| Polymorphisms in the Estrogen Receptor 1 and Vitamin C and Matrix Metalloproteinase Gene Families Are Associated with Susceptibility to Lymphoma | C. F. Skibola, P. M. Bracci, E. Halperin, A. Nieters, A. Hubbard, R. A. Paynter, D. R. Skibola, A. Agana, N. Becker, P. Tessler, M. S. Forrest, S. Sankararaman, L. Conde, E. A. Holly, and M. T. Smith | PLoS ONE, Vol. 3, Issue 7, e2816 | June 2008 | Algorithms | [PDF]
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| On the Inference of Ancestries in Admixed Populations | S. Sankararaman, G. Kimmel, E. Halperin and M. I. Jordan | Genome Research, Vol 18, Issue 4, pp. 668-675 | April 2008 | Algorithms | [PDF]
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| Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles | I. Ulitzky, R. M. Karp, and R. Shamir | Proceedings of 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), Singapore, pp. 347-359 | March 2008 | Algorithms | |
| E-QED: An Efficient Method for Interpreting eQTL Associations Using Protein Networks | S. Suthram, A. Beyer, R. M. Karp, Y. Eldar, and T. Ideker | Molecular Systems Biology, Vol. 4 | March 2008 | Algorithms | |
| LAMP: Local Ancestry in adMixed Populations | S. Sankararaman, S. Sridhar, G. Kimmel, and E. Halperin | American Journal of Human Genetics, Vol. 82, Issue 2, American Society of Human Genetics, pp. 290-303 | February 2008 | Algorithms | |
| Estimating Local Ancestry in Admixed Populations | S. Sankararaman, S. Sridhar, G. Kimmel, and E. Halperin | The American Journal of Human Genetics, Vol. 82, Issue 2, pp. 290-303 | February 2008 | Algorithms | [PDF]
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| Linked Decomposition of Networks and the Power of Choice in Polya Urns | H. Lin, C. Amanatidis, M. Sideri, R. M. Karp, and C. Papadimitriou | Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 2008), pp. 993-1002, San Francisco, California | January 2008 | Algorithms | |
| Total Latency in Singleton Congestion Games | M. Gairing and F. Schoppmann | Proceedings of the Third International Workshop on Internet and Network Economics (WINE 2007), San Diego, California, pp. 381-387 | December 2007 | Algorithms | |
| Streaming Algorithms for Selection and Approximate Sorting | R. M. Karp | Proceedings of the IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, New Delhi, India, pp. 9-20 | December 2007 | Algorithms | |
| A Randomization Test for Controlling Population Stratification in Whole-Genome Association Studies | G. Kimmel, M. I. Jordan, E. Halperin, R. Shamir, and R. M. Karp | American Journal of Human Genetics, Vol. 81, Issue 5, pp. 895-905 | November 2007 | Algorithms | [PDF]
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| HAPLOPOOL: Improving Haplotype Frequency Estimation Through DNA Pools and Phylogenetic Modeling | B. Kirkpatrick, C. Santos Armendariz, R. M. Karp, and E. Halperin | Bioinformatics, Vol. 23, No. 22, pp. 3048-3055 | November 2007 | Algorithms | [PDF]
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| Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm | M. Narayanan and R. M. Karp | Journal of Computational Biology, Vol. 14, Issue 7, pp. 892-907 | September 2007 | Algorithms | [PDF]
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| Balancing the Traffic Load in Wireless Networks with Curveball Routing | L. Popa, A. Rostami, R. M. Karp, C. Papadimitriou, and I. Stoica | Proceedings of the 8th ACM International Symposium on Mobile Ad Hoc Networking and Computing (MobiHoc 2007), Montreal, Canada | September 2007 | Algorithms | |
| Leveraging the HapMap Correlation Structure in Association Studies | N. Zaitlen, H. M. Kang, E. Eskin, and E. Halperin | American Journal of Human Genetics, Vol. 80, Issue 4, pp. 683-691 | April 2007 | Algorithms | [PDF]
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| An Efficient and Accurate Graph-based Approach to Detect Population Substructure | S. Sridhar, S. Rao, and E. Halperin | Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), Oakland, California, pp. 503-517 | April 2007 | Algorithms | [PDF]
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| A Rigorous Analysis of Population Stratification with Limited Data | K. Chaudhuri, E. Halperin, S. Rao, and S. Zhou | Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA), New Orleans, Louisiana, pp. 1046-1055 | January 2007 | Algorithms | [PDF]
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| Noisy Binary Search | R. M. Karp and R. Kleinberg | Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), New Orleans, Louisiana, pp. 881-890 | January 2007 | Algorithms | |
| Using DNA Pools for Genotyping Trios | K.B. Beckman, K.A. Abel, A. Braun, and E. Halperin | Nucleic Acids Research, Vol. 34, No. 19, electronic article no. 129 | November 2006 | Algorithms | [PDF]
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| Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction | G.E. Blelloch, K. Dhamdhere, E. Halperin, R. Ravi, R. Schwartz, and S. Sridhar | Proceedings of the 33rd International Colloquium on Automata, Languages, and Programming (ICALP 2006), Venice, Italy, pp. 667-678 | July 2006 | Algorithms | |
| A Note on Optimally Phasing Long Genomic Regions Using Local Haplotype Predictions | E. Eskin, E. Halperin, and R. Sharan | Journal of Bioinformatics and Computational Biology, Vol. 4, No. 3, pp. 639-647 | June 2006 | Algorithms | |
| George Dantzig's Impact on the Theory of Computation | R. M. Karp | Discrete Optimization, Vol. 5, Issue 2, pp. 174-185 | May 2006 | Algorithms | |
| Lower Bounds for Reductions | M. Kaariainen and J. Langford | Presented at the Atomic Learning Workshop, Chicago, Illinois | March 2006 | Algorithms | |
| A Comparison of Phasing Algorithms for Trios and Unrelated Individuals | J. Marchini, D. Cutler, N. Patterson, M. Stephens, E. Eskin, E. Halperin, S. Lin, S. Qin, G. Abecassis, H. Munro, and P. Donnelly | American Journal of Human Genetics, Vol. 78, Issue 3, pp. 437-450 | March 2006 | Algorithms | |
| Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks | J. Scott, T. Ideker, R. M. Karp, and R. Sharan | Journal of Computational Biology, Vol. 13, Issue 2 pp. 133-144 | March 2006 | Algorithms | [PDF]
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| Optimal Flow Distribution Among Multiple Channels with Unknown Capacities | R. M. Karp, T. Nierhoff, and T. Tantau | Theoretical Computer Science: Essays in Memory of Shimon Even, O. Goldreich, A. L. Rosenberg, and A. L. Selman, eds., Lecture Notes in Computer Science, Vol. 3895, pp. 111-128, Springer-Verlag | 2006 | Algorithms | [PDF]
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| Fair Bandwidth Allocation Without Per-Flow State | R. M. Karp | In Essays in Theoretical Computer Science in Memory of Shimon Even, O. Goldreich, A. L. Rosenberg, and A. L. Selman, eds., pp. 88-110, Springer | 2006 | Algorithms | |
| The Minimum-Entropy Set Cover Problem | E. Halperin and R. M. Karp | Theoretical Computer Science, Vol. 348, Issue 2, pp. 240-250 | December 2005 | Algorithms | |
| A Probabilistic Model for the Survivability of Cells | I. Adler, H-S Ahn, R. M. Karp, and S.M. Ross | Journal of Applied Probability, Vol. 42, No. 4, pp. 919-931 | December 2005 | Algorithms | |
| On Active Learning in the Non-Realizable Case | M. Kaariainen | Proceedings of the Foundations of Active Learning Workshop at the 19th Annual Conference on Neural Information Processing Systems (NIPS), Vancouver, Canada | December 2005 | Algorithms | |
| Report of the SIGACT Committee on funding for Theoretical Computer Science | R. M. Karp | SIGACT (Special Interest Group on Algorithms and Computation Theory) News | December 2005 | Algorithms | |
| Active Learning Under Arbitrary Distributions | C. Monteleoni and M. Kaariainen | Poster at the Value of Information in Inference, Learning, and Decision-Making Workshop at the 19th Annual Conference on Neural Information Processing Systems (NIPS), Vancouver, Canada | December 2005 | Algorithms | |
| Inference and Analysis of Haplotypes from Combined Genotyping Studies Deposited in dbSNP | N.A. Zaitlen, H.M. Kang, M.L. Feolo, S.T. Sherry, E. Halperin, and E. Eskin | Genome Research, Vol. 15, No. 11, pp.1594-1600 | October 2005 | Algorithms | |
| Knowledge Discovery for Time Series | M. Saffell | Ph.D. Thesis, OGI School of Science and Engineering, Oregon Health and Science University | September 2005 | Algorithms | |
| A Comparison of Tight Generalization Error Bounds | M. Kaariainen and J. Langford | Proceedings of the 22nd International Conference on Machine Learning (ICML 2005), Bonn, Germany, pp. 409-416 | August 2005 | Algorithms | |
| Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data | R. Sharan, T. Ideker, B. P. Kelley, R. Shamir, and R. M. Karp | Journal of Computational Biology, Vol. 12, Issue 6, pp. 835-846; also in Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB'04), San Diego, California, pp. 282-289, March 2004 | July 2005 | Algorithms | |
| Asymmetric K-Center Is Log* N-Hard to Approximate | J. Chuzhoy, S. Guha, E. Halperin, S. Khanna, G. Kortsarz, R. Krauthgamer, and J. Naor | Journal of the ACM, Vol. 52, Issue 4, pp. 538-551 | July 2005 | Algorithms | |
| Optimal Flow Distribution Among Multiple Channels with Unknown Capacities | R. Karp, T. Nierhoff, and T. Tantau | Proceedings of the Second Brazilian Symposium of Graphs, Algorithms, and Combinatorics (GRACO 2005), Angra dos Reis, Brazil, pp. 225-231 | July 2005 | Algorithms | [PDF]
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| Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy | E. Halperin, G. Kimmel, and R. Shamir | Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, Michigan, pp. 195-203 | June 2005 | Algorithms | [PDF]
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| Generalization Error Bounds Using Unlabeled Data | M. Kaariainen | Proceedings of the 18th Annual Conference on Learning Theory (COLT 2005), Bertinoro, Italy, pp. 127-142 | June 2005 | Algorithms | |
| Estimating Haplotype Frequencies Efficiently | E. Halperin and E. Hazan | Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05), Cambridge, Massachusetts, pp. 553-568 | May 2005 | Algorithms | |
| Haplofreq - Estimating Haplotype Frequencies Efficiently | E. Halperin and E. Hazan | Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05), Cambridge, Massachusetts, pp. 553-568 | May 2005 | Algorithms | |
| Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks | J. Scott, T. Ideker, R. M. Karp, and R. Sharan | Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05), Cambridge, Massachusetts, pp. 133-144 | May 2005 | Algorithms | |
| Whole-Genome Patterns of Common DNA Variation in Three Human Populations | D. A. Hinds, L. L. Stuve, G. B. Nilsen, E. Halperin, E. Eskin, D. G. Ballinger, K. A. Frazer, and D. R. Cox | Science, Vol. 307, No. 5712, pp. 1072-1079. DOI:10.1126/science.1105436 | February 2005 | Algorithms | [PDF]
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| Performance Aspects of Distributed Caches Using TTL-Based Consistency | E. Cohen, E. Halperin, and H. Kaplan | Theoretical Computer Science, Vol. 331, Issue 1, pp. 73-96 | February 2005 | Algorithms | |
| Conserved Patterns of Protein Interaction in Multiple Species | R. Sharan, S. Sutharan, R. Kelley, T. Kuhn, S. McCuine, T.Sittler, R. Karp, and T. Ideker | Proceedings of National Academy of Science, Vol. 102, Issue 6, pp. 1974-1979 | February 2005 | Algorithms | [PDF]
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| Optimization Problems Related to Internet Congestion Control | R. M. Karp | Graph Theory, Combinatorics and Algorithms: Interdisciplinary Applications, M.C. Golumbic and I.B.-A. Hartman, eds., Springer-Verlag, New York | 2005 | Algorithms | |
| Stochastic Direct Reinforcement: Application to Simple Games with Recurrence | J. Moody, Y. Liu, M. Saffell, and K. Youn | Proceedings of the 2004 AAAI Fall Symposium on Artificial Multiagent Learning, Arlington, Virginia, pp. 23-34 | October 2004 | Algorithms | [PDF]
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| A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns | J. Gramm | Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics (WABI 2004), Bergen, Norway | September 05 2004 | Algorithms | |
| Perfect Path Phylogeny Haplotyping with Missing Data is Fixed-Parameter Tractable | J. Gramm, T. Nierhoff, and T. Tantau | Proceedings of the First International Workshop on Parameterized and Exact Computation (IWPEC 2004), Bergen, Norway | September 05 2004 | Algorithms | |
| A 1.5-Approximation Algorithm for Sorting by Transpositions and Transversals | T. Hartman and R. Sharan | Proceedings of WABI | September 05 2004 | Algorithms | |
