biology, 5 (10). 1086 - 1097.

Zhang, Z, Nguyen, T, Roehner, N, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Pocock, M, Oberortner, E, Samineni, M, Zundel, Z, Beal, J, Clancy, K, Wipat, A and Myers, CJ (2016) libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 1 (4). 34 - 37.

Misirli, G, Cavaliere, M, Waites, W, Pocock, M, Madsen, C, Gilfellon, O, Honorato-Zimmer, R, Zuliani, P, Danos, V and Wipat, A (2015) Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics, 32 (6). 908 - 917.

Bartley, B, Beal, J, Clancy, K, Misirli, G, Roehner, N, Oberortner, E, Pocock, M, Bissell, M, Madsen, C, Nguyen, T, Zhang, Z, Gennari, JH, Myers, C, Wipat, A and Sauro, H (2015) Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of integrative bioinformatics, 12 (2). 272 - ?.

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Hallinan, J and Wipat, A (2014) Composable Modular Models for Synthetic Biology. Journal on Emerging Technologies in Computing Systems, 11 (3). 22:1 - 22:1.

Misirli, G, Hallinan, J, Röttger, R, Baumbach, J and Wipat, A (2014) BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of integrative bioinformatics, 11 (2). 244 - ?.

Misirli, G, Hallinan, JS, Yu, T, Lawson, JR, Wimalaratne, SM, Cooling, MT and Wipat, A (2011) Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics, 27 (7). 973 - 979.

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Yang, B, James, K and Wipat, A Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits. bioRxiv. (Unpublished)

Conference or Workshop Item

Yang, B, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Wipat, A and Hallinan, J (2021) Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome. In: 2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 13/10/21-15/10/21.

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Yang, B and Wipat, A (2019) Model-driven design of genetic regulatory networks using virtual parts. In: 11th International Workshop on Bio-Design Automation (IWBDA 2019), 8-10 Jul 2019, Cambridge.

Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188, Beal, J, Gorochowski, T, Stan, G-B, Wipat, A and Myers, C (2019) SBOL Visual 2 Ontology. In: 11th International Workshop on Bio-Design Automation (IWBDA 2019), 8-10 Jul 2019, Cambridge.

Aksoy, D, Yilmaz, B, Kuran, S, Wipat, A, Pusane, AE, Misirli, G ORCID: https://orcid.org/0000-0002-2454-7188 and Tugcu, T (2019) Receiver Design Using Genetic Circuits in Molecular Communication. In: 4th workshop on Molecular Communications, 16-18 Apr 2019, Linz, Austria.

Misirli, G, Nguyen, T, McLaughlin, J, Myers, C and Wipat, A (2017) Standard Enabled Model Generator for Genetic Circuit Design. In: 9th International Workshop on Bio-Design Automation, 8th - 11th August 2017, Pittsburgh.

This list was generated on Wed Nov 1 01:51:36 2023 UTC.