Publications

My Google Scholar page

Refereed Journals

  1. P. R. Wilton, S. Carmi*, and A. Hobolth*. The SMC’ is a highly accurate approximation to the ancestral recombination graph. Genetics 200, 343 (2015).
  2. 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).
  3. S. Carmi, P. R. Wilton, J. Wakeley, and I. Pe’er. A renewal theory approach to IBD sharing. Theor. Popul. Biol. 97, 35 (2014).
  4. 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).
  5. 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).
  6. S. K. Gupta, V. Chikne, D. Eliaz, I. D. Tkacz, I. Naboishchikov, S. Carmi, H. Waldman Ben-Asher, and S. Michaeli. Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei. RNA Biol. 11, 715 (2014).
  7. 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).
  8. S. K. Gupta, I. Kosti, G. Plaut, A. Pivko, I. D. Tkacz, S. Cohen-Chalamish, D. K. Biswas, C. Wachtel, H. Waldman Ben-Asher, S. Carmi, F. Glaser, Y. Mandel-Gutfreund, and S. Michaeli. 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. 41, 6577 (2013).
  9. 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).
  10. Sachin Kumar Gupta, Shai Carmi, Hiba Waldman Ben-Asher, Itai Dov Tkacz, Ilana Naboishchikov, and Shulamit Michaeli. “Basal splicing factors regulate the stability of mature mRNAs in Trypanosomes“. J. Biol. Chem. 7 , 4991 (2013).
  11. S. Carmi and E. Barkai. Fractional Feynman-Kac equation for weak ergodicity breaking. Phys. Rev. E 84, 061104 (2011).
  12. Shai Carmi, George M. Church, and Erez Y. Levanon. “Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution“. Nat. Commun. 2, 519 (2011).
  13. S. Carmi, I. Borukhov, and E. Y. Levanon. Identification of widespread ultra-edited human RNAs. PLoS Genet. 7, e1002317 (2011).
  14. S. Carmi, L. Turgeman, and E. Barkai. On distributions of functionals of anomalous diffusion paths. J. Stat. Phys. 141, 1071 (2010).
  15. 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).
  16. R. Parshani, S. Carmi, and S. Havlin. Epidemic threshold for the Susceptible-Infectious-Susceptible model on random networks. Phys. Rev. Lett. 104, 258701 (2010).
  17. H. Goldshmidt, D. Matas, A. Kabi, S. Carmi, R. Hope, and S. Michaeli. Persistent ER stress induces the Spliced Leader RNA Silencing pathway (SLS), leading to programmed cell death in Trypanosoma brucei. PLoS Pathog. 6, e1000731 (2010).
  18. L. Turgeman, S. Carmi, and E. Barkai. Fractional Feynman-Kac equation for non-Brownian functionals. Phys. Rev. Lett. 103, 190201 (2009).
  19. S. Carmi, S. Carter, J. Sun, and D. ben-Avraham. Asymptotic behavior of the Kleinberg model. Phys. Rev. Lett. 102, 238702 (2009).
  20. 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).
  21. S. Carmi, E. Y. Levanon, and E. Eisenberg. Efficiency of complex production in changing environment. BMC Syst. Biol. 3:3 (2009).
  22. S. Carmi, P. L. Krapivsky, and D. ben-Avraham. Partition of networks into basins of attraction. Phys. Rev. E 78, 066111 (2008).
  23. A. Kittas, S. Carmi, S. Havlin, and P. Argyrakis. Trapping in complex networks. EPL 84, 40008 (2008).
  24. S Carmi, Z. Wu, S. Havlin, and H. E. Stanley. Transport in networks with multiple sources and sinks. EPL 84, 28005 (2008).
  25. M. Maragakis, S. Carmi, D. ben-Avraham, S. Havlin, and P. Argyrakis. Priority diffusion model in lattices and complex networks. Phys. Rev. E (Rapid Communication) 77, 020103 (2008).
  26. E. Lopez, R. Parshani, R. Cohen, S. Carmi, and S. Havlin. Limited path percolation in complex networks. Phys. Rev. Lett. 99, 188701 (2007).
  27. 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).
  28. S. Carmi, R. Cohen, and D. Dolev. Searching complex networks efficiently with minimal information. Europhys. Lett. 74, 1102 (2006).
  29. S. Carmi, E. Y. Levanon, S. Havlin, and E. Eisenberg. Connectivity and expression in protein networks: Proteins in a complex are uniformly expressed. Phys. Rev. E 73, 031909 (2006).

Refereed conferences

  1. S. Yang, S. Carmi, and I. Pe’er. Rapidly registering identity-by-descent across ancestral recombination graphs. Lect. Notes Comput. Sc.  9029, 340 (2015). [RECOMB 2015]

Conference and workshop proceedings in refereed journals

  1. S. Carmi, Z. Wu, E. Lopez, S. Havlin, and H. E. Stanley. Transport between multiple users in complex networks. Eur. Phys. J. B 57, 165 (2007). [Proceedings of the 5th International Conference “Applications of Physics in Financial Analysis” (APFA5), Torino, 2006]
  2. E. Lopez, S. Carmi, S. Havlin, S. Buldyrev, and H. E. Stanley. Anomalous electrical and frictionless flow conductance in complex networks. Physica D 224, 69 (2006). [Proceedings of the workshop “Dynamics on Complex Networks and Applications”, Dresden, 2006]

Book chapters

  1. S. Carmi and E. Barkai. Fractional Feynman-Kac equation for anomalous diffusion functionals. Chapter 8 in Fractional Dynamics: Recent advances, Eds.: J. Klafter, S. C. Lim, and R. Metzler (World Scientific, Singapore, 2011).