Publications

Publications marked with list authors in alphabetical order, as is common in mathematics and theoretical computer science.
Ashwin Gopinath, Chris Thachuk, Anya Mitskovets, Harry A. Atwater, David Kirkpatrick, Paul W. K. Rothemund (2021). Absolute and arbitrary orientation of single-molecule shapes. Science.

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Anne Condon, Chris Thachuk (2019). Towards space- and energy-efficient computations. The Energetics of Computing in Life and Machines.

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Keenan Breik, Chris Thachuk, Marijn Heule, David Soloveichik (2019). Computing properties of stable configurations of thermodynamic binding networks. Theoretical Computer Science.

Boya Wang, Chris Thachuk, Andrew D Ellington, Erik Winfree, David Soloveichik (2018). Effective design principles for leakless strand displacement systems. Proceedings of the National Academy of Sciences.

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Ashwin Gopinath, Chris Thachuk, Anya Mitskovets, Harry A Atwater, David Kirkpatrick, Paul WK Rothemund (2018). Absolute and arbitrary orientation of single molecule shapes. arXiv preprint arXiv:1808.04544.

Seung Woo Shin, Chris Thachuk, Erik Winfree (2017). Verifying chemical reaction network implementations: A pathway decomposition approach. Theoretical Computer Science.

David Doty, Trent A Rogers, David Soloveichik, Chris Thachuk, Damien Woods (2017). Thermodynamic binding networks. International Conference on DNA-Based Computers.

Boya Wang, Chris Thachuk, Andrew D Ellington, David Soloveichik (2017). The design space of strand displacement cascades with toehold-size clamps. International Conference on DNA-Based Computers.

Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree (2017). Inferring parameters for an elementary step model of DNA structure kinetics with locally context-dependent Arrhenius rates. International Conference on DNA-Based Computers.

Anupama J Thubagere, Chris Thachuk, Joseph Berleant, Robert F Johnson, Diana A Ardelean, Kevin M Cherry, Lulu Qian (2017). Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components. Nature communications.

Stefan Badelt, Seung Woo Shin, Robert F Johnson, Qing Dong, Chris Thachuk, Erik Winfree (2017). A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities. International Conference on DNA-Based Computers.

Ashwin Gopinath, David G Kirkpatrick, Paul WK Rothemund, Chris Thachuk (2016). Progressive Alignment of Shapes. CCCG.

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Chris Thachuk, Erik Winfree, David Soloveichik (2015). Leakless DNA strand displacement systems. International Workshop on DNA Computing and Molecular Programming.

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Anne Condon, Ján Maňuch, Chris Thachuk (2015). The complexity of string partitioning. Journal of Discrete Algorithms.

Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree (2015). Stochastic simulation of the kinetics of multiple interacting nucleic acid strands. International Workshop on DNA-Based Computers.

Frits Dannenberg, Marta Kwiatkowska, Chris Thachuk, Andrew J Turberfield (2015). DNA walker circuits: computational potential, design, and verification. Natural Computing.

Marta Z Kwiatkowska, Chris Thachuk (2014). Probabilistic Model Checking for Biology. Software Systems Safety.

Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang (2014). Fast algorithmic self-assembly of simple shapes using random agitation. International Workshop on DNA-Based Computers.

Chris Thachuk (2013). Logically and physically reversible natural computing: a tutorial. International Conference on Reversible Computation.

Chris Thachuk (2013). Indexing hypertext. Journal of Discrete Algorithms.

Chris Thachuk (2013). Compressed indexes for text with wildcards. Theoretical Computer Science.

Chris Thachuk, Anne Condon (2012). Space and energy efficient computation with DNA strand displacement systems. International Workshop on DNA-Based Computers.

Anne Condon, Alan J Hu, Ján Maňuch, Chris Thachuk (2012). Less haste, less waste: on recycling and its limits in strand displacement systems. Interface focus.

Anne Condon, Chris Thachuk (2012). Efficient codon optimization with motif engineering. Journal of Discrete Algorithms.

Chris Thachuk (2011). Succincter text indexing with wildcards. Annual Symposium on Combinatorial Pattern Matching.

Ján Maňuch, Chris Thachuk, Ladislav Stacho, Anne Condon (2011). NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. Natural Computing.

Chris Thachuk (2011). A succinct index for hypertext. International Symposium on String Processing andInformation Retrieval.

Ján Maňuch, Murray Patterson, Sheung-Hung Poon, Chris Thachuk (2010). Complexity of finding non-planar rectilinear drawings of graphs. International Symposium on Graph Drawing.

Chris Thachuk, Ján Maňuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon (2010). An algorithm for the energy barrier problem without pseudoknots and temporary arcs. Biocomputing 2010.

Chris Thachuk, José Crossa, Jorge Franco, Susanne Dreisigacker, Marilyn Warburton, Guy F Davenport (2009). Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures. BMC bioinformatics.

Anne Condon, Ján Maňuch, Chris Thachuk (2008). Complexity of a collision-aware string partition problem and its relation to oligo design for gene synthesis. International Computing and Combinatorics Conference.

Chris Thachuk, Anne Condon (2007). On the design of oligos for gene synthesis. IEEE 7th International Symposium on BioInformatics andBioEngineering.

Chris Thachuk (2007). Novel algorithms for in vitro gene synthesis.

Chris Thachuk, Alena Shmygelska, Holger H Hoos (2007). A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC bioinformatics.

Jose Crossa, Jorge Franco, Suketoshi Taba, Marilyn Warburton, Chris Thachuk, Guy Davenport (2006). Sampling Strategies for Forming Core Subsets. 1-page abstract.