updated: 30.05.2022


List of Publications


24. A. Dolitzky, G. Shapira, S. Grisaru-Tal, I. Hazut, S. Avlas, Y. Gordon, M. Itan, N. Shomron and A. Munitz (2021) Transcriptional Profiling of Mouse Eosinophils Identifies Distinct Gene Signatures Following Cellular ActivationFront. Immunol., 


23. G. Shapira, R. Abu Hamad, C. Weiner, N. Rainy, R. Sorek-Abramovich, P. Benveniste-Levkovitz, R. Rock, E. Avnat, O. Levtzion-Korach, A. Bar Chaim, N. Shomron (2022) Population differences in antibody response to SARS-CoV-2 infection and BNT162b2 vaccination. FASEB Journal,


22. K. Halabi, E. Levy Karin, L. Guéguen, I. Mayrose (2021) A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution. Systematic Biology, Volume 70, Issue 3, Pages 608–622, 


21. D. Groenewoud, A. Shye, R. Elkon (2022) Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool. PLoS Comp Bio.


20. A. Gayoso, Z. Steier, R. Lopez, J. Regier, K. L. Nazor, A. Streets & N. Yosef (2021) Joint probabilistic modeling of single-cell multi-omic data with totalVI. Nature Methods, volume 18, pages272–282 (2021).


19. T. A. Hait,  R. Elkon,  and R. Shamir (2022) CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps.  Nucleic Acids Research, gkac048, (2022).


18. H. Levi, N. Rahmanian, R. Elkon, R. Shamir (2022) The DOMINO web-server for active module identification analysisBioinformatics, btac067,  


17. B. Yao,  C. Hsu, G. Goldner, Y. Michaeli,  Y. Ebenstein,  and J. Listgarten (2021) Nanopore callers for epigenetics from limited supervised databioRxiv, doi:


16. G. Gilad, I. Sason and R. Sharan (2021) An automated approach for determining the number of components in non-negative matrix factorization with application to mutational signature learning (2021) Machine Learning: Science and Technology, Volume 2, Number 1, 015013.


15. Y. Kim,* M. D.M. Leiserson,* P. Moorjani,* R. Sharan,* D. Wojtowicz,* and T. M. Przytycka* (2021) "Mutational Signatures: From Methods to Mechanisms". Annual Review of Biomedical Data Science, Vol. 4:189-206 (Volume publication date July 2021), *equal contribution.


14. S. Bahiri Elitzur, R. Cohen-Kupiec, D. Yacobi, L. Fine, B. Apt, A. Diament & T. Tuller (2021) Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts. RNA Biology, Pages 684-698 | Published online: 29 Sep 2021,


13. I. Israel-Elgali, L. Hertzberg, G. Shapira, A. Segev, I. Krieger, U. Nitzan, Y. Bloch, N. Pillar, O. Mayer, A. Weizman, D. Gurwitz, N. Shomron (2021) Blood transcriptional response to treatment-resistant depression during electroconvulsive therapyJournal of Psychiatric Research, Volume 141, 2021, Pages 92-103, ISSN 0022-3956,


12.  S. Belaish,  I. Israel-Elgali,  G. Shapira,  I. Krieger, A. Segev, U. Nitzan, M. Majer, Y. Bloch, A. Weizman, D. Gurwitz, N. Shomron & L. Hertzberg (2021) Genome wide analysis implicates upregulation of proteasome pathway in major depressive disorder. Transl Psychiatry 11, 409 (2021).


11. K. Halabi, I. Mayrose (2021) Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. J Mol Evol (2021).


10. H. Levi, R. Elkon, R. Shamir (2021) "DOMINO - a novel network-based active module identification algorithm with reduced rate of false calls". Molecular Systems Biology 17:e9593 (2021).


9.  M. Levy, A. Frishberg, I. Gat-Viks (2020) Inferring cellular heterogeneity of associations from single cell genomics. Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3466–3473,


8.  D. Levin,  and  T. Tuller (2020) Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics. PLoS Compt. Biol.,


7. D.D. Erdmann-Pham, K. Dao Duc, and Y.S. Song (2020) The key parameters that govern translation efficiency. Cell Systems, Vol. 10, Issue 2, (2020) 183-192.e6.


6. T. S. Hsieh, C. Cattoglio, E. Slobodyanyuk, A. S. Hansen, O. J. Rando, R. Tjian, X. Darzacq (2020) Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Mol Cell. 2020 May 7;78(3):539-553.e8. 


5. H. Wang, L. Pipes, R. Nielsen (2020) Synonymous mutations and the molecular evolution of SARS-CoV-2 origins. Virus Evolution, veaa098, 


4. L. Pipes, H. Wang, J. P. Huelsenbeck, R. Nielsen (2020) Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny. Molecular Biology and Evolution, msaa316,


3. M. Chintalapati  and P. Moorjani (2020) Evolution of the mutation rate across primates. Current Opinion in Genetics & Development, 62, 58-64.


2. T. Kustin and A. Stern (2020) Biased mutation and selection in RNA virusesMolecular Biology and Evolution, msaa247,


1. G. Ling, D. Miller, R. Nielsen, A. Stern (2019) A Bayesian framework for inferring the influence of sequence context on point mutations. Molecular Biology and Evolution, msz248,



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