| Education | ||
| Degree | Ph.D. in Bioengineering (2014) | |
| Institution | University of Utah | Salt Lake City, UT |
| Degree | B.S. in Bioengineering (2010) | |
| Institution | University of Washington | Seattle, WA |
| Professional Appointments | ||
| Institution | Boston University/Broad Institute | Boston, MA/Cambridge, MA |
| Department | Electrical and Computer Engineering | |
| Title | Postdoctoral Researcher | |
| Period | 2014 – Present | |
| Publications | ||
| Journal Articles | ||
| 2016 | Nicholas Roehner et al., “Sharing structure and function in biological design with SBOL 2.0,” in ACS Synthetic Biology, vol. 5, pp. 498-506, 2016. | |
| Nicholas Roehner, Eric M. Young, Christopher A. Voigt, D. Benjamin Gordon, and Douglas Densmore, “Double Dutch: a tool for designing combinatorial libraries of biological systems,” in ACS Synthetic Biology, vol. 5, pp. 507-517, 2016. | ||
| Zhen Zhang et al., “libSBOLj 2.0: a Java library to support SBOL 2.0,” in IEEE Life Sciences Letters, vol. 1, pp. 34-37, 2016. | ||
| Tramy Nguyen, Nicholas Roehner, Zach Zundel, and Chris J. Myers, “A converter from the Systems Biology Markup Language to the Synthetic Biology Open Language,” in ACS Synthetic Biology, vol. 5, pp. 479-486, 2016. | ||
| 2015 | Nicholas Roehner, Zhen Zhang, Tramy Nguyen, and Chris J. Myers, “Generating Systems Biology Markup Language models from the Synthetic Biology Open Language,” in ACS Synthetic Biology, vol. 4, pp. 873-879, 2015. | |
| Prashant Vaidyanathan et al., “A framework for genetic logic synthesis,” in Proceedings of the IEEE, vol. 103, pp. 2196-2207, 2015. | ||
| Bryan Bartley et al., “Synthetic Biology Open Language (SBOL) 2.0.0,” in Journal of Integrative Bioinformatics, vol. 12, pp. 272, 2015. | ||
| Nicholas Roehner et al., “Proposed data model for the next version of the Synthetic Biology Open Language,” in ACS Synthetic Biology, vol. 4, pp. 57-71, 2015. | ||
| 2014 | Nicholas Roehner and Chris J. Myers, “Directed acyclic graph-based technology mapping of genetic circuit models,” in ACS Synthetic Biology, vol. 3, pp. 543-555, 2014. | |
| Nicholas Roehner and Chris. J Myers, “A methodology to annotate Systems Biology Markup Language models with the Synthetic Biology Open Language,” in ACS Synthetic Biology, vol. 3, pp. 57-66, 2014. | ||
| Michal Galdzicki et al., “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology,” in Nature Biotechnology, vol. 32, pp. 545-550, 2014. | ||
| Curtis Madsen, Zhen Zhang, Nicholas Roehner, Chris Winstead, and Chris Myers, “Stochastic model checking of genetic circuits,” in ACM Journal of Emerging Technologies in Computing Systems, vol. 11, pp. 23:1-23:21, 2014. | ||
| 2012 | Curtis Madsen, Chris J. Myers, Tyler Patterson, Nicholas Roehner, Jason T. Stevens, and Chris Winstead, “Design and test of genetic circuits using iBioSim,” in Design and Test of Computers, vol. 29, pp. 32-39, 2012. | |
| Book Chapters | ||
| 2015 | Chris Myers et al., “The Synthetic Biology Open Language,” in Computational Methods in Synthetic Biology (Methods in Molecular Biology Series 1244), Mario Marchisio, Ed., New York City, Springer New York, 2015, ch. 11, pp. 323-336. | |
| Curtis Madsen, Chris Myers, Nicholas Roehner, Chris Winstead, and Zhen Zhang, “Efficient analysis methods in synthetic biology,” in Computational Methods in Synthetic Biology (Methods in Molecular Biology Series 1244), Mario Marchisio, Ed., New York City, Springer New York, 2015, ch. 11, pp. 217-257. | ||
| Conference Papers | ||
| 2012 | Curtis Madsen, Chris J. Myers, Nicholas Roehner, Chris Winstead, and Zhen Zhang, “Utilizing stochastic model checking to analyze genetic circuits,” in 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), San Diego, CA, 9-12 May 2012, pp. 379-386. | |
| Technical Reports | ||
| 2015 | Bryan Bartley et al., “Synthetic Biology Open Language (SBOL) version 2.0.0,” BioBricks Foundation, BBF RFC 108, 2015, DOI: 1721.1/98369. | |
| 2012 | Michal Galdzicki et al., “Synthetic Biology Open Language (SBOL) version 1.1.0,” BioBricks Foundation, BBF RFC 87, 2012, DOI: 1721.1/73909. | |
| Awards | ||
| 2016 | 2nd Annual Allan Kuchinsky IWBDA Scholarship | |
| Conference Activity | ||
| Service | ||
| 2016 | Genetic logic session chair, 8th International Workshop on Bio-Design Automation (IWBDA), Newcastle Upon Type, UK, 16-18 Aug. 2016. | |
| Program committee member, 8th IWBDA, Newcastle Upon Type, UK, 16-18 Aug. 2016. | ||
| 2015 | Synthetic biology session chair, Computational Modeling in Biology Network (COMBINE) 2015, Salt Lake City, UT, 12-16 Oct. 2015. | |
| Program committee member, 7th IWBDA, Seattle, WA, 19-21 Aug. 2015. | ||
| Digital biological information panel member, NIST Synthetic Biology Standards Consortium (SBSC) Kick-Off Workshop, Stanford, CA, 31 Mar. 2015. | ||
| Talks | ||
| 2016 | “How to remember and revisit many genetic design variants automatically,” 8th IWBDA, Newcastle Upon Tyne, UK, 16-18 Aug. 2016. | |
| “How to remember and revisit many genetic designs automatically,” Synthetic Biology Engineering Research Center (Synberc) Spring 2016 Retreat, Berkeley, CA, 23-24 Mar. 2016. | ||
| 2015 | “Multiplicity of representation in SBOL 2.0,” COMBINE 2015, Salt Lake City, UT, 12-16 Oct. 2015. | |
| “Double Dutch: a tool for designing libraries of variant metabolic pathways,” 7th IWBDA, Seattle, WA, 19-21 Aug. 2015. | ||
| “The Synthetic Biology Open Language 2.0,” 7th IWBDA, Seattle, WA, 19-21 Aug. 2015. | ||
| 2014 | “Generating SBML models from SBOL,” COMBINE 2014, Los Angeles, CA, 18-22 Aug. 2014. | |
| “A proposed data model for the next version of the Synthetic Biology Open Language,” 2014 Synthetic Biology: Engineering, Evolution and Design (SEED), London, 14-17 Jul 2014. | ||
| 2013 | “Directed acyclic graph-based technology mapping of genetic circuit models,” 5th IWBDA, London, 12-13 Jul. 2013. | |
| 2012 | “A methodology to annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language,” Institute of Biological Engineering (IBE) 2012 Wetern Regional Conference, Logan, UT, Oct. 2012. | |
| “A methodology to annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language,” Special Interest Group on Biological Systems Design (BSD-SIG) at the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA, 13-17 Jul. 2012. | ||
| Teaching Experience | ||
| Course | Computational Synthetic Biology for Engineers | |
| Institution | Boston University | Boston, MA |
| Title | Co-Instructor | |
| Term | Spring 2016 | |
| Course | Bio-Signal Processing | |
| Institution | University of Utah | Salt Lake City, UT |
| Title | Teaching Assistant | |
| Term | Spring 2012 | |
| Research Experience | ||
| Institution | University of Utah | Salt Lake City, UT |
| Department | Bioengineering | |
| Title | Research Assistant | |
| Period | 2010-2014 | |
| Service to Profession | ||
| SBOL Developers Group | Member, 2011-Present | |
| Editor, 2013-2015 | ||
| ACS Synthetic Biology | Reviewer, 2016 | |
| IET Systems Biology | Reviewer, 2016 | |
| PLoS ONE | Reviewer, 2015 | |
| Mathematical Biosciences | Reviewer, 2015 | |
| Professional Skills | ||
| Programming Languages | Java, JavaScript, MATLAB, Python, C++ | |
| Domain-Specific Standards | Synthetic Biology Open Language (SBOL), Systems Biology Markup Language (SBML) | |
| Software Development Tools | Eclipse, Git, Maven | |
| Database Systems | Neo4j | |
| Genetic Engineering | Cell Culture, Flow Cytometry, Molecular Cloning | |