2012
97Feature-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. Bioinformatics (28): 167-175 (2012). Web SearchBibTeXDownload
96Analysis of energy-based algorithms for RNA secondary structure prediction. Monir Hajiaghayi, Anne Condon, Holger H. Hoos. BMC Bioinformatics (13): 22 (2012). Web SearchBibTeXDownload
95The complexity of string partitioning. Anne Condon, JŠn Manuch, Chris Thachuk. CoRR (abs/1204.2201) (2012). Web SearchBibTeXDownload
94The Complexity of String Partitioning. Anne Condon, JŠn Manuch, Chris Thachuk. CPM 2012, 159-172. Web SearchBibTeXDownload
93Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems. Anne Condon, Bonnie Kirkpatrick, JŠn Manuch. DNA 2012, 43-57. Web SearchBibTeXDownload
92Space and Energy Efficient Computation with DNA Strand Displacement Systems. Chris Thachuk, Anne Condon. DNA 2012, 135-149. Web SearchBibTeXDownload
91Efficient codon optimization with motif engineering. Anne Condon, Chris Thachuk. J. Discrete Algorithms (16): 104-112 (2012). Web SearchBibTeXDownload
2011
90Revenue monotonicity in deterministic, dominant-strategy combinatorial auctions. Baharak Rastegari, Anne Condon, Kevin Leyton-Brown. Artif. Intell. (175): 441-456 (2011). Web SearchBibTeXDownload
89Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems. Anne Condon, Alan J. Hu, JŠn Manuch, Chris Thachuk. DNA 2011, 84-99. Web SearchBibTeXDownload
88Efficient Codon Optimization with Motif Engineering. Anne Condon, Chris Thachuk. IWOCA 2011, 337-348. Web SearchBibTeXDownload
87NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. JŠn Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon. Natural Computing (10): 391-405 (2011). Web SearchBibTeXDownload
2010
86An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. Chris Thachuk, JŠn Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon. Pacific Symposium on Biocomputing 2010, 108-119. Web SearchBibTeXDownload
2009
85Algorithms for distributional and adversarial pipelined filter ordering problems. Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu. ACM Transactions on Algorithms (5) (2009). Cited by 2Web SearchBibTeXDownload
84NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. JŠn Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon. DNA 2009, 106-115. Web SearchBibTeXDownload
83An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids. Ho-Lin Chen, Anne Condon, Hosna Jabbari. Journal of Computational Biology (16): 803-815 (2009). Web SearchBibTeXDownload
82Stepwise randomized combinatorial auctions achieve revenue monotonicity. Baharak Rastegari, Anne Condon, Kevin Leyton-Brown. SODA 2009, 738-747. Web SearchBibTeXDownload
81Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. Anne Condon, Hosna Jabbari. Theor. Comput. Sci. (410): 294-301 (2009). Web SearchBibTeXDownload
2008
80RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. Mirela Andronescu, Vera Bereg, Holger H. Hoos, Anne Condon. BMC Bioinformatics (9) (2008). Web SearchBibTeXDownload
79Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. Anne Condon, JŠn Manuch, Chris Thachuk. COCOON 2008, 265-275. Web SearchBibTeXDownload
78Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding. Hosna Jabbari, Anne Condon, Shelly Zhao. Journal of Computational Biology (15): 139-163 (2008). Web SearchBibTeXDownload
77Computational Challenges and Opportunities in the Design of Unconventional Machines from Nucleic Acids. Anne Condon. UC 2008, 6. Web SearchBibTeXDownload
76Women in Computing. Denise W. GŁrer, Jennifer Light, Christina BjŲrkman, 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. Wiley Encyclopedia of Computer Science and Engineering 2008. Web SearchBibTeXDownload
2007
75Revenue Monotonicity in Combinatorial Auctions. Baharak Rastegari, Anne Condon, Kevin Leyton-Brown. AAAI 2007, 122-127. Web SearchBibTeXDownload
74On the Design of Oligos for Gene Synthesis. Chris Thachuk, Anne Condon. BIBE 2007, 123-130. Web SearchBibTeXDownload
73Computational RNA secondary structure design: empirical complexity and improved methods. RosalŪa Aguirre-HernŠndez, Holger H. Hoos, Anne Condon. BMC Bioinformatics (8) (2007). Web SearchBibTeXDownload
72Efficient parameter estimation for RNA secondary structure prediction. Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy. ISMB/ECCB (Supplement of Bioinformatics) 2007, 19-28. Web SearchBibTeXDownload
71Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications. Baharak Rastegari, Anne Condon. Journal of Computational Biology (14): 16-32 (2007). Web SearchBibTeXDownload
70Revenue monotonicity in combinatorial auctions. Baharak Rastegari, Anne Condon, Kevin Leyton-Brown. SIGecom Exchanges (7): 45-47 (2007). Web SearchBibTeXDownload
69HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding. Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop, Yinglei Zhao. WABI 2007, 323-334. Web SearchBibTeXDownload
2006
68RNA Molecules: Glimpses Through an Algorithmic Lens. Anne Condon. LATIN 2006, 8-10. Web SearchBibTeXDownload
67Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set. Mirela Andronescu, Anne Condon. Nanotechnology: Science and Computation 2006, 121-135. Web SearchBibTeXDownload
66Flow algorithms for two pipelined filter ordering problems. Anne Condon, Amol Deshpande, Lisa Hellerstein, Ning Wu. PODS 2006, 193-202. Cited by 9Web SearchBibTeXDownload
2005
65Linear Time Algorithm for Parsing RNA Secondary Structure. Baharak Rastegari, Anne Condon. WABI 2005, 341-352. Web SearchBibTeXDownload
2004
64Automatic Verification of Sequential Consistency for Unbounded Addresses and Data Values. Jesse D. Bingham, Anne Condon, Alan J. Hu, Shaz Qadeer, Zhichuan Zhang. CAV 2004, 427-439. Web SearchBibTeXDownload
63Guest editor's foreword. Binhai Zhu, Young J. Kim. J. Comput. Syst. Sci. (69): 1-2 (2004). Web SearchBibTeXDownload
62Classifying RNA pseudoknotted structures. Anne Condon, Beth Davy, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant. Theor. Comput. Sci. (320): 35-50 (2004). Web SearchBibTeXDownload
2003
61On the undecidability of probabilistic planning and related stochastic optimization problems. Omid Madani, Steve Hanks, Anne Condon. Artif. Intell. (147): 5-34 (2003). Web SearchBibTeXDownload
60Problems on RNA Secondary Structure Prediction and Design. Anne Condon. ICALP 2003, 22-32. Web SearchBibTeXDownload
59Algorithms 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. Natural Computing (2): 391-415 (2003). Web SearchBibTeXDownload
58RNAsoft: a suite of RNA secondary structure prediction and design software tools. Mirela Andronescu, RosalŪa Aguirre-HernŠndez, Anne Condon, Holger H. Hoos. Nucleic Acids Research (31): 3416-3422 (2003). Web SearchBibTeXDownload
57Toward a decidable notion of sequential consistency. Jesse D. Bingham, Anne Condon, Alan J. Hu. SPAA 2003, 304-313. Web SearchBibTeXDownload
56Automatable Verification of Sequential Consistency. Anne Condon, Alan J. Hu. Theory Comput. Syst. (36): 431-460 (2003). Web SearchBibTeXDownload
2002
55Algorithms 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. DNA 2002, 182-195. Web SearchBibTeXDownload
54From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. Christine E. Heitsch, Anne Condon, Holger H. Hoos. DNA 2002, 215-228. Web SearchBibTeXDownload
53Stochastic Local Search Algorithms for DNA Word Design. Dan C. Tulpan, Holger H. Hoos, Anne Condon. DNA 2002, 229-241. Web SearchBibTeXDownload
52Specifying 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 Distrib. Syst. (13): 556-578 (2002). Web SearchBibTeXDownload
51Strand design for biomolecular computation. Arwen Brenneman, Anne Condon. Theor. Comput. Sci. (287): 39-58 (2002). Web SearchBibTeXDownload
50Guest Editors' Foreword. Peter Gritzmann, Peter Bro Miltersen, Dorothea Wagner, Attila Sali, Ivan Porres. Theory Comput. Syst. (35): 469 (2002). Web SearchBibTeXDownload
2001
49Proving sequential consistency by model checking. Tim Braun, Anne Condon, Alan J. Hu, Kai S. Juse, Marius Laza, Michael Leslie, Rita Sharma. HLDVT 2001, 103-108. Web SearchBibTeXDownload
48On Combinatorial DNA Word Design. Amit Marathe, Anne Condon, Robert M. Corn. Journal of Computational Biology (8): 201-219 (2001). Web SearchBibTeXDownload
47Algorithms for graph partitioning on the planted partition model. Anne Condon, Richard M. Karp. Random Struct. Algorithms (18): 116-140 (2001). Web SearchBibTeXDownload
46Automatable verification of sequential consistency. Anne Condon, Alan J. Hu. SPAA 2001, 113-121. Web SearchBibTeXDownload
1999
45On the Undecidability of Probabilistic Planning and Infinite-Horizon Partially Observable Markov Decision Problems. Omid Madani, Steve Hanks, Anne Condon. AAAI/IAAI 1999, 541-548. Web SearchBibTeXDownload
44Using Lamport Clocks to Reason about Relaxed Memory Models. Anne Condon, Mark D. Hill, Manoj Plakal, Daniel J. Sorin. HPCA 1999, 270-278. Web SearchBibTeXDownload
43Algorithms for Graph Partitioning on the Planted Partition Model. Anne Condon, Richard M. Karp. RANDOM-APPROX 1999, 221-232. Web SearchBibTeXDownload
42A System-Level Specification Framework for I/O Architectures. Mark D. Hill, Anne Condon, Manoj Plakal, Daniel J. Sorin. SPAA 1999, 138-147. Web SearchBibTeXDownload
1998
41Upper and Lower Bounds for Selection in the Mesh. Anne Condon, Lata Narayanan. Algorithmica (20): 1-30 (1998). Web SearchBibTeXDownload
40On Approximation Algorithms for Hierarchical MAX-SAT. Sameet Agarwal, Anne Condon. J. Algorithms (26): 141-165 (1998). Web SearchBibTeXDownload
39DNA Models and Algorithms for NP-Complete Problems. Eric Bach, Anne Condon, Elton Glaser, Celena Tanguay. J. Comput. Syst. Sci. (57): 172-186 (1998). Web SearchBibTeXDownload
38A Surface-Based Approach to DNA Computation. Lloyd M. Smith, Robert M. Corn, Anne Condon, Max G. Lagally, Tony Frutos, Qinghua Liu, Andrew Thiel. Journal of Computational Biology (5): 255-267 (1998). Web SearchBibTeXDownload
37On the Power of Finite Automata with Both Nondeterministic and Probabilistic States. Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson. SIAM J. Comput. (27): 739-762 (1998). Web SearchBibTeXDownload
36Lamport Clocks: Verifying a Directory Cache-Coherence Protocol. Manoj Plakal, Daniel J. Sorin, Anne Condon, Mark D. Hill. SPAA 1998, 67-76. Web SearchBibTeXDownload
1997
35The 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. RECOMB 1997, 67-74. Web SearchBibTeXDownload
34Random Debaters and the Hardness of Approximating Stochastic Functions. Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor. SIAM J. Comput. (26): 369-400 (1997). Cited by 56Web SearchBibTeXDownload
33Strategic directions in research in theory of computing. 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. SIGACT News (28): 75-93 (1997). Web SearchBibTeXDownload
1996
32DNA Models and Algorithms for NP-complete Problems. Eric Bach, Anne Condon, Elton Glaser, Celena Tanguay. IEEE Conference on Computational Complexity 1996, 290-300. Web SearchBibTeXDownload
31Asynchronous Analysis of Parallel Dynamic Programming Algorithms. Gary Lewandowski, Anne Condon, Eric Bach. IEEE Trans. Parallel Distrib. Syst. (7): 425-438 (1996). Web SearchBibTeXDownload
30Parallel Implementation of Borvka's Minimum Spanning Tree Algorithm. Sun Chung, Anne Condon. IPPS 1996, 302-308. Web SearchBibTeXDownload
29Complexity of Sub-Bus Mesh Computations. Anne Condon, Richard E. Ladner, Jordan Lampe, Rakesh K. Sinha. SIAM J. Comput. (25): 520-539 (1996). Web SearchBibTeXDownload
1995
28Probabilistically Checkable Debate Systems and Nonapproximability of PSPACE-Hard Functions. Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor. Chicago J. Theor. Comput. Sci. (1995) (1995). Cited by 11Web SearchBibTeXDownload
27Interactive Proof Systems with Polynomially Bounded Strategies. Anne Condon, Richard E. Ladner. J. Comput. Syst. Sci. (50): 506-518 (1995). Web SearchBibTeXDownload
26Approximate solutions to problems in PSPACE. Anne Condon. SIGACT News (26): 4-13 (1995). Web SearchBibTeXDownload
25On Approximation Algorithms for Hierarchical MAX-SAT. Sameet Agarwal, Anne Condon. Structure in Complexity Theory Conference 1995, 214-226. Web SearchBibTeXDownload
1994
24A Theory of Strict P-Completeness. Anne Condon. Computational Complexity (4): 220-241 (1994). Web SearchBibTeXDownload
23On the Complexity of the Policy Improvement Algorithm for Markov Decision Processes. Mary Melekopoglou, Anne Condon. INFORMS Journal on Computing (6): 188-192 (1994). Web SearchBibTeXDownload
22PSPACE Is Provable by Two Provers in One Round. Jin-yi Cai, Anne Condon, Richard J. Lipton. J. Comput. Syst. Sci. (48): 183-193 (1994). Web SearchBibTeXDownload
21Random Walks on Colored Graphs. Anne Condon, Diane Hernek. Random Struct. Algorithms (5): 285-304 (1994). Web SearchBibTeXDownload
20On the power of finite automata with both nondeterministic and probabilistic states (preliminary version). Anne Condon, Lisa Hellerstein, Samuel Pottle, Avi Wigderson. STOC 1994, 676-685. Web SearchBibTeXDownload
19Random Debaters and the Hardness of Approximating Stochastic Functions. Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor. Structure in Complexity Theory Conference 1994, 280-293. Cited by 56Web SearchBibTeXDownload
1993
18The Complexity of the Max Word Problem and the Power of One-Way Interactive Proof Systems. Anne Condon. Computational Complexity (3): 292-305 (1993). Web SearchBibTeXDownload
17Random Walks on Colored Graphs. Anne Condon, Diane Hernek. ISTCS 1993, 134-140. Web SearchBibTeX
16Asynchronous Analysis of Parallel Dynamic Programming. Gary Lewandowski, Anne Condon, Eric Bach. SIGMETRICS 1993, 268-269. Web SearchBibTeXDownload
15Probabilistically checkable debate systems and approximation algorithms for PSPACE-hard functions. Anne Condon, Joan Feigenbaum, Carsten Lund, Peter W. Shor. STOC 1993, 305-314. Cited by 51Web SearchBibTeXDownload
1992
14The Complexity of Space Boundes Interactive Proof Systems. Anne Condon. Complexity Theory: Current Research 1992, 147-189. Web SearchBibTeX
13The Complexity of Stochastic Games. Anne Condon. Inf. Comput. (96): 203-224 (1992). Web SearchBibTeXDownload
12A Theory of Strict P-completeness. Anne Condon. STACS 1992, 33-44. Web SearchBibTeXDownload
11Interactive Proof Systems with Polynomially Bounded Strategies. Anne Condon, Richard E. Ladner. Structure in Complexity Theory Conference 1992, 282-294. Web SearchBibTeXDownload
10On Games of Incomplete Information. Jin-yi Cai, Anne Condon, Richard J. Lipton. Theor. Comput. Sci. (103): 25-38 (1992). Web SearchBibTeXDownload
1991
9Space-Bounded Probabilistic Game Automata. Anne Condon. J. ACM (38): 472-494 (1991). Web SearchBibTeXDownload
8The Complexity of the Max Word Problem. Anne Condon. STACS 1991, 456-465. Web SearchBibTeXDownload
7PSPACE Is Provable By Two Provers In One Round. Jin-yi Cai, Anne Condon, Richard J. Lipton. Structure in Complexity Theory Conference 1991, 110-115. Web SearchBibTeXDownload
1990
6Playing Games of Incomplete Information. Jin-yi Cai, Anne Condon, Richard J. Lipton. STACS 1990, 58-69. Web SearchBibTeXDownload
5On Bounded Round Multi-Prover Interactive Proof Systems. Jin-yi Cai, Anne Condon, Richard J. Lipton. Structure in Complexity Theory Conference 1990, 45-54. Web SearchBibTeXDownload
1989
4On the Complexity of Space Bounded Interactive Proofs (Extended Abstract). Anne Condon, Richard J. Lipton. FOCS 1989, 462-467. Web SearchBibTeXDownload
1988
3Probabilistic Game Automata. Anne Condon, Richard E. Ladner. J. Comput. Syst. Sci. (36): 452-489 (1988). Web SearchBibTeXDownload
2Space bounded probabilistic game automata. Anne Condon. Structure in Complexity Theory Conference 1988, 162-174. Web SearchBibTeXDownload
1986
1Probabilistic Game Automata. Anne Condon, Richard E. Ladner. Structure in Complexity Theory Conference 1986, 144-162. Web SearchBibTeXDownload
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