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School of Public Health: Carmi Shai

Researchers / חוקרים

 Last updated February 2023 - School of Public Health

List of Publications

(1) Rappoport N, Aviel G, Shahian DM, Korach A, Carmi S, Keaney JF, et al. Resternotomy Coronary Artery Bypass 1999-2018: Insights From The Society of Thoracic Surgeons Adult Cardiac Surgery Database. Ann Thorac Surg 2023;115(1):62-71.

(2) Waldman S, Backenroth D, Harney É, Flohr S, Neff NC, Buckley GM, et al. Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century. Cell 2022;185(25):4703-4716.e16.

(3) Cotter DJ, Severson AL, Carmi S, Rosenberg NA. Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating. Theor Popul Biol 2022;147:1-15.

(4) Pereira S, Carmi S, Altarescu G, Austin J, Barlevy D, Hershlag A, et al. Polygenic embryo screening: Four clinical considerations warrant further attention. Hum Reprod 2022;37(7):1375-1378.

(5) Lieberman S, Chen-Shtoyerman R, Levi Z, Shkedi-Rafid S, Zuckerman S, Bernstein-Molho R, et al. Common founder BRCA2 pathogenic variants and breast cancer characteristics in Ethiopian Jews. Breast Cancer Res Treat 2022;193(1):217-224.

(6) Privé F, Aschard H, Carmi S, Folkersen L, Hoggart C, O'Reilly PF, et al. Erratum: Portability of 245 polygenic scores when derived from the UK Biobank and applied to 9 ancestry groups from the same cohort (The American Journal of Human Genetics (2022) 109(1) (12–23), (S0002929721004201), (10.1016/j.ajhg.2021.11.008)). Am J Hum Genet 2022;109(2):373.

(7) Tessler I, Goudot G, Albuisson J, Reshef N, Zwas DR, Carmi S, et al. Is Bicuspid Aortic Valve Morphology Genetically Determined? A Family-Based Study. Am J Cardiol 2022;163:85-90.

(8) Privé F, Aschard H, Carmi S, Folkersen L, Hoggart C, O'Reilly PF, et al. Portability of 245 polygenic scores when derived from the UK Biobank and applied to 9 ancestry groups from the same cohort. Am J Hum Genet 2022;109(1):12-23.

(9) Barlevy D, Lencz T, Carmi S, Kostick-Quenet KM, Mukherjee M, Pereira S, et al. Capacities and Limitations of Using Polygenic Risk Scores for Reproductive Decision Making. Am J Bioethics 2022;22(2):42-45.

(10) Agranat-Tamir L, Waldman S, Rosen N, Yakir B, Carmi S, Carmel L. LINADMIX: Evaluating the effect of ancient admixture events on modern populations. Bioinformatics 2021;37(24):4744-4755.

(11) Arciero E, Dogra SA, Malawsky DS, Mezzavilla M, Tsismentzoglou T, Huang QQ, et al. Fine-scale population structure and demographic history of British Pakistanis. Nat Commun 2021;12(1).

(12) Lencz T, Backenroth D, Granot-Hershkovitz E, Green A, Gettler K, Cho JH, et al. Utility of polygenic embryo screening for disease depends on the selection strategy. eLife 2021;10.

(13) Tessler I, Albuisson J, Goudot G, Carmi S, Shpitzen S, Messas E, et al. Bicuspid Aortic Valve: Genetic and Clinical Insights. AORTA 2021;9(4):139-146.

(14) Lázaro-Muñoz G, Pereira S, Carmi S, Lencz T. Screening Embryos for Polygenic Conditions and Traits: Ethical Considerations for an Emerging Technology. Obstet Gynecol Surv 2021;76(8):458-459.

(15) Ben Shachar S, Barda N, Manor S, Israeli S, Dagan N, Carmi S, et al. MHC Haplotyping of SARS-CoV-2 Patients: HLA Subtypes Are Not Associated with the Presence and Severity of COVID-19 in the Israeli Population. J Clin Immunol 2021;41(6):1154-1161.

(16) Zeevi DA, Backenroth D, Hakam-Spector E, Renbaum P, Mann T, Zahdeh F, et al. Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing. Gen Med 2021;23(7):1334-1340.

(17) Azulai S, Grinbaum R, Beglaibter N, Eldar SM, Rubin M, Carmi S, et al. Bariatric surgery affects plasma levels of alanine aminotransferase independent of weight loss: A registry-based study. J Clin Med 2021;10(12).

(18) Severson AL, Carmi S, Rosenberg NA. Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population. Theor Popul Biol 2021;139:50-65.

(19) Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, et al. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021;109(9):1465-1478.e4.

(20) Fridman H, Yntema HG, Mägi R, Andreson R, Metspalu A, Mezzavila M, et al. The landscape of autosomal-recessive pathogenic variants in European populations reveals phenotype-specific effects. Am J Hum Genet 2021;108(4):608-619.

(21) Lázaro-Muñoz G, Pereira S, Carmi S, Lencz T. Screening embryos for polygenic conditions and traits: ethical considerations for an emerging technology. Gen Med 2021;23(3):432-434.

(22) Hagbi-Levi S, Tiosano L, Rinsky B, Levinger N, Elbaz-Hayoun S, Carmi S, et al. Anti-tumor necrosis factor alpha reduces the proangiogenic effectof activated macrophages derived from patients with age-related macular degeneration. Mol Vision 2021;27:622-631.

(23) Agranat-Tamir L, Waldman S, Martin MAS, Gokhman D, Mishol N, Eshel T, et al. The Genomic History of the Bronze Age Southern Levant. Cell 2020;181(5):1146-1157.e11.

(24) Fridman H, Behar DM, Carmi S, Levy-Lahad E. Preconception carrier screening yield: effect of variants of unknown significance in partners of carriers with clinically significant variants. Gen Med 2020;22(3):646-653.

(25) Grunin M, Beykin G, Rahmani E, Schweiger R, Barel G, Hagbi-Levi S, et al. Association of a variant in VWA3A with response to anti-vascular endothelial growth factor treatment in neovascular AMD. Invest Ophthalmol Vis Sci 2020;61(2).

(26) Carmi S. Genealogy: The challenges of maintaining genetic privacy. eLife 2020;9.

(27) Clark DW, Okada Y, Moore KHS, Mason D, Pirastu N, Gandin I, et al. Associations of autozygosity with a broad range of human phenotypes. Nat Commun 2019;10(1).

(28) Karavani E, Zuk O, Zeevi D, Barzilai N, Stefanis NC, Hatzimanolis A, et al. Screening Human Embryos for Polygenic Traits Has Limited Utility. Cell 2019;179(6):1424-1435.e8.

(29) Backenroth D, Carmi S. A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations. Heredity 2019;123(4):470-478.

(30) Schweiger R, Erlich Y, Carmi S. FactorialHMM: Fast and exact inference in factorial hidden Markov models. Bioinformatics 2019;35(12):2162-2164.

(31) Backenroth D, Zahdeh F, Kling Y, Peretz A, Rosen T, Kort D, et al. Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy. Gen Med 2019;21(6):1390-1399.

(32) Severson AL, Carmi S, Rosenberg NA. The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 2019;212(1):305-316.

(33) Zeevi DA, Zahdeh F, Kling Y, Carmi S, Altarescu G. Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications. J Assisted Reprod Genet 2019;36(4):727-739.

(34) Caballero M, Seidman DN, Qiao Y, Sannerud J, Dyer TD, Lehman DM, et al. Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. PLoS Genet 2019;15(12).

(35) Winther M, Shpitzen S, Yaacov O, Landau J, Oren L, Foroozan-Rosenberg L, et al. In search of a genetic explanation for LDLc variability in an FH family: Common SNPs and a rare mutation in MTTP explain only part of LDL variability in an FH family. J Lipid Res 2019;60(10):1733-1740.

(36) Granot-Hershkovitz E, Karasik D, Friedlander Y, Rodriguez-Murillo L, Dorajoo R, Liu J, et al. A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure. Eur J Hum Genet 2018;26(12):1848-1858.

(37) Erlich Y, Shor T, Pe’er I, Carmi S. Identity inference of genomic data using long-range familial searches. Sci 2018;362(6415):690-694.

(38) Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, et al. Germline DNA replication timing shapes mammalian genome composition. Nucleic Acids Res 2018;46(16):8299-8310.

(39) King L, Wakeley J, Carmi S. A non-zero variance of Tajima's estimator for two sequences even for infinitely many unlinked loci. Theor Popul Biol 2018;122:22-29.

(40) Lencz T, Yu J, Palmer C, Carmi S, Ben-Avraham D, Barzilai N, et al. High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. Hum Genet 2018;137(4):343-355.

(41) Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 2018;555(7695):210-215.

(42) Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu N-, et al. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med 2018;10(423).

(43) Learning binary latent variable models: A tensor eigenpair approach. 35th International Conference on Machine Learning, ICML 2018; 2018.

(44) Rosner G, Gluck N, Carmi S, Bercovich D, Fliss-Issakov N, Ben-Yehoyada M, et al. POLD1 and POLE gene mutations in jewish cohorts of early-onset colorectal cancer and of multiple colorectal adenomas. Dis Colon Rectum 2018;61(9):1073-1079.

(45) Behar DM, Saag L, Karmin M, Gover MG, Wexler JD, Sanchez LF, et al. The genetic variation in the R1a clade among the Ashkenazi Levites' y chromosome. Sci Rep 2017;7(1).

(46) Einhorn Y, Weissglas-Volkov D, Carmi S, Ostrer H, Friedman E, Shomron N. Differential analysis of mutations in the Jewish population and their implications for diseases. Genet Res 2017;99.

(47) Xue J, Lencz T, Darvasi A, Pe’er I, Carmi S. The time and place of European admixture in Ashkenazi Jewish history. PLoS Genet 2017;13(4).

(48) Gilbert E, Carmi S, Ennis S, Wilson JF, Cavalleri GL. Genomic insights into the population structure and history of the Irish Travellers. Sci Rep 2017;7.

(49) Jaron R, Rosenfeld N, Zahdeh F, Carmi S, Beni-Adani L, Doviner V, et al. Expanding the phenotype of CRB2 mutations – A new ciliopathy syndrome? Clin Genet 2016;90(6):540-544.

(50) Vijai J, Topka S, Villano D, Ravichandran V, Maxwell KN, Maria A, et al. A recurrent ERCC3 truncating mutation confers moderate risk for breast cancer. Cancer Discov 2016;6(11):1267-1275.

(51) Hope R, Egarmina K, Voloshin K, Waldman Ben-Asher H, Carmi S, Eliaz D, et al. Transcriptome and proteome analyses and the role of atypical calpain protein and autophagy in the spliced leader silencing pathway in Trypanosoma brucei. Mol Microbiol 2016;102(1):1-21.

(52) Yang S, Carmi S, Pe'er I. Rapidly registering identity-by-descent across ancestral recombination graphs. J Comput Biol 2016;23(6):495-507.

(53) Baskovich B, Hiraki S, Upadhyay K, Meyer P, Carmi S, Barzilai N, et al. Expanded genetic screening panel for the Ashkenazi Jewish population. Gen Med 2016;18(5):522-528.

(54) Quint A, Sagi M, Carmi S, Daum H, Macarov M, Ben Neriah Z, et al. An Ashkenazi founder mutation in the PKHD1 gene. Eur J Med Genet 2016;59(2):86-90.

(55) Zidan J, Ben-Avraham D, Carmi S, Maray T, Friedman E, Atzmon G. Genotyping of geographically diverse Druze trios reveals substructure and a recent bottleneck. Eur J Hum Genet 2015;23(8):1093-1099.

(56) Wilton PR, Carmi S, Hobolth A. The SMC' is a highly accurate approximation to the ancestral recombination graph. Genetics 2015;200(1):343-355.

(57) Yang S, Carmi S, Pe’er I. Rapidly registering identity-by-descent across ancestral recombination graphs. Lect Notes Comput Sci 2015;9029:340-353.

(58) Carmi S, Wilton PR, Wakeley J, Pe'er I. A renewal theory approach to IBD sharing. Theor Popul Biol 2014;97:35-48.

(59) Porath HT, Carmi S, Levanon EY. A genome-wide map of hyper-edited RNA reveals numerous new sites. Nat Commun 2014;5.

(60) Carmi S, Hui KY, Kochav E, Liu X, Xue J, Grady F, et al. Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. Nat Commun 2014;5.

(61) Gupta SK, Chikne V, Eliaz D, Tkacz ID, Naboishchikov I, Carmi S, et al. Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei. RNA Biol 2014;11(6).

(62) Bastas N, Maragakis M, Argyrakis P, Ben-Avraham D, Havlin S, Carmi S. Random walk with priorities in communicationlike networks. Phys Rev E Stat Nonlinear Soft Matter Phys 2013;88(2).

(63) Gupta SK, Kosti I, Plaut G, Pivko A, Tkacz ID, Cohen-Chalamish S, et al. The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability. Nucleic Acids Res 2013;41(13):6577-6594.

(64) Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I. The variance of identity-by-descent sharing in the wright-fisher model. Genetics 2013;193(3):911-928.

(65) Gupta SK, Carmi S, Ben-Asher HW, Tkacz ID, Naboishchikov I, Michaeli S. Basal splicing factors regulate the stability of mature mRNAs in trypanosomes. J Biol Chem 2013;288(7):4991-5006.

(66) Carmi S, Barkai E. Fractional Feynman-Kac equation for weak ergodicity breaking. Phys Rev E Stat Nonlinear Soft Matter Phys 2011;84(6).

(67) Carmi S, Borukhov I, Levanon EY. Identification of widespread ultra-edited human RNAs. PLoS Genet 2011;7(10).

(68) Carmi S, Barkai E. Fractional feynman–kac equation for anomalous diffusion functionals. Fractional Dynamics: Recent Advances; 2011. p. 185-207.

(69) Carmi S, Church GM, Levanon EY. Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat Commun 2011;2(1).

(70) Carmi S, Turgeman L, Barkai E. On Distributions of Functionals of Anomalous Diffusion Paths. J Stat Phys 2010;141(6):1071-1092.

(71) Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C. The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog 2010;6(9).

(72) Parshani R, Carmi S, Havlin S. Epidemic threshold for the susceptible-infectious-susceptible model on random networks. Phys Rev Lett 2010;104(25).

(73) Goldshmidt H, Matas D, Kabi A, Carmi S, Hope R, Michaeli S. Persistent ER stress induces the spliced leader RNA silencing pathway (SLS), leading to programmed cell death in Trypanosoma brucei. PLoS Pathog 2010;6(1).

(74) Turgeman L, Carmi S, Barkai E. Fractional Feynman-Kac Equation for Non-Brownian Functionals. Phys Rev Lett 2009;103(19).

(75) Carmi S, Havlin S, Song C, Wang K, Makse HA. Energy-landscape network approach to the glass transition. J Phys Math Theor 2009;42(10).

(76) Carmi S, Carter S, Sun J, Ben-Avraham D. Asymptotic behavior of the Kleinberg model. Phys Rev Lett 2009;102(23).

(77) Carmi S, Levanon EY, Eisenberg E. Efficiency of complex production in changing environment. BMC Syst Biol 2009;3.

(78) Kittas A, Carmi S, Havlin S, Argyrakis P. Trapping in complex networks. EPL 2008;84(4).

(79) Carmi S, Krapivsky PL, Ben-Avraham D. Partition of networks into basins of attraction. Phys Rev E Stat Nonlinear Soft Matter Phys 2008;78(6).

(80) Carmi S, Wu Z, Havlin S, Stanley HE. Transport in networks with multiple sources and sinks. EPL 2008;84(2).

(81) Maragakis M, Carmi S, Ben-Avraham D, Havlin S, Argyrakis P. Priority diffusion model in lattices and complex networks. Phys Rev E Stat Nonlinear Soft Matter Phys 2008;77(2).

(82) López E, Parshani R, Cohen R, Carmi S, Havlin S. Limited path percolation in complex networks. Phys Rev Lett 2007;99(18).

(83) Carmi S, Havlin S, Kirkpatrick S, Shavitt Y, Shir E. A model of Internet topology using k-shell decomposition. Proc Natl Acad Sci U S A 2007;104(27):11150-11154.

(84) Carmi S, Wu Z, López E, Havlin S, Eugene Stanley H. Transport between multiple users in complex networks. Eur Phys J B 2007;57(2):165-174.

(85) Carmi S, Cohen R, Dolev D. Searching complex networks efficiently with minimal information. Europhys Lett 2006;74(6):1102-1108.

(86) Carmi S, Levanon EY, Havlin S, Eisenberg E. Connectivity and expression in protein networks: Proteins in a complex are uniformly expressed. Phys Rev E Stat Nonlinear Soft Matter Phys 2006;73(3).

(87) López E, Carmi S, Havlin S, Buldyrev SV, Stanley HE. Anomalous electrical and frictionless flow conductance in complex networks. Phys D Nonlinear Phenom 2006;224(1-2):69-76.