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Research


Bioinformatics

My current research interests are in developing computational methods for genomics and proteomics. In the genomics area, I am interested in the analysis of the next generation sequencing (NGS) data. The NGS technologies, such as Illumina, 454, APG, Helicos, Pacific Biosciences, and Ion Torrent, produce hundreds of gigabytes of data in a single run (hence also called high-throughput), with many applications, including cancer research, genetic disorders, disease control, neurological research, personalized medicine, etc. The impact of these technologies for everyday life is very far reaching and yet to be fully understood. I am currently interested in developing algorithms and software for genome assembly, read correction, read mapping, genomic variation detection, and DNA oligonucleotide design. In the area of proteomics, I am interested in protein-protein interaction prediction and alignment of biological networks. My work involves tools from algorithms, stringology, combinatorics, graph theory, (parallel) programming, probabilities, and statistics.

Stringology

I am as well interested in fundamental research in stringology, both in algorithms and combinatorics of strings.