The latest instalment of this blog post series is by Omar Wagih (@omarwagih, Gscholar) who has just last month successfully defended his PhD. Along with Marco, Omar has been part of the group working on studying how DNA variants relate to phenotypes. He developed the mutfunc resource and the fantastic guess the correlation game.What was the path the brought you to the group? Where are you from and what did you work on before arriving in the group?
My love of genetics is, in more ways that one biologically ingrained. Growing up in a family of scientists, I was always surrounded by a wealth of information which I instinctually sought to organise. For this, I pursued my undergraduate and masters degree at the University of Toronto, majoring in computational biology and computer science, respectively. Along the way, I was fortunate to work in some of the leading computational biology labs in Canada including those of Gary Bader, Philip Kim, Charlie Boone, Brenda Andrews, Andrew Fraser and Andrew Emili. I worked on a range of projects which ranged from analysing images of genetic screens of yeast to determining the impact of disease mutations on kinase-substrate phosphorylation. These experiences led me to develop an interest in understanding how changes in the genome translate to variability in cellular physiology, and ultimately phenotype, which prompted me to pursue my PhD.
What are you currently working on?
My current project involves working towards a deeper understanding of how changes in the genome propagate to phenotypic variability by predicting which cellular mechanisms are likely to be impacted. For the past several years I have been developing and using computational methodologies to assess the mechanistic impact of natural and disease-causing mutations. I have been applying these to yeast, human and bacteria models in hopes of streamlining hypothesis-driven variant annotation. I have also been utilising these predictions to assess the overall burden these mutations impose on gene function and putting such information towards conducting gene-phenotype associations.
What are some of the areas of research that excite you right now?
I'm intrigued by novel mutagenesis technologies that are allowing us experimentally assess the impact of genetic variants on cellular fitness and function in a massively parallel fashion. Technologies like deep mutational scanning CRISPR are becoming increasingly common in achieving this and their off-target effects are steadily being reduced.
With such massive amounts of mutagenesis data, I'm also interested in how machine learning methodologies such as deep learning can be applied to learn how mutations collectively impinge on cellular function and ultimately phenotype. This would significantly improve the precision of variant impact predictors and, in my opinion, will have crucial roles in shaping the development of novel and personalised drug therapies.
What sort of things do you like outside of the science?Whether I'm skiing, hiking, camping or exploring the city, or you'll more likely than less find me outdoors. I often partake in sports. During my time in Cambridge, I rowed for my college and was part of the university boxing team.
I have been fascinated by drones for a while and own a DJI Phantom 3, which I often use for aerial filming. I also enjoy landscape and portrait photography, particularly with my 50mm lens. If I still have extra time on my hands, you'll find me implementing silly ideas that come to mind into apps or games. Here are a few I've made: genewords, pubtex, and guess the correlation.