Publications


Selected

  • Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe’er I Whole Population, Genome-Wide Mapping of Hidden Relatedness Genome Research, 2009 Feb;19(2):318-26
  • Sarin S, Prabhu S, O'Meara MM, Pe’er I+, Hobert O, Caenorhabditis elegans mutant allele identification by whole-genome sequencing, Nat Methods, 2008, 5:865-867:663-667
  • 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.
  • 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


Complete


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. The International HapMap Consortium&, A haplotype map of the human genome. Nature 437, 1299-1320. 2005
  18. Bonnen PE, Pe’er I*, 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
  19. 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
  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
  21. Wang H, Thomas DC, Pe’er I, Stram DO. Optimal two stage designs for genomewide association scans. Genet Epi.. 2006;30(4):356-368.
  22. Grossman I, Avidan N, Singer C, Goldstaub D, Hayardeny L, Eyal E, Ben-Asher E, Paperna T, Pe’er I Lancet D, Beckmann JS, Miller A, Pharmacogenetics of Glatiramer acetate therapy for multiple sclerosis reveals drug-response markers, Pharmacogenetics and Genomics, (2007) 17(8):657-666.
  23. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES; The International HapMap Consortium&, Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18;449(7164):913-8
  24. The International HapMap Consortium&, A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861. 2007.
  25. Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, Pe’er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, Neale BM, Izmailova E, Roubenoff R, Parker AN, Glass R, Karlson EW, Maher N, Hafler DA, Lee DM, Seldin MF, Remmers EF, Lee AT, Padyukov L, Alfredsson L, Coblyn J, Weinblatt ME, Gabriel SB, Purcell S, Klareskog L, Gregersen PK, Shadick NA, Daly MJ, Altshuler D, Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007 Dec;39(12):1477-82
  26. Barzuza T, Beckmann JS, Shamir R, Pe’er I, Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele, IEEE Transactions on Computational Biology and Bioinformatics, advanced online publication, 2008 Jan-Mar;5(1):101-9.
  27. Stoyanovich J, Pe’er I MutaGeneSys: Estimating Individual Disease Susceptibility Based on Genome-Wide SNP Array Data, Bioinformatics, 2008 Feb 1;24(3):440-2
    Link to paper
  28. Pe’er I, Yelensky R, Altshuler D, Daly MJ, Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol. 2008 May;32(4):381-5
  29. Sarin S, Prabhu S, O'Meara MM, Pe’er I*, Hobert O, Caenorhabditis elegans mutant allele identification by whole-genome sequencing, Nat Methods, 2008, Aug 1st;:663-667
  30. Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe’er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM, Breslow JL Common SNPs in HMGCR in Micronesians and Whites Associated With LDL-Cholesterol Levels Affect Alternative Splicing of Exon13. Arterioscler Thromb Vasc Biol. 2008 Nov;28(11):2078-84
  31. Shen Y, Sarin S, Liu Y, Hobert O, Pe’er I. Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS ONE. 2008;3(12):e4012 { Supplementary data: Solexa reads; SOLiD reads. }
  32. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe’er I Whole Population, Genome-Wide Mapping of Hidden Relatedness Genome Research, 2009 Feb;19(2):318-26
  33. Lowe JK, Julian B. Maller, Pe’er I, Neale BM. Neale, Salit J, Kenny EE, Shea JL, Burkhardt R, Smith G, Ji W, Noel M, Foo JN, Blundell ML, Skilling V, Garcia L, Sullivan ML, Lee HE, Labek A, Ferdowsian H, Auerbach SB, Lifton RP, Newton-Cheh C, Breslow JL,Stoffel M, Daly MJ, Altshuler DM, Friedman JM. Genome-wide association studies in an isolated founder population from the Pacific island of Kosrae. PLoS Genetics, 2009, Feb;5(2):e1000365
  34. Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe’er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR, Graham J, Park BK, Dillon JF, Bernal W, Cordell HJ, Pirmohamed M, Aithal GP, Day CP for the DILIGEN study and International SAE Consortium, HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin, Nature Genetics, 2009 Jul;41(7):816-9.
  35. Prabhu S, Pe’er I. Overlapping pools for high throughput targeted resequencing. Genome Res. 2009 Jul;19(7):1254-61.
  36. Kenny EE, Gusev A, Riegel K, Latjohannd D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman DM, Breslow JL, Pe’er I*, Sehayek E. Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. PNAS. 2009, Aug;106(33):13886-91.
  37. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe’er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Crowe RR, Oksenberg JR, Mirel DB, Kendler KS, Freedman R, Gejman PV. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature. 2009, Aug;460(7256):753-7
  38. Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. Eur J Hum Genet.2010; 18(3):309-316Â
  39. LaFramboise T, Dewal NP, Wilkins K, Pe'er I, Freedman M. Allelic Selection of Amplicons in Glioblastoma Revealed by Combining Somatic and Germline Analysis. PloS Genetics. In press.
  40. Dewal N, Freedman ML, Laframboise T, Pe'er I , Power to Detect Selective Allelic Amplification in Genome-wide Scans of Tumor Data. Bioinformatics. 26(4):518-28.
  41. Atzmon G, Hao L, Pe'er I2, Velez C, Pearlman A, Palamara PF, Morrow B, Friedman E, Oddoux C, Burns E, Ostrer H, Abraham’s Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry, Am J Hum Genet. Epub june 2010.


Book Chapters


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
  11. Prabhu S, Pe'er I. Overlapping pools for high throughput targeted resequencing. Proceedings of the Annual International Conference on Computational Biology. 2009 (extended abstract selected to a special journal issue, thus omitted from proceedings)
  12. Setty M, Gusev A Pe'er I. HLA type inference via haplotypes identical by descent. Proceedings of the Annual International Conference on Computational Biology. 2010. To appear.


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)

+ Joint last authorship status
& Consortium Member
* Joint first authorship status