| 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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| 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 | |
| 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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| 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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| 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 | |
| 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 | |
| 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 | |
| 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 | |
