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Philippos Tsourkas

Assistant Professor
School of Life Sciences
Office: WHI 107
Mail Code: 4004
Phone: 702-895-3390
Fax: 702-895-3956


The primary goal of my research is to generate insight into important questions in biology using bioinformatics and computational biology methods. I am also interested in developing bioinformatics and computational tools for use by the biological community. In addition, I am also interested in aiding my colleagues with analysis of large biological data sets as the need arises. Outlined below are some of the research projects currently pursued in my lab.

A meta-tool for bacteriophage gene prediction and genome annotation

Bacteriophages are the most numerous and diverse entities on Earth, with an estimated 10 31 particles in the biospher. The rapid decrease in cost of sequencing technology has resulted in an explosion in the number of published phage genomes. Consequently, accurate gene prediction and start codon calling (in cases where a gene has more than one possible start codon) for newly assembled phage genomes is of great importance.  There are currently several gene calling programs (Glimmer, GeneMark, GeneMark.hmm) that are widely used to annotate new phage genomes in an automated manner. While producing rapid results, such programs occasionally produce false positives and missed calls (false negatives.)  Furthermore, these programs may not necessarily be in agreement in many cases, complicating the process of gene and start codon calling. Accurate genome annotation thus requires manual curation, using additional information such as expert knowledge, BLAST results, gene length, and overlap with other genes (since bacteriophage genes seldom overlap with each other). However, when the number of sequenced phages is large, manual curation becomes prohibitively time-consuming.  To this end we are working towards developing a genome annotation meta-tool for bacteriophages that integrates all readily available information to call genes and start codons, thereby combining as many of the advantages of manual curation as possible, while retaining the speed of automation.

Identification of gene regulatory networks controlling obesity in starvation selected Drosophila melanogaster

The identification of genes and gene regulatory networks implicated in control of obesity is of great importance in biology and health. In collaboration with the Gibbs lab at UNLV, we are interested in identifying gene regulatory networks that play a central role in regulating obesity in D. melanogaster.  Successive generations of D. melanogaster have been subjected to starvation conditions, such that in each generation, only 15% of the individuals survive. In the next generation, the survivors are allowed to breed to replenish the population, and the population is again subjected to starvation conditions. This process has been repeated for >90 generations, resulting in a population of starvation-selected D. melanogaster. D. melanogaster subjected to this kind of starvation selection are prone to obesity when fed a normal diet. We plan to collect gene expression data by RNA-Seq for each generation of starvation selected D. melanogaster and identify genes that are overexpressed in the starvation selected individuals by statistical comparison with a control population.  By taking expression profiles at each generation we will have time-course expression data, which we hope to use to infer gene regulatory networks that play a role in obesity.

Investigation into the use of extrinsic kinases in lymphocyte receptor signaling

Signaling by receptors is in many cases mediated by a tyrosine kinase domain that transfers a phosphate group from an ATP molecule to a cytosolic signaling molecule, initiating a cascade that eventually leads to gene transcription. Most commonly, the receptor’s kinase domain is an intrinsic part of the receptor itself (e.g. in the EGFR family of receptors, insulin receptors, etc…). In lymphocytes however (T and B cells), the intracellular domain of the lymphocyte antigen receptor (the receptor dedicated to detecting foreign pathogens, known as the “B cell receptor” or “BCR” in B cells, and the “T cell receptor”, or “TCR” in T cells) does not possess a kinase domain. Rather, kinase activity is carried out by an extrinsic family of molecules known as Src-family kinases that carry out their signaling function by binding to an Immuno-Tyrosine Activation Motif (ITAM) on the intracellular domain of the receptor following antigen ligation to the receptor’s extracellular domain.  It is currently not known why lymphocyte antigen receptor signaling differs from other receptor families in this respect. One reason could be that lymphocyte antigen receptors, in contrast to other receptor families, encounter an essentially infinite variety of antigenic ligands. We are currently developing a mathematical model that we hope will generate useful insight into the differences between extrinsic and intrinsic kinase-mediated signaling cascades.


Bioinformatics, Mathematical Modeling


Ph.D. University of California, Berkeley