Bio

I have a PhD in Computer science from School of Computer Science and Communication, KTH Royal institute of Technology (Supervisor: Lars Arvestad). Before my PhD I earned a bachelor's degree in mathematics (my Bachelor thesis on theoretcal properties of splines) and a master's degree in mathematical statistics (my Master thesis on convergence and burn-in estimation of MCMC output) from Stockholm University, Sweden. I'm currently a postdoctoral researcher (started October 2015) at Penn State University in Paul Medvedev's group.

Current research

During my PhD I developed algorithms for genome assembly (scaffolding in particular) and Structural variation detection using Illumina paired end and mate-pair data. Recent advances in sequencing techniques listed in GIAB preprint has opened up the possibility for obtaining accurate haplotype phased genome assemblies, detecting large and complex structural variation, or obtaining fully phased haplotype specific transcript isoforms. A lot is still needed on the computational method development side to fully make use of the data that these techniques provide. My postdoctoral research focuses on this. Specifically I work with algorithm development within transcriptome analysis, structural variation and genome assembly where, in addition to Illumina paired-end/mate-pairs, I use sequencing data such as pacbio CCS reads, synthetic long reads.

Motivation and interests

I'm interested in applications of statistical and mathematical methods and algorithms to analyze data. I'm also strongly motivated by developing sustainable and easily accesibele open source software --- all my code can be found on GitHub.