Author: 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

Several LifeForm-related  internships took place this spring and summer; let us start with the French side:

• Clara Scherbaum worked at LSV on Computing Cut Sets for Petri Nets; she developped unfolding-based techniques for determining sets of conditions to block from being satisfied so that some given place in the Net remains unmarked; such cut sets allow to ensure health properties in biological networks.
• Juraj Kolčák studied Efficient Analysis of Boolean Networks under Parameter Uncertainty  in his master’s thesis accepted at Masaryk University, Brno, Czech Republic; the research was carried out at LSV under the joint supervision of Stefan Haar and Loïc Paulevé, together with master’s advisor David Safranek at Brno.
• Hugues Mandon successfully completed his master’s thesis on Algorithms for cellular reprogramming  with Loïc Paulevé and Stefan Haar at LRI; he is now continuing as a PhD student at LSV under Stefan Haar and Loïc Paulevé.
• Céline CHEVALIER worked with Loïc Paulevé at LRI on a logical model for transcription regulation in Bacillus subtilis ; the results of her internship are presented here .

In Newcastle,

• Delia Casas Pastor did her MSc internship at Newcastle University under the supervision of  Anil Wipat, Goksel Misirli and Wendy Smith and in cooperation with Victor Khomenko, on Deriving stress-specific biomarkers for Bacillus subtilis from the integration of RNA-seq and tiling data.