| Probabilistic Inference of Viral Quasispecies Subject to Recombination | A. Topfer, O. Zagordi, S. Prabhakaran, V. Roth, E. Halperin, and N. Beerenwinkel | Journal of Computational Biology, Vol. 20, No. 2, pp. 113-123 | February 2013 | Algorithms | |
| Identifying Personal Genomes by Surname Inference | M. Gymrek, A. L. McGuire, D. Golan, E. Halperin, and Y. Erlich | Science, Vol. 339, No. 6117, pp. 321-324 | January 2013 | Algorithms | |
| A Model-Based Approach for Analysis of Spatial Structure in Genetic Data | W. Yang, J. Novembre, E. Eskin, and E. Halperin | Presented at the Annual Meeting of the American Society of Human Genetics, San Francisco, California | November 2012 | Algorithms | |
| Probabilistic Convergence Guarantees for Type-II Pulse-Coupled Oscillators | J. Nishimura and E. Friedman | Physical Review E, Vol. 86, Issue 2 | August 2012 | Algorithms | |
| Common Variation at 6p21.31 (BAK1) Influences the Risk of Chronic Lymphocytic Leukemia | S. L. Slager, C. F. Skibola,..., E. Halperin, et al. | Blood, Vol. 120, No. 4, pp. 843-846 | July 2012 | Algorithms | |
| Theory of Computation as an Enabling Tool for the Sciences | R. Karp | Presented at the Turing Centennial Celebration, Princeton, New Jersey. Also presented at the 9th Annual Conference on Theory and Applications of Models of Computation (TAMC 2012), Turing Centenary Meeting, Beijing, China | May 2012 | Algorithms | |
| Fast and Accurate Inference of Local Ancestry in Latino Populations | Y. Baran, B. Pasaniuc, S. Sankararaman, D. G. Torgerson, C. Gignoux, C. Eng, W. Rodriguez-Cintron, R. Chapela, J. G. Ford, P. C. Avila, J. Rodriguez-Santana, E. G. Burchard, and E. Halperin | Bioinformatics, Vol. 28, Issue 10, pp. 1359-1367 | May 2012 | Algorithms | [PDF]
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| A Model-Based Approach for Analysis of Spatial Structure in Genetic Data | W.-Y. Yang, J. Novembre, E. Eskin, and E. Halperin | Nature Genetics, Vol. 44, pp. 725-731 | May 2012 | Algorithms | [PDF]
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| Probabilistic Inference of Viral Quasispecies Subject to Recombination | O. Zagordi, A. Topfer, S. Prabhakaran, V. Roth, E. Halperin, and N. Beerenwinkel | Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain, pp.342-354 | April 2012 | Algorithms | [PDF]
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| MGMR: Leveraging RNA-Seq Population Data to Optimize Expression Estimation | R. Rozov, E. Halperin, and R. Shamir | Proceedings of the Second Annual Satellite Workshop on Massively Parallel Sequencing at the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain. Published in BMC Bioinformatics, Vol. 13, Suppl. 6:S2 | April 2012 | Algorithms | [PDF]
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| CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping | Z. Wang, F. Hormozdiari, W.-Y. Yang, E. Halperin, and E. Eskin | Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain, pp. 326-340 | April 2012 | Algorithms | |
| Haplotype Reconstruction Using Perfect Phylogeny and Sequence Data | A. Efros and E. Halperin | Proceedings of the Second Annual Satellite Workshop on Massively Parallel Sequencing at the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain. Published in BMC Bioinformatics, Vol. 13, Suppl. 6:S2 | April 2012 | Algorithms | [PDF]
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| Reconstructing Boolean Models of Signaling | R. Sharan and R. M. Karp | Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain, pp. 261-271 | April 2012 | Algorithms | |
| Joint Analysis of Multiple Metagenomic Samples | Y. Baran and E. Halperin | PLOS Computational Biology, accepted for publication | 2012 | Algorithms | |
| Comparing Pedigree Graphs | B. Kirkpatrick, Y. Reshef, H. Finucane, H. Jiang, B. Zhu, and R. M. Karp | Journal of Computational Biology | 2012 | Algorithms | [PDF]
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| Combinatorial Games with a Pass: A dynamical systems approach | R. Morrison, E. Friedman, and A. Landsberg | Chaos, Vol. 21, No. 4 | December 2011 | Algorithms | |
| Novel Associations for Coronary Artery Disease Derived from Genome Wide Association Studies Are Not Associated with Increased Carotid Intima-Media Thickness.... | L. Conde, S. Bevan, M. Sitzer, N. Klopp, T. Illig, J. Thiery, J. Seissler, J. Baumert, O. Raitakari, M. Khnen, L. P. Lyytikinen, R. Laaksonen, J. Viikari, T. Lehtimki, W. Koernig, E. Halperin, H. S. Markus | Atherosclerosis, Vol. 219, No 2, pp. 684-689 | December 2011 | Algorithms | |
| Faster and More Accurate Sequence Alignment with SNAP | M. Zaharia, W. J. Bolosky, K. Curtis, A. Fox, D. Patterson, S. Shenker, I. Stoica, R. M. Karp, and T. Sittler | arXiv.org under arXiv:1111.5572v1 | November 2011 | Algorithms | [PDF]
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| Asymmetric Cost Sharing Mechanisms | E. Friedman | Games and Economic Behavior, available at http://dx.doi.org/10.1016/j.geb.2011.09.009 | October 2011 | Algorithms | |
| Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values | K. Stephens and B. Kirkpatrick | Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI 2011), Saarbrücken, Germany | September 2011 | Algorithms | |
| Using Contiguous Bi-Clustering for Data Driven Temporal Analysis of fMRI Based Functional Connectivity | A. Maron-Katz, E. B. Simon, Y. Jacob, K. Rosenberg, R. M. Karp, T. Hendler, and R. Shamir | Proceedings of the 4th Annual INCF Neuroinformatics Congress, Boston, Massachusetts | September 2011 | Algorithms | [PDF]
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| Inhibition of Activated Pericentromeric SINE/Alu Repeat Transcription in Senescent Human Adult Stem Cells Reinstates Self-Renewal | J. Wang, G. J. Geesman, S. L. Hostikka, M. Atallah, B. Blackwell, E. Lee, P. J. Cook, B. Pasaniuc, G. Shariat, E. Halperin, M. Dobke, M. G. Rosenfeld, I. K. Jordan, and V. V. Lunyak | Cell Cycle, Vol. 10, No.17, pp. 3016-3030 | September 2011 | Algorithms | |
| Algorithms to Detect Multiprotein Modularity Conserved During Evolution | L. Hodgkinson and R. M. Karp | IEEE/ACM Transactions on Computational Biology and Bioinformatics, PMID: 21968956 | September 2011 | Algorithms | [PDF]
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| Effective Heuristics for NP-Hard Problems | R. M. Karp | Presented at the Michael Rabin Celebration, Cambridge, Massachusetts | August 2011 | Algorithms | |
| A Search for Overlapping Genetic Susceptibility Loci Between Non-Hodgkin Lymphoma and Autoimmune Diseases | L. Conde, P. M. Bracci, E. Halperin, and C. F. Skibola | Genomics, Vol. 98, No. 1, pp. 9-14 | July 2011 | Algorithms | |
| Domination When the Stars Are Out | D. Hermelin, M. Mnich, E. J. van Leeuwen, and G. J. Woeginger | Proceedings of the 38th International Colloquium on Automata, Languages and Programming (ICALP 2011), pp. 432-473, Zurich, Switzerland | July 2011 | Algorithms | |
| Planar k-Path in Subexponential Time and Polynomial Space | D. Lokshtanov, M. Mnich, and S. Saurabh | Proceedings of the 37th International Workshop on Graph-Theoretic Concepts in Computer Science (WG '11), Teplá-Klášter, Czech Republic | June 2011 | Algorithms | |
| Algorithms to Detect Multiprotein Modularity Conserved During Evolution | L. Hodgkinson and R. M. Karp | Proceedings of the 7th International Symposium on Bioinformatics Research
and Applications (ISBRA 2011), Changsha, China. Also in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011. | May 2011 | Algorithms | [PDF]
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| Review of F. V. Fomin and D. Kratsch, "Exact Exponential Algorithms" | M. Mnich | Operations Research Letters, Vol. 39, No. 3, pp. 229-230 | May 2011 | Algorithms | |
| Combinatorial Games with a Pass: A Dynamical Systems Approach | R. Morrison, E. Friedman, and A. Landsberg | Proceedings of the 4th International Conference on Chaotic Modeling, Simulation, and Applications (CHAOS2011), Agios Nikolaos, Greece | May 2011 | Algorithms | [PDF]
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| Robust Convergence in Pulse Coupled Oscillators with Delays | J. Nishimura and E. Friedman | In Physical Review Letters, Vol. 106, No. 19, DOI:10.1103/PhysRevLett.106.194101 | May 2011 | Algorithms | |
| Short-Term Wind Energy Forecasting Using Support Vector Regression | O. Kramer and F. Gieseke | Proceedings of the International Conference on Soft Computing Models in Industrial and Environmental Applications (SoCo), Salamanca, Spain | April 2011 | Algorithms | [PDF]
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| Self-Stabilization in Hierarchically Structured Energy Markets | J. Laessig, B. Satzger, and O. Kramer | Proceedings of the 8th International Conference on Information Technology: New Generations (ITNG 2011), pp. 803-809, Las Vegas, Nevada | April 2011 | Algorithms | |
| Pedigree Reconstruction Using Identity by Descent | B. Kirkpatrick, S. C. Li, R. M. Karp, and E. Halperin | Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011),Vancouver, British Columbia, Canada, pp. 136-152. Also appeared in Journal of Computational Biology, Vol. 18, No. 11, pp. 1481-1493, November 2011. | March 2011 | Algorithms | [PDF]
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| Genotyping Common and Rare Variation Using Overlapping Pool Sequencing | D. He, N. Zaitlen, B. Pasaniuc, E. Eskin, and E. Halperin | BMC Informatics, Vol. 12, Suppl. 6. Also appears in the proceedings of the First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq), Vancouver, Canada, pp. 26-27 | March 2011 | Algorithms | [PDF]
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| Large-scale Association Analysis Identifies 13 New Susceptibility Loci for Coronary Artery Disease | The CARDIoGRAM Consortium | Nature Genetics, Vol. 43, No. 4, pp. 333-338 | March 2011 | Algorithms | |
| Genotype Is a Stronger Determinant than Sex of the Mouse Gut Microbiota | A. Kovacs, N. Ben-Jacob, H. Tayem, E. Halperin, F. A. Iraqi, and U. Gophna | Microbial Ecology, Vol. 61, No. 2, pp. 423-428 | February 2011 | Algorithms | |
| Autonomous and Scalable Failure Detection in Distributed Systems | B. Satzger, A. Pietzowski, and T. Ungerer | International Journal of Autonomous and Adaptive Communications Systems, Vol. 4, No.1, pp. 61-77 | January 2011 | Algorithms | |
| Simple Max-Min Ant Systems and the Optimization of Linear Pseudo-Boolean Functions | T. Koetzing, F. Neumann, D. Sudholt, and M. Wagner | Proceedings of the 11th Foundations of Genetic Algorithms Workshop (FOGA XI), pp. 209-218, Schwarzenberg, Austria | January 2011 | Algorithms | [PDF]
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| Adaptive Population Models for Offspring Populations and Parallel Evolutionary Algorithms | J. Laessig and D. Sudholt | Proceedings of the 11th Foundations of Genetic Algorithms Workshop (FOGA XI), pp. 181-192, Schwarzenberg, Austria | January 2011 | Algorithms | [PDF]
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| Using Markov-Chain Mixing Time Estimates for the Analysis of Ant Colony Optimization | D. Sudholt | Proceedings of the 11th Foundations of Genetic Algorithms Workshop (FOGA XI), pp. 139-150, Schwarzenberg, Austria | January 2011 | Algorithms | [PDF]
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| Algorithms for Implicit Hitting Set Problems | K. Chandrasekaran, R. Karp, E. Moreno-Centeno, and S. Vempala | Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2011), pp. 614-629, San Francisco, California | January 2011 | Algorithms | [PDF]
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| Machine Symbol Grounding and Optimization | O. Kramer | Proceedings of the Third International Conference on Agents and Artificial Intelligence (ICAART 2011), Rome, Italy | January 2011 | Algorithms | [PDF]
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| Algorithms to Detect Multi-Protein Modularity Conserved During Evolution | L. Hodgkinson and R. M. Karp | EECS Department, UC Berkeley Technical Report No. UCB/EECS-2011-7, Berkeley, California | January 2011 | Algorithms | |
| Heuristic Algorithms in Computations Molecular Biology | R. M. Karp | Journal of Computer and System Sciences, Special Issue: Celebrating Karp's Kyoto Prize, Vol. 77, No. 1, pp. 122-128 | January 2011 | Algorithms | |
| Approximating Covering Problems by Randomized Search Heuristics using Multi-Objective Models | T. Friedrich, J. He, N. Hebbinghaus, F. Neumann, and C. Witt | Evolutionary Computation, Vol. 18, No. 4, pp. 617-633, Winter 2010 | December 2010 | Algorithms | [PDF]
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| On the Power and Limits of Evolutionary Conservation -- Unraveling Bacterial Gene Regulatory Networks | J. Baumbach | Nucleic Acids Research, Vol. 38, No. 22, pp. 7877-7884 | December 2010 | Algorithms | [PDF]
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| Analysis of an Iterated Local Search Algorithm for Vertex Coloring | D. Sudholt and C. Zarges | Proceedings of the 21st International Symposium on Algorithms and Computation (ISAAC 2010), Jeju Island, Korea | December 2010 | Algorithms | |
| A Generic Coalescent-Based Framework for the Selection of a Reference Panel for Imputation | B. Pasanuic, R. Avinery, T. Gur, C. F. Skibola, P. M. Bracci, and E. Halperin | Genetic Epidemiology, Vol. 34, Issue 8, pp. 773-782 | December 2010 | Algorithms | [PDF]
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| Presymptomatic Risk Assessment for Chronic Non-Communicable Diseases | B. Padhukasahasram, E. Halperin, J. Wessel, D. J. Thomas, E. Silver, H. Trumbower, M. Cargill, and D. A. Stephan | PLoS ONE Vol. 5, No. 12. doi:10.1371/journal.pone.0014338 | December 2010 | Algorithms | |
