How to cite j5, and publications citing j5

If you want to cite j5, our core algorithm for specifying robust and optimal DNA assembly instructions, please use this reference:

Hillson, N.J., Rosengarten, R.D., and Keasling J.D. (2012) j5 DNA Assembly Design Automation Software. ACS Synthetic Biology 1 (1), 14-21. DOI: 10.1021/sb2000116

Here is a list of other publications citing j5:

  1. Linshiz, G., Stawski, N., Goyal, G., Bi, C., Poust, S., Sharma, M., Mutalik, V., Keasling, J.D., and Hillson, N.J. (2014). PR-PR: Cross-Platform Laboratory Automation System. ACS Synthetic Biology. DOI: 10.1021/sb4001728

  2. Douglas M. Densmore, Swapnil Bhatia. (2013) "Bio-design automation: software + biology + robots". Trends in Biotechnology. DOI: 10.1016/j.tibtech.2013.10.005.

  3. Liu, Wusheng; Yuan, Joshua S.; Stewart, C. Neal, Jr. (2013) "Advanced genetic tools for plant biotechnology". Nature Reviews Genetics 14 (11), 781-793. DOI: 10.1038/nrg3583.

  4. Bi, C., Su, P., Müller, J., Yeh, Y.C., Chhabra, S.R., Beller, H.R., Singer, S.W., and Hillson, N.J. (2013) "Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production". Microbial Cell Factories 12:107. DOI: 10.1186/1475-2859-12-107

  5. Fisher, A.B., Canfield, A.B., Hayward, L.C., Fong, S.S., and McArthur IV, G.H. (2013) "Ex vivo DNA assembly". Front. Bioeng. Biotechnol. DOI: 10.3389/fbioe.2013.00012.

  6. Cobb RE, Ning JC, Zhao H. (2013) "DNA assembly techniques for next-generation combinatorial biosynthesis of natural products". J Ind Microbiol Biotechnol. Oct 15. [Epub ahead of print] PubMed PMID: 24127070.

  7. Yifan Li , Qun Gu , Zhenquan Lin , Zhiwen Wang , Tao Chen *, and Xueming Zhao. (2013) "Multiplex Iterative Plasmid Engineering for Combinatorial Optimization of Metabolic Pathways and Diversification of Protein Coding Sequences". ACS Synth. Biol. DOI: 10.1021/sb400051t

  8. Sang Yup Lee, Seung Bum Sohn, Yu Bin Kim, Jae Ho Shin, Jin Eyun Kim, Tae Yong Kim. (2013) "Chapter 8 – Computational Methods for Strain Design" in Synthetic Biology Tools and Applications. Huimin Zhao, Editor(s), Academic Press, Boston, Pages 141-156.

  9. Sean C. Sleight and Herbert M. Sauro. (2013) "Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits". ACS Synth. Biol. DOI: 10.1021/sb400055h

  10. Thomas Landrain, Morgan Meyer, Ariel Martin Perez, and Remi Sussan. (2013) "Do-it-yourself biology: challenges and promises for an open science and technology movement". Systems and Synthetic Biology. DOI: 10.1007/s11693-013-9116-4

  11. Carothers, J. (2013) "Design-driven, multi-use research agendas to enable applied synthetic biology for global health". Syst Synth Biol. DOI 10.1007/s11693-013-9118-2

  12. Narjeskhatoon Habibi, Siti Zaiton Mohd Hashim, Cesar A. Rodriguez, Mohd Razip Samian. (2013) "A Review of CADs, Languages and Data Models for Synthetic Biology" Jurnal Teknologi 63 (1): DOI: 10.11113/jt.v63.1644

  13. Sleight, S.C. and Sauro, H.M. (2013) "Randomized BioBrick Assembly: A novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways" ACS Synth. Biol., DOI: 10.1021/sb4000542

  14. Cox III, R.S., Koro Nishikata, K., Shimoyama, S., Yoshida, Y., Matsui, M., Makita, Y., and Toyoda, T. (2013) PromoterCAD: data-driven design of plant regulatory DNA. Nucl. Acids Res. DOI: 10.1093/nar/gkt518

  15. Kahl, L.J., and Endy, D. (2013) A survey of enabling technologies in synthetic biology. Journal of Biological Engineering 7:13 DOI:10.1186/1754-1611-7-13.

  16. Chen, W.H., Qin, Z.J., Zhao, G.P. (2013) The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Research 41 (8), e93. DOI:10.1093/nar/gkt122

  17. Mackenzie, A. (2013) Realizing the promise of biotechnology: Infrastructural-icons in synthetic biology. Futures. DOI:10.1016/j.futures.2013.02.003

  18. Linshiz, G., Goldberg, A., Konry, T., and Hillson, N.J. (2013) The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology. Perspectives in Biology and Medicine 55 (4), 503-520. DOI: 10.1353/pbm.2012.0044

  19. Stephen Van Dien. (2013) From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals. Current Opinion in Biotechnology. DOI:10.1016/j.copbio.2013.03.002

  20. Peng Xu, Namita Bhan, and Mattheos AG Koffas. (2013). "Engineering plant metabolism into microbes: from systems biology to synthetic biology". Current Opinion in Biotechnology 24(2):291.

  21. Chen, J, Densmore, D, Ham, TS, Keasling, JD and Hillson, N.J. (2012) "DeviceEditor visual biological CAD canvas". Journal of Biological Engineering 6:1

  22. Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Quynh-Anh Mai, Marc Juul Christoffersen, Lance Martin, Ayumi Yu, Colin Lam, Cesar Rodriguez, Gaymon Bennett, Jay D Keasling, Drew Endy, and Adam P Arkin. (2013) Quantitative estimation of activity and quality for collections of functional genetic elements. Nature Methods. doi:10.1038/nmeth.2403

  23. W.H. Chen, Z.J. Qin, J. Wang, G.P. Zhao, (2013)The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Research. doi:10.1093/nar/gkt122

  24. Esvelt, K.M., and Wang, H.H. (2013) Genome-scale engineering for systems and synthetic biology. Molecular Systems Biology 9:641. doi:10.1038/msb.2012.66

  25. Stevens, J.T., and Myers, C.J. (2012) Dynamic Modeling of Cellular Populations within iBioSim. ACS Synthetic Biology. DOI: 10.1021/sb300082b

  26. Perkel, JM. (2012). Genome engineering: writing a better genome. BioTechniques, Vol. 53, No. 4, October 2012, pp. 213–217. http://www.biotechniques.com/BiotechniquesJournal/2012/October/Genome-engineering-writing-a-better-genome/biotechniques-336011.html

  27. Linshiz, G., Stawski, N., Poust, S., Bi, C., Keasling, J.D., and Hillson, N.J. (2012). PaR-PaR Laboratory Automation platform. ACS Synthetic Biology. DOI: 10.1021/sb300075t

  28. Xu P, Bhan N, Koffas MA. (2012) Engineering plant metabolism into microbes: from systems biology to synthetic biology. Curr Opin Biotechnol. doi: 10.1016/j.copbio.2012.08.010. PubMed PMID: 22985679.

  29. Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman. (2012) An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synthetic Biology. DOI: 10.1021/sb300030d

  30. Yaman F, Bhatia S, Adler A, Densmore D, and Beal J. (2012) Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks. ACS Synthetic Biology. DOI: 10.1021/sb300032y.

  31. Kitney R, Freemont P. (2012) Synthetic biology - the state of play. FEBS Lett. DOI: 10.1016/j.febslet.2012.06.002 PubMed PMID: 22704968.

  32. Ham, T.S., Dmytriv, Z. Plahar, H., Chen, J., Hillson, N.J., and Keasling, J.D. (2012) Design, Implementation and Practice of JBEI-ICE: An Open Source Biological Part Registry Platform and Tools. Nucleic Acids Research. DOI: 10.1093/nar/gks531.

  33. Allen Cheng and Timothy K. Lu. (2012) Synthetic Biology: An Emerging Engineering Discipline. Annu. Rev. Biomed. Eng. 2012. 14:155–78. DOI: 10.1146/annurev-bioeng-071811–150118.

  34. Michael G Montague, Carole Lartigue, Sanjay Vashee. (2012) Synthetic genomics: potential and limitations. Current Opinion in Biotechnology, DOI:10.1016/j.copbio.2012.01.014.

  35. Synthetic Biology. Wikigenes collaborative publishing.

  36. Artificial gene synthesis. Wikipedia, the free encyclopedia.

  37. (2012) In This Issue. ACS Synthetic Biology 1 (1), 3-3. DOI: 10.1021/sb3000047.

  38. Holtz, William J (2011) Engineering Scalable Combinational Logic in Escherichia coli Using Zinc Finger Proteins. UC Berkeley Technical Report EECS-2011-59.

  39. Baker M. (2011) Synthetic genomes: The next step for the synthetic genome. Nature. 473(7347):403, 405-8. DOI:10.1038/473403a. PubMed PMID: 21593873.

  40. Hillson NJ. (2011) "DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 295-314.

  41. Beal, J., Phillips, A., Densmore, D., and Cai, Y.(2011) "High-Level Programming Languages for Bio-Molecular Systems" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 225-252.

  42. Chandran D, Bergmann FT, Sauro HM, Densmore D. (2011) "Computer-Aided Design for Synthetic Biology" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 203-224.

  43. Ellis T, Adie T, Baldwin GS. DNA assembly for synthetic biology: from parts to pathways and beyond (2011). Integr Biol (Camb). 3, 109-118. DOI: 10.1039/C0IB00070A. PubMed PMID: 21246151.