PROGRAMMABLE BIOLOGY

BIBLIOGRAPHY

Class 1: Introduction
• Synthetic Biology in 2 hours for computer scientists - FAQ Talk Alfonso
Rodríguez-Patón Valencia junio 2017 www.lia.upm.es

Class 2: Classic DNA Computing

• Adleman, L.M. (1994). Molecular computation of solutions to combinatorial
problems. Science, 266 5187, 1021-4.
• Ehud Shapiro, Y. Benenson. Bringing DNA computers to life. Scientific
American 294, 44 - 51 (2006) doi:10.1038/scientificamerican0506-44

Class 3: DNA Computing II

DNA Nanotechnology:
• El robot de ADN ya está aquí _ Ciencia Home _ EL MUNDO
• Thubagere, A.J., Li, W., Johnson, R.F., Chen, Z., Doroudi, S., Lee, Y.L., Izatt, G.,
Wittman, S., Srinivas, N., Woods, D., Winfree, E., & Qian, L. (2017). A cargo-
sorting DNA robot. Science, 357 6356.
• Chatterjee, G., Dalchau, N., Muscat, R.A., Phillips, A., & Seelig, G. (2017). A
spatially localized architecture for fast and modular DNA computing. Nature
nanotechnology, 12 9, 920-927.
• Estevez-Torres, A., & Rondelez, Y. (2017). DNA computing: Spatially localized
DNA domino. Nature nanotechnology, 12 9, 842-843.
• Gines, G., Zadorin, A.S., Galas, J., Fujii, T., Estevez-Torres, A., & Rondelez, Y.
(2017). Microscopic agents programmed by DNA circuits. Nature
nanotechnology, 12 4, 351-359.
• Chen, Y., Groves, B., Muscat, R.A., & Seelig, G. (2015). DNA nanotechnology
from the test tube to the cell. Nature nanotechnology, 10 9, 748-60.
• Zhang, D.Y., & Seelig, G. (2011). Dynamic DNA nanotechnology using strand-
displacement reactions. Nature chemistry, 3 2, 103-13.

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 strand displacement:

• Seelig, G., Soloveichik, D., Zhang, D.Y., & Winfree, E. (2006). Enzyme-free
nucleic acid logic circuits. Science, 314 5805, 1585-8.
• W. Fontana, "Chemistry. pulling strings." Science (New York, N.Y.), vol. 314, no.
5805, pp. 1552-1553, Dec. 2006. [Online]. Available:
http://dx.doi.org/10.1126/science.1135101
• Zhang, D.Y., & Seelig, G. (2011). Dynamic DNA nanotechnology using strand-
displacement reactions. Nature chemistry, 3 2, 103-13.

DNA Computing. Additional readings:

• Macdonald, J., Stefanovic, D., & Stojanovic, M.N. (2008). DNA computers for
work and play. Scientific American, 299 5, 84-91.
• Ran, T., Kaplan, S., & Shapiro, E. (2009). Molecular implementation of simple
logic programs. Nature nanotechnology, 4 10, 642-8.
• Chen, X., & Ellington, A.D. (2010). Shaping up nucleic acid
computation. Current opinion in biotechnology, 21 4, 392-400.
• Rodríguez-Patón, A., Larrea, J.M., & Murieta, I.S. (2010). Inference with DNA
Molecules. UC.
• Andy Extance, DNA gets with the program. 27 January 2015.
https://www.chemistryworld.com/feature/dna-gets-with-the-
program/8190.article

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.

Class 4: IBM and Gro simulator

Gro:
• Jang, S.S., Oishi, K.T., Egbert, R.G., & Klavins, E. (2012). Specification and
simulation of synthetic multicelled behaviors. ACS synthetic biology, 1 8, 365-74.
• Gutiérrez, M., Gregorio-Godoy, P., Pulgar, G.P., Munoz, L.E., Sáez, S., &
Rodríguez-Patón, A. (2017). A New Improved and Extended Version of the
Multicell Bacterial Simulator gro. ACS synthetic biology, 6 8, 1496-1508.

IBM, ABM, reviews:

• Kreft, J., Plugge, C.M., Grimm, V., Prats, C., Leveau, J.H., Banitz, T., Baines,
S.B., Clark, J., Ros, A., Klapper, I., Topping, C.J., Field, A.J., Schuler, A.J.,
Litchman, E., & Hellweger, F.L. (2013). Mighty small: Observing and modeling
individual microbes becomes big science. Proceedings of the National Academy
of Sciences of the United States of America, 110 45, 18027-8.
• Rudge, T.J., Steiner, P.J., Phillips, A., & Haseloff, J. (2012). Computational
modeling of synthetic microbial biofilms. ACS synthetic biology, 1 8, 345-52.
• Hellweger, F.L., Clegg, R.J., Clark, J.R., Plugge, C.M., & Kreft, J. (2016).
Advancing microbial sciences by individual-based modelling. Nature Reviews
Microbiology, 14, 461-471.
• Gorochowski, T.E. (2016). Agent-based modelling in synthetic biology. Essays
in biochemistry.

Class 5: Bioblocks – Programming biological experiments

• Gupta, V., Irimia, J., Pau, I., & Rodríguez-Patón, A. (2017). BioBlocks:
Programming Protocols in Biology Made Easier. ACS synthetic biology, 6 7,
1230-1232.
• Ananthanarayanan, V., & Thies, W. (2010). Biocoder: A programming language
for standardizing and automating biology protocols. Journal of biological
engineering.
• Vishal Gupta. Tesis doctoral: An end-to-end solution for automation of biological
protocols http://oa.upm.es/48791/
• Kulkarni, C.D., Xu, W., Ritter, A., & Machiraju, R. (2018). An Annotated Corpus
for Machine Reading of Instructions in Wet Lab Protocols.
• Bitbloq framework for programming open-source biolabs

Class 6: Intro to SynBio

Introduction to SynBio:
• Synthetic Biology in 2 hours for computer scientists - FAQ Talk Alfonso
Rodríguez-Patón Valencia junio 2017.pdf (available in www.lia.upm.es )
• Gene expression regulation intro SLIDES.pdf
• Meehan, D.A., Khalil, A.S., & Bashor, C.J. (2013). Engineering Life | The
Scientist Magazine®.
• Group, B.F., Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J.B.,
Keasling, J.D., Modrich, P.L., Smolke, C.D., & Weiss, R. (2006). Engineering
life: building a fab for biology. Scientific American, 294 6, 44-51.

Pioneer genetic circuits:

• Rosenfeld, N., Elowitz, M.B., & Alon, U. (2002). Negative autoregulation speeds
the response times of transcription networks. Journal of molecular biology, 323
5, 785-93.
• Becskei and L. Serrano, "Engineering stability in gene networks by
autoregulation." Nature, vol. 405, no. 6786, pp. 590-593, Jun. 2000. [Online].
Available: http://dx.doi.org/10.1038/35014651
• Gardner, T.S., & Collins, J. (2000). Neutralizing noise in gene networks. Nature,
405 6786, 520-1.

A genetic oscillator – Repressilator:

• Elowitz, M.B., & Leibler, S. (2000). A synthetic oscillatory network of
transcriptional regulators. Nature, 403, 335-338.
• SLIDES pioneer genetic circuits.pdf

Genetic Toggle Switch:

• Gardner, T.S., Cantor, C.R., & Collins, J.J. (2000). Construction of a genetic
toggle switch in Escherichia coli. Nature, 403, 339-342.
• Tinkering With Life _ The Scientist.pdf
• 10_11_Designing-Genetic-Circuits.pdf

Boolean Logic Gates with Genes in vivo:

• Circuitos booleanos de Ron Weiss.pptx
• Weiss, R., Basu, S., Hooshangi, S., Kalmbach, A., Karig, D.K., Mehreja, R.,
& Netravali, I. (2003). Genetic circuit building blocks for cellular
computation, communications, and signal processing. Natural Computing, 2,
47-84.

Class 7: Gene networks motifs and genetic oscillators

• SLIDES gene network motifs and oscillators.pdf
• Riccione, K.A., Smith, R.P., Lee, A.J., & You, L. (2012). A synthetic biology
approach to understanding cellular information processing. ACS synthetic
biology, 1 9, 389-402.

Gene networks motifs:

 • Schaerli, Y., Munteanu, A., Gili, M., Cotterell, J., Sharpe, J., & Isalan, M.
(2014). A unified design space of synthetic stripe-forming networks. Nature
communications.
• Alon, U. (2007). Network motifs: theory and experimental approaches. Nature
Reviews Genetics, 8, 450-461.

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

Class 8: Quorum Sensing

Biology of QS – intro and Bassler video:
• Waters, C.M., & Bassler, B.L. (2005). Quorum sensing: cell-to-cell
communication in bacteria. Annual review of cell and developmental biology, 21,
319-46.
• BonnieBassler_2009-480p-es.mp4

SynBio using QS – Pioneer Works:

• Balagaddé, F.K., Song, H., Ozaki, J., Collins, C.H., Barnet, M., Arnold, F.H.,
Quake, S.R., & You, L. (2008). A synthetic Escherichia coli predator–prey
ecosystem. Molecular Systems Biology, 4, 187 - 187.
• Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H., & Weiss, R. (2005). A
synthetic multicellular system for programmed pattern formation. Nature, 434,
1130-1134.
• You, L., Cox, R.S., Weiss, R., & Arnold, F.H. (2004). Programmed population
control by cell–cell communication and regulated killing. Nature, 428, 868-871.
• Tabor, J.J., Salis, H.M., Simpson, Z.B., Chevalier, A.A., Levskaya, A., Marcotte,
E.M., Voigt, C.A., & Ellington, A.D. (2009). A Synthetic Genetic Edge Detection
Program. Cell, 137, 1272-1281.

Multicellular computing using chemical wires:

• Tamsir, A., Tabor, J.J., & Voigt, C.A. (2011). Robust multicellular computing
using genetically encoded NOR gates and chemical ‘wires’. Nature, 469, 212-
215.
• Regot, S., Macía, J., Conde-Pueyo, N., Furukawa, K., Kjellén, J., Peeters, T.,
Hohmann, S., Nadal, E.D., Posas, F., & Solé, R.V. (2011). Distributed biological
computation with multicellular engineered networks. Nature, 469, 207-211.
Class 9: RNA Synthetic Biology

Slides RNA Synthetic Biology- CRISPR and RNA switches 2017.pdf

RNA Switches - STAR and Toehold switches

Toehold switches Collins:
• Green, A.A., Silver, P.A., Collins, J.J., & Yin, P. (2014). Toehold Switches: De-
Novo-Designed Regulators of Gene Expression. Cell, 159, 925-939.
• Pardee, K.I., Green, A.A., Ferrante, T., Cameron, D.E., DaleyKeyser, A.J., Yin,
P., & Collins, J.J. (2014). Paper-Based Synthetic Gene Networks. Cell, 159, 940-
954.

STAR – Julius Lucks:

• Chappell, J., Takahashi, M.K., & Lucks, J.B. (2015). Creating small transcription
activating RNAs. Nature chemical biology, 11 3, 214-20.
• Lucks, J.B., & Arkin, A.P. (2011). The hunt for the biological transistor. IEEE
Spectrum, 48.

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

Short CRISPR intro videos:

• Short CRISPR intro videos.pdf

Reviews on RNA SynBio:

• Chappell, J., Watters, K.E., Takahashi, M.K., & Lucks, J.B. (2015). A renaissance
in RNA synthetic biology: new mechanisms, applications and tools for the
future. Current opinion in chemical biology, 28, 47-56.
• Christine Gorman y Dina Fine Maron La revolución del ARN. Investigación y
Ciencia. Junio 2014.
Gene Drive:
• The extinction invention. MIT Tech Review.
https://www.technologyreview.com/s/601213/the-extinction-invention/
• Esvelt, K.M., Smidler, A.L., Catteruccia, F., & Church, G.M. (2014). Concerning
RNA-guided gene drives for the alteration of wild populations. eLife.
• Gene drives FAQ FINAL.pdf

Germline editing – risks:

• Engineering the Perfect Baby - MIT Technology Review.
https://www.technologyreview.com/s/535661/engineering-the-perfect-baby/
• Should you edit your children’s genes?.pdf
• Lanphier, E., Urnov, F.D., Haecker, S.E., Werner, M., & Smolenski, J. (2015).
Don’t edit the human germ line. Nature, 519, 410-411.

Class 10: PLASWIRES and EVOPROG projects

www.plaswires.eu
www.evoprog.eu