Anne Condon

ORCID

Publication Activity (10 Years)

Years Active: 1986-2024
Publications (10 Years): 27

Top Venues

Publications

Chenwei Zhang, Anne Condon, Khanh Dao Duc
Synthetic High-resolution Cryo-EM Density Maps with Generative Adversarial Networks. CoRR (2024)
Aryan Tajmir Riahi, Geoffrey Woollard, Frédéric Poitevin, Anne Condon, Khanh Dao Duc
AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon
Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. DNA (2023)
Joseph Berleant, Kristin Sheridan, Anne Condon, Virginia Vassilevska Williams, Mark Bathe
Isometric Hamming embeddings of weighted graphs. Discret. Appl. Math. 332 (2023)
Chenwei Zhang, Khanh Dao Duc, Anne Condon
Visualizing DNA reaction trajectories with deep graph embedding approaches. CoRR (2023)
Kristin Sheridan, Joseph Berleant, Mark Bathe, Anne Condon, Virginia Vassilevska Williams
Factorization and pseudofactorization of weighted graphs. Discret. Appl. Math. 337 (2023)
Anne Condon, Yuval Emek, Noga Harlev
On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions. CoRR (2023)
Chenwei Zhang, Jordan Lovrod, Boyan Beronov, Khanh Dao Duc, Anne Condon
ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings. CoRR (2023)
Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt, Anne Condon, Erik Winfree
Predicting DNA kinetics with a truncated continuous-time Markov chain method. Comput. Biol. Chem. 104 (2023)
Anne Condon, Yuval Emek, Noga Harlev
On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions. DNA (2023)
Chenwei Zhang, Jordan Lovrod, Boyan Beronov, Khanh Dao Duc, Anne Condon
ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings. MLCB (2023)
Hope Amber Johnson, Anne Condon
A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems. DNA (2022)
Anne Condon, Monir Hajiaghayi, Chris Thachuk
Predicting Minimum Free Energy Structures of Multi-Stranded Nucleic Acid Complexes Is APX-Hard. DNA (2021)
Kristin Sheridan, Joseph Berleant, Mark Bathe, Anne Condon, Virginia Vassilevska Williams
Factorization and pseudofactorization of weighted graphs. CoRR (2021)
Joseph Berleant, Kristin Sheridan, Anne Condon, Virginia Vassilevska Williams, Mark Bathe
Isometric Hamming embeddings of weighted graphs. CoRR (2021)
Hooman Hashemi, Ben Chugg, Anne Condon
Composable Computation in Leaderless, Discrete Chemical Reaction Networks. DNA (2020)
Anne Condon, Monir Hajiaghayi, David G. Kirkpatrick, Ján Manuch
Approximate majority analyses using tri-molecular chemical reaction networks. Nat. Comput. 19 (1) (2020)
Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon
Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains. DNA (2019)
Allison Tai, Anne Condon
Error-Free Stable Computation with Polymer-Supplemented Chemical Reaction Networks. DNA (2019)
Ben Chugg, Anne Condon, Hooman Hashemi
Output-Oblivious Stochastic Chemical Reaction Networks. CoRR (2018)
Anne Condon
On Design and Analysis of Chemical Reaction Network Algorithms. CIAA (2018)
Ben Chugg, Hooman Hashemi, Anne Condon
Output-Oblivious Stochastic Chemical Reaction Networks. OPODIS (2018)
Martyn Amos, Anne Condon
Preface. Nat. Comput. 17 (2) (2018)
Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree
Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates. DNA (2017)
Anne Condon, Bonnie Kirkpatrick, Ján Manuch
Design of nucleic acid strands with long low-barrier folding pathways. Nat. Comput. 16 (2) (2017)
Anne Condon, Monir Hajiaghayi, David G. Kirkpatrick, Ján Manuch
Simplifying Analyses of Chemical Reaction Networks for Approximate Majority. DNA (2017)
Jiarui Ding, Sohrab P. Shah, Anne Condon
densityCut: an efficient and versatile topological approach for automatic clustering of biological data. Bioinform. 32 (17) (2016)
Leigh-Anne Mathieson, Anne Condon
On Low Energy Barrier Folding Pathways for Nucleic Acid Sequences. DNA (2015)
Anne Condon, Ján Manuch, Chris Thachuk
The complexity of string partitioning. J. Discrete Algorithms 32 (2015)
Baharak Rastegari, Anne Condon, Nicole Immorlica, Robert W. Irving, Kevin Leyton-Brown
Reasoning about optimal stable matchings under partial information. EC (2014)
Hosna Jabbari, Anne Condon
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures. BMC Bioinform. 15 (2014)
Anne Condon, Bonnie Kirkpatrick, Ján Manuch
Reachability bounds for chemical reaction networks and strand displacement systems. Nat. Comput. 13 (4) (2014)
Baharak Rastegari, Anne Condon, Nicole Immorlica, Kevin Leyton-Brown
Two-sided matching with partial information. EC (2013)
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
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinform. 28 (2) (2012)
Monir Hajiaghayi, Anne Condon, Holger H. Hoos
Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinform. 13 (2012)
Chris Thachuk, Anne Condon
Space and Energy Efficient Computation with DNA Strand Displacement Systems. DNA (2012)
Anne Condon, Bonnie Kirkpatrick, Ján Manuch
Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems. DNA (2012)
Anne Condon, Ján Manuch, Chris Thachuk
The complexity of string partitioning CoRR (2012)
Anne Condon, Chris Thachuk
Efficient codon optimization with motif engineering. J. Discrete Algorithms 16 (2012)
Anne Condon, Ján Manuch, Chris Thachuk
The Complexity of String Partitioning. CPM (2012)
Baharak Rastegari, Anne Condon, Kevin Leyton-Brown
Revenue monotonicity in deterministic, dominant-strategy combinatorial auctions. Artif. Intell. 175 (2) (2011)
Anne Condon
Molecular programming: DNA and the brain. Nat. 475 (7356) (2011)
Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon
NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. Nat. Comput. 10 (1) (2011)
Anne Condon, Chris Thachuk
Efficient Codon Optimization with Motif Engineering. IWOCA (2011)
Anne Condon, Alan J. Hu, Ján Manuch, Chris Thachuk
Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems. DNA (2011)
Chris Thachuk, Ján Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon
An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. Pacific Symposium on Biocomputing (2010)
Baharak Rastegari, Anne Condon, Kevin Leyton-Brown
Stepwise randomized combinatorial auctions achieve revenue monotonicity. SODA (2009)
Anne Condon, Hosna Jabbari
Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. Theor. Comput. Sci. 410 (4-5) (2009)
Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon
NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. DNA (2009)
Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu
Algorithms for distributional and adversarial pipelined filter ordering problems. ACM Trans. Algorithms 5 (2) (2009)
Ho-Lin Chen, Anne Condon, Hosna Jabbari
) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids. J. Comput. Biol. 16 (6) (2009)
Mirela Andronescu, Vera Bereg, Holger H. Hoos, Anne Condon
RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinform. 9 (2008)
Anne Condon, Ján Manuch, Chris Thachuk
Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. COCOON (2008)
Anne Condon
Computational Challenges and Opportunities in the Design of Unconventional Machines from Nucleic Acids. UC (2008)
Hosna Jabbari, Anne Condon, Shelly Zhao
Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding. J. Comput. Biol. 15 (2) (2008)
Baharak Rastegari, Anne Condon
Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications. J. Comput. Biol. 14 (1) (2007)
Baharak Rastegari, Anne Condon, Kevin Leyton-Brown
Revenue Monotonicity in Combinatorial Auctions. AAAI (2007)
Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy
Efficient parameter estimation for RNA secondary structure prediction. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Rosalía Aguirre-Hernández, Holger H. Hoos, Anne Condon
Computational RNA secondary structure design: empirical complexity and improved methods. BMC Bioinform. 8 (2007)
Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop, Yinglei Zhao
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding. WABI (2007)
Chris Thachuk, Anne Condon
On the Design of Oligos for Gene Synthesis. BIBE (2007)
Baharak Rastegari, Anne Condon, Kevin Leyton-Brown
Revenue monotonicity in combinatorial auctions. SIGecom Exch. 7 (1) (2007)
Mirela Andronescu, Anne Condon
Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set. Nanotechnology: Science and Computation (2006)
Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu
Flow algorithms for two pipelined filter ordering problems. PODS (2006)
Anne Condon
RNA Molecules: Glimpses Through an Algorithmic Lens. LATIN (2006)
Baharak Rastegari, Anne Condon
Linear Time Algorithm for Parsing RNA Secondary Structure. WABI (2005)
Anne Condon
Guest editor's foreword. J. Comput. Syst. Sci. 69 (1) (2004)
Anne Condon, Beth Davy, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant
Classifying RNA pseudoknotted structures. Theor. Comput. Sci. 320 (1) (2004)
Jesse D. Bingham, Anne Condon, Alan J. Hu, Shaz Qadeer, Zhichuan Zhang
Automatic Verification of Sequential Consistency for Unbounded Addresses and Data Values. CAV (2004)
Omid Madani, Steve Hanks, Anne Condon
On the undecidability of probabilistic planning and related stochastic optimization problems. Artif. Intell. 147 (1-2) (2003)
Mirela Andronescu, Danielle Dees, Laura Slaybaugh, Yinglei Zhao, Anne Condon, Barry Cohen, Steven Skiena
Algorithms for testing that sets of DNA words concatenate without secondary structure. Nat. Comput. 2 (4) (2003)
Jesse D. Bingham, Anne Condon, Alan J. Hu
Toward a decidable notion of sequential consistency. SPAA (2003)
Anne Condon, Alan J. Hu
Automatable Verification of Sequential Consistency. Theory Comput. Syst. 36 (5) (2003)
Anne Condon
Problems on RNA Secondary Structure Prediction and Design. ICALP (2003)
Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon, Holger H. Hoos
RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res. 31 (13) (2003)
Mitsunori Ogihara, Anne Condon
Guest Editors' Foreword. Theory Comput. Syst. 35 (5) (2002)
Mirela Andronescu, Danielle Dees, Laura Slaybaugh, Yinglei Zhao, Anne Condon, Barry Cohen, Steven Skiena
Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure. DNA (2002)
Dan C. Tulpan, Holger H. Hoos, Anne Condon
Stochastic Local Search Algorithms for DNA Word Design. DNA (2002)
Arwen Brenneman, Anne Condon
Strand design for biomolecular computation. Theor. Comput. Sci. 287 (1) (2002)
Daniel J. Sorin, Manoj Plakal, Anne Condon, Mark D. Hill, Milo M. K. Martin, David A. Wood
Specifying and Verifying a Broadcast and a Multicast Snooping Cache Coherence Protocol. IEEE Trans. Parallel Distributed Syst. 13 (6) (2002)
Christine E. Heitsch, Anne Condon, Holger H. Hoos
From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. DNA (2002)
Tim Braun, Anne Condon, Alan J. Hu, Kai S. Juse, Marius Laza, Michael Leslie, Rita Sharma
Proving sequential consistency by model checking. HLDVT (2001)
Anne Condon, Alan J. Hu
Automatable verification of sequential consistency. SPAA (2001)
Amit Marathe, Anne Condon, Robert M. Corn
On Combinatorial DNA Word Design. J. Comput. Biol. 8 (3) (2001)
Anne Condon, Richard M. Karp
Algorithms for graph partitioning on the planted partition model. Random Struct. Algorithms 18 (2) (2001)
Anne Condon, Richard M. Karp
Algorithms for Graph Partitioning on the Planted Partition Model. RANDOM-APPROX (1999)
Amit Marathe, Anne Condon, Robert M. Corn
On combinatorial DNA word design. DNA Based Computers (1999)
Omid Madani, Steve Hanks, Anne Condon
On the Undecidability of Probabilistic Planning and Infinite-Horizon Partially Observable Markov Decision Problems. AAAI/IAAI (1999)
Anne Condon, Mark D. Hill, Manoj Plakal, Daniel J. Sorin
Using Lamport Clocks to Reason about Relaxed Memory Models. HPCA (1999)
Mark D. Hill, Anne Condon, Manoj Plakal, Daniel J. Sorin
A System-Level Specification Framework for I/O Architectures. SPAA (1999)
Eric Bach, Anne Condon, Elton Glaser, Celena Tanguay
DNA Models and Algorithms for NP-Complete Problems. J. Comput. Syst. Sci. 57 (2) (1998)
Manoj Plakal, Daniel J. Sorin, Anne Condon, Mark D. Hill
Lamport Clocks: Verifying a Directory Cache-Coherence Protocol. SPAA (1998)
Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson
On the Power of Finite Automata with Both Nondeterministic and Probabilistic States. SIAM J. Comput. 27 (3) (1998)
Lloyd M. Smith, Robert M. Corn, Anne Condon, Max G. Lagally, Tony Frutos, Qinghua Liu, Andrew Thiel
A Surface-Based Approach to DNA Computation. J. Comput. Biol. 5 (2) (1998)
Sameet Agarwal, Anne Condon
On Approximation Algorithms for Hierarchical MAX-SAT. J. Algorithms 26 (1) (1998)
Anne Condon, Lata Narayanan
Upper and Lower Bounds for Selection in the Mesh. Algorithmica 20 (1) (1998)
Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor
Random Debaters and the Hardness of Approximating Stochastic Functions. SIAM J. Comput. 26 (2) (1997)
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
The power of surface-based DNA computation (extended abstract). RECOMB (1997)
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
Strategic directions in research in theory of computing. SIGACT News 28 (3) (1997)
Gary Lewandowski, Anne Condon, Eric Bach
Asynchronous Analysis of Parallel Dynamic Programming Algorithms. IEEE Trans. Parallel Distributed Syst. 7 (4) (1996)

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Publication Activity (10 Years)

Top Topics

Top Venues

Anne Condon