Adi Stern



Jointly affiliated with UCSF, lab of Raul Andino

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Research Overview

I am interested in the evolution of RNA viruses, many of which pose major threats to global human health (e.g., Influenza, Dengue virus, Hepatitis, and SARS). One of the reasons for this is that RNA viruses display very high mutation rates, allowing them to evade the host immune system and therapeutic interventions. I aim to study: (a) the fitness of RNA viruses as a function of their interaction with the host and (b) the process by which cross-species transmissions occur, often leading to emerging infectious diseases.

In general, I have always been interested in the evolutionary arms race that develops between any type of host (be it human, insect or bacteria) to any parasite (e.g., bacterial, viral, or phage). I am also interested in general processes that lead to genomic innovation, such as lateral gene transfer, gene duplication, and dynamics of mobile elements.

Selected Publications

Stern A., Sorek R. The phage-host arms race: shaping the evolution of microbes. Bioessays. BioEssays, 33(1):43-51 (2011).

Stern A., Keren L., Wurtzel O., Amitai G., Sorek R. Widespread targeting of self-DNA by the prokaryotic CRISPR immune system: gene regulation or autoimmunity? Trends in Genetics. 2010 26(8):335-340.

Stern A., Mayrose I., Shaul S., Gophna U., Pupko T. An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes. Systematic Biology. 59(2): 212-225.

Sela N, Stern, A., Pupko, T., Ast, G. Transduplication resulted in incorporation of a conserved protein domain sequence within the transposable element Harbinger Turmoil-1 in C. elegans. Biology Direct. 2008 Oct 8;3:41

Penn O.*, Stern A.*, Rubinstein N., Dutheil J., Bacharach E., Galtier N., Pupko T. 2008. Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Computational Biology. 2008 Nov;4(11):e1000214. *Authors contributed equally.

Cohen, O., Rubinstein, ND., Stern, A., Gophna, U., and Pupko, T. A likelihood framework to analyze phyletic patterns. Proceedings of The Royal Society of London Series B-Biological Sciences. 2008 Dec 27;363(1512):3903-11.

Stern, A., Doron-Faigenboim, A., Erez, E., Martz, E., Bacharach, E., Pupko, T. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Research. 35: W506-W511.

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: 392-400

Doron-Faigenboim, A.*, Stern, A.*, Mayrose, I., Bacharach, E., and Pupko, T. 2005. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21(9): 2101-2103. *Authors contributed equally.