Rottenstreich S. A Stationary Phase Approach to the Weak Coupling Schrodinger Equation. Jour. Stat. Phys. v.124, n.1 (2006) 47-86. link
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
Rottenstreich S., Hamilton M., Miller J. Dynamics of Fst for the Island Model. Theoretical Population Biology. v.72 (2007) 485-503. link
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
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
Leviyang S., Hamilton M. Properties of Weir and CockerhamÃs Fst estimators and associated bootstrap confidence intervals. Theo. Pop. Biology, v.79, (2011) 39-52. link
Leviyang S. Sampling HIV Intrahost Genealogies Based on a Model of Acute Stage CTL Response. Bull Math Biol. v.3, (2012) 509-35
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
Leviyang S. The Coalescence of Intrahost HIV Lineages Under Symmetric CTL Attack. Bull. Math. Bio. v. 74, n.3, (2012), 509-535. link
Leviyang S. Computational Inference Methods for Selective Sweeps Arising in Acute HIV Infection. Genetics. v. 194, n. 3 (2013) 737-752. link
Leviyang S. Constructing Lower-Bounds for CTL Escape Rates in Early SIV Infection. J. Theor. Bio. v. 352, n. 7 (2014), 82-91. link
Leviyang S. and Ganusov, V.V. Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes. PLOS-Computational Biology (2015). link
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
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
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
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
Leviyang S, Strawn N, Griva I. Regulation of interferon stimulated gene expression levels at homeostasis. Cytokine (2019). link
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.
Leviyang S. Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state. Cytokine X (2021). link.
George T, Strawn N, and Leviyang S. Tree Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated with Hematopoietic Lineage Structure. Frontiers in Genetics (2021). link.
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.
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.
Leviyang, S. Analysis of a Single Cell RNA-seq Workflow by Random Matrix Methods. (2024). Bulletin of Mathematical Biology. link
Leviyang, S. Resolution Tradeoffs in Modularity Clustering of Single Cell RNA-Seq Datasets. (2025). IEEE Transactions on Computational Biology and Bioinformatics link
Leviyang, S. A Metacell Model of Single Cell RNA-seq Counts Yields a Gaussian Mixture Model in PCA Space. (2026). bioRxiv. link