| 2025 | DNA | A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs. | Hope Amber Johnson, Anne Condon |
| 2023 | DNA | On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions. | Anne Condon, Yuval Emek, Noga Harlev |
| 2023 | DNA | Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. | Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon |
| 2022 | DNA | A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems. | Hope Amber Johnson, Anne Condon |
| 2021 | DNA | Predicting Minimum Free Energy Structures of Multi-Stranded Nucleic Acid Complexes Is APX-Hard. | Anne Condon, Monir Hajiaghayi, Chris Thachuk |
| 2020 | DNA | Composable Computation in Leaderless, Discrete Chemical Reaction Networks. | Hooman Hashemi, Ben Chugg, Anne Condon |
| 2019 | DNA | Error-Free Stable Computation with Polymer-Supplemented Chemical Reaction Networks. | Allison Tai, Anne Condon |
| 2019 | DNA | Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains. | Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Ct, Mark Schmidt, Anne Condon |
| 2018 | OPODIS | Output-Oblivious Stochastic Chemical Reaction Networks. | Ben Chugg, Hooman Hashemi, Anne Condon |
| 2017 | DNA | Simplifying Analyses of Chemical Reaction Networks for Approximate Majority. | Anne Condon, Monir Hajiaghayi, David G. Kirkpatrick, Jn Manuch |
| 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 | On Low Energy Barrier Folding Pathways for Nucleic Acid Sequences. | Leigh-Anne Mathieson, Anne Condon |
| 2012 | CPM | The Complexity of String Partitioning. | Anne Condon, Jn Manuch, Chris Thachuk |
| 2012 | DNA | Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems. | Anne Condon, Bonnie Kirkpatrick, Jn Manuch |
| 2012 | DNA | Space and Energy Efficient Computation with DNA Strand Displacement Systems. | Chris Thachuk, Anne Condon |
| 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 |
| 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 |
| 2009 | SODA | Stepwise randomized combinatorial auctions achieve revenue monotonicity. | Baharak Rastegari, Anne Condon, Kevin Leyton-Brown |
| 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 |
| 2008 | UC | Computational Challenges and Opportunities in the Design of Unconventional Machines from Nucleic Acids. | Anne Condon |
| 2007 | AAAI | Revenue Monotonicity in Combinatorial Auctions. | Baharak Rastegari, Anne Condon, Kevin Leyton-Brown |
| 2007 | BIBE | On the Design of Oligos for Gene Synthesis. | Chris Thachuk, Anne Condon |
| 2007 | ISMB | Efficient parameter estimation for RNA secondary structure prediction. | Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy |
| 2007 | WABI | HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding. | Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop, Yinglei Zhao |
| 2006 | LATIN | RNA Molecules: Glimpses Through an Algorithmic Lens. | Anne Condon |
| 2006 | PODS | Flow algorithms for two pipelined filter ordering problems. | Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu |
| 2005 | WABI | Linear Time Algorithm for Parsing RNA Secondary Structure. | Baharak Rastegari, Anne Condon |
| 2004 | CAV | Automatic Verification of Sequential Consistency for Unbounded Addresses and Data Values. | Jesse D. Bingham, Anne Condon, Alan J. Hu, Shaz Qadeer, Zhichuan Zhang |
| 2003 | ICALP | Problems on RNA Secondary Structure Prediction and Design. | Anne Condon |
| 2003 | SPAA | Toward a decidable notion of sequential consistency. | Jesse D. Bingham, Anne Condon, Alan J. Hu |
| 2002 | DNA | Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure. | Mirela Andronescu, Danielle Dees, Laura Slaybaugh, Yinglei Zhao, Anne Condon, Barry Cohen, Steven Skiena |
| 2002 | DNA | From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. | Christine E. Heitsch, Anne Condon, Holger H. Hoos |
| 2002 | DNA | Stochastic Local Search Algorithms for DNA Word Design. | Dan C. Tulpan, Holger H. Hoos, Anne Condon |
| 2001 | SPAA | Automatable verification of sequential consistency. | Anne Condon, Alan J. Hu |
| 1999 | AAAI | On the Undecidability of Probabilistic Planning and Infinite-Horizon Partially Observable Markov Decision Problems. | Omid Madani, Steve Hanks, Anne Condon |
| 1999 | HPCA | Using Lamport Clocks to Reason about Relaxed Memory Models. | Anne Condon, Mark D. Hill, Manoj Plakal, Daniel J. Sorin |
| 1999 | SPAA | A System-Level Specification Framework for I/O Architectures. | Mark D. Hill, Anne Condon, Manoj Plakal, Daniel J. Sorin |
| 1998 | SPAA | Lamport Clocks: Verifying a Directory Cache-Coherence Protocol. | Manoj Plakal, Daniel J. Sorin, Anne Condon, Mark D. Hill |
| 1997 | RECOMB | The power of surface-based DNA computation (extended abstract). | Weiping Cai, Anne Condon, Robert M. Corn, Elton Glaser, Zhengdong Fei, Tony Frutos, Zhen Guo, Max G. Lagally, Qinghua Liu, Lloyd M. Smith, Andrew Thiel |
| 1994 | STOC | On the power of finite automata with both nondeterministic and probabilistic states (preliminary version). | Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson |
| 1993 | STOC | Probabilistically checkable debate systems and approximation algorithms for PSPACE-hard functions. | Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor |
| 1993 | SIGMETRICS | Asynchronous Analysis of Parallel Dynamic Programming. | Gary Lewandowski, Anne Condon, Eric Bach |
| 1992 | STACS | A Theory of Strict P-completeness. | Anne Condon |
| 1991 | STACS | The Complexity of the Max Word Problem. | Anne Condon |
| 1990 | STACS | Playing Games of Incomplete Information. | Jin-yi Cai, Anne Condon, Richard J. Lipton |
| 1989 | FOCS | On the Complexity of Space Bounded Interactive Proofs (Extended Abstract) | Anne Condon, Richard J. Lipton |