For the full list of publications, see Google Scholar

Applied population genetics

Ashkenazi Jews

• J. Xue, T. Lencz, A. Darvasi, I. Pe’er, and S. Carmi. The Time and Place of European Admixture in the Ashkenazi Jewish History. PLoS Genet. 13, e1006644 (2017).
• D. M. Behar, L. Saag, M. Karmin, …, S. Carmi, S. Tzur, …, K. Skorecki, M. Metspalu, S. Rootsi, R. Villems. The genetic variation in the R1a clade among the Ashkenazi Levites’ Y chromosome. Sci. Rep. 7, 14969 (2017).

Other populations

• E. Arciero, M. Mezzavilla, …, S. Carmi, M. M. Iles, and H. C. Martin. Fine-scale population structure and demographic history of British Pakistanis. Nat. Commun. 12, 7189 (2021). (Code for the ROH models)
• E. Gilbert, S. Carmi, S. Ennis, J. F. Wilson, G. L. Cavalleri. Genomic insights into the population structure and history of the Irish Travellers. Sci. Rep. 7, 42187 (2017).
• J. Zidan*, D. Ben-Avraham*, S. Carmi*, …, E. Friedman, and G. Atzmon. Genotyping of geographically diverse Druze trios reveals substructure and a recent bottleneck. Eur. J. Hum. Genet. 23, 1093 (2015).

Ancient DNA

• S. Waldman, D. Backenroth, É. Harney, S. Flohr, …, K. Sczech, S. Carmi*, and D. Reich*. Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century. Cell 185, 4703 (2022) (Genotypes) (Questions and answers for lay readers) (A popular article in The Conversation) (A commentary by C. Lalueza-Fox)
• L. Agranat-Tamir, S. Waldman, …, S. Tzur, …, B. Yakir, R. Pinhasi*, S. Carmi*, I. Finkelstein*, L. Carmel*, and D. Reich*. The Genomic History of the Bronze Age Southern Levant. Cell 181, 1146 (2020). (A commentary by L. Orlando) (Software for the pseudo-haploid ChromoPainter model)

Theoretical population genetics

IBD sharing and genetic genealogy

• Y. Huang, S. Carmi, and H. Ringbauer. Estimating effective population size trajectories from time-series Identity-by-Descent (IBD) segments. (2024).
• S. Carmi and H. Ringbauer. DNA says you’re related to a Viking, a medieval German Jew or a 1700s enslaved African? What a genetic match really means. The Conversation (2024).
• D. J. Cotter, A. L. Severson, J. T. L. Kang, H. N. Godrej, S. Carmi, and N. A. Rosenberg. Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3: Genes Genomes Genet. 14, jkad264 (2024)
• Y. Huang, S. Carmi, D. E. Reich, and H. Ringbauer. Genetic estimates of the initial peopling of Polynesian islands actually reflect later inter-island contacts. (2022)
• E. Petter, R. Schweiger, …, S. Carmi, J. H. Li, T. Berisa, J. K. Pickrell, Y. Erlich. Relative matching using low coverage sequencing. (2020).
• M. Caballero, D. N. Seidman, Y. Qiao, …, S. Carmi, and A. L. Williams. Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. PLoS Genet. 15, e1007979 (2019).
• A. L. Severson, S. Carmi, and N. A. Rosenberg. The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 212, 305 (2019).
• S. Yang, S. Carmi, and I. Pe’er. Rapidly registering identity-by-descent across ancestral recombination graphs. J. Comput. Biol. 23, 495 (2016). (Software)
• S. Carmi, P. R. Wilton, J. Wakeley, and I. Pe’er. A renewal theory approach to IBD sharing. Theor. Popul. Biol. 97, 35 (2014).
• S. Carmi, P. F. Palamara, V. Vacic, …, and I. Pe’er. The variance of identity-by-descent sharing in the Wright-Fisher model. Genetics 193, 911 (2013).

The coalescent and admixture

• D. J. Cotter, A. L. Severson, S. Carmi, and N. A. Rosenberg. Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating. Theor. Popul. Biol. 147, 1 (2022).
• A. L. Severson, S. Carmi, and N. A. Rosenberg. Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population. Theor. Popul. Biol. 139, 50 (2021). (A short (popular) explanation in Hebrew)
• L. Agranat-Tamir, S. Waldman, N. Rosen, B. Yakir*, S. Carmi*, and L. Carmel*. LINADMIX: Evaluating the effect of ancient admixture events on modern populations. Bioinformatics 37, 4744 (2021).
• S. Carmi. The distances between tree changes under SMC for any n and under SMC’ for n=3. Unpublished. (2020). (Manuscript)
• A. Jaffe, R. Weiss, S. Carmi, Y. Kluger, and B. Nadler. Learning Binary Latent Variable Models: A Tensor Eigenpair Approach. ICML 2018 (arXiv:1802.09656). (Code)
• L. King, J. Wakeley, and S. Carmi. A non-zero variance of Tajima’s estimator for two sequences even for infinitely many unlinked loci. Theor. Popul. Biol. 122, 22 (2018).
• P. R. Wilton, S. Carmi*, and A. Hobolth*. The SMC’ is a highly accurate approximation to the ancestral recombination graph. Genetics 200, 343 (2015).

Genetic privacy and forensics

• G. Azhari, S. Waldman, N. Ofer, Y. Keller, S. Carmi, and G. Yaari. Decomposition of Individual SNP Patterns from Mixed DNA Samples. Forensic Sci. 2, 455 (2022). (Software)
• S. Carmi. Genealogy: The challenges of maintaining genetic privacy. eLife 9, e51810 (2020). Insight on Edge and Coop, eLife, 2020.
• Y. Erlich, T. Shor, I. Pe’er, and S. Carmi. Identity inference of genomic data using long-range familial searches. Science 362, 690 (2018). Covered in Science Magazine’s 10 breakthroughs of 2018.

Preimplantation genetic testing

Our website on polygenic embryo screening

• A. Capalbo, G. de Wert, H. Mertes, L. Klausner, …, K. Sermon, N. Vermeulen, T. Lencz, and S. Carmi. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum. Reprod. Update dmae012 (2024).
• R. A. Furrer, D. Barlevy, S. Pereira, S. Carmi, T. Lencz, and G. Lázaro-Muñoz. Public Attitudes, Interests, and Concerns Regarding Polygenic Embryo Screening. JAMA Netw. Open 7, e2410832 (2024).
• D. Barlevy, I. Cenolli, T. Campbell, R. Furrer, M. Mukherjee, K. M. Kostick-Quenet, S. Carmi, T. Lencz, G. Lázaro-Muñoz, and S. Pereira. Patient interest in and clinician reservations on polygenic embryo screening: a qualitative study of stakeholder perspectives. J. Assist. Reprod. Genet. 41, 1221 (2024).
• D. Backenroth*, G. Altarescu*, F. Zahdeh, T. Mann, O. Murik, P. Renbaum, R. Segel, S. Zeligson, E. Hakam-Spector, S. Carmi*, and D. A. Zeevi*. SHaploseek: A sequencing-only high-resolution implementation of comprehensive preimplantation genetic testing. Sci. Rep. 13, 18036 (2023).
• T. Lencz and S. Carmi. Selected before birth: Embryo risk screening could lower the odds of illnesses ranging from depression to diabetes. Can it be ethically done? Aeon (2023). (Magazine article)
• Pereira, S. Carmi, …, G. Lázaro-Muñoz, and T. Lencz. Polygenic embryo screening: four clinical considerations warrant further attention. Hum. Reprod. 37, 1375 (2022).
• D. A. Zeevi*, D. Backenroth*, …, S. Carmi*, G. Altarescu*. Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing. Genet. Med. 23, 1334 (2021).
• T. Lencz, D. Backenroth, E. Granot-Hershkovitz, A. Green, …, O. Zuk, and S. Carmi. Utility of polygenic embryo screening for disease depends on the selection strategy. eLife 10, e64716 (2021). (Code for all calculations and simulations) (Q&A) (See also a commentary by J. M. Fletcher, Y. Wu, and Q. Lu.) Online risk reduction calculator
• G. Lázaro-Muñoz, S. Pereira, S. Carmi, and T. Lencz. Screening Embryos for Polygenic Conditions and Traits: Ethical Considerations for an Emerging Technology. Genet. Med. 23, 432 (2021).
• E. Karavani*, O. Zuk*, D. Zeevi, …, T. Lencz*, and S. Carmi*. Screening human embryos for polygenic traits has limited utility. Cell 179, 1424 (2019) (Q&A) (Code)
• D. A. Zeevi, F. Zahdeh, Y. Kling, S. Carmi, and G. Altarescu. Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications. J. Assist. Reprod. Gen. 36, 727 (2019).
• D. Backenroth, F. Zahdeh, Y. Kling, …, G. Altarescu*, S. Carmi*, and D. A. Zeevi*. Haploseek: A 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy. Genet. Med. 21, 1390 (2019).

Preconception and prenatal carrier screening

• C. Gafni-Amsalem, …, S. Carmi, and S. A. Shalev. The distribution of regions of homozygosity (ROH) among consanguineous populations – implications for a routine genetic counseling service (2024).
• R. Furrer, S. Carmi, T. Lencz, and G. Lázaro-Muñoz. Nurtured Genetics: Prenatal Testing and the Anchoring of Genetic Expectancies. Am. J. Bioeth. 23, 42 (2023).
• D. Barlevy, T. Lencz, S. Carmi, K. M. Kostick-Quenet, M. Mukherjee, S. Pereira, and G. Lázaro-Muñoz. Capacities and Limitations of Using Polygenic Risk Scores for Reproductive Decision Making. Am. J. Bioeth. 22, 45 (2022).
• H. Fridman, …, S. Carmi, E. Levy-Lahad, C. Gilissen, and H. Brunner. The landscape of autosomal-recessive pathogenic variants in European populations reveals phenotype-specific effects. Am. J. Hum. Genet. 108, 608 (2021).
• H. Fridman, D. Behar, S. Carmi, and E. Levy-Lahad. Preconception carrier screening yield: effect of variants of unknown significance in partners of carriers with clinically significant variants. Genet. Med. 22, 646 (2020).
• B. Baskovich, S. Hiraki, K. Upadhyay, …, S. Carmi, …, H. Ostrer, and C. Oddoux. Expanded Genetic Screening Panel for the Ashkenazi Jewish Population. Genet. Med. 18, 522 (2016).

Statistical genetics

• M. Krichevski, R. Calderon-Margalit, S. Carmi*, and R. Raz*. The Heritability of Weight Gain in Infancy: A Population-Based Twin Study. Paediatr. Perinat. Epidemiol. 37, 577 (2023).
• D. Backenroth and S. Carmi. A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations. Heredity, 123, 470 (2019). (Software)
• R. Schweiger, Y. Erlich, and S. Carmi. FactorialHMM: Fast and exact inference in factorial hidden Markov models. Bioinformatics 35, 2162 (2019). (Software)
• D. Clark, Y. Okada, …, A. Halevy, S. Carmi, …, J. Wilson. Associations of autozygosity with a broad range of human phenotypes. Nat. Commun. 10, 4957 (2019).
• D. Rothschild, O. Weissbrod, E. Barkan, …, S. Carmi, …, E. Elinav, and E. Segal. Environmental factors dominate over host genetics in shaping human gut microbiota composition. Nature 555, 210 (2018).

Polygenic scores

• D. Gokhman, K. D. Harris, S. Carmi, and G. Greenbaum. Predicting the direction of phenotypic difference. (2024).
• F. Privé, H. Aschard, S. Carmi, …, and B. J. Vilhjálmsson. High-resolution portability of 245 polygenic scores when derived and applied in the same cohort. Am. J. Hum. Genet. 109, 12 (2022).
• S. Carmi. Cascade screening following a polygenic risk score test: what is the disease risk of a sibling conditional on a high score of a proband? (2021)

Ashkenazi Jewish genetics

• E. Granot-Hershkovitz, D. Karasik, Y. Friedlander, …, I. Peter, S. Carmi*, and H. Hochner*. A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure. Eur. J. Hum. Genet. 26, 1848 (2018).
• T. Lencz, J. Yu, C. Palmer, S. Carmi, …., and I. Pe’er. High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. Hum. Genet. 137, 343 (2018).
• S. Carmi, K. Y. Hui, E. Kochav, …, T. Lencz, and I. Pe’er. Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. Nat. Commun. 5, 4835 (2014).

Other medical genetics and epidemiology (selected)

Cardiology

• I. Tessler, …, S. Carmi, …, and R. Durst. Novel Association of the NOTCH Pathway Regulator MIB1 Gene With the Development of Bicuspid Aortic Valve. JAMA Cardiol. 8, 721 (2023). (A commentary by B. M Kuehn)
• N. Rappoport, …, S. Carmi, J. F. Keaney Jr., and O. M. Shapira. Resternotomy Coronary Artery Bypass 1999-2018: Insights From The Society of Thoracic Surgeons Adult Cardiac Surgery Database. Ann. Thorac. Surg. 115, 62 (2023).
• I. Tessler, …, S. Carmi, …, D. Gilon, and R. Durst. Is Bicuspid Aortic Valve Morphology Genetically Determined? A Family-Based Study. Am. J. Cardiol. 163, 85 (2022).
• I. Tessler, …, S. Carmi, …, D. Gilon, and R. Durst. Bicuspid Aortic Valve: Genetic and Clinical Insights. Aorta 9, 139 (2021). (A review)
• M. Winther, S. Shpitzen, O. Yaacov, J. Landau, …, S. Carmi, M. R. Hayden, E. Leitersdorf, and R. Durst. In search for genetic explanation for LDLc variabily in an FH family: Common SNPs and a rare mutation in microsomal triglyceride transfer protein explain only part of LDL variability in an FH family. J. Lipid Res. 60, 1733 (2019).

Oncology

• H. Levi, S. Carmi, S. Rosset, …, S. Ben-Sachar, N. Elefant, R. Shamir, and R. Elkon. Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel. J. Med. Genet. (2023).
• S. Lieberman, …, S. Carmi, E. Levy-Lahad, and Y. Goldberg. Common founder BRCA2 pathogenic variants and breast cancer characteristics in Ethiopian Jews. Breast Cancer Res. Treat. 193, 217 (2022).
• G. Rosner, N. Gluck, S. Carmi, …, and R. Kariv. POLD1 and POLE Gene Mutations in Jewish Cohorts of Early-Onset Colorectal Cancer and of Multiple Colorectal Adenomas. Dis. Colon Rectum 61, 1073 (2018)
• J. Vijai, …, S. Carmi, …, G. Rennert, and K. Offit. A Recurrent ERCC3 Truncating Mutation Confers Moderate Risk for Breast Cancer. Cancer Discov. 6, 1267 (2016)

Ophthalmology

• M. Grunin, D. Triffon, …, S. Carmi*, and I. Chowers*. Genome-wide association study and genomic risk prediction of age-related macular degeneration in Israel. Sci. Rep. 14, 13034 (2024).
• M. Grunin, G. Beykin, E. Rahmani, …, S. Carmi, E. Halperin, I. Chowers. Association of a variant in VWA3A with response to anti-VEGF treatment in neovascular age-related macular degeneration. Invest. Ophthalmol. Vis. Sci. 61, 48 (2020).

Psychiatry

• T. Lencz, J. Yu, R. Rashid Khan, E. Flaherty, S. Carmi, …, and I. Pe’er. Novel Ultra-Rare Exonic Variants Identified in a Founder Population Implicate Cadherins in Schizophrenia. Neuron 109, 1465 (2021). (Perspective)

Gastroenterology

• S. Azulai, …, S. Carmi, R. Ben-Haroush Schyr, O. Romano-Zelekha, and D. Ben-Zvi. Bariatric surgery affects plasma levels of alanine aminotransferase independent of weight-loss: a registry-based study. J. Clin. Med. 10, 2724 (2021).
• K. Y. Hui, H. Fernandez-Hernandez, J. Hu, …, S. Carmi, …, J. H. Cho, and I. Peter. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn’s disease and Parkinson’s disease. Sci. Transl. Med. 10, eaai7795 (2018)

COVID-19

• S. Ben-Shachar, N. Barda, …, S. Carmi, R. Balicer, B. Zisser, and Y. Louzoun. 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. 41, 1154 (2021).

Selected past publications in computational biology

RNA and DNA editing

• H. T. Porath, S. Carmi, and E. Y. Levanon. A genome-wide map of hyper-edited RNA reveals numerous new sites. Nat. Commun. 5, 4726 (2014).
• S. Carmi, G. M. Church, and E. Y. Levanon. Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat. Commun. 2, 519 (2011).
• S. Carmi, I. Borukhov, and E. Y. Levanon. Identification of widespread ultra-edited human RNAs. PLoS Genet. 7, e1002317 (2011).

Trypanosoma brucei cell biology

• S. K. Gupta, S. Carmi, H. Waldman Ben-Asher, …, and S. Michaeli. “Basal splicing factors regulate the stability of mature mRNAs in Trypanosomes“. J. Biol. Chem. 7 , 4991 (2013).
• N. G. Kolev, J. B. Franklin, S. Carmi, …, S. Michaeli, and C. Tschudi. The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog. 6, e1001090 (2010).

Biophysical modeling

• S. Carmi, Y. Brody, N. Neufeld, and Y. Shav-Tal.  Extracting kinetic parameters from FRAP and FLIP experiments. Unpublished. (2011). (Manuscript)

Selected past publications in physics

• N. Bastas, M. Maragakis, P. Argyrakis, D. ben-Avraham, S. Havlin, and S. Carmi. Random walk with priorities in communicationlike networks. Phys. Rev. E 88, 022803 (2013).
• S. Carmi and E. Barkai. Fractional Feynman-Kac equation for weak ergodicity breaking. Phys. Rev. E 84, 061104 (2011).
• S. Carmi, L. Turgeman, and E. Barkai. On distributions of functionals of anomalous diffusion paths. J. Stat. Phys. 141, 1071 (2010).
• S. Carmi, S. Carter, J. Sun, and D. ben-Avraham. Asymptotic behavior of the Kleinberg model. Phys. Rev. Lett. 102, 238702 (2009).
• S. Carmi, S. Havlin, C. Song, K. Wang, and H. A. Makse. Energy-landscape network approach to the glass transition. J. Phys. A: Math. Theor. 42, 105101 (2009).
• S. Carmi, P. L. Krapivsky, and D. ben-Avraham. Partition of networks into basins of attraction. Phys. Rev. E 78, 066111 (2008).
• S. Carmi, Z. Wu, S. Havlin, and H. E. Stanley. Transport in networks with multiple sources and sinks. EPL 84, 28005 (2008).
• S. Carmi, S. Havlin, S. Kirkpatrick, Y. Shavitt, and E. Shir. A model of Internet topology using k-shell decomposition. P. Natl. Acad. Sci. USA 104, 11150 (2007).