| Idetifying Blocks and Sub-Populations in Noisy SNP Data | G. Kimmel, R. Sharan, and R. Shamir | Proceedings of the Third Workshop on Algorithms in Bioinformatics (WABI'03), pp. 303-319 | 2003 | Algorithms | |
| Regularizers and Priors for Feed-Forward Networks | J. Moody and T. Rognvaldsson | Submitted for publication 2003 | 2003 | Algorithms | |
| Detecting Excess Radical Replacements in Phylogenetic Trees | T. Pupko, R. Sharan, M. Hasegawa, R. Shamir, and D. Graur | Gene, 319, pp. 127-135 | 2003 | Algorithms | |
| Load Balancing in Structured P2P Systems | A. Rao, K. Lakshminarayanan, S. Surana, R.M. Karp, and I. Stoica | Second International Workshop on Peer-to-Peer Systems | 2003 | Algorithms | |
| CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data | R. Sharan, A. Maron-Katz, and R. Shamir | Bioinformatics, 19, pp. 1787-1799 | 2003 | Algorithms | |
| CRÈME: A Framework for Identifying Cis-Regulatory Modules in Human-Mouse Conserved Segments | R. Sharan, I. Ovcharenko, A. Ben-Hur, and R. M. Karp | Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology (ISMB'03), Bioinformatics 19, Supplement 1, pp. 1283-1291 | 2003 | Algorithms | |
| LOGOS: A Modular Bayesian Model for de Novo Motif Detection | E.P. Xing, W. Wu, M. Jordan, and R.M. Karp | Proceedings of IEEE Computer Society Bioinformatic Conference IPTPS | 2003 | Algorithms | |
| Large-Scale Reconstruction of Haplotype Structure via Perfect Phylogeny | E. Eskin, E. Halperin, and R.M. Karp | EECS Department, UC Berkeley Technical Report No. UCB/CSD 2-1196, Berkeley, California | August 2002 | Algorithms | [PDF]
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| Large-Scale Recovery of Haplotypes from Genotype Data Using Imperfect Phylogeny | E. Halperin and E. Eskin | EECS Department, UC Berkeley Technical Report No. UCB/CSD-1-1196, Berkeley, California | August 2002 | Algorithms | [PDF]
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| Selfish Behavior and Stability of the Internet: A Game-Theoretic Analysis of TCP | A. Akella, R.M. Karp, S. Seshan, S. Shenker, and C. Papadimitriou. | Proceedings ACM SIGCOMM 2002. | 2002 | Algorithms | |
| Multiple Sequence Alighment with Arbitrary Gap Costs: Computing an Optimal Solution Using Polydhedral Combinatorics | E. Althaus, A. Caprara, H.P. Lenhof, and K. Reinert | ECCB, 4-16, 2002. | 2002 | Algorithms | |
| A Polyhedral Approach to Surface Reconstruction from Planar Contours | E. Althaus and C. Fink | Proceedings of the Ninth Conference on Integer Programming and Combinatorial Optimization. Lecture Notes in Computer Science, 2002. | 2002 | Algorithms | |
| Constant-Factor Approximation of Vertex-Cuts in Planar Graphs | E. Amir, R. Krathgamer, and S. Rao | Manuscript, 2002. | 2002 | Algorithms | |
| The Efficiency of Resolution and Davis-Putnamn Procedures | P. Beame, R. M. Karp, T. Pitassi, and M. Saks | SIAM Journal of Computing, Vol. 31, No. 4, pp. 1048-1075 | 2002 | Algorithms | |
| Discovering Local Structure in Gene Expression Data: The Order Preserving Submatrix Problem | A. Ben-Dor, B. Chor, R.M. Karp, and Z. Yakhini | Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB'02) | 2002 | Algorithms | |
| The Restriction Scaffold Problem | A. Ben-Dor, R.M. Karp, B Schwikowski, and R. Shamir | Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB'02), 2002. | 2002 | Algorithms | |
| Idempotents Among Partesan Games | E. Berlekamp | More Games of No Chance, MSRI Publicatons vol. 42, pp 3-23, Cambridge University Press, 2002. | 2002 | Algorithms | |
| Improved Approximation Algorithms for the Partial Vertex Cover Problem | E. Halperin and R. Srinivasan | Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization, (APPROX), 185-199, Springer, 2002. | 2002 | Algorithms | |
| Mathematical Challenges from Genomics and Molecular Biology | R. M. Karp | Notices of the American Mathematical Society, Vol. 49, No. 5, pp. 544-553 | 2002 | Algorithms | |
| Hardness of Approximation for Vertex-Connectivity Network Design Problems | G. Kortsarz, R. Krauthgamer, and J.R. Lee | Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization (APPROX), 185-199, Springer, 2002. | 2002 | Algorithms | |
| The Intrinsic Dimensionality of Graphs | R. Krauthgamer and J.R. Lee | Manuscript, 2002. | 2002 | Algorithms | |
| Online Scheduling for Sorting Buffers | H. Racke, C. Sohler, and M. Westermann | European Symposium on Algorithms, 820-832, 2002. | 2002 | Algorithms | |
| Go Thermography: The 4/12/98 Jiang-Rui Environmental Endgame | B. Spight | More Games of No Chance, MSRI Publictations vo. 42, Cambridge University Press, 2002. | 2002 | Algorithms | |
| Distributed Caching Independent of the Network Size | M. Westermann | Symposium on Parallel Algorithms and Archiectures, 31-40, 2002. | 2002 | Algorithms | |
| Distance Metric Learning, with Application to Clustering with Side-Information | E.P. Xing, A.Y. Ng, M.I. Jordan, and S. Russell | Neural Information Processing Systems, 2002. | 2002 | Algorithms | |
| A Hierarchical Bayesian Markovian Model for Motifs in Biopolymer Sequences | E.P. Xing, M.I. Jordan, R.M. Karp, and S. Russell | Neural Information Processing Systems, 2002. | 2002 | Algorithms | |
| Neural Networks for Time Series Analysis | Y Liao, J. Moody, and L. Wu | Handbook on Neural Network Signal Processing, edited by Y-H Hu and J-N Hwang, CRC Press 2001. | 2002 | Algorithms | |
| Learning to Trade via Direct Reinforcement | J. Moody and M. Saffell | IEEE Transactions on Neural Networks, Vol. 12, No. 4, July 2001. | July 2001 | Algorithms | |
| CLIFF: Clustering of High-Dimensional Microarray Data via Iterative Feature Filtering Using Normalized Cuts | E. P. Xing and R. M. Karp | Proceedings for the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, Denmark, Vol. 17, Supplement 1, pp. S306-S315 | July 2001 | Algorithms | [PDF]
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| Feature Selection for High-Dimensional Genomic Microarray Data | E. P. Xing, M. I. Jordan, and R. M. Karp | Proceedings of the 18th International Conference on Machine Learning (ICML 2001), Williamstown, Massachusetts, pp. 601-608 | June 2001 | Algorithms | [PDF]
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| Curve Reconstruction and the Traveling Salsman Problem. | E. Althaus | Ph.D. Thesis, Universitat des Saarlandes. 2001. | 2001 | Algorithms | |
| TSP-Based Curve Reconstruction in Polynomial Time | E. Althaus and K. Melhorn | SIAM Journal of Computing 31(1), 2001. | 2001 | Algorithms | |
| Developments in Forecast Combination and Portfolio Choice | C. Dunis, A. Timmermann, and J. Moody, editors | Wiley Financial Economics, London, 2001. | 2001 | Algorithms | |
| A Maximun Likelihood Polynomial Time Syndrome Decoder to Correct Linearly Independent Errors | G.B. Horn and R.M. Karp | Proceedings of International Symposium on Information Theory | 2001 | Algorithms | |
| Approximation Algorithms for Data Management in Networks | C. Krick, H. Racke, and M. Westermann | Proceedings of the Thirteenth ACM Symposium on Parallel Algorithms and Architectures (SPAA) pp. 237-246, 2001. | 2001 | Algorithms | |
| Approximation Algorithms for Data Management in Networks | C. Krick, H. Racke, and M. Westermann | Theory of Computing Systems, 2001. | 2001 | Algorithms | |
| On Approximating Optimal Auctions | A. Ronen | The Third ACM Conference on Electronic Commerce (EC01), 11-17, 2001. | 2001 | Algorithms | |
| Discrete Prediction Games with Arbitrary Feedback and Loss | A. Piccolboni and C. Schindelhauer | Universitat zu Lubeck Technical Report No. AIIM-TR-A-00-18 | November 2000 | Algorithms | |
| Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design | T.E. Ideker, V. Thorsson, and R.M. Karp | Proceedings of Pacific Symposium on Biocomputing (PSB 2000), Oahu, Hawaii, pp. 302-313 | January 2000 | Algorithms | [PDF]
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| TSP-Based Curve Reconstruction in Polynomial Time | E. Althaus and K. Melhorn | Proceedings of the Eleventh Symposium on Discrete Algorithms, pp. 686-695, 2000. | 2000 | Algorithms | |
| Experiments on Curve Reconstruction | E. Althaus, K. Melhorn. S Naher, and S. Schirra | Proceedings of the Second Workshop Algorithm Engineering and Experiments (ALENEX00). Lecture Notes in Computer Science, Springer-Verlag, 2000. | 2000 | Algorithms | |
| A Branch and Cut Algorithm for the Optimal Solution of the Side Chain Placement Problem | E. Althaus, O. Kohlbacher, H.P. Lenhof, and P. Muller | Technical Report Vol.2000-1-001, Max-Planck-Institut fur Informatik: Foschungsbericht, 2000. | 2000 | Algorithms | |
| A Combinatorial Approach to Protein Docking with Flexible Side-Chains | E. Althaus, O. Kohlbacher, H.P. Lenhof, and P. Muller | Proceedings of the Fourth Annual International conference on Computational Molecular Biology (RECOMB-00), Tokyo, Japan, 2000. | 2000 | Algorithms | |
| Universal DNA Tag Systems: A Combinatorial Design Scheme | A. Ben-Dor, R. Karp, B. Schwikowski, and Z. Yakhini | Proceedings of RECOMB 2000. | 2000 | Algorithms | |
| An Optimal Algorithm for Monte Carlo Estimation | P. Dagum, R.M. Karp, M. Luby, and S. Ross | SIAM Journal on Computing, SIAM J. Comput. (USA), vol.29, (no.5), SIAM, 2000. p.1484-96. | 2000 | Algorithms | |
| Topologically-Aware Overlay Construction and Server Selection | M. Handley, R.M. Karp, S. Ratnasamy, and S. Shenker | Proceedings, INFOCOM 2000. | 2000 | Algorithms | |
| Constructing Heterogeneous Committees via Input Feature Grouping | Y. Liao and J. Moody | Advances in Neural Information Processing Systems, Vol.12, S.A. Solla, T.K. Leen and K.-R. Muller (eds.),MIT Press, 2000. | 2000 | Algorithms | |
| Minimizing Downside Risk via Stochastic Dynamic Programming | J. Moody and M. Saffell | Computational Finance 1999, edited by Y. S. Abu-Mostafa, B. LeBaron, A. W. Lo, and A. S. Weigend, MIT Press, Cambridge, MA, 2000. | 2000 | Algorithms | |
| Term Structure of Interactions of Foreign Exchange Rates | J. Moody and H. Yang | Computational Finance 1999, edited by Y. S. Abu-Mostafa, B. LeBaron, A. W. Lo, and A. S. Weigend, MIT Press, Cambridge, MA, 2000. | 2000 | Algorithms | |
| Data Visualization and Feature Selection: New Algorithms for Nongaussian Data | H. Yang and J. Moody | Advances in Neural Information Processing Systems, Vol.12, S.A. Solla, T.K. Leen and K.R. Muller (eds.), MIT Press, 2000. | 2000 | Algorithms | |
