| 2025 | DNA | Leakless Polymerase-Dependent Strand Displacement Systems. | Zo Evelyn Mohalakealoha Derauf, Chris Thachuk |
| 2023 | DNA | Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. | Ahmed Shalaby, Chris Thachuk, Damien Woods |
| 2022 | DNA | Fast and Robust Strand Displacement Cascades via Systematic Design Strategies. | Tiernan Kennedy, Cadence Pearce, Chris Thachuk |
| 2021 | DNA | Predicting Minimum Free Energy Structures of Multi-Stranded Nucleic Acid Complexes Is APX-Hard. | Anne Condon, Monir Hajiaghayi, Chris Thachuk |
| 2017 | DNA | A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. | Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, Erik Winfree |
| 2017 | DNA | Thermodynamic Binding Networks. | David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods |
| 2017 | DNA | The Design Space of Strand Displacement Cascades with Toehold-Size Clamps. | Boya Wang, Chris Thachuk, Andrew D. Ellington, David Soloveichik |
| 2017 | DNA | Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates. | Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree |
| 2015 | DNA | Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. | Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree |
| 2015 | DNA | Leakless DNA Strand Displacement Systems. | Chris Thachuk, Erik Winfree, David Soloveichik |
| 2014 | DNA | Fast Algorithmic Self-assembly of Simple Shapes Using Random Agitation. | Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang |
| 2013 | DNA | DNA Walker Circuits: Computational Potential, Design, and Verification. | Frits Dannenberg, Marta Z. Kwiatkowska, Chris Thachuk, Andrew J. Turberfield |
| 2013 | RC | Logically and Physically Reversible Natural Computing: A Tutorial. | Chris Thachuk |
| 2012 | CPM | The Complexity of String Partitioning. | Anne Condon, Jn Manuch, Chris Thachuk |
| 2012 | DNA | Space and Energy Efficient Computation with DNA Strand Displacement Systems. | Chris Thachuk, Anne Condon |
| 2011 | CPM | Succincter Text Indexing with Wildcards. | Chris Thachuk |
| 2011 | DNA | Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems. | Anne Condon, Alan J. Hu, Jn Manuch, Chris Thachuk |
| 2011 | IWOCA | Efficient Codon Optimization with Motif Engineering. | Anne Condon, Chris Thachuk |
| 2011 | SPIRE | A Succinct Index for Hypertext. | Chris Thachuk |
| 2010 | GD | Complexity of Finding Non-Planar Rectilinear Drawings of Graphs. | Jn Manuch, Murray Patterson, Sheung-Hung Poon, Chris Thachuk |
| 2010 | PSB | An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. | Chris Thachuk, Jn Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon |
| 2009 | DNA | NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. | Jn Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon |
| 2008 | COCOON | Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. | Anne Condon, Jn Manuch, Chris Thachuk |
| 2007 | BIBE | On the Design of Oligos for Gene Synthesis. | Chris Thachuk, Anne Condon |