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  2. Rottenstreich S., Miller J., Hamilton M. Steady state of homozygosity and Gst for the island model. Theoretical Population Biology. v.72 (2007) 231-244. link

  3. Rottenstreich S., Hamilton M., Miller J. Dynamics of Fst for the Island Model. Theoretical Population Biology. v.72 (2007) 485-503. link

  4. Leviyang S. Fst for the Island Model in the Weak Mutation, Large Sample Limit. Stoch. Anal. App. v.28, n,4 (2010) 577 - 601. link

  5. Leviyang S. The Distribution of Fst and other Genetic Statistics for a Class of Population Structure Models. J. Math. Biology, v.62, n.2, (2011) 203-289. link

  6. Leviyang S., Hamilton M. Properties of Weir and Cockerhamís Fst estimators and associated bootstrap confidence intervals. Theo. Pop. Biology, v.79, (2011) 39-52. link

  7. Leviyang S. Sampling HIV Intrahost Genealogies Based on a Model of Acute Stage CTL Response. Bull Math Biol. v.3, (2012) 509-35

  8. Leviyang S. Analysis of a Stochastic Predator-Prey Model with Applications to Intrahost HIV Genetics. J. Math. Bio. v. 65, iss 6-7, (2012) 1285-1336. link

  9. Leviyang S. The Coalescence of Intrahost HIV Lineages Under Symmetric CTL Attack. Bull. Math. Bio. v. 74, n.3, (2012), 509-535. link

  10. Leviyang S. Computational Inference Methods for Selective Sweeps Arising in Acute HIV Infection. Genetics. v. 194, n. 3 (2013) 737-752. link

  11. Leviyang S. Constructing Lower-Bounds for CTL Escape Rates in Early SIV Infection. J. Theor. Bio. v. 352, n. 7 (2014), 82-91. link

  12. Leviyang S. and Ganusov, V.V. Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes. PLOS-Computational Biology (2015). link

  13. Leviyang S., Griva I., Ita S, and Johnson W. A Penalized Regression Approach to Haplotype Reconstruction of Viral Populations Arising in Early HIV/SIV Infection. Bioinformatics (2017). link

  14. Gustavo H. Kijak, Eric Sanders-Buell1, Agnes-Laurence Chenine, Michael A. Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, Elizabeth A. Harbolick, Meera Bose, Phuc Pham, Celina Oropeza, Kultida Poltavee, Annemarie OSullivan, Erik Billings, Melanie Merbah, Margaret Costanzo, Joanna Warren, Bonnie Slike, Hui Li, Kristina K. Peachman, Will Fischer, Feng Gao, Claudia Cicala, James Arthos, Leigh A. Eller, Robert J. OConnell, Samuel Sinei, Lucas Maganga, Hannah Kibuuka, Sorachai Nitayaphan, Mangala Rao, Mary A. Marovich, Shelly J. Krebs, Morgane Rolland, Bette T. Korber, George M. Shaw, Nelson L. Michael, Merlin L. Robb, Sodsai Tovanabutra, Jerome H. Kim. Rare HIV-1 Transmitted/Founder Lineages Identified by Deep Viral Sequencing Contribute to Rapid Shifts in Dominant Quasispecies during Acute and Early Infection. PLOS-Pathogens (2017). link

  15. Ita S., Hill A.K., Lam E.C., Dufort F.J., Yang X., Newman R., Leviyang S., Fofana I.B., Johnson W.E. High-Resolution Sequencing of Viral Populations During Early SIV Infection Reveals Evolutionary Strategies for Rapid Escape from Emerging Env-Specific Antibody Responses. Journal of Virology (2018). link

  16. Leviyang S., Griva I Investigating Functional Roles for Positive Feedback and Cellular Heterogeneity in the Type I Interferon Response to Viral Infection. Viruses (2018). link

  17. Leviyang S, Strawn N, Griva I. Regulation of interferon stimulated gene expression levels at homeostasis. Cytokine (2019). link

  18. Wu F, Ourmanov I, Kirmaier A, Leviyang S, LaBranche C, Huang J, Whitted S, Matsude K, Montefiori D, Hirsch V.M. SIV Infection Duration Largely Determines Broadening of Neutralizing Antibody Response in Macaques. Journal of Clinical Investigation (2020). link.

  19. Leviyang S. Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state. Cytokine X (2021). link.

  20. George T, Strawn N, and Leviyang S. Tree Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated with Hematopoietic Lineage Structure. Bioarxiv (2021). link.

  21. Sah P, Otterstatter M, Leu ST, Leviyang S, Bansal S. Revealing mechanisms of infectious disease spread through empirical contact networks. PLOS-Computational Biology (2021). link.

  22. De Marco C, Marscio N, et al. Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Infection, Genetics, and Evolution (2022). link.