Postgraduate Researcher at Edwards Lab (2008-2011)
Current location: UCSD Bioengineering 426
Phone: +1 (858) 822 1144
Bio (updated on 11/11/11)
Ramy finds it weird to refer to himself in the third person and thinks that bios written in third person—like many other aspects of scientific writing—are pretentious because they are almost always written by the “first person.” Thus, I will write my bio using the first person “I.”
– I am currently a Visiting Scientist at UCSD’s Systems Biology Research Group (AKA Palsson lab). I also hold a tenured Assistant Professor position in the Department of Microbiology, Faculty of Pharmacy, Cairo University (FOPCU).
– I have been in-and-out the Edwards lab between April 2008 and September 2011. During that period, though, my position (or affiliation) and my physical position (location) have changed a few times. One of the most common questions I get asked is: “where are you exactly working?” The right answer is: online!
- When I joined the lab, I was first appointed as an adjunct faculty member at the Computational Science Research Center of SDSU, a position which I still hold. In July 2008, I was appointed by the University of Chicago as a Research Associate (to work on the NMPDR project while physically at SDSU) then, between July 2009-2011, as a Research Associate at SDSU, instead.
- Between 2008 and 2011, I was also a lecturer (i.e., a tenured junior faculty member involved in teaching and conducting research without taking primary credit for it) in the Department of Microbiology and Immunology at FOPCU. I actually got this position in July 2006. As a lecturer, I taught microbiology and immunology to undergraduate and graduate students between 2006-2008. In addition I started a series of workshops between 2006-2010 on bioinformatics, pharmacogenetics/pharmacogenomics, and gene therapy in FOPCU and in the German University in Cairo (GUC). I also supervised or co-supervised a few undergraduate students and six graduate students (one of whom received her PhD in 2008; two received their MS degrees in 2009 and 2010; while three of them are still–more ore less–working on their master’s projects).
- My main projects at SDSU were to (i) devlop (better) tools and methods for annotating bacteriophage genomes; (ii) annotate phage genomes using the subsystems technology; and (iii) use these tools and annotations for the interpretation of phage genomes and, by extension, microbial genomes, viral, and microbial metagenomes. More details can be found in the Phage Annotation Tools and Methods (PhAnToMe) website.
- My broader research interests are in the evolution of virulence in bacteria (but also in other pathogenic organisms like archaea, unicellular eukaryotes, and Homo sapiens). Because bacterial virulence, like many other bacterial phenotypes, is contributed by bacteriophages, viruses that infect bacteria, I got interested into studying bacteriophages as well. During my PhD project and my first postdoctoral training, I have discovered a variant of a bacterial toxin (streptodornase 1) encoded by a bacteriophage that resides in the genome of the human-restricted pathogen Streptococcus pyogenes (a.k.a. Strep). Strep causes sore throat, pharyngitis, and skin diseases, but can turn into a killer monster (a.k.a. flesh-eating bacteria).
- Finally, I am also interested in several topics that came out of the studies mentioned above. These inclue immunogenetics (how different animals and humans react differently to bacterial infections), reconstructing bacterial virulomes from genomic data, and integrating diverse microarray data to improve the biological relevance of their interpretation.
- PhD in Microbiology and immunology from the University of Tennessee Health Science Center (UTHSC) at Memphis TN (defended December 2004 and officially earned May 2005). Coincidentally, Robert A. Edwards, PhD, was one of my committee members–those who tell you that you are “free to go.”
- BSc in Pharmacy and Pharmaceutical Chemistry from the Faculty of Pharmacy, Cairo University, June 1995.