| 2024 | PODC | Brief Announcement: Optimally Encoding Information in Chemical Reaction Networks. | Austin Luchsinger, David Doty, David Soloveichik |
| 2024 | UC | Rate-Independent Continuous Inhibitory Chemical Reaction Networks Are Turing-Universal. | Kim Calabrese, David Doty |
| 2023 | DNA | Accelerating Self-Assembly of Crisscross Slat Systems. | David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, Lukas A. Vaughan |
| 2023 | DNA | Optimal Information Encoding in Chemical Reaction Networks. | Austin Luchsinger, David Doty, David Soloveichik |
| 2023 | DNA | Thermodynamically Driven Signal Amplification. | Joshua Petrack, David Soloveichik, David Doty |
| 2021 | DNA | Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. | David Haley, David Doty |
| 2021 | FOCS | A time and space optimal stable population protocol solving exact majority. | David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Przemyslaw Uznanski, Grzegorz Stachowiak |
| 2021 | PODC | Time-Optimal Self-Stabilizing Leader Election in Population Protocols. | Janna Burman, Ho-Lin Chen, Hsueh-Ping Chen, David Doty, Thomas Nowak, Eric E. Severson, Chuan Xu |
| 2021 | PODC | Brief Announcement: A Time and Space Optimal Stable Population Protocol Solving Exact Majority. | David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Grzegorz Stachowiak, Przemyslaw Uznanski |
| 2020 | DNA | scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. | David Doty, Benjamin L. Lee, Tristan Strin |
| 2019 | PODC | Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols. | David Doty, Mahsa Eftekhari |
| 2019 | PODC | Composable Computation in Discrete Chemical Reaction Networks. | Eric E. Severson, David Haley, David Doty |
| 2018 | SOFSEM | Computational Complexity of Atomic Chemical Reaction Networks. | David Doty, Shaopeng Zhu |
| 2017 | DNA | Thermodynamic Binding Networks. | David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods |
| 2017 | ICALP | Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols. | Amanda Belleville, David Doty, David Soloveichik |
| 2016 | DNA | Robustness of Expressivity in Chemical Reaction Networks. | Robert Brijder, David Doty, David Soloveichik |
| 2016 | ISIT | Design of geometric molecular bonds. | David Doty, Andrew Winslow |
| 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 |
| 2014 | DNA | Probability 1 Computation with Chemical Reaction Networks. | Rachel Cummings, David Doty, David Soloveichik |
| 2014 | SODA | Timing in chemical reaction networks. | David Doty |
| 2014 | UC | Producibility in Hierarchical Self-assembly. | David Doty |
| 2013 | DNA | Leaderless Deterministic Chemical Reaction Networks. | David Doty, Monir Hajiaghayi |
| 2012 | DNA | Deterministic Function Computation with Chemical Reaction Networks. | Ho-Lin Chen, David Doty, David Soloveichik |
| 2012 | FOCS | The Tile Assembly Model is Intrinsically Universal. | David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, Damien Woods |
| 2012 | SODA | Parallelism and time in hierarchical self-assembly. | Ho-Lin Chen, David Doty |
| 2011 | ISAAC | Program Size and Temperature in Self-Assembly. | Ho-Lin Chen, David Doty, Shinnosuke Seki |
| 2011 | SODA | The Power of Nondeterminism in Self-Assembly. | Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki |
| 2010 | DNA | Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. | Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki |
| 2010 | DNA | Negative Interactions in Irreversible Self-assembly. | David Doty, Lila Kari, Benot Masson |
| 2010 | FOCS | Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature. | David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, Scott M. Summers |
| 2010 | STACS | Intrinsic Universality in Self-Assembly. | David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods |
| 2009 | DNA | A Domain-Specific Language for Programming in the Tile Assembly Model. | David Doty, Matthew J. Patitz |
| 2009 | DNA | Limitations of Self-assembly at Temperature One. | David Doty, Matthew J. Patitz, Scott M. Summers |
| 2009 | FOCS | Randomized Self-Assembly for Exact Shapes. | David Doty |
| 2009 | UC | Random Number Selection in Self-assembly. | David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods |
| 2007 | CiE | Constructive Dimension and Weak Truth-Table Degrees. | Laurent Bienvenu, David Doty, Frank Stephan |
| 2007 | CiE | Feasible Depth. | David Doty, Philippe Moser |
| 2006 | CiE | Every Sequence Is Decompressible from a Random One. | David Doty |
| 2006 | ICALP | Finite-State Dimension and Real Arithmetic. | David Doty, Jack H. Lutz, Satyadev Nandakumar |
| 2005 | MFCS | Zeta-Dimension. | David Doty, Xiaoyang Gu, Jack H. Lutz, Elvira Mayordomo, Philippe Moser |
| 2004 | CEC | Nonlocal evolutionary adaptation in gridplants. | David Doty |
| 2003 | CEC | Morphometric grayscale texture analysis using foot patterns. | Dan Ashlock, Dean C. Adams, David Doty |