I am primarily interested in sequence analysis in the context of metagenomics and phylogenetics. I develop tools that target efficient analysis of large-scale genomic datasets. Some examples are:
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CONSULT-II – using locality-sensitive hashing for taxonomic identification
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KRANK – memory-bound and taxonomy-aware k-mer selection algorithm
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krepp – reads to genome distance estimation and phylogenetic placement
I also briefly worked in network analysis: see our community detection method for dynamic gene co-expression networks (MuDCoD – community detection in multi-subject dynamic networks from scRNA-seq data).
During my master’s, my focus was mostly on (applied) machine learning, in particular time series analysis in the context of computational ethology (basty – behavioral analysis of sleep in fruit flies), and natural language processing (active learning for named entity detection).