Research on Language and Biology
The theory: Formal language and Genetic
This is related to the work I have done at Peccoud’s synthetic biology lab from 2008 to 2013:
- Formal languages and DNA molecules
- Design of Languages for Systems and Synthetic Biology
- Biological Languages to Design Natural Genomes
- [Slides] Formal languages to map Genotype to Phenotype in Natural Genomes.
Application: BioCAD tools
This is related to the work I have done at Peccoud’s synthetic biology lab from 2008 to 2013:
- My work on GenoCAD v2: design to simulation based on domain specific genetic langauges (GenoCAD.org)
Overview:
My phd defense, GBCB program at VT from 2009-2013:
My Related Publications:
Peer-‐Reviewed Journal Articles
Michal Galdzicki, Mandy L Wilson, Cesar A Rodriguez, Ernst Oberortner, Matthew Pocock, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J Hillson, Haiyao Huang, Jeffrey D Johnson, Allan Kuchinsky, Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Herbert M Sauro. (2014). SBOL: A community standard for communicating designs in synthetic biology. Nature Biotechnology, vol. 32, no. 6, pp. 545–550.
M. L. Wilson, S. Okumoto, L. Adam, and J. Peccoud (2013). Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. Bioinformatics, pp. 1–7.
Cai, Y., Lux, M. W., Adam, L., & Peccoud, J. (2009). Modeling structure-‐function relationships in synthetic DNA sequences using attribute grammars. PLoS computational biology, 5(10).
Book Chapter/Others
Mandy L. Wilson, Russell Hertzberg, Laura Adam, and Jean Peccoud (2011). A Step-‐by-‐Step Introduction to Rule-‐Based Design of Synthetic Genetic Constructs Using GenoCAD. Methods in Enzymology/ Volume 498 -‐ Synthetic Biology, Part B-‐ Chapter 8
Wipat, Anil; Villalobos, Alan; Stan, Guy-‐Bart; Smith, Trevor; Sauro, Herbert; Roehner, Nicholas; Pocock, Matthew; Plahar, Hector; Peccoud, Jean; Myers, Chris; Misirli, Goksel; Madsen, Curtis; Lux, Matthew; Kuchinsky, Allan; Ham, Timothy; Grünberg, Raik; Gennari, John; Endy, Drew; Drory, Omri; Densmore, Douglas; Chandran, Deepak; Beal, Jacob; Anderson, J. Christopher; Adler, Aaron; Adam, Laura; Rodriguez, Cesar; Wilson, Mandy; Galdzicki, Michal (2011). Synthetic Biology Open Language (SBOL)Version1.0.0. BBFRFC#84(http://hdl.handle.net/1721.1/66172)