Adi Stern

My main research interest lies in host-pathogen interactions, particularly the fascinating patterns of co-evolution that hosts and viruses display. In my Ph.D. studies in Tel-Aviv University (Prof. Tal Pupko) I focused on developing novel evolutionary models and methodologies, and used these models to study the interactions between HIV and the human host.

In my post-doctoral studies in the lab of Dr. Rotem Sorek (Weizmann Institute) I studied the interaction between phages (bacterial viruses and the recently discovered CRISPR system, an adaptive immune system in prokaryotes.

Currently my research interests revolve around trying to understand what governs the evolution of RNA viruses and their interactions with hosts. I am combining phylogenetics, population genetics, and experiments to study:

·      The effect of recombination and convergent evolution on viral populations

·      Mutational robustness in RNA viruses

·      The structure of viral populations and how they evolve

·      Discovering novel antiviral systems

I am a post-doctoral fellow in the labs of: • Raul Andino, Department of Microbiology & Immunology, UCSF and • Rasmus Nielsen, Department of Integrative Biology, UC Berkeley

Mayrose I, Stern A, Burdelova EO, Sabo Y, Laham-Karam N, Zamostiano R, Bacharach E, Pupko T. 2013. Synonymous site conservation in the HIV-1 genome. BMC Evol Biol. 13:164.

Mick E, Stern A, Sorek R. 2013. Holding a grudge: persisting anti-phage CRISPR immunity in multiple human gut microbiomes. RNA Biol. 10(5):900-6. 

Stern A, Mick E, Tirosh I, Sagy O, Sorek R. 2012. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. 22(10):1985-94.

Stern A, Sorek R. 2011. The phage-host arms race: shaping the evolution of microbes.


Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. 2010. Self-targeting by CRISPR: gene regulation or autoimmunity? 26(8):335-40.

Stern A, Mayrose I, Penn O, Shaul S, Gophna U, Pupko T. 2010. An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst Biol. 59(2):212-25.

Sela N, Stern A, Makalowski W, Pupko T, Ast G. 2008. Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans. Biol Direct. 3:41. 

Penn O*, Stern A *, Rubinstein ND, Dutheil J, Bacharach E, Galtier N, Pupko T. 2008. Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

PLoS Comput Biol. 4(11):e1000214.

*Authors contributed equally

Cohen O, Rubinstein ND, Stern A, Gophna U, Pupko T. 2008. A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci. 363(1512):3903-11. 

Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, Pupko T. 2007. Selecton

2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res. 35(Web Server issue):W506-11.

Stern A, Privman E, Rasis M, Lavi S, Pupko T. 2007. Evolution of the metazoan protein phosphatase 2C superfamily. J Mol Evol. 64(1):61-70.

Stern A, Pupko T. 2006. An evolutionary space-time model with varying among-site dependencies. Mol Biol Evol. 23(2):392-400.

Doron-Faigenboim A*, Stern A *, Mayrose I, Bacharach E, Pupko T. 2005. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21(9):2101-3.

*Authors contributed equally