I obtainedmy 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
I use mathematics, modeling, algorithms and simulations to understand problems in biology. My main focus has been on developing algorithms to analyze DNA and RNA sequencing data for problems related to genome assembly, structural variation detection, and transcriptome analysis. Recent reasearch involves transcript reconstruction, isoform detection, and SNV calling in long-read sequencing data (paperd
), and long-read clustering techniques (manuscript
). I have also worked a lot with genomic (short) read sequencing for genome assembly, e.g., for scaffolding
and structural variation detection
. I'm looking into aproaches integrating both long and short as well as genomic and transcriptomic datasets for, e.g., intron and UTR variation detection, isoform specific expression analysis.
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.