Itsik Pe'er - Publications

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Journal Articles

  1. Pe'er I, Shamir R: Satisfiability problems on intervals and unit intervals. TCS 175(2): 349-372 (1997)

  2. Pe'er I, Shamir R: Realizing interval graphs with size and distance constraints. SIAM Journal on Discrete Mathematics 10(4): 662-687 (1997)

  3. Karp RM, Pe'er I, Shamir R: An algorithm combining discrete and continuous methods for optical mapping. Journal of Computational Biology 7(5): 745-760 (2000)

  4. Pupko T, Pe'er I, Shamir R, Graur D: A fast algorithm for joint reconstruction of ancestral amino acid sequences. Molecular Biology and Evolution. 17(6):890-6 (2000)

  5. Ben-Dor A, Pe'er I, Shamir R, Sharan R: On the complexity of positional sequencing by hybridization. Journal of Computational Biology 8(4): 361-371 (2002)

  6. Friedman N, Ninio M, Pe'er I, Pupko T: A structural EM algorithm for phylogenetic inference. Journal of Computational Biology 9(2): 331-353 (2002)

  7. Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N: A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics 18(8): 1116-1123 (2002)

  8. Pe’er I, Arbili N, Shamir R. A computational method for resequencing long DNA targets by universal oligonucleotide arrays. PNAS (USA) 99:15492-6. 2002.

  9. Pe'er I, Arbili N, Liu Y, Enck C, Gelfand CA, Shamir R. Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays. Nucleic Acids Research. 31:5667-75. 2003.

  10. Pe'er I, Beckman JS. On the applicability of a haplotype map to unassayed populations. Human Genetics. 114:214-7. 2004.

  11. Pe'er I, Felder CE, Man O, Silman I, Sussman JL, Beckman JS. Proteomic signatures: amino acid and oligopeptide compositions defferentiante between phyla. Proteins 54:20-40. 2004.

  12. Pe'er I, Beckman JS. Recovering frequencies of known haplotype blocks from SNP allele frequencies. Genetics. 166:2001-6. 2004.

  13. Pe'er I, Shamir R, Sharan R. Incomplete directed perfect phylogeny. SIAM J on Comput. 33(3): 590-607. 2004.

  14. Singer C, Grossman I, Avidan N, Beckmann JS, Pe'er I. Trick or treat: The effect of placebo on the power of pharmacogenetic association studies. Hum Genomics. 2005;2(1):28-38

  15. Barzuza T, Beckmann JS, Shamir R, Pe'er I. Typing without calling the allele: a strategy for inferring SNP haplotypes. Eur J Hum Genet. 2005;13(8):898-901.

  16. de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D. Efficiency and power in genetic association studies. Nat Genet. 2005; 37(11):1217-1223.

  17. Bonnen PE, Pe’er I1, Plenge RM, Salit J, Lowe JK, Shapero MH, Lifton RP, Breslow JL, Daly MJ, Reich DE, Jones KW, Stoffel M, Altshuler D, Friedman JM. Evaluating potential for whole genome studies in Kosrae, an isolated population in Micronesia. Nat Genet. 2006;38(2):214-7

  18. Pe’er I, Chretien YR, de Bakker PIW, Barrett JC, Daly MJ, Altshuler D. Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am J Hum Genet., 2006;78(4):588-603

  19. Wang H, Thomas DC, Pe’er I, Stram DO. Optimal two stage designs for genomewide association scans. Genet Epi.. 2006;30(4):356-368.

  20. Pe’er I, de Bakker PIW, Maller J, Yelensky R, Altshuler D, Daly MJ, Evaluating and Improving Power in Whole Genome Association Studies using Fixed Marker Sets, Nat Genet, 2006;38(6):663-667


Book Chapters

  1. Pe’er I, Shamir R. Approximation algorithms for the permutations median problem in the breakpoint model in comparative genomics. In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families. David Sankoff and Joseph H. Nadeau, eds. Dordrecht, The Netherlands: Kluwer Academic Press, 2000, pp 225-241

Reviewed Extended Abstracts

  1. Pe’er I, Shamir R. Interval Graphs with Side (and Size) Constraints. Proceedings of the European Symposium on Algorithms. 1995; 3:142-154

  2. Ben-Dor A, Pe’er I, Shamir R, Sharan R. On the Complexity of Positional Sequencing by Hybridization. Annual Symposium on Combinatorial Pattern Matching. 1999;10:88-100

  3. Karp RM, Pe'er I, Shamir R. An algorithm combining discrete and continuous methods for optical mapping. Proceedings of the International Conference on Intelligent Systems for Molecular Biology. 1999;7:159-68.

  4. Pe’er I, Shamir R, Sharan R. Incomplete Directed Perfect Phylogeny. Annual Symposium on Combinatorial Pattern Matching. 2000; 11:143-153

  5. Pe'er I, Shamir R. Spectrum alignment: efficient resequencing by hybridization. Proceedings of the International Conference on Intelligent Systems for Molecular Biology. 2000;8:260-8.

  6. Friedman N, Ninio M, Pe'er I, Pupko T. A structural EM algorithm for phylogenetic inference. Proceedings of the Annual International Conference on Computational Biology. 2001;10:132-140

  7. Pe’er I, Shamir R, Sharan R. On the Generality of Phylogenies from Incomplete Directed Characters. Scandinavian Workshop on Algorithmic Theory. 2002; 8:358-367

  8. Pe'er I, Beckmann JS. Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples. Proceedings of the Annual International Conference on Computational Biology. 2003; 12:237-246

  9. Pe'er I, de Bakker PIW, Barrett JC, Altshuler D, Daly MJ. A Branch-and-Bound Algorithm for the Chromosome Tagging Problem Proc. RECOMB Workshop on Computational Methods for SNPs and Haplotypes. 2004; 89-97

  10. Barzuza T, Beckmann JS, Shamir R, Pe'er I. Annual Symp. on Combinatorial Pattern Matching. 2004;15:14

Reviewed E-journals

  1. Pe’er I, Shamir R. The median problems for breakpoints are NP-complete. Electronic Colloquium on Computational Complexity. 1998;5(71)

  2. Berman P, Ben-Dor A., Pe’er I, Shamir R, Sharan R. On the Complexity of Positional Sequencing by Hybridization. Electronic Colloquium on Computational Complexity. 8(54): (2001)

1 Joint first authorship status

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