Matthew Lakin

Matthew Lakin

Research Assistant Professor
Department of Computer Science
Department of Chemical & Biological Engineering
Center for Biomedical Engineering
University of New Mexico

Email: <firstinitial><lastname> AT cs.unm.edu
Curriculum Vitae
Google Scholar page

Research interests: Molecular computing, theoretical computer science, formal methods, declarative programming, pathogen detection, nanomedicine, synthetic biology.

Research


Funding


Publications

Publications are tagged by subject area: [MC-T] molecular computing (theoretical), [MC-E] molecular computing (experimental), [PL] programmming languages, [DS] dynamical systems.

Journal publications

  1. M. R. Lakin and D. Stefanovic, Supervised learning in adaptive DNA strand displacement networks. ACS Synthetic Biology, published online, 2016.
    [MC-T] [abstract] [bib] [doi: 10.1021/acssynbio.6b00009]

  2. D. Mo, M. R. Lakin, and D. Stefanovic, Logic circuits based on molecular spider systems. BioSystems, published online, 2016.
    [MC-T] [abstract] [bib] [doi: 10.1016/j.biosystems.2016.03.008]

  3. M. R. Lakin, D. Stefanovic, and A. Phillips, Modular verification of chemical reaction network encodings via serializability analysis. Theoretical Computer Science, published online, 2015.
    [MC-T] [abstract] [bib] [doi: 10.1016/j.tcs.2015.06.033]

  4. R. L. Petersen, M. R. Lakin, and A. Phillips, A strand graph semantics for DNA-based computation. Theoretical Computer Science, published online, 2015.
    [MC-T] [abstract] [bib] [doi: 10.1016/j.tcs.2015.07.041]

  5. C. W. Brown III, M. R. Lakin, A. Fabry-Wood, E. K. Horwitz, N. A. Baker, D. Stefanovic, and S. W. Graves, A unified sensor architecture for isothermal detection of double-stranded DNA, small molecules, and oligonucleotides. ChemBioChem, volume 16, pages 725-730, 2015.
    This paper was selected to appear on the journal cover.
    [MC-E] [abstract] [bib] [doi: 10.1002/cbic.201402615]

  6. M. R. Lakin, C. W. Brown. III, E. K. Horwitz, M. L. Fanning, H. E. West, D. Stefanovic, and S. W. Graves, Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering. PLoS ONE, volume 9, number 10, e110986, 2014.
    [MC-E] [abstract] [bib] [doi: 10.1371/journal.pone.0110986]

  7. C. W. Brown, III, M. R. Lakin, E. K. Horwitz, M. L. Fanning, H. E. West, D. Stefanovic, and S. W. Graves, Signal propagation in multi-layer DNAzyme cascades using structured chimeric substrates. Angewandte Chemie, volume 53, number 28, pages 7183-7187, 2014.
    This paper was selected as a "Hot Paper." Hot Papers are chosen by the Editors for their importance in a rapidly evolving field of high current interest.
    [MC-E] [abstract] [bib] [doi: 10.1002/anie.201402691]

  8. M. R. Lakin, A. Minnich, T. Lane, and D. Stefanovic, Design of a biochemical circuit motif for learning linear functions. Journal of the Royal Society Interface, volume 11, number 101, 20140902, 2014.
    [MC-T] [abstract] [bib] [doi: 10.1098/rsif.2014.0902]

  9. C. W. Brown III, M. R. Lakin, D. Stefanovic, and S. W. Graves, Catalytic molecular logic devices by DNAzyme displacement. ChemBioChem, volume 15, pages 950-954, 2014.
    This paper was selected to appear on the journal cover.
    [MC-E] [abstract] [bib] [doi: 10.1002/cbic.201400047]

  10. M. R. Lakin and A. 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.
    [PL] [abstract] [bib] [pdf] [doi: 10.1017/S0956796813000245]

  11. P. Banda, C. Teuscher, and M. R. Lakin, Online learning in a chemical perceptron. Artificial Life, volume 19, number 2, pages 195-219, 2013.
    [MC-T] [abstract] [bib] [doi: 10.1162/ARTL_a_00105]

  12. M. R. Lakin, D. Parker, L. Cardelli, M. Kwiatkowska, and A. 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.
    [MC-T] [abstract] [bib] [doi: 10.1098/rsif.2011.0800]

  13. M. R. Lakin, L. Paulevé, and A. Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science, volume 431, pages 181-206, 2012.
    [MC-T] [abstract] [bib] [doi: 10.1016/j.tcs.2011.12.057]

  14. M. R. Lakin, S. Youssef, L. Cardelli, and A. Phillips. Abstractions for DNA circuit design. Journal of the Royal Society Interface, volume 9, number 68, pages 470-486, 2012.
    [MC-T] [abstract] [bib] [doi: 10.1098/rsif.2011.0343]

  15. M. R. Lakin, S. Youssef, F. Polo, S. Emmott, and A. Phillips. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics, volume 27, issue 22, pages 3211-3213, 2011.
    [MC-T] [abstract] [bib] [doi: 10.1093/bioinformatics/btr543]

  16. M. R. Lakin and A. M. Pitts, Encoding abstract syntax without fresh names. Journal of Automated Reasoning, volume 49, number 2, pages 115-140, 2012.
    [PL] [abstract] [bib] [doi: 10.1007/s10817-011-9220-7]

  17. M. R. Lakin. Constraint solving in non-permutative nominal abstract syntax. Logical Methods in Computer Science, volume 7 (3:06), pages 1-31, 2011.
    [PL] [abstract] [bib] [doi: 10.2168/LMCS-7(3:6)2011]

Conference publications

  1. M. R. Lakin and D. Stefanovic, Supervised learning in an adaptive DNA strand displacement circuit. In A. Phillips and P. Yin (eds.), Proceedings of the 21st International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 9211, pages 154-167, 2015.
    [MC-T] [abstract] [bib] [draft pdf] [doi: 10.1007/978-3-319-21999-8_10]

  2. D. Mo, M. R. Lakin, and D. Stefanovic, Scalable design of logic circuits using an active molecular spider system. In M. Lones, A. Tyrrell, S.Smith, and G. 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, 2015.
    [MC-T] [abstract] [bib] [doi: 10.1007/978-3-319-23108-2_2]

  3. M. R. Lakin, R. Petersen, K. E. Gray, and A. Phillips. Abstract modelling of tethered DNA circuits. In S. Murata and S. 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-Verlag, 2014.
    [MC-T] [abstract] [bib] [pdf] [appendices] [doi: 10.1007/978-3-319-11295-4_9]

  4. M. R. Lakin and D. Stefanovic, Pattern formation by spatially organized approximate majority reactions. In O. H. Ibarra, L. Kari and S. Kopecki (eds.), UCNC 2014, Lecture Notes in Computer Science, volume 8553, pages 254-266, Springer-Verlag, 2014.
    [MC-T] [abstract] [bib] [pdf] [doi: 10.1007/978-3-319-08123-6_21]

  5. M. R. Lakin and A. 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.
    [PL] [abstract] [bib] [pdf] [doi: 10.1007/978-3-319-04132-2_6]

  6. A. Goudarzi, M. R. Lakin, D. Stefanovic, and C. 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, 2014.
    [DS] [abstract] [bib] [pdf] [doi: 10.1109/NANOARCH.2014.6880504]

  7. A. Goudarzi, M. R. Lakin, and D. Stefanovic, Reservoir computing approach to robust computation using unreliable nanoscale networks. In O. H. Ibarra, L. Kari and S. Kopecki (eds.), UCNC 2014, Lecture Notes in Computer Science, volume 8553, pages 164-176, Springer-Verlag, 2014.
    [DS] [abstract] [bib] [pdf] [doi: 10.1007/978-3-319-08123-6_14]

  8. M. R. Lakin, A. Phillips, and D. 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. (This paper was selected as a "conference highlight".)
    [MC-T] [abstract] [bib] [pdf] [appendices] [doi: 10.1007/978-3-319-01928-4_10]

  9. A. Goudarzi, M. R. Lakin, and D. 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.
    [DS] [abstract] [bib] [pdf] [appendices] [doi: 10.1007/978-3-319-01928-4_6]

  10. M. R. Lakin, A. Minnich, T. Lane, and D. Stefanovic, Towards a biomolecular learning machine. In J. Durand-Lose and N. Jonoska (eds.): UCNC 2012, Lecture Notes in Computer Science, volume 7445, pages 152-163, Springer-Verlag, 2012.
    [MC-T] [abstract] [bib] [doi: 10.1007/978-3-642-32894-7_15]

  11. M. R. Lakin and A. 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.
    [MC-T] [abstract] [bib] [supplementary files] [doi: 10.1007/978-3-642-23638-9_12]

  12. A. Phillips, M. R. Lakin, and L. 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.
    [MC-T] [abstract] [bib] [doi: 10.4204/EPTCS.40.1]

  13. L. Paulevé, S. Youssef, M. R. Lakin, and A. 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.
    [MC-T] [abstract] [bib] [doi: 10.1145/1839764.1839771]

  14. M. R. Lakin and A. M. Pitts. Resolving inductive definitions with binders in higher-order typed functional programming. In Programming Languages and Systems: Proceedings of the 18th European Symposium on Programming (ESOP 2009), York, UK, Lecture Notes in Computer Science, volume 5502, pages 47-61. Springer-Verlag, 2009.
    [PL] [abstract] [bib] [pdf © 2009 Springer-Verlag] [doi: 10.1007/978-3-642-00590-9_4]

  15. M. R. Lakin and A. M. Pitts. A metalanguage for structural operational semantics. In M. T. Morazán (ed.), Trends in Functional Programming, volume 8, pages 19-35. Intellect, 2008.
    [PL] [abstract] [bib] [pdf © 2008 Intellect]

Ph.D. dissertation


Software


Teaching

At the University of New Mexico, I have lectured for the following courses:

At the University of Cambridge, I supervised the following courses for Queens' College, New Hall, and various other colleges:

My supervision question sets use the following convention for naming tripos questions: year of examination followed by CST paper number (in roman numerals) followed by question number.


Sun May 1 19:27:33 MDT 2016