L A K I N   L A B
Programmable Biology

University of New Mexico

Publications

2022

David Arredondo and Matthew R. Lakin. Operant conditioning of stochastic chemical reaction networks. PLOS Computational Biology. Published online ahead of print, 2022. Link to article. BibTeX.

Tracy L. Mallette and Matthew R. Lakin. Protecting heterochiral DNA nanostructures against exonuclease-mediated degradation. ACS Synthetic Biology, volume 11, number 7, pages 2222–2228, 2022. Link to article. BibTeX.

David Arredondo and Matthew R. Lakin. Supervised learning in a multilayer, nonlinear chemical neural network. IEEE Transactions on Neural Networks and Learning Systems. Published online ahead of print, 2022. Link to article. BibTeX.

2021

David Arredondo and Matthew R. Lakin. Robust finite automata in stochastic chemical reaction networks. Royal Society Open Science, volume 8, number 12, 211310, 2021. Link to article. BibTeX.

Oskar Staufer, Jacqueline A. De Lora, Eleonora Bailoni, Alisina Bazrafshan, Amelie S. Benk, Kevin Jahnke, Zachary A. Manzer, Lado Otrin, Telmo Díez Pérez, Judee Sharon, Jan Steinkühler, Katarzyna P. Adamala, Bruna Jacobson, Marileen Dogterom, Kerstin Göpfrich, Darko Stefanovic, Susan R. Atlas, Michael Grunze, Matthew R. Lakin, Andrew P. Shreve, Joachim P. Spatz, and Gabriel P. López. Building a community to engineer synthetic cells and organelles from the bottom-up. eLife, volume 10, e73556, 2021. Link to article. BibTeX.

Matthew R. Lakin and Petr Šulc (eds.). 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), volume 205. Schloss Dagstuhl – Leibniz-Zentrum für Informatik, 2021. Link to volume. BibTeX.

Matthew R. Lakin, Darko Stefanovic, and Milan N. Stojanovic. Diverse applications of DNAzymes in computing and nanotechnology. In Sabine Müller, Benoît Masquida, and Wade Winkler (eds.), Ribozymes, chapter 25, pages 633–660. Wiley, 2021. Link to article. BibTeX.

Sarika Kumar, Julian M. Weisburd, and Matthew R. Lakin. Structure sampling for computational estimation of localized DNA interaction rates. Scientific Reports, volume 11, 12730, 2021. Link to article. BibTeX.

David Arredondo, Matthew R. Lakin, Darko Stefanovic, and Milan N. Stojanovic. Development and application of catalytic DNA in nanoscale robotics. In Evgeny Katz (ed.), DNA- and RNA-Based Computing Systems, chapter 15, pages 293–306. Wiley, 2021. Link to article. BibTeX.

2020

Matthew R. Lakin and Andrew Phillips. Domain-specific programming languages for computational nucleic acid systems. ACS Synthetic Biology, volume 9, number 7, pages 1499–1513, 2020. Link to article. BibTeX.

Tracy L. Mallette, Milan N. Stojanovic, Darko Stefanovic, and Matthew R. Lakin. Robust heterochiral strand displacement using leakless translators. ACS Synthetic Biology, volume 9, number 7, pages 1907–1910, 2020. Link to article. BibTeX.

2019

Carlo Spaccasassi, Matthew R. Lakin, and Andrew Phillips. A logic programming language for computational nucleic acid devices. ACS Synthetic Biology, volume 8, number 7, pages 1530–1547, 2019. Link to article. BibTeX.

Aurora Fabry-Wood, Madalyn Elise Fetrow, Ayomide Oloyede, Kyung-Ae Yang, Milan N. Stojanovic, Darko Stefanovic, Steven W. Graves, Nick J. Carroll, and Matthew R. Lakin. Microcompartments for protection and isolation of nanoscale DNA computing elements. ACS Applied Materials and Interfaces, volume 11, number 12, pages 11262–11269, 2019. Link to article. BibTeX.

2018

Matthew R. Lakin and Andrew Phillips. Automated analysis of tethered DNA nanostructures using constraint solving. Natural Computing, volume 17, number 4, pages 709–722, 2018. Link to article. BibTeX.

Sandeep Pallikkuth, Cheyenne Martin, Farzin Farzam, Jeremy S. Edwards, Matthew R. Lakin, Diane S. Lidke, and Keith A. Lidke. Sequential super-resolution imaging using DNA strand displacement. PLOS ONE, volume 13, number 8, e0203291, 2018. Link to article. BibTeX.

2017

Aurora Fabry-Wood, Madalyn Elise Fetrow, Carl W. Brown, III, Nicholas A. Baker, Nadiezda Fernandez Oropeza, Andrew P. Shreve, Gabriel A. Montaño, Darko Stefanovic, Matthew R. Lakin, and Steven W. Graves. A microsphere-supported lipid bilayer platform for DNA reactions on a fluid surface. ACS Applied Materials and Interfaces, volume 9, number 35, pages 30185–30195, 2017. Link to article. BibTeX.

Matthew R. Lakin, Milan N. Stojanovic, and Darko Stefanovic. Implementing molecular logic gates, circuits, and cascades using DNAzymes. In Andrew Adamatzky (ed.), Advances in Unconventional Computing Volume 2: Prototypes, Models and Algorithms, Emergence, Complexity, and Computation, volume 23, chapter 1, pages 1–28. Springer International Publishing, 2017. Link to article. BibTeX.

Matthew R. Lakin and Andrew Phillips. Automated, constraint-based analysis of tethered DNA nanostructures. In R. Brijder and L. Qian (eds.), Proceedings of the 23rd International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 10467, pages 1–16. Springer, Cham, 2017. Link to article. Draft PDF. Appendices. BibTeX.

Matthew R. Lakin and Darko Stefanovic. Towards temporal logic computation using DNA strand displacement reactions. In M. J. Patitz and M. Stannett (eds.), Unconventional Computation and Natural Computation 2017, Lecture Notes in Computer Science, volume 10240, pages 41–55. Springer, Cham, 2017. Link to article. Draft PDF. Appendices. BibTeX.

2016

Matthew R. Lakin and Darko Stefanovic. Supervised learning in adaptive DNA strand displacement networks. ACS Synthetic Biology, volume 5, number 8, pages 885–897, 2016. Link to article. BibTeX.

Dandan Mo, Matthew R. Lakin, and Darko Stefanovic. Logic circuits based on molecular spider systems. BioSystems, volume 146, pages 10–25, 2016. Link to article. BibTeX.

Matthew R. Lakin, Darko Stefanovic, and Andrew Phillips. Modular verification of chemical reaction network encodings via serializability analysis. Theoretical Computer Science, volume 632, pages 21–42, 2016. Link to article. BibTeX.

Rasmus L. Petersen, Matthew R. Lakin, and Andrew Phillips. A strand graph semantics for DNA-based computation. Theoretical Computer Science, volume 632, pages 43–73, 2016. Link to article. BibTeX.

2015

Carl W. Brown, III, Matthew R. Lakin, Aurora Fabry-Wood, Eli K. Horwitz, Nicholas A. Baker, Darko Stefanovic, and Steven W. Graves. A unified sensor architecture for isothermal detection of double-stranded DNA, oligonucleotides, and small molecules. ChemBioChem, volume 16, number 5, pages 725–730, 2015. Link to article. BibTeX.

Matthew R. Lakin and Darko Stefanovic. Supervised learning in an adaptive DNA strand displacement circuit. In Andrew Phillips and Peng Yin (eds.), Proceedings of the 21st International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 9211, pages 154–167. Springer International Publishing, 2015. Link to article. Draft PDF. BibTeX.

Dandan Mo, Matthew R. Lakin, and Darko Stefanovic. Scalable design of logic circuits using an active molecular spider system. In Michael Lones, Andy Tyrrell, Stephen Smith, and Gary Fogel (eds.), Proceedings of the 10th International Conference on Information Processing in Cells and Tissues, Lecture Notes in Computer Science, volume 9303, pages 13–28. Springer International Publishing, 2015. Link to article. BibTeX.

2014

Matthew R. Lakin, Carl W. Brown, III, Eli K. Horwitz, M. Leigh Fanning, Hannah E. West, Darko Stefanovic, and Steven W. Graves. Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering. PLOS ONE, volume 9, number 10, e110986, 2014. Link to article. BibTeX.

Carl W. Brown, III, Matthew R. Lakin, Eli K. Horwitz, M. Leigh Fanning, Hannah E. West, Darko Stefanovic, and Steven W. Graves. Signal propagation in multi-layer DNAzyme cascades using structured chimeric substrates. Angewandte Chemie International Edition, volume 53, number 28, pages 7183–7187, 2014. Link to article. BibTeX.

Matthew R. Lakin, Amanda Minnich, Terran Lane, and Darko Stefanovic. Design of a biochemical circuit motif for learning linear functions. Journal of the Royal Society Interface, volume 11, number 101, 20140902, 2014. Link to article. BibTeX.

Carl W. Brown, III, Matthew R. Lakin, Darko Stefanovic, and Steven W. Graves. Catalytic molecular logic devices by DNAzyme displacement. ChemBioChem, volume 15, number 7, pages 950–954, 2014. Link to article. BibTeX.

Matthew R. Lakin, Rasmus Petersen, Kathryn E. Gray, and Andrew Phillips. Abstract modelling of tethered DNA circuits. In Satoshi Murata and Satoshi Kobayashi (eds.), Proceedings of the 20th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 8727, pages 132–147. Springer International Publishing, 2014. Link to article. Draft PDF. Appendices. BibTeX.

Matthew R. Lakin and Darko Stefanovic. Pattern formation by spatially organized approximate majority reactions. In O. H. Ibarra, L. Kari, and S. Kopecki (eds.), Unconventional Computation and Natural Computation 2014, Lecture Notes in Computer Science, volume 8553, pages 254–266. Springer International Publishing, 2014. Link to article. Draft PDF. BibTeX.

Matthew R. Lakin and Andrew Phillips. Compiling DNA strand displacement reactions using a functional programming language. In M. Flatt and H.-F. Guo (eds.), Proceedings of Practical Aspects of Declarative Languages 2014, Lecture Notes in Computer Science, volume 8324, pages 81–86. Springer International Publishing Switzerland, 2014. Link to article. Draft PDF. BibTeX.

Alireza Goudarzi, Matthew R. Lakin, Darko Stefanovic, and Christof Teuscher. A model for variation- and fault-tolerant digital logic using self-assembled nanowire architectures. In Proceedings of the 2014 IEEE/ACM International Symposium on Nanoscale Architectures (NANOARCH), pages 116–121. IEEE Press, 2014. Link to article. BibTeX.

Alireza Goudarzi, Matthew R. Lakin, and Darko Stefanovic. Reservoir computing approach to robust computation using unreliable nanoscale networks. In O. H. Ibarra, L. Kari, and S. Kopecki (eds.), Unconventional Computation and Natural Computation 2014, Lecture Notes in Computer Science, volume 8553, pages 164–176. Springer International Publishing, 2014. Link to article. BibTeX.

2013

Matthew R. Lakin and Andrew M. Pitts. Contextual equivalence for inductive definitions with binders in higher-order typed functional programming. Journal of Functional Programming, volume 23, number 6, pages 658–700, 2013. Link to article. BibTeX.

Peter Banda, Christof Teuscher, and Matthew R. Lakin. Online learning in a chemical perceptron. Artificial Life, volume 19, number 2, pages 195–219, 2013. Link to article. BibTeX.

Matthew R. Lakin, Andrew Phillips, and Darko Stefanovic. Modular verification of DNA strand displacement networks via serializability analysis. In D. Soloveichik and B. Yurke (eds.), Proceedings of the 19th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 8141, pages 133–146. Springer-Verlag, 2013. Link to article. Draft PDF. Appendices. BibTeX.

Alireza Goudarzi, Matthew R. Lakin, and Darko Stefanovic. DNA reservoir computing: a novel molecular computing approach. In D. Soloveichik and B. Yurke (eds.), Proceedings of the 19th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 8141, pages 76–89. Springer-Verlag, 2013. Link to article. Draft PDF. Appendices. BibTeX.

2012

Matthew R. Lakin, David Parker, Luca Cardelli, Marta Kwiatkowska, and Andrew Phillips. Design and analysis of DNA strand displacement devices using probabilistic model checking. Journal of the Royal Society Interface, volume 9, number 72, pages 1470–1485, 2012. Link to article. BibTeX.

Matthew R. Lakin, Loïc Paulevé, and Andrew Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science, volume 431, pages 181–206, 2012. Link to article. BibTeX.

Matthew R. Lakin, Simon Youssef, Luca Cardelli, and Andrew Phillips. Abstractions for DNA circuit design. Journal of the Royal Society Interface, volume 9, number 68, pages 460–486, 2012. Link to article. BibTeX.

Matthew R. Lakin and Andrew M. Pitts. Encoding abstract syntax without fresh names. Journal of Automated Reasoning, volume 49, number 2, pages 115–140, 2012. Link to article. BibTeX.

Matthew R. Lakin, Amanda Minnich, Terran Lane, and Darko Stefanovic. Towards a biomolecular learning machine. In J. Durand-Lose and N. Jonoska (eds.), Unconventional Computation and Natural Computation 2012, Lecture Notes in Computer Science, volume 7445, pages 152–163. Springer-Verlag, 2012. Link to article. BibTeX.

2011

Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, and Andrew Phillips. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics, volume 27, number 22, pages 3211–3213, 2011. Link to article. BibTeX.

Matthew R. Lakin. Constraint solving in non-permutative nominal abstract syntax. Logical Methods in Computer Science, volume 7, number 3:06, pages 1–31, 2011. Link to article. BibTeX.

Matthew R. Lakin and Andrew Phillips. Modelling, simulating and verifying Turing-powerful strand displacement systems. In L. Cardelli and W. Shih (eds.), Proceedings of the 17th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 6937, pages 130–144. Springer-Verlag, 2011. Link to article. Appendices. BibTeX.

2010

Andrew Phillips, Matthew R. Lakin, and Loïc Paulevé. Stochastic simulation of process calculi for biology. In G. Ciobanu and M. Koutny (eds.), Membrane Computing and Biologically Inspired Process Calculi 2010, Electronic Proceedings in Theoretical Computer Science, volume 40, pages 1–5, 2010. Link to article. BibTeX.

Loïc Paulevé, Simon Youssef, Matthew R. Lakin, and Andrew Phillips. A generic abstract machine for stochastic process calculi. In CMSB 2010: Proceedings of the 8th International Conference on Computational Methods in Systems Biology, Trento, Italy, pages 43–54. ACM, 2010. Link to article. BibTeX.

Matthew R. Lakin. An executable meta-language for inductive definitions with binders. Ph.D. thesis, University of Cambridge, 2010. Link to document. BibTeX. Software.

2009

Matthew R. Lakin and Andrew M. Pitts. Resolving inductive definitions with binders in higher-order typed functional programming. In G. Castagna (ed.), 18th European Symposium on Programming (ESOP '09), Lecture Notes in Computer Science, volume 5502, pages 47–61. Springer, 2009. Link to article. BibTeX.

2008

Matthew R. Lakin and Andrew M. Pitts. A Metalanguage for Structural Operational Semantics. In M. T. Morazán (ed.), Trends in Functional Programming, Volume 8, pages 19–35. Intellect, 2008. Draft PDF. BibTeX.