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Researchers
  • Dr.  Shai Carmi
Dr Shai Carmi
 
Research Interests
 
Research in the lab involves developing 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
    • Sequencing Ashkenazi genomes for disease mapping, clinical genetics, and carrier screening​
    • Reconstructing demographic events in the Ashkenazi history
    • Association studies of various phenotypes​
     
  • Haplotype sharing in founder populations
    • Theory for the number and length of shared segments
    • 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
    • Estimating the time of origin of rare mutations
    • Modeling the effect of recombination parameters on patterns of genetic variation
    • Markovian approximations of the coalescent with recombination
 
Unofficial lab website​
 
Open positions We are looking for talented and motivated students to join exciting research projects. Positions are available for MSc and PhD students, as well as for a post-doc. Projects are available across the wide spectrum of statistical, population, and medical genetics. Day-to-day work ranges between hands-on medical data analysis and probabilistic modeling, and could therefore fit students with diverse backgrounds such as physics, math, statistics, computer science, biology, and medicine.
 
Selected publications 
​Ashkenazi Jewish genetic​​s
 
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
 
​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).

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
 
Education
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
Modeling transport processes on random networks
 
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