• [DOI] C. Myers, K. Clancy, G. Misirli, E. Oberortner, M. Pocock, J. Quinn, N. Roehner, and H. Sauro, “The synthetic biology open language,” in Computational methods in synthetic biology, M. A. Marchisio, Ed., Springer New York, 2015, vol. 1244, pp. 323-336.
    [Bibtex]
    @incollection{Myers2015,
    year={2015},
    isbn={978-1-4939-1877-5},
    booktitle={Computational Methods in Synthetic Biology},
    volume={1244},
    series={Methods in Molecular Biology},
    editor={Marchisio, Mario Andrea},
    doi={10.1007/978-1-4939-1878-2_16},
    title={The Synthetic Biology Open Language},
    url={http://dx.doi.org/10.1007/978-1-4939-1878-2_16},
    publisher={Springer New York},
    keywords={Synthetic biology; Standards; Engineering design},
    author={Myers, Chris and Clancy, Kevin and Misirli, Goksel and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline and Roehner, Nicholas and Sauro, HerbertM.},
    pages={323-336},
    language={English}
    }
  • [DOI] G. Misirli, J. Hallinan, and A. Wipat, “Composable modular models for synthetic biology,” Acm journal on emerging technologies in computing systems, vol. 11, iss. 3, pp. 1-19, 2014.
    [Bibtex]
    @ARTICLE{Misirli2014a,
    title = {Composable Modular Models for Synthetic Biology},
    author = {Misirli, Goksel and Hallinan, Jennifer and Wipat, Anil},
    year = 2014,
    doi = {10.1145/2631921},
    month = dec,
    journal = {ACM Journal on Emerging Technologies in Computing Systems},
    volume = {11},
    number = {3},
    pages = {1--19}
    }
  • [DOI] G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, and A. Wipat, “Bacillusregnet: a transcriptional regulation database and analysis platform for bacillus species,” Journal of integrative bioinformatics, vol. 11, iss. 2, p. 244, 2014.
    [Bibtex]
    @ARTICLE{Misirli2014,
    title = {BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species},
    author = {Misirli, G. and Hallinan, J. and Röttger, R. and Baumbach, J. and Wipat, A.},
    year = 2014,
    doi = {10.2390/biecoll-jib-2014-244},
    journal = {Journal of Integrative Bioinformatics},
    volume = {11},
    number = {2},
    pages = {244}
    }
  • [DOI] N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, and C. J. Myers, “Proposed data model for the next version of the synthetic biology open language,” Acs synthetic biology, 2014.
    [Bibtex]
    @article{doi:10.1021/sb500176h,
    author = {Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Beal, Jacob and Clancy, Kevin and Madsen, Curtis and Misirli, Goksel and Wipat, Anil and Sauro, Herbert and Myers, Chris J.},
    title = {Proposed Data Model for the Next Version of the Synthetic Biology Open Language},
    journal = {ACS Synthetic Biology},
    year = {2014},
    doi = {10.1021/sb500176h},
    note ={PMID: 24896221},
    URL = { http://dx.doi.org/10.1021/sb500176h}
    }
  • [DOI] J. S. Hallinan, O. Gilfellon, G. Misirli, and A. Wipat, “Tuning receiver characteristics in bacterial quorum communication: an evolutionary approach using standard virtual biological parts,” in 2014 ieee conference on computational intelligence in bioinformatics and computational biology, Honolulu, HI, USA, 2014, pp. 1-8.
    [Bibtex]
    @INPROCEEDINGS{Hallinan2014,
    title = {Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts},
    author = {Hallinan, J. S. and Gilfellon, O. and Misirli, G. and Wipat, A.},
    year = 2014,
    doi = {10.1109/CIBCB.2014.6845520},
    month = may,
    booktitle = {2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology},
    pages = {1--8},
    address = {Honolulu, HI, USA}
    }
  • [DOI] M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, C. J. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grünberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro, “The synthetic biology open language (sbol) provides a community standard for communicating designs in synthetic biology,” Nature biotechnology, vol. 32, iss. 6, pp. 545-550, 2014.
    [Bibtex]
    @ARTICLE{Galdzicki2014,
    title = {The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology},
    author = {Galdzicki, Michal and Clancy, Kevin P and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y and Rodriguez, Cesar A and Roehner, Nicholas and Wilson, Mandy L and Adam, Laura and Anderson, J Christopher and Bartley, Bryan A and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Grünberg, Raik and Hallinan, Jennifer and Hillson, Nathan J and Johnson, Jeffrey D and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A and Sirin, Evren and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Gennari, John H and Myers, Chris J and Sauro, Herbert M},
    year = 2014,
    doi = {10.1038/nbt.2891},
    month = jun,
    journal = {Nature Biotechnology},
    volume = {32},
    number = {6},
    pages = {545--550}
    }
  • [DOI] S. Pohl, G. Bhavsar, J. Hulme, A. E. Bloor, G. Misirli, M. W. Leckenby, D. S. Radford, W. Smith, A. Wipat, D. E. Williamson, C. R. Harwood, and R. M. Cranenburgh, “Proteomic analysis of bacillus subtilis strains engineered for improved production of heterologous proteins,” Proteomics, vol. 13, iss. 22, pp. 3298-3308, 2013.
    [Bibtex]
    @ARTICLE{Pohl2013,
    title = {Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins},
    author = {Pohl, Susanne and Bhavsar, Gaurav and Hulme, Joanne and Bloor, Alexandra E. and Misirli, Goksel and Leckenby, Matthew W. and Radford, David S. and Smith, Wendy and Wipat, Anil and Williamson, E. Diane and Harwood, Colin R. and Cranenburgh, Rocky M.},
    year = 2013,
    doi = {10.1002/pmic.201300183},
    month = nov,
    journal = {PROTEOMICS},
    volume = {13},
    number = {22},
    pages = {3298--3308}
    }
  • M. Galdzicki, E. Oberortner, M. Pocock, J. Quinn, M. L. Wilson, E. Appleton, B. Bartley, J. Beal, S. Bhatia, R. Cox, R. Grunberg, G. Misirli, H. Plahar, N. Roehner, L. Soldotova, G. Stan, D. Densmore, C. Myers, H. Sauro, and A. Wipat, “Recent advances in the synthetic biology open language,” , 2013.
    [Bibtex]
    @article{8,
    author = {Galdzicki, Michal and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline and Wilson, Mandy L. and Appleton, Evan and Bartley, Bryan and Beal, Jacob and Bhatia, Swapnil and Cox, Robert and Grunberg, Raik and Misirli, Goksel and Plahar, Hector and Roehner, Nicholas and Soldotova, Larisa and Stan, Guy-Bart and Densmore, Doug and Myers, Chris and Sauro, Herbert and Wipat, Anil },
    title = { Recent Advances in the Synthetic Biology Open Language},
    month = {July 12-13},
    year = {2013}
    }
  • [DOI] C. R. Harwood, S. Pohl, W. Smith, and A. Wipat, “Chapter 4 – bacillus subtilis: model gram-positive synthetic biology chassis,” in Microbial synthetic biology, C. Harwood and A. Wipat, Eds., Academic Press, 2013, vol. 40, pp. 87-117.
    [Bibtex]
    @incollection{Harwood201387,
    title = "Chapter 4 - Bacillus subtilis: Model Gram-Positive Synthetic Biology Chassis ",
    editor = "Colin Harwood and Anil Wipat",
    booktitle = "Microbial Synthetic Biology",
    publisher = "Academic Press",
    year = "2013",
    volume = "40",
    pages = "87 - 117",
    series = "Methods in Microbiology ",
    issn = "0580-9517",
    doi = "http://dx.doi.org/10.1016/B978-0-12-417029-2.00004-2",
    url = "http://www.sciencedirect.com/science/article/pii/B9780124170292000042",
    author = "Colin R. Harwood and Susanne Pohl and Wendy Smith and Anil Wipat",
    keywords = "Bacillus subtilis",
    keywords = "Reporter genes",
    keywords = "Genome engineering",
    keywords = "Transcription profiling",
    keywords = "Markerless deletions",
    keywords = "Sigma factors",
    keywords = "Computational resources "
    }
  • [DOI] G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, and J. Hallinan, “Bacillondex: an integrated data resource for systems and synthetic biology,” Journal of integrative bioinformatics, vol. 10, iss. 2, p. 224, 2013.
    [Bibtex]
    @ARTICLE{Misirli2013,
    title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
    author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J.},
    year = 2013,
    doi = {10.2390/biecoll-jib-2013-224},
    journal = {Journal of Integrative Bioinformatics},
    volume = {10},
    number = {2},
    pages = {224}
    }
  • [DOI] J. S. Hallinan, “Chapter 1 – computational intelligence in the design of synthetic microbial genetic systems,” in Microbial synthetic biology, C. Harwood and A. Wipat, Eds., Academic Press, 2013, vol. 40, pp. 1-37.
    [Bibtex]
    @incollection{Hallinan20131,
    title = "Chapter 1 - Computational Intelligence in the Design of Synthetic Microbial Genetic Systems ",
    editor = "Colin Harwood and Anil Wipat",
    booktitle = "Microbial Synthetic Biology",
    publisher = "Academic Press",
    year = "2013",
    volume = "40",
    pages = "1 - 37",
    series = "Methods in Microbiology ",
    issn = "0580-9517",
    doi = "http://dx.doi.org/10.1016/B978-0-12-417029-2.00001-7",
    url = "http://www.sciencedirect.com/science/article/pii/B9780124170292000017",
    author = "Jennifer S. Hallinan",
    keywords = "Evolutionary algorithms",
    keywords = "Neural networks",
    keywords = "Machine learning",
    keywords = "Synthetic genetic circuits",
    keywords = "Circuit design "
    }