| 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 | |
| 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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| Coalescing Times for IID Random Variables | I. Adler, H.S. Ahn, R.M. Karp, and S.M. Ross | Random Structures and Algorithms | 2003 | Algorithms | |
| A Stochastic Process on the Hypercube with Applications to Peer to Peer Networks | M. Adler, E. Halperin, R.M. Karp, and V. Vazirani | Proceedings of the 35th Annual ACM Symposium on Theory of Computing (STOC), 575-584 | 2003 | Algorithms | |
| Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem | A. Ben-Dor, B. Chor, R. M. Karp, and Z. Yakhini | Journal of Computational Biology, Vol. 10, No. 3-4, pp. 385-398 | 2003 | Algorithms | |
| Towards Optimally Multiplexed Applications of Universal DNA Tag Systems | A. Ben-Dor, T. Hartman, B. Schwikowski, R. Sharan, and Z. Yakhini | Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'03), ACM Press, 48-56 | 2003 | Algorithms | |
| The Restriction Scaffold Problem | A. Ben-Dor, R.M. Karp, B. Schwikowski, and R. Shamir | Journal of Computational Biology, Vol. 10, No. 3-4, pp. 385-398 | 2003 | Algorithms | |
| A Heuristic for the Stacker Crane Problem on Trees Which is Almost Surely Exact | A. Coja-Oghlan, S.O. Krumke, and T. Nierhoff | Algorithms and Computation, 14th International Sympsium, ISAAC 2003, LNCS 2906, pp. 605-614, Springer | 2003 | Algorithms | |
| Genome-Wide In-silico Determination of Transcriptional Regulation Modules Controlling Cell Cycle in Human Cells | R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh | Genome Research, 13, pp. 773-780 | 2003 | Algorithms | |
| Large Scale Reconstruction of Haplotypes from Genotype Data | E. Eskin, E. Halperin, and R.M. Karp | Proceedings of the Seventh Conference on Research in Computational Biology (RECOMB), 104-113 | 2003 | Algorithms | |
| Efficient Reconstruction of Haplotype Structure Via Perfect Phylogeny | E. Eskin, E. Halperin, and R.M. Karp | Journal of Bioinformatics and Computational Biology (JBCB) 1(1) 1-20 | 2003 | Algorithms | |
| Stock Returns: Momentum, Volatility and Interest Rates | Y. Fang, S. Wada, and J. Moody | Proceedings of Computational Intelligence in Financial Engineering, IEEE Press | 2003 | Algorithms | |
| Scoring Clustering Solutions by Their Biological Relevance | I. Gat-Viks, R. Sharan, and R. Shamir | Bioinformatics, 19,pp 2381-2389 | 2003 | Algorithms | |
| Detecting Protein Sequences via Metric Embeddings | E. Halperin, J. Buhler, R. M. Karp, R. Krauthgamer, and B. Westover | Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 122-129 | 2003 | Algorithms | |
| Integrality Ratio for Group Steiner Trees and Directed Steiner Trees | E. Halperin, G. Kortsarz, R. Krauthgamer, A. Srinivasan, and N. Wang | Proceedings of the Twelfth Symposium on Discrete Algorithms (SODA), 275-284 | 2003 | Algorithms | |
| Polylogarithmic Inapproximability | E. Halperin and R. Krauthgamer | Proceedings of the 35th Annual ACM Symposium on Theory of Computing (STOC), 585-594 | 2003 | Algorithms | |
| A Gambling Game and its Application to the Analysis of Adaptive Randomized Rounding | R.M. Karp and C. Kenyon | Springer-Verlag Lecture Notes in Computer Science, Volume 2764 (RANDOM 03), 329-340 | 2003 | Algorithms | |
| Load Balancing in Structured P2P Systems | R.M. Karp, A. Rao, K. Lakshminarayanan, S. Surana, and I. Stoica | Proceedings of the Second International Workshop on Peer-to-Peer Systems | 2003 | Algorithms | |
| A Simple Algorithm for Finding Frequent Elements in Streams and Bags | R.M. Karp, S. Shenker, and C.H. Papadimitriou | Transactions on Database Systems | 2003 | Algorithms | |
| 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 | |
| Conserved Pathways Within Bacteria and Yeast as Revealed by Global Protein Network Alignment | B. P. Kelley, R. Sharan, R. M. Karp, E.T. Sittler, D. E. Root, B. R. Stockwell, and T. Ideker | Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 20, pp. 11394-11399. DOI:10.1073/pnas.1534710100. | September 2003 | Algorithms | [PDF]
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| Global Synchronization in Sensornets | J. Elson, R.M. Karp, C.H. Papadimitriou, and S. Shenker | Proceedings of LATIN, 609-624, 2004. | 2004 | Algorithms | |
| Computing the Similarity of Two Sequences with Nested Arc Annotations | J. Alber, J. Gramm, J. Guo, and R. Niedermeier | Theoretical Computer Science, Vol. 312, Issues 2-3, pp. 337-358 | January 2004 | Algorithms | |
| Towards Optimally Multiplexed Applications of Universal Arrays | A. Ben-Dor, T. Hartman, R. M. Karp, B. Schwikowski, R. Sharan, and Z. Yakhini | Journal of Computational Biology, Vol. 11, Nos. 2-3, pp. 477-493 | January 2004 | Algorithms | [PDF]
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| Tight Lower Bounds for the Asymetric k-Center Problem | J. Chuzhoy, S. Guha, E. Halperin, S. Khanna, G. Kortsarz and S. Naor | In Proceedings of the 36th Annual ACM Symposium on Theory of Computing (STOC04) | January 05 2004 | Algorithms | |
| Optimally Phasing Long Genomic Regions using Local Haplotype Predictions | E. Eskin, E. Halperin, and R. Sharan | In Proceedings of the Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, pp. 13-16 | January 05 2004 | Algorithms | |
| Reconstructing Chain Functions in Genetic Networks | I. Gat-Viks, R. Shamir, R.M. Karp, and R. Sharan | Proceedings of the Ninth Pacific Symposium on Biocomputing (PSB'04), pp. 498-509 | January 05 2004 | Algorithms | |
| Load Balancing in Dynamic Structured P2P Systems | B. Godfrey, R.M. Karp, K. Lakshminarayanan, S. Surana, and I. Stoica | Proceedings of INFOCOMM | January 05 2004 | Algorithms | |
| Experimental Design for Multiplexed SNP Genotyping | J. Gramm, A. Ben-Dor, and R. Sharan | Manuscript | January 05 2004 | Algorithms | |
| Graph-Modeled Data Clustering: Fixed-Parameter Algorithms for Clique Generation | J. Gramm, J. Guo, F. Hüffner, and R. Niedermeier | Theory of Computing Systems | January 05 2004 | Algorithms | |
| Automated Generation of Search Tree Algorithms for Hard Graph-Modification Problems | J. Gramm, J. Guo, F. Hüffner, and R. Niedermeier | Algorithmica, 39(4):321-347 | January 05 2004 | Algorithms | |
| Parameterized Intractability of Distinguishing Substring Selection | J. Gramm, J. Guo, and R. Niedermeier | Theory of Computing Systems | January 05 2004 | Algorithms | |
| Pattern Matching for Arc-Annotated Sequences | J. Gramm, J. Guo, and R. Niedermeier | Journal of Algorithms | January 05 2004 | Algorithms | |
| On the Complexity of Haplotyping via Perfect Phylogeny | J. Gramm, T. Nierhoff, R. Sharan, and T. Tantau | Proceedings of the Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, pp. 35-46 | January 05 2004 | Algorithms | |
| Haplotype Reconstruction from Genotype Data Using Imperfect Phylogeny | E. Halperin and E. Eskin | Bioinformatics | January 05 2004 | Algorithms | |
| Perfect Phylogeny and Haplotype Assignment | E. Halperin and R.M. Karp | In Proceedings of RECOMB | January 05 2004 | Algorithms | |
| The Minimum-Entropy Set Cover Problem | E. Halperin and R.M. Karp | Proceedings of ICALP | January 05 2004 | Algorithms | |
| Finite-Length Analysis of LT-codes | R.M. Karp, M. Luby, and A. Shokrollahi | Proceedings of International Symposium on Information Theory (ISIT) | January 05 2004 | Algorithms | |
| PathBLAST: A Tool for Alignment of Protein Interaction Networks | B.P. Kelley, B. Yuan, F. Lewitter, R. Sharan, B.R. Stockwell, and T. Ideker | Nucleic Acids Research 32, pp. W83-W88 | January 05 2004 | Algorithms | |
| Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification and Population Stratification | G. Kimmel, R. Sharan, and R. Shamir | INFORMS Journal on Computing, in press | January 05 2004 | Algorithms | |
| On the Reducibility of Sets Inside with Low Information Content | M. Ogihara and T. Tantau | In JCSS | January 05 2004 | Algorithms | |
| Incomplete Directed Perfect Phylogeny | I. Pe'er, T. Pupko, R. Shamir, and R. Sharan | SIAM Journal on Computing 33(3), pp. 590-607 | January 05 2004 | Algorithms | |
