I have recently earned my PhD under the supervision of Prof Dan Graur. The Graur lab deals with various subjects in molecular evolution such as multiple sequence alignment, genome composition, and critiquing other people's work.

My own research focuses on overlapping genes. Overlapping genes were suggested to have multiple functions, such as regulation of gene expression, translational coupling, and genome imprinting. In addition, overlapping genes were hypothesized to be a means of genome size reduction, as well as a mechanism for creating new genes. My first paper on the subject examines the distribution of overlapping genes across genomes. In contrast to previous studies, which suggested that selection shaped the distribution of overlapping genes in the possible overlap phases, we provide a simple explanation based on the structure of the genetic code and the abundance of amino-acids in protein coding genes. A short talk describing this study, which I gave at the SMBE 2008 conference, can be found here.

Inferring the intensity of selection in protein-coding genes is important, since such selection is used to shed light on the process of adaptation. However, such inference in overlapping genes is difficult because the standard approaches do not take into account the interdependence between the overlapping sequences and the unique evolutionary constraints due to interdependence. We developed a new method for the simultaneous estimation of selection intensities in overlapping genes. The source code for the program (written in Matlab) can be downloaded here. The paper describing the method was published in PLoS ONE.

Detection of functional overlapping genes has been proven to be another difficult task. For example, the eleventh protein-coding gene in the influenza A genome, PB1-F2 (which overlaps PB1), was discovered 20 years after the initial annotation of its genome, thereby increasing the proteome repertoire by 10% (Chen et al. 2001). We demonstrated how our method for the estimation of selection intensity can be used to detect functional overlapping genes (Sabath, Price, and Graur 2009). We presented a discovery of a new overlapping gene in the genomes of Israeli Acute Paralysis Virus (IAPV) and three other viruses. IAPV infects honeybees and is associated with colony collapse disorder, a syndrome characterized by the mass disappearance of bees from hives (Cox-Foster et al. 2007).

General Interests: