On the Design of Oligos for Gene Synthesis. - Chris Thachuk; Anne Condon (BIBE, 2007)

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

Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. - Anne Condon; Ján Manuch; Chris Thachuk (COCOON, 2008)

NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. - Ján Manuch; Chris Thachuk; Ladislav Stacho; Anne Condon (DNA, 2009)

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

Complexity of Finding Non-Planar Rectilinear Drawings of Graphs. - Ján Manuch; Murray Patterson; Sheung-Hung Poon; Chris Thachuk (GD, 2010)

An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. - Chris Thachuk; Ján Manuch; Arash Rafiey; Leigh-Anne Mathieson; Ladislav Stacho; Anne Condon (Pacific Symposium on Biocomputing, 2010)

Succincter Text Indexing with Wildcards. - Chris Thachuk (CPM, 2011)

Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems. - Anne Condon; Alan J. Hu; Ján Manuch; Chris Thachuk (DNA, 2011)

A Succinct Index for Hypertext. - Chris Thachuk (SPIRE, 2011)

NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. - Ján Manuch; Chris Thachuk; Ladislav Stacho; Anne Condon (Nat. Comput., 2011)

Space and Energy Efficient Computation with DNA Strand Displacement Systems. - Chris Thachuk; Anne Condon (DNA, 2012)

Efficient codon optimization with motif engineering. - Anne Condon; Chris Thachuk (J. Discrete Algorithms, 2012)

Logically and Physically Reversible Natural Computing: A Tutorial. - Chris Thachuk (RC, 2013)

Indexing hypertext. - Chris Thachuk (J. Discrete Algorithms, 2013)

Compressed indexes for text with wildcards. - Chris Thachuk (Theor. Comput. Sci., 2013)

Fast Algorithmic Self-assembly of Simple Shapes Using Random Agitation. - Ho-Lin Chen; David Doty; Dhiraj Holden; Chris Thachuk; Damien Woods; Chun-Tao Yang (DNA, 2014)

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

Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. - Joseph Malcolm Schaeffer; Chris Thachuk; Erik Winfree (DNA, 2015)

Leakless DNA Strand Displacement Systems. - Chris Thachuk; Erik Winfree; David Soloveichik (DNA, 2015)

The complexity of string partitioning. - Anne Condon; Ján Manuch; Chris Thachuk (J. Discrete Algorithms, 2015)

DNA walker circuits: computational potential, design, and verification. - Frits Dannenberg; Marta Z. Kwiatkowska; Chris Thachuk; Andrew J. Turberfield (Nat. Comput., 2015)

Progressive Alignment of Shapes. - Ashwin Gopinath; David G. Kirkpatrick; Paul W. K. Rothemund; Chris Thachuk (CCCG, 2016)

Preface. - Marta Kwiatkowska; Andrew Phillips; Chris Thachuk (Theor. Comput. Sci., 2016)

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 (DNA, 2017)

Thermodynamic Binding Networks. - David Doty; Trent A. Rogers; David Soloveichik; Chris Thachuk; Damien Woods (DNA, 2017)

The Design Space of Strand Displacement Cascades with Toehold-Size Clamps. - Boya Wang; Chris Thachuk; Andrew D. Ellington; David Soloveichik (DNA, 2017)

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 001; Chris Thachuk; Erik Winfree (DNA, 2017)

Computing properties of stable configurations of thermodynamic binding networks. - Keenan Breik; Lakshmi Prakash; Chris Thachuk; Marijn Heule; David Soloveichik (CoRR, 2017)

Computing properties of stable configurations of thermodynamic binding networks. - Keenan Breik; Chris Thachuk; Marijn Heule; David Soloveichik (Theor. Comput. Sci., 2019)

Verifying chemical reaction network implementations: A pathway decomposition approach. - Seung Woo Shin; Chris Thachuk; Erik Winfree (Theor. Comput. Sci., 2019)

Predicting Minimum Free Energy Structures of Multi-Stranded Nucleic Acid Complexes Is APX-Hard. - Anne Condon; Monir Hajiaghayi; Chris Thachuk (DNA, 2021)

Fast and Robust Strand Displacement Cascades via Systematic Design Strategies. - Tiernan Kennedy; Cadence Pearce; Chris Thachuk (DNA, 2022)

Fridge Compiler: Optimal Circuits from Molecular Inventories. - Lancelot Wathieu; Gus Henry Smith; Luis Ceze; Chris Thachuk (CMSB, 2023)

Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. - Ahmed Shalaby 005; Chris Thachuk; Damien Woods (DNA, 2023)

Leakless Polymerase-Dependent Strand Displacement Systems. - Zoë Evelyn Mohalakealoha Derauf; Chris Thachuk (DNA, 2025)