Programmable Biology Bibliography: Class 1: Introduction
Programmable Biology Bibliography: Class 1: Introduction
Programmable Biology Bibliography: Class 1: Introduction
BIBLIOGRAPHY
Class 1: Introduction
• Synthetic Biology in 2 hours for computer scientists - FAQ Talk Alfonso
Rodríguez-Patón Valencia junio 2017 www.lia.upm.es
DNA Automaton:
• Ehud Shapiro, Y. Benenson. Bringing DNA computers to life. Scientific
American 294, 44 - 51 (2006) doi:10.1038/scientificamerican0506-44
• Kahana, M., Gila, B., Adara, R., & Shapiroa, E. (2008). Towards molecular
computers that operate in a biological environment. Physica D 237.
• Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., & Shapiro, E.Y.
(2001). Programmable and autonomous computing machine made of
biomolecules. Nature, 414, 430-434.
• Benenson, Y., Gil, B.G., Ben-Dor, U., Adar, R., & Shapiro, E. (2004). An
autonomous molecular computer for logical control of gene expression. Nature,
429, 423-429.
DNA storage:
• Digital DNA. https://www.nature.com/news/how-dna-could-store-all-the-world-
s-data-1.20496
• Extance, A. (2016). How DNA could store all the world’s data. Nature, 537, 22-
24.
• Blawat, M., Gaedke, K., Huetter, I., Chen, X., Turczyk, B., Inverso, S., Pruitt, B.,
& Church, G. (2016). Forward Error Correction for DNA Data Storage. ICCS.
• Shipman, S.L., Nivala, J., Macklis, J.D., & Church, G.M. (2017). CRISPR-Cas
encoding of a digital movie into the genomes of a population of living
bacteria. Nature.
• Erlich, Y., & Zielinski, D. (2017). DNA Fountain enables a robust and efficient
storage architecture. Science, 355 6328, 950-954.
• Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E.M., Sipos, B., &
Birney, E. (2013). Towards practical, high-capacity, low-maintenance
information storage in synthesized DNA. Nature, 494, 77-80.
• Church, G.M., Gao, Y., & Kosuri, S. (2012). Next-generation digital information
storage in DNA. Science, 337 6102, 1628.
• Yazdi, S.M., Yuan, Y., Ma, J., Zhao, H., & Milenkovic, O. (2015). A Rewritable,
Random-Access DNA-Based Storage System. Scientific reports.
• Zhirnov, V., Zadegan, R.M., Sandhu, G.S., Church, G.M., & Hughes, W.L.
(2016). Nucleic acid memory. Nature materials, 15 4, 366-70.
• Bornholt, J., Lopez, R., Carmean, D.M., Ceze, L., Seelig, G., & Strauss, K. (2016).
A DNA-Based Archival Storage System. ASPLOS.
• Zakeri, B., Carr, P.A., & Lu, T.K. (2016). Multiplexed Sequence Encoding: A
Framework for DNA Communication. PloS one.
Gene oscillators:
• Purcell, O., Savery, N.J., Grierson, C.S., & Bernardo, M.D. (2010). A
comparative analysis of synthetic genetic oscillators. Journal of the Royal
Society, Interface, 7 52, 1503-24.
• Miró-Bueno, J.M., & Rodríguez-Patón, A. (2011). A Simple Negative
Interaction in the Positive Transcriptional Feedback of a Single Gene Is
Sufficient to Produce Reliable Oscillations. PloS one.
Hasty oscillator:
• Stricker, J., Cookson, S.W., Bennett, M.R., Mather, W.H., Tsimring, L.S.,
& Hasty, J. (2008). A fast, robust and tunable synthetic gene
oscillator. Nature, 456, 516-519.
• Video negative feedback oscillator nature07389-s12.mov
CRISPR:
• CRISPR Bibliography.pdf
• Charpentier, E., & Doudna, J.A. (2013). Biotechnology: Rewriting a
genome. Nature, 495, 50-51.
• Shipman, S.L., Nivala, J., Macklis, J.D., & Church, G.M. (2017). CRISPR-Cas
encoding of a digital movie into the genomes of a population of living
bacteria. Nature.
• Michael Specter. The gene hackers. A powerful new technology enables us to
manipulate our DNA more easily than ever before. Annals of Science. Nov. 2015.
• H. Ledford, "CRISPR, the disruptor," Nature, vol. 522, no. 7554, pp. 20-24.
[Online]. Available: http://dx.doi.org/10.1038/522020a
• E. Pennisi, "The CRISPR craze," Science, vol. 341, no. 6148, pp. 833-836, Aug.
2013. [Online]. Available: http://dx.doi.org/10.1126/science.341.6148.833
• L. A. Marraffini, "CRISPR-cas immunity in prokaryotes," Nature, vol. 526, no.
7571, pp. 55-61, Oct. 2015. [Online]. Available:
http://dx.doi.org/10.1038/nature15386
• A. K. Nielsen and C. A. Voigt, "Multi-input CRISPR/cas genetic circuits that
interface host regulatory networks," Molecular Systems Biology, vol. 10, no. 763,
2014. [Online]. Available: http://view.ncbi.nlm.nih.gov/pubmed/25422271
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