About me...

I earned a B.S. in Electrical Engineering from Faculty of Electrical Engineering, University of Sarajevo, Bosnia and Herzegovina, in 2005. and a Ph.D. in Computer Science from University of California, Irvine, in 2010.

During my Ph.D., I worked with Prof. Natasa Przulj in the field of Computational and Systems Biology and Bioinformatics. The main focus of my research was on the analysis and modelling large molecular network wiring patterns, with aim to gain deeper understanding of underlying biomedical processes and complement the information that can be obtained using the genomic data. My Ph.D. dissertation title is "Uncovering Biological Knowledge from Network Structure."

Previously, I was a research scientist at Biotechnology HPC Software Application Institute (BHSAI), working on interdisciplinary projects with researchers in the fields of molecular biology, microbiology, and immunology. The main focus of my research was on the analysis of host-pathogen interactions, with the aim to identify specific targets for future biochemical and immunological work. I created an integrative computational analysis workflow that uses various types of high-throughput molecular data to investigated mechanisms that pathogens use to invade the host cell, evade the host’s immune response, and survive within the host. I also developed a novel application that can identify mechanisms that are conserved among pathogens.

My research as a word-clould These methods helped identify novel pathogen proteins required for virulence in two different pathogenic species (B. mallei and F. tularensis). Subsequent animal experiments confirmed their virulence. Insights gathered from working on the host-pathogen interactions project lead to the creation of Database of Burkholderia secretion systems (DBSecSys), a comprehensive and manually curated resource for studying Burkholderia secretion systems. For more details, see Publications

While working at BHSAI, I also had a chance to get hands-on experience learning about computational methods for expression data analysis (microarrays, protein arrays, and RNAseq), next generation sequencing analysis, and pharmacokinetic/pharmacodynamics modeling and simulation. The later one inspired me to try to develop an R package sysBio for systems biology modeling.

I am also interested in large scale data visualization techniques, especially network visualization techniques. I discussed some of the network visualization approaches in my R blog posts Network visualization techniques in R. Although I often use R for my work, the blog mainly contains discussions of various non-bioinformatics related packages or functions.

While I enjoy doing research, I also have many other interests. I enjoy reading, traveling, photography, and various outdoor activities, especially tennis and hiking. I am an avid coffee fan and I enjoy trying different varieties and different preparation methods. Whenever I travel, besides all the touristy things, local coffee shops are always on my "must see" list. Naturally, some of my hobbies are not that far away from my professional interests - I enjoy playing with Lego Mindstorms and doing Arduino projects. Generally, I am always trying to find fun in things I do (or just do fun things), because I believe that people who enjoy and have fun doing things can achieve better results. I am very competitive and I rarely say no to a challenge, I am always looking for new things to learn, and often, I feel that days are just too short.

Contact: vesna [at] vesnam [dot] com