Anne Condon

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. Bioinformatics 28(2): 167-175 (2012)

Monir Hajiaghayi, Anne Condon, Holger H. Hoos: Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinformatics 13: 22 (2012)

Anne Condon, Chris Thachuk: Efficient codon optimization with motif engineering. J. Discrete Algorithms 16: 104-112 (2012)

Anne Condon, Ján Manuch, Chris Thachuk: The Complexity of String Partitioning. CPM 2012: 159-172

Anne Condon, Bonnie Kirkpatrick, Ján Manuch: Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems. DNA 2012: 43-57

Chris Thachuk, Anne Condon: Space and Energy Efficient Computation with DNA Strand Displacement Systems. DNA 2012: 135-149

Anne Condon, Ján Manuch, Chris Thachuk: The complexity of string partitioning. CoRR abs/1204.2201 (2012)

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown: Revenue monotonicity in deterministic, dominant-strategy combinatorial auctions. Artif. Intell. 175(2): 441-456 (2011)

Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon: NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. Natural Computing 10(1): 391-405 (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: 84-99

Anne Condon, Chris Thachuk: Efficient Codon Optimization with Motif Engineering. IWOCA 2011: 337-348

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: 108-119

Ho-Lin Chen, Anne Condon, Hosna Jabbari: An O(n⁵) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids. Journal of Computational Biology 16(6): 803-815 (2009)

Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu: Algorithms for distributional and adversarial pipelined filter ordering problems. ACM Transactions on Algorithms 5(2) (2009)

Anne Condon, Hosna Jabbari: Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. Theor. Comput. Sci. 410(4-5): 294-301 (2009)

Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon: NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. DNA 2009: 106-115

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown: Stepwise randomized combinatorial auctions achieve revenue monotonicity. SODA 2009: 738-747

Mirela Andronescu, Vera Bereg, Holger H. Hoos, Anne Condon: RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics 9 (2008)

Hosna Jabbari, Anne Condon, Shelly Zhao: Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding. Journal of Computational Biology 15(2): 139-163 (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: 265-275

Anne Condon: Computational Challenges and Opportunities in the Design of Unconventional Machines from Nucleic Acids. UC 2008: 6

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: Women in Computing. Wiley Encyclopedia of Computer Science and Engineering 2008

Rosalía Aguirre-Hernández, Holger H. Hoos, Anne Condon: Computational RNA secondary structure design: empirical complexity and improved methods. BMC Bioinformatics 8 (2007)

Baharak Rastegari, Anne Condon: Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications. Journal of Computational Biology 14(1): 16-32 (2007)

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown: Revenue monotonicity in combinatorial auctions. SIGecom Exchanges 7(1): 45-47 (2007)

Baharak Rastegari, Anne Condon, Kevin Leyton-Brown: Revenue Monotonicity in Combinatorial Auctions. AAAI 2007: 122-127

Chris Thachuk, Anne Condon: On the Design of Oligos for Gene Synthesis. BIBE 2007: 123-130

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: 19-28

Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop, Yinglei Zhao: HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding. WABI 2007: 323-334

Anne Condon: RNA Molecules: Glimpses Through an Algorithmic Lens. LATIN 2006: 8-10

Mirela Andronescu, Anne Condon: Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set. Nanotechnology: Science and Computation 2006: 121-135

Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu: Flow algorithms for two pipelined filter ordering problems. PODS 2006: 193-202

Baharak Rastegari, Anne Condon: Linear Time Algorithm for Parsing RNA Secondary Structure. WABI 2005: 341-352

Anne Condon: Guest editor's foreword. J. Comput. Syst. Sci. 69(1): 1-2 (2004)

Anne Condon, Beth Davy, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant: Classifying RNA pseudoknotted structures. Theor. Comput. Sci. 320(1): 35-50 (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: 427-439

Omid Madani, Steve Hanks, Anne Condon: On the undecidability of probabilistic planning and related stochastic optimization problems. Artif. Intell. 147(1-2): 5-34 (2003)

Anne Condon, Alan J. Hu: Automatable Verification of Sequential Consistency. Theory Comput. Syst. 36(5): 431-460 (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 Research 31(13): 3416-3422 (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. Natural Computing 2(4): 391-415 (2003)

Anne Condon: Problems on RNA Secondary Structure Prediction and Design. ICALP 2003: 22-32

Jesse D. Bingham, Anne Condon, Alan J. Hu: Toward a decidable notion of sequential consistency. SPAA 2003: 304-313

Mitsunori Ogihara, Anne Condon: Guest Editors' Foreword. Theory Comput. Syst. 35(5): 469 (2002)

Arwen Brenneman, Anne Condon: Strand design for biomolecular computation. Theor. Comput. Sci. 287(1): 39-58 (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 Distrib. Syst. 13(6): 556-578 (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: 182-195

Christine E. Heitsch, Anne Condon, Holger H. Hoos: From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. DNA 2002: 215-228

Dan C. Tulpan, Holger H. Hoos, Anne Condon: Stochastic Local Search Algorithms for DNA Word Design. DNA 2002: 229-241

Amit Marathe, Anne Condon, Robert M. Corn: On Combinatorial DNA Word Design. Journal of Computational Biology 8(3): 201-219 (2001)

Anne Condon, Richard M. Karp: Algorithms for graph partitioning on the planted partition model. Random Struct. Algorithms 18(2): 116-140 (2001)

Tim Braun, Anne Condon, Alan J. Hu, Kai S. Juse, Marius Laza, Michael Leslie, Rita Sharma: Proving sequential consistency by model checking. HLDVT 2001: 103-108

Anne Condon, Alan J. Hu: Automatable verification of sequential consistency. SPAA 2001: 113-121

Anne Condon, Grzegorz Rozenberg (Eds.): DNA Computing, 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 13-17, 2000, Revised Papers. Lecture Notes in Computer Science 2054, Springer 2001, isbn 3-540-42076-2

Omid Madani, Steve Hanks, Anne Condon: On the Undecidability of Probabilistic Planning and Infinite-Horizon Partially Observable Markov Decision Problems. AAAI/IAAI 1999: 541-548

Anne Condon, Mark D. Hill, Manoj Plakal, Daniel J. Sorin: Using Lamport Clocks to Reason about Relaxed Memory Models. HPCA 1999: 270-278

Anne Condon, Richard M. Karp: Algorithms for Graph Partitioning on the Planted Partition Model. RANDOM-APPROX 1999: 221-232

Mark D. Hill, Anne Condon, Manoj Plakal, Daniel J. Sorin: A System-Level Specification Framework for I/O Architectures. SPAA 1999: 138-147

Anne Condon, Lata Narayanan: Upper and Lower Bounds for Selection in the Mesh. Algorithmica 20(1): 1-30 (1998)

Sameet Agarwal, Anne Condon: On Approximation Algorithms for Hierarchical MAX-SAT. J. Algorithms 26(1): 141-165 (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. Journal of Computational Biology 5(2): 255-267 (1998)

Eric Bach, Anne Condon, Elton Glaser, Celena Tanguay: DNA Models and Algorithms for NP-Complete Problems. J. Comput. Syst. Sci. 57(2): 172-186 (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): 739-762 (1998)

Manoj Plakal, Daniel J. Sorin, Anne Condon, Mark D. Hill: Lamport Clocks: Verifying a Directory Cache-Coherence Protocol. SPAA 1998: 67-76

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor: Random Debaters and the Hardness of Approximating Stochastic Functions. SIAM J. Comput. 26(2): 369-400 (1997)

Anne Condon, Faith 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): 75-93 (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: 67-74

Anne Condon, Richard E. Ladner, Jordan Lampe, Rakesh K. Sinha: Complexity of Sub-Bus Mesh Computations. SIAM J. Comput. 25(3): 520-539 (1996)

Gary Lewandowski, Anne Condon, Eric Bach: Asynchronous Analysis of Parallel Dynamic Programming Algorithms. IEEE Trans. Parallel Distrib. Syst. 7(4): 425-438 (1996)

Eric Bach, Anne Condon, Elton Glaser, Celena Tanguay: DNA Models and Algorithms for NP-complete Problems. IEEE Conference on Computational Complexity 1996: 290-300

Sun Chung, Anne Condon: Parallel Implementation of Borvka's Minimum Spanning Tree Algorithm. IPPS 1996: 302-308

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor: Probabilistically Checkable Debate Systems and Nonapproximability of PSPACE-Hard Functions. Chicago J. Theor. Comput. Sci. 1995 (1995)

Anne Condon, Richard E. Ladner: Interactive Proof Systems with Polynomially Bounded Strategies. J. Comput. Syst. Sci. 50(3): 506-518 (1995)

Anne Condon: Approximate solutions to problems in PSPACE. SIGACT News 26(2): 4-13 (1995)

Sameet Agarwal, Anne Condon: On Approximation Algorithms for Hierarchical MAX-SAT. Structure in Complexity Theory Conference 1995: 214-226

Anne Condon: A Theory of Strict P-Completeness. Computational Complexity 4: 220-241 (1994)

Mary Melekopoglou, Anne Condon: On the Complexity of the Policy Improvement Algorithm for Markov Decision Processes. INFORMS Journal on Computing 6(2): 188-192 (1994)

Jin-yi Cai, Anne Condon, Richard J. Lipton: PSPACE Is Provable by Two Provers in One Round. J. Comput. Syst. Sci. 48(1): 183-193 (1994)

Anne Condon, Diane Hernek: Random Walks on Colored Graphs. Random Struct. Algorithms 5(2): 285-304 (1994)

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor: Random Debaters and the Hardness of Approximating Stochastic Functions. Structure in Complexity Theory Conference 1994: 280-293

Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson: On the power of finite automata with both nondeterministic and probabilistic states (preliminary version). STOC 1994: 676-685

Anne Condon: The Complexity of the Max Word Problem and the Power of One-Way Interactive Proof Systems. Computational Complexity 3: 292-305 (1993)

Anne Condon, Diane Hernek: Random Walks on Colored Graphs. ISTCS 1993: 134-140

Gary Lewandowski, Anne Condon, Eric Bach: Asynchronous Analysis of Parallel Dynamic Programming. SIGMETRICS 1993: 268-269

Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor: Probabilistically checkable debate systems and approximation algorithms for PSPACE-hard functions. STOC 1993: 305-314

Anne Condon: The Complexity of Stochastic Games. Inf. Comput. 96(2): 203-224 (1992)

Jin-yi Cai, Anne Condon, Richard J. Lipton: On Games of Incomplete Information. Theor. Comput. Sci. 103(1): 25-38 (1992)

Anne Condon, Richard E. Ladner: Interactive Proof Systems with Polynomially Bounded Strategies. Structure in Complexity Theory Conference 1992: 282-294

Anne Condon: The Complexity of Space Boundes Interactive Proof Systems. Complexity Theory: Current Research 1992: 147-189

Anne Condon: A Theory of Strict P-completeness. STACS 1992: 33-44

Anne Condon: Space-Bounded Probabilistic Game Automata. J. ACM 38(2): 472-494 (1991)

Jin-yi Cai, Anne Condon, Richard J. Lipton: PSPACE Is Provable By Two Provers In One Round. Structure in Complexity Theory Conference 1991: 110-115

Anne Condon: The Complexity of the Max Word Problem. STACS 1991: 456-465

Jin-yi Cai, Anne Condon, Richard J. Lipton: On Bounded Round Multi-Prover Interactive Proof Systems. Structure in Complexity Theory Conference 1990: 45-54

Jin-yi Cai, Anne Condon, Richard J. Lipton: Playing Games of Incomplete Information. STACS 1990: 58-69

Anne Condon, Richard J. Lipton: On the Complexity of Space Bounded Interactive Proofs (Extended Abstract). FOCS 1989: 462-467

Anne Condon, Richard E. Ladner: Probabilistic Game Automata. J. Comput. Syst. Sci. 36(3): 452-489 (1988)

Anne Condon: Space bounded probabilistic game automata. Structure in Complexity Theory Conference 1988: 162-174

Anne Condon, Richard E. Ladner: Probabilistic Game Automata. Structure in Complexity Theory Conference 1986: 144-162