Publications of LifeForm – Website of project LifeForm

Papers from the Newcastle group
- Goksel Misirli, Jennifer Hallinan, and Anil Wipat. 2014. Composable Modular Models for Synthetic Biology. J. Emerg. Technol. Comput. Syst. 11, 3, Article 22 (December 2014), 19 pages. DOI
- Curtis Madsen^†^‡, James Alastair McLaughlin^†, Göksel Mısırlı^†, Matthew Pocock^†^§, Keith Flanagan^†, Jennifer Hallinan^†, and Anil Wipat^*^†The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.
  
  ACS Synth. Biol., 2016, 5 (6), pp 487–497.DOI
- Bartley, Bryan ; Beal, Jacob ; Clancy, Kevin ; Misirli, Goksel ; Roehner, Nicholas ; Oberortner, Ernst ; Pocock, Matthew ; Bissell, Michael ; Madsen, Curtis ; Nguyen, Tramy ; Zhang, Zhen ; Gennari, John H. ; Myers, Chris J. ; Wipat, Anil ; Sauro, Herbert . Synthetic Biology Open Language (SBOL) Version 2.0.0.
  Journal of Integrative Bioinformatics – JIB (ISSN 1613-4516).DOI
- Göksel Mısırlı^†, Jennifer Hallinan^†∥, Matthew Pocock^†^‡, Phillip Lord^†, James Alastair McLaughlin^†, Herbert Sauro^§, and Anil Wipat^*^†. Data Integration and Mining for Synthetic Biology Design. ACS Synth. Biol., 2016, 5 (10), pp. 1086–1097. DOI
- Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, McLaughlin JA, Misirli G, Nguyen T, Oberortner E, Samineni M, Wipat A, Zhang M, Zundel Z. A standard-enabled workflow for synthetic biology. Biochemical Society Transactions 2017, 45(3), 793-803.
French side
- H. Mandon, S. Haar and L. Paulevé. Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph. In HSB’16, LNBI. Springer, 2016. To appear. ( PDF | BibTeX + Abstract )
- J. Kolcák, D. Šafránek, S. Haar and L. Paulevé. Unfolding of Parametric Logical Regulatory Networks. In SASB’16, ENTCS. Elsevier Science Publishers, 2016. To appear. ( HAL | PDF | BibTeX + Abstract )
- Loïc Paulevé. Goal-Oriented Reduction of Automata Networks. In CMSB 2016 – 14th conference on Computational Methods for Systems Biology, volume 9859 of Lecture Notes in Bioinformatics. Springer, 2016. [ DOI:10.1007/978-3-319-45177-0_16 | PDF | URL | Bibtex ]
- H. Mandon, S. Haar and L. Paulevé. Temporal Reprogramming of Boolean Networks. In CMSB’17, LNBI 10545, pages 179-195. Springer-Verlag, 2017. ( PDF | BibTeX + Abstract )
- Th. Chatain and L. Paulevé. Goal-Driven Unfolding of Petri Nets. In CONCUR’17, Leibniz International Proceedings in Informatics 85, pages 18:1-18:16. Leibniz-Zentrum für Informatik, 2017. ( Web page | PDF | BibTeX + Abstract )
Miscellaneous
- Internship reports:
  - J. Kolcák: Efficient Analysis of Boolean Networks under Parameter Uncertainty
  - Clara Scherbaum: Computing Cut Sets for Petri Nets
  - Hugues Mandon: Algorithms for cellular reprogramming