Anne Condon

According to our database1, Anne Condon authored at least 116 papers between 1986 and 2018.

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Awards

ACM Fellow

ACM Fellow 2010, "For contributions in complexity theory and leadership in advancing women in computing.".

Timeline

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PhD thesis 
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Bibliography

2018
Preface.
Natural Computing, 2018

On Design and Analysis of Chemical Reaction Network Algorithms.
Proceedings of the Implementation and Application of Automata, 2018

2017
Design of nucleic acid strands with long low-barrier folding pathways.
Natural Computing, 2017

Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates.
Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

Simplifying Analyses of Chemical Reaction Networks for Approximate Majority.
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.
Bioinformatics, 2016

2015
The complexity of string partitioning.
J. Discrete Algorithms, 2015

On Low Energy Barrier Folding Pathways for Nucleic Acid Sequences.
Proceedings of the DNA Computing and Molecular Programming - 21st International Conference, 2015

2014
Reachability bounds for chemical reaction networks and strand displacement systems.
Natural Computing, 2014

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.
BMC Bioinformatics, 2014

Reasoning about optimal stable matchings under partial information.
Proceedings of the ACM Conference on Economics and Computation, 2014

2013
Two-sided matching with partial information.
Proceedings of the ACM Conference on Electronic Commerce, 2013

2012
Efficient codon optimization with motif engineering.
J. Discrete Algorithms, 2012

The complexity of string partitioning
CoRR, 2012

Analysis of energy-based algorithms for RNA secondary structure prediction.
BMC Bioinformatics, 2012

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
Bioinformatics, 2012

Space and Energy Efficient Computation with DNA Strand Displacement Systems.
Proceedings of the DNA Computing and Molecular Programming - 18th International Conference, 2012

Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems.
Proceedings of the DNA Computing and Molecular Programming - 18th International Conference, 2012

The Complexity of String Partitioning.
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011
NP-completeness of the energy barrier problem without pseudoknots and temporary arcs.
Natural Computing, 2011

Molecular programming: DNA and the brain.
Nature, 2011

Revenue monotonicity in deterministic, dominant-strategy combinatorial auctions.
Artif. Intell., 2011

Efficient Codon Optimization with Motif Engineering.
Proceedings of the Combinatorial Algorithms - 22nd International Workshop, 2011

Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems.
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.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009
Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges.
Theor. Comput. Sci., 2009

Algorithms for distributional and adversarial pipelined filter ordering problems.
ACM Trans. Algorithms, 2009

An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids.
Journal of Computational Biology, 2009

Stepwise randomized combinatorial auctions achieve revenue monotonicity.
Proceedings of the Twentieth Annual ACM-SIAM Symposium on Discrete Algorithms, 2009

NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots.
Proceedings of the DNA Computing and Molecular Programming, 15th International Conference, 2009

2008

Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding.
Journal of Computational Biology, 2008

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database.
BMC Bioinformatics, 2008

Computational Challenges and Opportunities in the Design of Unconventional Machines from Nucleic Acids.
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.
Proceedings of the Computing and Combinatorics, 14th Annual International Conference, 2008

2007
Revenue monotonicity in combinatorial auctions.
SIGecom Exchanges, 2007

Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications.
Journal of Computational Biology, 2007

Computational RNA secondary structure design: empirical complexity and improved methods.
BMC Bioinformatics, 2007

HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Efficient parameter estimation for RNA secondary structure prediction.
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.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

Revenue Monotonicity in Combinatorial Auctions.
Proceedings of the Twenty-Second AAAI Conference on Artificial Intelligence, 2007

2006
Flow algorithms for two pipelined filter ordering problems.
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.
Proceedings of the Nanotechnology: Science and Computation, 2006

RNA Molecules: Glimpses Through an Algorithmic Lens.
Proceedings of the LATIN 2006: Theoretical Informatics, 2006

2005
Linear Time Algorithm for Parsing RNA Secondary Structure.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2004
Classifying RNA pseudoknotted structures.
Theor. Comput. Sci., 2004

Guest editor's foreword.
J. Comput. Syst. Sci., 2004

Automatic Verification of Sequential Consistency for Unbounded Addresses and Data Values.
Proceedings of the Computer Aided Verification, 16th International Conference, 2004

2003
Algorithms for testing that sets of DNA words concatenate without secondary structure.
Natural Computing, 2003

RNAsoft: a suite of RNA secondary structure prediction and design software tools.
Nucleic Acids Research, 2003

Automatable Verification of Sequential Consistency.
Theory Comput. Syst., 2003

On the undecidability of probabilistic planning and related stochastic optimization problems.
Artif. Intell., 2003

Toward a decidable notion of sequential consistency.
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.
Proceedings of the Automata, Languages and Programming, 30th International Colloquium, 2003

2002
Specifying and Verifying a Broadcast and a Multicast Snooping Cache Coherence Protocol.
IEEE Trans. Parallel Distrib. Syst., 2002

Strand design for biomolecular computation.
Theor. Comput. Sci., 2002

Guest Editors' Foreword.
Theory Comput. Syst., 2002

Stochastic Local Search Algorithms for DNA Word Design.
Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

From RNA Secondary Structure to Coding Theory: A Combinatorial Approach.
Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure.
Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

2001
Algorithms for graph partitioning on the planted partition model.
Random Struct. Algorithms, 2001

On Combinatorial DNA Word Design.
Journal of Computational Biology, 2001

Automatable verification of sequential consistency.
SPAA, 2001

Proving sequential consistency by model checking.
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.
SPAA, 1999

Algorithms for Graph Partitioning on the Planted Partition Model.
Proceedings of the Randomization, 1999

Using Lamport Clocks to Reason about Relaxed Memory Models.
Proceedings of the Fifth International Symposium on High-Performance Computer Architecture, 1999

On combinatorial DNA word design.
Proceedings of the DNA Based Computers, 1999

On the Undecidability of Probabilistic Planning and Infinite-Horizon Partially Observable Markov Decision Problems.
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.
SIAM J. Comput., 1998

DNA Models and Algorithms for NP-Complete Problems.
J. Comput. Syst. Sci., 1998

A Surface-Based Approach to DNA Computation.
Journal of Computational Biology, 1998

On Approximation Algorithms for Hierarchical MAX-SAT.
J. Algorithms, 1998

Upper and Lower Bounds for Selection in the Mesh.
Algorithmica, 1998

Lamport Clocks: Verifying a Directory Cache-Coherence Protocol.
SPAA, 1998

1997
Strategic directions in research in theory of computing.
SIGACT News, 1997

Random Debaters and the Hardness of Approximating Stochastic Functions.
SIAM J. Comput., 1997

The power of surface-based DNA computation (extended abstract).
Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

1996
Asynchronous Analysis of Parallel Dynamic Programming Algorithms.
IEEE Trans. Parallel Distrib. Syst., 1996

Complexity of Sub-Bus Mesh Computations.
SIAM J. Comput., 1996

Parallel Implementation of Borvka's Minimum Spanning Tree Algorithm.
Proceedings of IPPS '96, 1996

A surface-based approach to DNA computation.
Proceedings of the DNA Based Computers, 1996

DNA Models and Algorithms for NP-complete Problems.
Proceedings of the Eleveth Annual IEEE Conference on Computational Complexity, 1996

1995
Approximate solutions to problems in PSPACE.
SIGACT News, 1995

Interactive Proof Systems with Polynomially Bounded Strategies.
J. Comput. Syst. Sci., 1995

Probabilistically Checkable Debate Systems and Nonapproximability of PSPACE-Hard Functions.
Chicago J. Theor. Comput. Sci., 1995

On Approximation Algorithms for Hierarchical MAX-SAT.
Proceedings of the Tenth Annual Structure in Complexity Theory Conference, 1995

1994
Random Walks on Colored Graphs.
Random Struct. Algorithms, 1994

PSPACE Is Provable by Two Provers in One Round.
J. Comput. Syst. Sci., 1994

On the Complexity of the Policy Improvement Algorithm for Markov Decision Processes.
INFORMS Journal on Computing, 1994

A Theory of Strict P-Completeness.
Computational Complexity, 1994

On the power of finite automata with both nondeterministic and probabilistic states (preliminary version).
Proceedings of the Twenty-Sixth Annual ACM Symposium on Theory of Computing, 1994

Upper and lower bounds for selection on the mesh.
Proceedings of the Sixth IEEE Symposium on Parallel and Distributed Processing, 1994

Random Debaters and the Hardness of Approximating Stochastic Functions.
Proceedings of the Ninth Annual Structure in Complexity Theory Conference, Amsterdam, The Netherlands, June 28, 1994

1993
The Complexity of the Max Word Problem and the Power of One-Way Interactive Proof Systems.
Computational Complexity, 1993

Probabilistically checkable debate systems and approximation algorithms for PSPACE-hard functions.
Proceedings of the Twenty-Fifth Annual ACM Symposium on Theory of Computing, 1993

Asynchronous Analysis of Parallel Dynamic Programming.
Proceedings of the 1993 ACM SIGMETRICS conference on Measurement and modeling of computer systems, 1993

Random Walks on Colored Graphs.
Proceedings of the Second Israel Symposium on Theory of Computing Systems, 1993

Experiments with parallel graph coloring heuristics and applications of graph coloring.
Proceedings of the Cliques, 1993

1992
The Complexity of Stochastic Games
Inf. Comput., February, 1992

On Games of Incomplete Information.
Theor. Comput. Sci., 1992

A Theory of Strict P-completeness.
Proceedings of the STACS 92, 1992

The Complexity of Space Boundes Interactive Proof Systems.
Proceedings of the Complexity Theory: Current Research, 1992

Interactive Proof Systems with Polynomially Bounded Strategies.
Proceedings of the Seventh Annual Structure in Complexity Theory Conference, 1992

1991
Space-Bounded Probabilistic Game Automata.
J. ACM, 1991

The Complexity of the Max Word Problem.
Proceedings of the STACS 91, 1991

PSPACE Is Provable By Two Provers In One Round.
Proceedings of the Sixth Annual Structure in Complexity Theory Conference, Chicago, Illinois, USA, June 30, 1991

1990
Playing Games of Incomplete Information.
Proceedings of the STACS 90, 1990

On Algorithms for Simple Stochastic Games.
Proceedings of the Advances In Computational Complexity Theory, 1990

On Bounded Round Multi-Prover Interactive Proof Systems.
Proceedings of the Proceedings: Fifth Annual Structure in Complexity Theory Conference, 1990

1989
On the Complexity of Space Bounded Interactive Proofs (Extended Abstract)
Proceedings of the 30th Annual Symposium on Foundations of Computer Science, Research Triangle Park, North Carolina, USA, 30 October, 1989

Computational models of games.
ACM distinguished dissertations, MIT Press, ISBN: 978-0-262-03152-3, 1989

1988
Probabilistic Game Automata.
J. Comput. Syst. Sci., 1988

Space bounded probabilistic game automata.
Proceedings of the Proceedings: Third Annual Structure in Complexity Theory Conference, 1988

1986
Probabilistic Game Automata.
Proceedings of the Structure in Complexity Theory, 1986


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