Morphometric grayscale texture analysis using foot patterns. - Dan Ashlock; Dean C. Adams; David Doty (IEEE Congress on Evolutionary Computation, 2003)

Nonlocal evolutionary adaptation in gridplants. - David Doty (IEEE Congress on Evolutionary Computation, 2004)

Zeta-Dimension. - David Doty; Xiaoyang Gu; Jack H. Lutz; Elvira Mayordomo; Philippe Moser (MFCS, 2005)

Every Sequence Is Decompressible from a Random One. - David Doty (CiE, 2006)

Finite-State Dimension and Lossy Decompressors - David Doty; Philippe Moser (CoRR, 2006)

Dimension Extractors. - David Doty (Electron. Colloquium Comput. Complex., 2006)

Finite-State Dimension and Real Arithmetic. - David Doty; Jack H. Lutz; Satyadev Nandakumar (Electron. Colloquium Comput. Complex., 2006)

Constructive Dimension and Weak Truth-Table Degrees. - Laurent Bienvenu; David Doty; Frank Stephan 001 (CiE, 2007)

Feasible Depth. - David Doty; Philippe Moser (CiE, 2007)

Pushdown dimension. - David Doty; Jared Nichols (Theor. Comput. Sci., 2007)

Limitations of Self-Assembly at Temperature One (extended abstract) - David Doty; Matthew J. Patitz; Scott M. Summers (CSP, 2008)

Dimension Extractors and Optimal Decompression. - David Doty (Theory Comput. Syst., 2008)

A Domain-Specific Language for Programming in the Tile Assembly Model. - David Doty; Matthew J. Patitz (DNA, 2009)

Limitations of Self-assembly at Temperature One. - David Doty; Matthew J. Patitz; Scott M. Summers (DNA, 2009)

Random Number Selection in Self-assembly. - David Doty; Jack H. Lutz; Matthew J. Patitz; Scott M. Summers; Damien Woods (UC, 2009)

Constructive Dimension and Turing Degrees. - Laurent Bienvenu; David Doty; Frank Stephan 001 (Theory Comput. Syst., 2009)

Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. - Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki 001 (DNA, 2010)

Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature. - David Doty; Matthew J. Patitz; Dustin Reishus; Robert T. Schweller; Scott M. Summers (FOCS, 2010)

Intrinsic Universality in Self-Assembly. - David Doty; Jack H. Lutz; Matthew J. Patitz; Scott M. Summers; Damien Woods (STACS, 2010)

An Oracle Strongly Separating Deterministic Time from Nondeterministic Time, via Kolmogorov Complexity - David Doty (CoRR, 2010)

The Power of Nondeterminism in Self-Assembly. - Nathaniel Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki 001 (Electron. Colloquium Comput. Complex., 2010)

Parallelism, Program Size, Time, and Temperature in Self-Assembly. - Ho-Lin Chen; David Doty; Shinnosuke Seki 001; David Soloveichik (Electron. Colloquium Comput. Complex., 2010)

Randomized Self-Assembly for Exact Shapes. - David Doty (SIAM J. Comput., 2010)

Limitations of self-assembly at temperature 1. - David Doty; Matthew J. Patitz; Scott M. Summers (Theor. Comput. Sci., 2011)

The Tile Assembly Model is Intrinsically Universal. - David Doty; Jack H. Lutz; Matthew J. Patitz; Robert T. Schweller; Scott M. Summers; Damien Woods (FOCS, 2012)

Theory of algorithmic self-assembly. - David Doty (Commun. ACM, 2012)

Negative Interactions in Irreversible Self-assembly. - David Doty; Lila Kari; Benoît Masson (Algorithmica, 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)

Rate-independent computation in continuous chemical reaction networks. - Ho-Lin Chen; David Doty; David Soloveichik (ITCS, 2014)

Timing in chemical reaction networks. - David Doty (SODA, 2014)

Deterministic function computation with chemical reaction networks. - Ho-Lin Chen; David Doty; David Soloveichik (Nat. Comput., 2014)

Program Size and Temperature in Self-Assembly. - Ho-Lin Chen; David Doty; Shinnosuke Seki 001 (Algorithmica, 2015)

Leaderless deterministic chemical reaction networks. - David Doty; Monir Hajiaghayi (Nat. Comput., 2015)

Robustness of Expressivity in Chemical Reaction Networks. - Robert Brijder; David Doty; David Soloveichik (DNA, 2016)

Pattern overlap implies runaway growth in hierarchical tile systems. - David Doty; Ho-Lin Chen; Ján Manuch; Arash Rafiey; Ladislav Stacho (J. Comput. Geom., 2016)

Probability 1 computation with chemical reaction networks. - Rachel Cummings; David Doty; David Soloveichik (Nat. Comput., 2016)

Producibility in hierarchical self-assembly. - David Doty (Nat. Comput., 2016)

Hierarchical Self-Assembly. - David Doty (Encyclopedia of Algorithms, 2016)

Randomized Self-Assembly. - David Doty (Encyclopedia of Algorithms, 2016)

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

Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols. - Amanda Belleville; David Doty; David Soloveichik (ICALP, 2017)

Speed faults in computation by chemical reaction networks. - Ho-Lin Chen; Rachel Cummings; David Doty; David Soloveichik (Distributed Comput., 2017)

Parallelism and Time in Hierarchical Self-Assembly. - Ho-Lin Chen; David Doty (SIAM J. Comput., 2017)

Design of Geometric Molecular Bonds. - David Doty; Andrew Winslow (IEEE Trans. Mol. Biol. Multi Scale Commun., 2017)

Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time. - David Doty; Mahsa Eftekhari; Othon Michail; Paul G. Spirakis; Michail Theofilatos (DISC, 2018)

Exact size counting in uniform population protocols in nearly logarithmic time. - David Doty; Mahsa Eftekhari; Othon Michail; Paul G. Spirakis; Michail Theofilatos (CoRR, 2018)

Stable leader election in population protocols requires linear time. - David Doty; David Soloveichik (Distributed Comput., 2018)

Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks. - Robert Brijder; David Doty; David Soloveichik (Nat. Comput., 2018)

Computational complexity of atomic chemical reaction networks. - David Doty; Shaopeng Zhu (Nat. Comput., 2018)

Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols. - David Doty; Mahsa Eftekhari (PODC, 2019)

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. - Damien Woods; David Doty; Cameron Myhrvold; Joy Hui; Felix Zhou 001; Peng Yin; Erik Winfree (Nat., 2019)

scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. - David Doty; Benjamin L. Lee; Tristan Stérin (DNA, 2020)

Message Complexity of Population Protocols. - Talley Amir; James Aspnes; David Doty; Mahsa Eftekhari; Eric E. Severson (DISC, 2020)

scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures. - David Doty; Benjamin L. Lee; Tristan Stérin (CoRR, 2020)

Preface. - David Doty; Hendrik Dietz (Nat. Comput., 2020)

Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols. - David Doty; Eric E. Severson (CMSB, 2021)

Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. - David Haley; David Doty (DNA, 2021)

A time and space optimal stable population protocol solving exact majority. - David Doty; Mahsa Eftekhari; Leszek Gasieniec; Eric E. Severson; Przemyslaw Uznanski; Grzegorz Stachowiak (FOCS, 2021)

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 002 (PODC, 2021)

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 (PODC, 2021)

Composable computation in discrete chemical reaction networks. - Eric E. Severson; David Haley; David Doty (Distributed Comput., 2021)

Preface. - David Doty; Rudolf Freund; Natasa Jonoska; Jarkko Kari (Nat. Comput., 2021)

Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks. - Keenan Breik; Cameron T. Chalk; David Doty; David Haley; David Soloveichik (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A survey of size counting in population protocols. - David Doty; Mahsa Eftekhari (Theor. Comput. Sci., 2021)

Dynamic Size Counting in Population Protocols. - David Doty; Mahsa Eftekhari (SAND, 2022)

Simulating 3-Symbol Turing Machines with SIMD||DNA. - David Doty; Aaron Ong (SAND, 2022)

Accelerating Self-Assembly of Crisscross Slat Systems. - David Doty; Hunter Fleming; Daniel Hader; Matthew J. Patitz; Lukas A. Vaughan (DNA, 2023)

Optimal Information Encoding in Chemical Reaction Networks. - Austin Luchsinger; David Doty; David Soloveichik (DNA, 2023)

Thermodynamically Driven Signal Amplification. - Joshua Petrack; David Soloveichik; David Doty (DNA, 2023)

Harvesting Brownian Motion: Zero Energy Computational Sampling. - David Doty; Niels Kornerup; Austin Luchsinger; Leo Orshansky; David Soloveichik; Damien Woods (CoRR, 2023)

Is stochastic thermodynamics the key to understanding the energy costs of computation? - David H. Wolpert; Jan Korbel; Christopher Lynn; Farita Tasnim; Joshua A. Grochow; Gülce Kardes; James B. Aimone; Vijay Balasubramanian; Eric De Giuli; David Doty; Nahuel Freitas; Matteo Marsili; et al. (CoRR, 2023)

Rate-independent Computation in Continuous Chemical Reaction Networks. - Ho-Lin Chen; David Doty; Wyatt Reeves; David Soloveichik (J. ACM, 2023)

Brief Announcement: Optimally Encoding Information in Chemical Reaction Networks. - Austin Luchsinger; David Doty; David Soloveichik (PODC, 2024)

Rate-Independent Continuous Inhibitory Chemical Reaction Networks Are Turing-Universal. - Kim Calabrese; David Doty (UCNC, 2024)

The Computational Power of Discrete Chemical Reaction Networks with Bounded Executions. - David Doty; Ben Heckmann (DISC, 2024)

Robust predicate and function computation in continuous chemical reaction networks. - Kim Calabrese; David Doty; Mina Latifi (CoRR, 2025)

Exactly simulating stochastic chemical reaction networks in sub-constant time per reaction. - Joshua Petrack; David Doty (CoRR, 2025)

Analog computation with transcriptional networks. - David Doty; Mina Latifi; David Soloveichick (CoRR, 2025)