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  • Dr.  Shai Carmi
Dr Shai Carmi
Research Interests
We develop methods and theory in statistical and population genetics, with applications to medicine, biology, and history, in particular in the context of the Jewish population. Current research is focused on the following projects.​
  • Ashkenazi Jewish genetics
    • Association studies of various phenotypes
    • Polygenic risk predictio​n
    • Reconstructing demographic events in the Ashkenazi history
  • Haplotype sharing in founder populations
    • Patterns of sharing under sex-biased demography and consanguinity
    • Methods for reconstructing the demography of modern and ancient populations
    • Applications for low-coverage sequencing, in particular in reproductive genetics
  • Theoretical population genetics and applications
    • Modeling ancestry in admixed populations
    • Modeling the effect of recombination on genetic variation
    • Approximations of the coalescent with recombination
Open positions We are looking for talented and motivated PhD students/post-docs with quantitative​ skills to join the lab. Experience in programming, computer science, and/or statistics is a prerequisite. Projects are available across the spectrum of statistical, population, and medical genetics. Day-to-day work ranges between hands-on medical data analysis and probabilistic modeling, and could fit students with diverse backgrounds and interests.
Selected publications 
​Ashkenazi Jewish genetic​​s
T. Lencz, J. Yu, C. Palmer, S. Carmi, …., I. Pe’er. High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation​. Hum. Genet. 137, 343 (2018).

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).

E. Granot-Hershkovitz, D. Karasik, Y. Friedlander, L. Rodriguez-Murillo, R. Dorajoo, J. Liu, A. Sewda, I. Peter, S. Carmi*, and H. Hochner*. A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure. Submitted (2018).

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).

J. Xue, T. Lencz, A. Darvasi, I. Pe'er, and S. CarmiThe time and place of European admixture in Ashkenazi Jewish history​. PLoS Genet. 13, e1006644 (2017).

B. Baskovich, S. Hiraki, K. Upadhyay, P. Meyer, S. Carmi, N. Barzilai, A. Darvasi, K. Offit, S. Bressman, L. Ozelius, I. Peter, J. Cho, G. Atzmon, L. Clark, T. Lencz, I. Pe’er, H. Ostrer, and C. Oddoux. Expanded Genetic Screening Panel for the Ashkenazi Jewish Population. Genet. Med. 18, 522 (2016).​

S. Carmi, K. Y. Hui, E. Kochav, X. Liu, J. Xue, F. Grady, S. Guha, K. Upadhyay, D. Ben-Avraham, S. Mukherjee, B. M. Bowen, T. Thomas, J. Vijai, M. Cruts, G. Froyen, D. Lambrechts, S. Plaisance, C. Van Broeckhoven, P. Van Damme, H. Van Marck, N. Barzilai, A. Darvasi, K. Offit, S. Bressman, L. J. Ozelius, I. Peter, J. H. Cho, H. Ostrer, G. Atzmon, L. N. Clark, 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).

Statistical and pop​​ulation ​genetics
Y. Erlich, T. Shor, S. Carmi, and I. Pe’er. Re-identification of genomic data using long range familial searches. Submitted (2018).

D. Backenroth, F. Zahdeh, Y. Kling, A. Peretz, T. Rosen, D. Kort, S. Zeligson, T. Dror, S. Kirshberg, E. Burak, E. Levy-Lahad, D. Zangen, 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. Submitted (2018).

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).
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., in press (2017).

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).

S. Yang, S. Carmi, and I. Pe’er. Rapidly registering identity-by-descent across ancestral recombination graphs. J. Comput. Biol. 23, 495 (2016). 
[RECOMB 2015]
P. R. Wilton, S. Carmi*, and A. Hobolth*. The SMC’ is a highly accurate approximation to the ancestral recombination graph. Genetics 200, 343 (2015).
J. Zidan*, D. Ben-Avraham*, S. Carmi*, T. Maray, E. Friedman, and G. Atzmon. Genotyping of geographically diverse Druze trios reveals substructure and a recent bottleneck. Eur. J. Hum. Genet. 23, 1093 (2015).
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. Francesco Palamara, V. Vacic, T. Lencz, A. Darvasi, and I. Pe’er. The variance of identity-by-descent sharing in the Wright-Fisher model. Genetics 193, 911 (2013).
Selected recent 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 RNA processing
S. K. Gupta, S. Carmi, H. Waldman Ben-Asher, I. Dov Tkacz, I. Naboishchikov, 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, H. Shi, S. Michaeli, and C. Tschudi. The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog. 6, e1001090 (2010).
Brief CV
2011-2015     Post-doctoral scientist, Department of Computer Science, Columbia University. Mentor: Prof. Itsik Pe’er.
2010-2011     Post-doctoral fellow, Faculty of Life Sciences, Bar-Ilan University, Israel. Mentor: Dr. Erez Levanon.
2005-2010     M.Sc. and Ph.D., Physics , Bar-Ilan University, Israel. Advisor: Prof. Shlomo Havlin.
2002-2005     B.Sc., Physics and Computer Science, Bar-Ilan University, Israel.
Major honors
Bar-Ilan dean’s list (4x), rector’s list
Wolf foundation​ (2x)
Adams fellowship
Human Frontier Science Program Post-doctoral Fellowship
Alon fellowship (declined)
TheMarker Magazine 40 most promising under 40 (link​)
Past research interests
RNA and DNA editing
RNA processing in Trypanosoma brucei
Anomalous diffusion
Models of transport processes on networks
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