Peer Reviewed

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert M. Sauro, and John H. Gennari (2011) Standard Biological Parts Knowledgebase. PLoS ONE. 6(2): e17005. doi:10.1371/journal.pone.0017005

Jean Peccoud, J Christopher Anderson, Deepak Chandran, Douglas Densmore, Michal Galdzicki, Matthew W Lux, Cesar A Rodriguez, Guy-Bart Stan, and Herbert M Sauro (2011) Essential information for synthetic DNA sequences. Nature Biotechnology. 29, 22. doi:10.1038/nbt.1753

BioBrick Foundation Request for Comments Documents

Michal Galdzicki, Mandy L. Wilson, Cesar A. Rodriguez, Laura Adam, Aaron Adler, J. Christopher Anderson, Jacob Beal, Deepak Chandran, Douglas Densmore, Omri A. Drory, Drew Endy, John H. Gennari, Raik Grünberg, Timothy S. Ham, Allan Kuchinsky, Matthew W. Lux, Curtis Madsen, Goksel Misirli, Chris J. Myers, Jean Peccoud, Hector Plahar, Matthew R. Pocock, Nicholas Roehner, Trevor F. Smith, Guy-Bart Stan, Alan Villalobos, Anil Wipat, and Herbert M. Sauro (2011) Synthetic Biology Open Language (SBOL) Version 1.0.0. BBF RFC #84 doi: 1721.1/66172


Jeff Johnson, Michal Galdzicki, Herbert Sauro (2010) Standard for the Electronic Distribution of SBOLv Diagrams. BBF RFC #68. doi: 1721.1/60086

Jannetta S. Steyn, Anil Wipat, Jennifer Hallinan, Matthew Pocock, Rachel May Boyd, Harsh Sheth, Alan Koh, Phil Hall, Deena Tsu, Steven Woodhouse and Younus Essa (2010) A RESTful API for Supporting Automated BioBrick Model Assembly. BBF RFC #66. doi: 1721.1/60085

Cesar Rodriguez, Suzie Bartram, Anusuya Ramasubramanian, and Drew Endy Synthetic Biology Open Language Visual (SBOLv) Specification. BBF RFC #16. doi: 1721.1/49523 2009

Michal Galdzicki, Deepak Chandran, Alec Nielsen, Jason Morrison, Mackenzie Cowell, Raik Grunberg, Sean Sleight, Herbert Sauro (2009) Provisional BioBrick Language (PoBoL). BBF RFC #31. doi: 1721.1/45537

Raik Grünberg (2009) Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data. BBF RFC #30 doi: 1721.1/45143 2009

Conference Abstracts

Michal Galdzicki, Laura Adam, J. Christopher Anderson, Deepak Chandran, Douglas Densmore, Drew Endy, John H Gennari, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay Maheshwari, Barry Moore, Chris J. Myers, Jean Peccoud, Cesar A. Rodriguez, Nicholas Roehner, Guy-Bart Stan, Mandy Wilson, Herbert M. Sauro. (2011) Synthetic Biology Open Language: A standardized information exchange framework for synthetic biologists. The 5th International Meeting on Synthetic Biology, Stanford University, Stanford, CA, June 15-17, 2011.

Michal Galdzicki, Cesar Rodriguez, Herbert Sauro, Laura Adam, J. Christopher Anderson, Deepak Chandran, Douglas Densmore, Drew Endy, John H. Gennari, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay Maheshwari, Barry Moore, Chris J. Myers, Jean Peccoud, Nicholas Roehner, Guy-Bart Stan, Mandy Wilson, Herbert M. Sauro. (2011) Evolution of SBOL: design information exchange standard. International Workshop on Bio-Design and Automation 2011, San Diego Convention Center, San Diego, CA, June 6-7, 2011.

“Design, Implementation, and Deployment of Electronic Datasheets”
Cesar Rodriguez, Michal Galdzicki
International Workshop on Bio-Design Automation
San Diego, CA, June 6-7, 2011

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, John Gennari and Herbert Sauro. (2010) A Semantic Knowledge Base of Standard Biological Parts. International Workshop on Bio-Design and Automation 2010, Anaheim, CA

Michal Galdzicki, Deepak Chandran, Herbert Sauro, Daniel Cook, and John Gennari. (2009) Bridging Synthetic Biology Models and Experiments using PoBoL. 
International Workshop on Bio-Design and Automation 2009, San Francisco, CA

Deepak Chandran, Michal Galdzicki, and Alec Nielsen. (2009) Bridging Synthetic Biology Design and Experiments using PoBoL. International Workshop on Bio-Design and Automation 2009, San Francisco, CA

Publications Citing SBOL

Karsten Temme, Dehua Zhaob, Christopher A. Voigt. (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proceedings of the National Academy of Science, Online Publication April 16, 2012. doi:10.1073/pnas.1120788109 

Joanna Chen, Douglas Densmore, Timothy S Ham, Jay D Keasling, and Nathan J Hillson. (2012) DeviceEditor visual biological CAD canvas. Journal of Biological Engineering, 6:1.  doi:10.1186/1754-1611-6-1

Matthew W Lux, Brian W Bramlett, David A Ball, Jean Peccoud. (2012) Genetic design automation: engineering fantasy or scientific renewal? Trends in Biotechnology, 30(2), 120-126. doi:10.1016/j.tibtech.2011.09.001

Madsen C, Myers C J, Patterson T, Roehner N, Stevens J T, Winstead C. (2012) Design and Test of Genetic Circuits using iBioSim. Design & Test of Computers, PP(99), 1 - 1. doi:10.1109/MDT.2012.2187875 

Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J. Christopher Anderson, Douglas Densmore. (2011) Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems. PLoS ONE 6(4): e18882. doi:10.1371/journal.pone.0018882

Yuting Zheng and Ganesh Sriram, “Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology,” Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 541609, 16 pages, 2010. doi:10.1155/2010/541609

Deepak Chandran, Frank T Bergmann, Herbert M Sauro. TinkerCell: modular CAD tool for synthetic biology. Journal of Biological Engineering 2009, 3:19 doi:10.1186/1754-1611-3-19