Anne Condon

According to our database, Anne Condon authored at least 112 papers between 1988 and 2023.

Collaborative distances:

• Dijkstra number of two.
• Erdős number of three.

2023

Factorization and pseudofactorization of weighted graphs.

Kristin Sheridan, Joseph Berleant, Mark Bathe, Anne Condon, Virginia Vassilevska Williams

Discret. Appl. Math., October, 2023

Isometric Hamming embeddings of weighted graphs.

Joseph Berleant, Kristin Sheridan, Anne Condon, Virginia Vassilevska Williams, Mark Bathe

Discret. Appl. Math., June, 2023

Predicting DNA kinetics with a truncated continuous-time Markov chain method.

Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt, Anne Condon, Erik Winfree

Comput. Biol. Chem., June, 2023

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps.

Aryan Tajmir Riahi, Geoffrey Woollard, Frédéric Poitevin, Anne Condon, Khanh Dao Duc

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings.

Chenwei Zhang, Jordan Lovrod, Boyan Beronov, Khanh Dao Duc, Anne Condon

CoRR, 2023

Visualizing DNA reaction trajectories with deep graph embedding approaches.

Chenwei Zhang, Khanh Dao Duc, Anne Condon

CoRR, 2023

Revisiting Hybridization Kinetics with Improved Elementary Step Simulation.

Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon

Proceedings of the 29th International Conference on DNA Computing and Molecular Programming, 2023

On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions.

Anne Condon, Yuval Emek, Noga Harlev

Proceedings of the 29th International Conference on DNA Computing and Molecular Programming, 2023

2022

A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems.

Hope Amber Johnson, Anne Condon

Proceedings of the 28th International Conference on DNA Computing and Molecular Programming, 2022

2021

Predicting Minimum Free Energy Structures of Multi-Stranded Nucleic Acid Complexes Is APX-Hard.

Anne Condon, Monir Hajiaghayi, Chris Thachuk

Proceedings of the 27th International Conference on DNA Computing and Molecular Programming, 2021

2020

Approximate majority analyses using tri-molecular chemical reaction networks.

Anne Condon, Monir Hajiaghayi, David G. Kirkpatrick, Ján Manuch

Nat. Comput., 2020

Composable Computation in Leaderless, Discrete Chemical Reaction Networks.

Hooman Hashemi, Ben Chugg, Anne Condon

Proceedings of the 26th International Conference on DNA Computing and Molecular Programming, 2020

2019

Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains.

Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon

Proceedings of the DNA Computing and Molecular Programming - 25th International Conference, 2019

Error-Free Stable Computation with Polymer-Supplemented Chemical Reaction Networks.

Allison Tai, Anne Condon

Proceedings of the DNA Computing and Molecular Programming - 25th International Conference, 2019

2018

Preface.

Martyn Amos, Anne Condon

Nat. Comput., 2018

On Design and Analysis of Chemical Reaction Network Algorithms.

Anne Condon

Proceedings of the Implementation and Application of Automata, 2018

Output-Oblivious Stochastic Chemical Reaction Networks.

Ben Chugg, Hooman Hashemi, Anne Condon

Proceedings of the 22nd International Conference on Principles of Distributed Systems, 2018

2017

Design of nucleic acid strands with long low-barrier folding pathways.

Anne Condon, Bonnie Kirkpatrick, Ján Manuch

Nat. Comput., 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, Chris Thachuk, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

Simplifying Analyses of Chemical Reaction Networks for Approximate Majority.

Anne Condon, Monir Hajiaghayi, David G. Kirkpatrick, Ján Manuch

Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

2016

densityCut: an efficient and versatile topological approach for automatic clustering of biological data.

Jiarui Ding, Sohrab P. Shah, Anne Condon

Bioinform., 2016

2015

The complexity of string partitioning.

Anne Condon, Ján Manuch, Chris Thachuk

J. Discrete Algorithms, 2015

On Low Energy Barrier Folding Pathways for Nucleic Acid Sequences.

Leigh-Anne Mathieson, Anne Condon

Proceedings of the DNA Computing and Molecular Programming - 21st International Conference, 2015

2014

Reachability bounds for chemical reaction networks and strand displacement systems.

Anne Condon, Bonnie Kirkpatrick, Ján Manuch

Nat. Comput., 2014

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.

Hosna Jabbari, Anne Condon

BMC Bioinform., 2014

Reasoning about optimal stable matchings under partial information.

Baharak Rastegari, Anne Condon, Nicole Immorlica, Robert W. Irving, Kevin Leyton-Brown

Proceedings of the ACM Conference on Economics and Computation, 2014

2013

Two-sided matching with partial information.

Baharak Rastegari, Anne Condon, Nicole Immorlica, Kevin Leyton-Brown

Proceedings of the fourteenth ACM Conference on Electronic Commerce, 2013

2012

Efficient codon optimization with motif engineering.

Anne Condon, Chris Thachuk

J. Discrete Algorithms, 2012

Analysis of energy-based algorithms for RNA secondary structure prediction.

Monir Hajiaghayi, Anne Condon, Holger H. Hoos

BMC Bioinform., 2012

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.

Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A. Marra, Anne Condon, Sam Aparicio, Sohrab P. Shah

Bioinform., 2012

Space and Energy Efficient Computation with DNA Strand Displacement Systems.

Chris Thachuk, Anne Condon

Proceedings of the DNA Computing and Molecular Programming - 18th International Conference, 2012

2011

NP-completeness of the energy barrier problem without pseudoknots and temporary arcs.

Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon

Nat. Comput., 2011

Molecular programming: DNA and the brain.

Anne Condon

Nat., 2011

Revenue monotonicity in deterministic, dominant-strategy combinatorial auctions.

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown

Artif. Intell., 2011

Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems.

Anne Condon, Alan J. Hu, Ján Manuch, Chris Thachuk

Proceedings of the DNA Computing and Molecular Programming - 17th International Conference, 2011

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

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges.

Anne Condon, Hosna Jabbari

Theor. Comput. Sci., 2009

Algorithms for distributional and adversarial pipelined filter ordering problems.

Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu

ACM Trans. Algorithms, 2009

An <i>O</i>(<i>n</i>⁵) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids.

Ho-Lin Chen, Anne Condon, Hosna Jabbari

J. Comput. Biol., 2009

Stepwise randomized combinatorial auctions achieve revenue monotonicity.

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown

Proceedings of the Twentieth Annual ACM-SIAM Symposium on Discrete Algorithms, 2009

NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots.

Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon

Proceedings of the DNA Computing and Molecular Programming, 15th International Conference, 2009

2008

Women in Computing.

Denise W. Gürer, Jennifer Light, Christina Björkman, Rhian Davies, Mark S. Hancock, Anne Condon, Annemieke Craig, Vashti Galpin, Ursula Martin, Margit Pohl, Sylvia Wiltner, M. Suriya, Ellen Spertus, Joanne McGrath Cohoon, Gloria Childress Townsend, Paula Gabbert

Proceedings of the Wiley Encyclopedia of Computer Science and Engineering, 2008

Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding.

Hosna Jabbari, Anne Condon, Shelly Zhao

J. Comput. Biol., 2008

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database.

Mirela Andronescu, Vera Bereg, Holger H. Hoos, Anne Condon

BMC Bioinform., 2008

Computational Challenges and Opportunities in the Design of Unconventional Machines from Nucleic Acids.

Anne Condon

Proceedings of the Unconventional Computing, 7th International Conference, 2008

Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis.

Anne Condon, Ján Manuch, Chris Thachuk

Proceedings of the Computing and Combinatorics, 14th Annual International Conference, 2008

2007

Revenue monotonicity in combinatorial auctions.

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown

SIGecom Exch., 2007

Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications.

Baharak Rastegari, Anne Condon

J. Comput. Biol., 2007

Computational RNA secondary structure design: empirical complexity and improved methods.

Rosalía Aguirre-Hernández, Holger H. Hoos, Anne Condon

BMC Bioinform., 2007

HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding.

Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop, Yinglei Zhao

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Efficient parameter estimation for RNA secondary structure prediction.

Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

On the Design of Oligos for Gene Synthesis.

Chris Thachuk, Anne Condon

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

Flow algorithms for two pipelined filter ordering problems.

Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu

Proceedings of the Twenty-Fifth ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, 2006

Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set.

Mirela Andronescu, Anne Condon

Proceedings of the Nanotechnology: Science and Computation, 2006

RNA Molecules: Glimpses Through an Algorithmic Lens.

Anne Condon

Proceedings of the LATIN 2006: Theoretical Informatics, 2006

2005

Linear Time Algorithm for Parsing RNA Secondary Structure.

Baharak Rastegari, Anne Condon

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2004

Classifying RNA pseudoknotted structures.

Anne Condon, Beth Davy, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant

Theor. Comput. Sci., 2004

Guest editor's foreword.

Anne Condon

J. Comput. Syst. Sci., 2004

Automatic Verification of Sequential Consistency for Unbounded Addresses and Data Values.

Jesse D. Bingham, Anne Condon, Alan J. Hu, Shaz Qadeer, Zhichuan Zhang

Proceedings of the Computer Aided Verification, 16th International Conference, 2004

2003

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

Nat. Comput., 2003

RNAsoft: a suite of RNA secondary structure prediction and design software tools.

Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon, Holger H. Hoos

Nucleic Acids Res., 2003

Automatable Verification of Sequential Consistency.

Anne Condon, Alan J. Hu

Theory Comput. Syst., 2003

On the undecidability of probabilistic planning and related stochastic optimization problems.

Omid Madani, Steve Hanks, Anne Condon

Artif. Intell., 2003

Toward a decidable notion of sequential consistency.

Jesse D. Bingham, Anne Condon, Alan J. Hu

Proceedings of the SPAA 2003: Proceedings of the Fifteenth Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2003

Problems on RNA Secondary Structure Prediction and Design.

Anne Condon

Proceedings of the Automata, Languages and Programming, 30th International Colloquium, 2003

2002

Specifying and Verifying a Broadcast and a Multicast Snooping Cache Coherence Protocol.

Daniel J. Sorin, Manoj Plakal, Anne Condon, Mark D. Hill, Milo M. K. Martin, David A. Wood

IEEE Trans. Parallel Distributed Syst., 2002

Strand design for biomolecular computation.

Arwen Brenneman, Anne Condon

Theor. Comput. Sci., 2002

Guest Editors' Foreword.

Mitsunori Ogihara, Anne Condon

Theory Comput. Syst., 2002

Stochastic Local Search Algorithms for DNA Word Design.

Dan C. Tulpan, Holger H. Hoos, Anne Condon

Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

From RNA Secondary Structure to Coding Theory: A Combinatorial Approach.

Christine E. Heitsch, Anne Condon, Holger H. Hoos

Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

2001

Algorithms for graph partitioning on the planted partition model.

Anne Condon, Richard M. Karp

Random Struct. Algorithms, 2001

On Combinatorial DNA Word Design.

Amit Marathe, Anne Condon, Robert M. Corn

J. Comput. Biol., 2001

Proving sequential consistency by model checking.

Tim Braun, Anne Condon, Alan J. Hu, Kai S. Juse, Marius Laza, Michael Leslie, Rita Sharma

Proceedings of the Sixth IEEE International High-Level Design Validation and Test Workshop 2001, 2001

1999

A System-Level Specification Framework for I/O Architectures.

Mark D. Hill, Anne Condon, Manoj Plakal, Daniel J. Sorin

Proceedings of the Eleventh Annual ACM Symposium on Parallel Algorithms and Architectures, 1999

Using Lamport Clocks to Reason about Relaxed Memory Models.

Anne Condon, Mark D. Hill, Manoj Plakal, Daniel J. Sorin

Proceedings of the Fifth International Symposium on High-Performance Computer Architecture, 1999

On the Undecidability of Probabilistic Planning and Infinite-Horizon Partially Observable Markov Decision Problems.

Omid Madani, Steve Hanks, Anne Condon

Proceedings of the Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence, 1999

1998

On the Power of Finite Automata with Both Nondeterministic and Probabilistic States.

Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson

SIAM J. Comput., 1998

DNA Models and Algorithms for NP-Complete Problems.

Eric Bach, Anne Condon, Elton Glaser, Celena Tanguay

J. Comput. Syst. Sci., 1998

A Surface-Based Approach to DNA Computation.

Lloyd M. Smith, Robert M. Corn, Anne Condon, Max G. Lagally, Tony Frutos, Qinghua Liu, Andrew Thiel

J. Comput. Biol., 1998

On Approximation Algorithms for Hierarchical MAX-SAT.

Sameet Agarwal, Anne Condon

J. Algorithms, 1998

Upper and Lower Bounds for Selection in the Mesh.

Anne Condon, Lata Narayanan

Algorithmica, 1998

Lamport Clocks: Verifying a Directory Cache-Coherence Protocol.

Manoj Plakal, Daniel J. Sorin, Anne Condon, Mark D. Hill

Proceedings of the Tenth Annual ACM Symposium on Parallel Algorithms and Architectures, 1998

1997

Strategic directions in research in theory of computing.

Anne Condon, Faith E. Fich, Greg N. Frederickson, Andrew V. Goldberg, David S. Johnson, Michael C. Loui, Steven Mahaney, Prabhakar Raghavan, John E. Savage, Alan L. Selman, David B. Shmoys

SIGACT News, 1997

Random Debaters and the Hardness of Approximating Stochastic Functions.

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor

SIAM J. Comput., 1997

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

Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

1996

Asynchronous Analysis of Parallel Dynamic Programming Algorithms.

Gary Lewandowski, Anne Condon, Eric Bach

IEEE Trans. Parallel Distributed Syst., 1996

Complexity of Sub-Bus Mesh Computations.

Anne Condon, Richard E. Ladner, Jordan Lampe, Rakesh K. Sinha

SIAM J. Comput., 1996

Parallel Implementation of Borvka's Minimum Spanning Tree Algorithm.

Sun Chung, Anne Condon

Proceedings of IPPS '96, 1996

A surface-based approach to DNA computation.

Qinghua Liu, Zhen Guo, Zhengdong Fei, Anne Condon, Robert M. Corn, Max G. Lagally, Lloyd M. Smith

Proceedings of the DNA Based Computers, 1996

1995

Approximate solutions to problems in PSPACE.

Anne Condon

SIGACT News, 1995

Interactive Proof Systems with Polynomially Bounded Strategies.

Anne Condon, Richard E. Ladner

J. Comput. Syst. Sci., 1995

Probabilistically Checkable Debate Systems and Nonapproximability of PSPACE-Hard Functions.

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor

Chic. J. Theor. Comput. Sci., 1995

1994

Random Walks on Colored Graphs.

Anne Condon, Diane Hernek

Random Struct. Algorithms, 1994

PSPACE Is Provable by Two Provers in One Round.

Jin-yi Cai, Anne Condon, Richard J. Lipton

J. Comput. Syst. Sci., 1994

On the Complexity of the Policy Improvement Algorithm for Markov Decision Processes.

Mary Melekopoglou, Anne Condon

INFORMS J. Comput., 1994

A Theory of Strict P-Completeness.

Anne Condon

Comput. Complex., 1994

On the power of finite automata with both nondeterministic and probabilistic states (preliminary version).

Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson

Proceedings of the Twenty-Sixth Annual ACM Symposium on Theory of Computing, 1994

1993

The Complexity of the Max Word Problem and the Power of One-Way Interactive Proof Systems.

Anne Condon

Comput. Complex., 1993

Probabilistically checkable debate systems and approximation algorithms for PSPACE-hard functions.

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor

Proceedings of the Twenty-Fifth Annual ACM Symposium on Theory of Computing, 1993

Asynchronous Analysis of Parallel Dynamic Programming.

Gary Lewandowski, Anne Condon, Eric Bach

Proceedings of the 1993 ACM SIGMETRICS conference on Measurement and modeling of computer systems, 1993

Experiments with parallel graph coloring heuristics and applications of graph coloring.

Gary Lewandowski, Anne Condon

Proceedings of the Cliques, 1993

1992

The Complexity of Stochastic Games

Anne Condon

Inf. Comput., February, 1992

On Games of Incomplete Information.

Jin-yi Cai, Anne Condon, Richard J. Lipton

Theor. Comput. Sci., 1992

The Complexity of Space Boundes Interactive Proof Systems.

Anne Condon

Proceedings of the Complexity Theory: Current Research, 1992

1991

Space-Bounded Probabilistic Game Automata.

Anne Condon

J. ACM, 1991

The Complexity of the Max Word Problem.

Anne Condon

Proceedings of the STACS 91, 1991

1990

Playing Games of Incomplete Information.

Jin-yi Cai, Anne Condon, Richard J. Lipton

Proceedings of the STACS 90, 1990

On Algorithms for Simple Stochastic Games.

Anne Condon

Proceedings of the Advances In Computational Complexity Theory, 1990

On Bounded Round Multi-Prover Interactive Proof Systems.

Jin-yi Cai, Anne Condon, Richard J. Lipton

Proceedings of the Proceedings: Fifth Annual Structure in Complexity Theory Conference, 1990

1989

On the Complexity of Space Bounded Interactive Proofs (Extended Abstract)

Anne Condon, Richard J. Lipton

Proceedings of the 30th Annual Symposium on Foundations of Computer Science, Research Triangle Park, North Carolina, USA, 30 October, 1989

Computational models of games.

Anne Condon

ACM distinguished dissertations, MIT Press, ISBN: 978-0-262-03152-3, 1989

1988

Probabilistic Game Automata.

Anne Condon, Richard E. Ladner

J. Comput. Syst. Sci., 1988