Our main research areas

Annotation of tRNA-derived fragments

Several studies have been initiated towards functional characterization of non-coding RNA molecules, derived from tRNA (tRFs) in a variety of model organisms. However, a global perspective of the biogenesis of this interesting group of ncRNAs is largely missing.

Using Arabidopsis thaliana as a model organism, we aim at identification and characterization of the components involved in tRNA and microRNA biogenesis pathways that may play a role in generation of tRFs. We are presenting our results of a global, high-throughput characterization of small RNA fragments originating from Arabidopsis tRNA and tRNA-like genomic sequences.

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Alignment-free sequence comparison

With a bang, alignment-free (AF) sequence analysis tools have exploded into biological research. As AF methods offer computational speed many hundreds of times faster than the comparable alignment-based approaches, they have been applied to problems such as NGS analysis, whole-genome/proteome phylogeny, identification of horizontally transferred genes or recombined sequences — and many more.

We established a consortium (AFproject) for objective performance comparison of alignment-free sequence comparison tools on different datasets. This community developed web-service aims at simplyfing and standardizing the benchmarking of alignment-free tools. And for the users, the benchmarks provide a way to identify the most effective methods for the problem at hand.

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Prediction of hosts based on virus genome sequences

Prokaryotes (bacteria and archaea) play important roles in many ecosystems and significantly impact the health of humans, animals, and plants. However, much less is known about the viruses that infect prokaryotes. Experimental techniques to detect the potential host of the virus are low-throughput and require robust growth of the target host strain, which very often is not possible for many bacteria and archaea

The primary goal of the project is to create a universal and high-throughput computational pipeline (metaprogram) for prediction of host organisms from viral DNA sequences. The metaprogram will integrate multiple state-of-the-art alignment-free sequence comparison methods to provide the most likely host candidates for experimental testing. The large-scale application of the metaprogram to available viral and prokaryotic genomic sequences will provide a baseline for understanding virus-prokaryote interactions in natural systems and coevolution of viruses and their hosts.

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Transcriptome-wide RNA structure dynamics

In recent years RNA is emerging as the key regulator of gene expression. In most of known cases, the regulatory function fulfilled by RNA molecule is highly dependent on the accommodated secondary and tertiary structure.

The aim of the project is to develop both, the experimental and computational methods for identification of novel RNA-based regulatory mechanisms, relying solely on dynamic changes in RNA structure. Our research focuses on high throughput, transcriptome-wide approaches based on NGS technology.

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Database & Software Development

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