| 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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| 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 | |
| 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 | |
| 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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| 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 | |
| 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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| 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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| Probabilistic Analysis of Linear Programming Decoding | C. Daskalakis, A. G. Dimakis, R. M. Karp, and M. J. Wainwright | IEEE Transactions on Information Theory, Vol. 54, Issue 8, pp. 3565-3578 | August 2008 | Algorithms | |
| Malicious Bayesian Congestion Games | M. Gairing | Proceedings of the 6th Workshop on Approximation and Online Algorithms (WAOA'08), Universität Karlsruhe, Germany, pp. 119-132 | September 2008 | Algorithms | [PDF]
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| Average Update Times for Fully-Dynamic All-Pairs Shortest Paths | T. Friedrich and N. Hebbinghaus | Proceedings of International Symposium on Algorithms and Computation (ISAAC), Gold Coast, Australia, pp. 693-704 | December 2008 | Algorithms | [PDF]
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| Approximating the Volume of Unions and Intersections of High-Dimensional Geometric Objects | K. Bringmann and T. Friedrich | Proceedings of International Symposium on Algorithms and Computation (ISAAC), Gold Coast, Australia, pp. 436-447 | December 2008 | Algorithms | [PDF]
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| Association Mapping and Significance Estimation via the Coalescent | G. Kimmel, R. M. Karp, M. A. Jordan, and E. Halperin | Journal of Human Genetics, Vol. 83, Issue 6, pp. 675-683 | December 2008 | Algorithms | [PDF]
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| Computing Single Source Shortest Paths Using Single-Objective Fitness Functions | S. Baswana, S. Biswas, DB. Doerr, T. Friedrich, P. Kurur, and F. Neumann | Proceedings of the 10th Foundations of Genetic Algorithms Workshop (FOGA X), Orlando, Florida, pp. 59-66 | January 2009 | Algorithms | [PDF]
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| Quasirandom Rumor Spreading: An Experimental Analysis | B. Doerr, T. Friedrich, M. Künneman, and T. Sauerwald | Proceedings of the Workshop on Algorithm Engineering and Experiments (ALENEX09), New York, New York, pp. 145-153 | January 2009 | Algorithms | [PDF]
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| Don’t Be Greedy When Calculating Hypervolume Contributions. | K. Bringmann and T. Friedrich. | Proceedings of the 10th Foundations of Genetic Algorithms Workshop (FOGA X), Orlando, Florida, pp. 103-112 | January 2009 | Algorithms | [PDF]
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| Towards the Integrated Analysis, Visualization, and Reconstruction of Microbial Gene Regulatory Networks | J. Baumbach, S. Rahmann, and A. Tauch | Briefings in Bioinformatics, Vol. 10, Issue 1, pp. 75-83 | January 2009 | Algorithms | [PDF]
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| Reliable Transfer of Transcriptional Gene Regulatory Networks Between Taxonomically Related Organisms | J. Baumbach, S. Rahmann, and A. Tauch | BMC Systems Biology, Vol. 3, Issue 8 | January 2009 | Algorithms | [PDF]
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| Sorting and Selection in Posets | C. Daskalakis, R. M. Karp, E. Mossel, S. Riesenfeld, and E. Verbin | Proceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms, New York, New York, pp. 392-401 | January 2009 | Algorithms | [PDF]
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| Dynamic Network Topology Changes in Functional Modules Predict Responses to Oxidative Stress in Yeast | P. V. Gopalacharyulu, V. R. Velagapudi, E. Lindfors, E. Halperin, and M. Orešič | Molecular BioSystems, Vol. 5, Issue 3, pp. 276-287 | March 2009 | Algorithms | |
| Maximizing Power in Association Studies | E. Halperin and D. A. Stephan | Nature Biotechnology, Vol. 27, Issue 3, pp. 255-256 | March 2009 | Algorithms | [PDF]
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| Approximating the Least Hypervolume Contributor : NP-Hard in General, but Fast in Practice | K. Bringmann and T. Friedrich | Proceedings of the Fifth International Conference on Evolutionary Multi-Criterion Optimization (EMO 2009), Nantes, France, pp. 6-20 | April 2009 | Algorithms | [PDF]
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| SNP Imputation in Association Studies | E. Halperin and D. A. Stephan | Nature Biotechnology, Vol. 27, No. 4, pp. 349-351 | April 2009 | Algorithms | [PDF]
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| Adaptive Concept Drift Detection | A. Dries and U. Rueckert | Best paper, proceedings of the 9th SIAM International Conference on Data Mining, Sparks, Nevada, pp. 235-246 | April 2009 | Algorithms | [PDF]
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| Near-Perfect Load Balancing by Randomized Rounding | T. Friedrich and T. Sauerwald | Proceedings of the 41st ACM Symposium on Theory of Computing (STOC 2009), Bethesda, Maryland, pp. 121-130 | May 2009 | Algorithms | [PDF]
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| Imputation-Based Local Ancestry Inference in Admixed Populations | B. Pasaniuc, J. Kennedy, and I. I. Mandoiu | Proceedings of the Fifth International Symposium on Bioinformatics Research and Applications (ISBRA 2009), Fort Lauderdale, Florida, pp. 221-233 | May 2009 | Algorithms | [PDF]
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| MotifAdjuster: A Tool for Computational Reassessment of Transcription Factor Binding Site Annotations | J. Keilwagen, J. Baumbach, T. Kohl, and I. Grosse | Genome Biology, Vol. 10, Issue 5, p. R46 | May 2009 | Algorithms | [PDF]
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| Haplotype Inference in Complex Pedigrees | B. Kirkpatrick, J. Rosa, E. Halperin, and R. M. Karp | Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB2009), Tucson, Arizona, pp. 108-120 | May 2009 | Algorithms | [PDF]
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| Torque: Topology-Free Querying of Protein Interaction Networks | S. Bruckner, F. Hüffner, R. M. Karp, R. Shamir, and R. Sharan | Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), Tucson, Arizona, pp. 74-89 | May 2009 | Algorithms | |
| Integrated Analysis and Reconstruction of Microbial Transcriptional Gene Regulatory Networks Using CoryneRegNet | J. Baumbach, T. Wittkop, C. K. Kleindt, and A. Tauch | Nature Protocols, Vol. 4, Issue 6, pp. 992-1005 | June 2009 | Algorithms | |
| On the Effects of Adding Objectives to Plateau Functions | D. Brockhoff, T. Friedrich, N. Hebbinghaus, C. Klein, F. Neumann, and E. Zitzler | IEEE Transactions on Evolutionary Computation, Vol. 13, Issue 3, pp. 591-603 | June 2009 | Algorithms | [PDF]
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| Inference of Locus-Specific Ancestry in Closely Related Populations | B. Pasaniuc, S. Sankararaman, G. Kimmel, and E. Halperin | Proceedings of the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden. In Bioinformatics, Vol. 25, No. 12, pp. 213-221 | June 2009 | Algorithms | [PDF]
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| Three Combinatorial Problems in Computational and Genomic Biology | R. Karp | IFORS Distinguished Lecture at the Joint International Meeting of the Canadian Operational Research Society and the Institute for Operations Research and the Management Sciences (CORS-INFORMS International), Toronto, Canada | June 2009 | Algorithms | |
| Dynamic Portfolio Management with Transaction Costs | A. Suarez, J. Moody, and M. Saffell | Proceedings of the International Workshop on Advances in Machine Learning for Computational Finance, London, United Kingdom. Also presented at the Multidisciplinary Symposium on Reinforcement Learning, Montreal, Canada, June 2009 | July 2009 | Algorithms | [PDF]
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| Multiplicative Approximations and the Hypervolume Indicator | T. Friedrich, C. Horoba, and F. Neumann | Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2009), Montreal, Canada, pp. 571-578 | July 2009 | Algorithms | [PDF]
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| Quasirandom Rumor Spreading: Expanders, Push vs. Pull, and Robustness | B. Doerr, T. Friedrich, and T. Sauerwald | Proceedings of the 36th International Colloquium on Automata, Languages, and Programming (ICALP 2009), Rhodes, Greece, pp. 366-377 | July 2009 | Algorithms | [PDF]
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| Smoothed Analysis of Balancing Networks | T. Friedrich, T. Sauerwald, and D. Vilenchik | Proceedings of the 36th International Colloquium on Automata, Languages, and Programming (ICALP 2009), Rhodes, Greece, pp. 472-483 | July 2009 | Algorithms | [PDF]
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| Tight Bounds for the Cover Time of Multiple Random Walks | R. Elsässer and T. Sauerwald | Proceedings of the 36th International Colloquium on Automata, Languages, and Programming (ICALP 2009), Rhodes, Greece, pp. 415-426 | July 2009 | Algorithms | [PDF]
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| The Weighted Coupon Collector's Problem and Applications | P. Berenbrink and T. Sauerwald | Proceedings of the 15th International Computing and Combinatorics Conference (COCOON 2009), Niagra Falls, New York, pp. 449-458 | July 2009 | Algorithms | |
| Torque: Topology-Free Querying of Protein Interaction Networks | S. Bruckner, F. Hueffner, R. M. Karp, R. Shamir, and R. Sharan | Nucleic Acids Research, Vol. 37, pp. 106-108 | July 2009 | Algorithms | [PDF]
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| From Corynebacterium Glutamicum to Mycobacterium Tuberculosis - Towards Transfers of Gene Regulatory Networks and Integrated Data Analyses with MycoRegNet | J. Krawczyk, T. A. Kohl, A. Goesmann, J. Kalinowski, and J. Baumbach | Nucleic Acids Research, Vol. 37, No. 14, e97 | August 2009 | Algorithms | [PDF]
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| A Randomized, O(log w)-Depth 2-Smoothing Network | M. Mavronicolas and T. Sauerwald | Proceedings of the 21st ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2009), Calgary, Canada, pp. 178-187 | August 2009 | Algorithms | [PDF]
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| On the Runtime and Robustness of Randomized Broadcasting | R. Elsässer and T. Sauerwald | Theoretical Computer Science, Vol. 410, Issue 36, pp. 3414-3427 | August 2009 | Algorithms | [PDF]
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| Genetic Variants at 6p21.33 Are Associated with Susceptibility to Follicular Lymphoma | C. F. Skibola, P. M. Bracci, E. Halperin, L. Conde, D. W. Craig, L. Agana, K. Iyadurai, N. Becker, A. Brooks-Wilson, J. D. Curry, J. J. Spinelli, E. A. Holly, J. Riby, L. Zhang, A. Nieters, M. T. Smith, and K. M. Brown | Nature Genetics, Vol. 41, No. 8, pp. 873-875 | August 2009 | Algorithms | [PDF]
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| On the Price of Heterogeneity in Parallel Systems | P. Brighten Godfrey and R. M. Karp | Theory of Computing Systems, Vol. 45, No. 2, pp. 280-301 | August 2009 | Algorithms | [PDF]
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| Capacity Control for Partially Ordered Feature Sets | U. Rueckert | Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2009), Part II, Bled, Slovenia, pp. 318-333 | September 2009 | Algorithms | [PDF]
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| Genomic Privacy and Limits of Individual Detection in a Pool | S. Sankararaman, G. Obozinski, M. I. Jordan, and E. Halperin | Nature Genetics, Vol. 41, No. 9, pp. 965-967 | September 2009 | Algorithms | [PDF]
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