BI project

Development and improvement search strategies in the GeneQuery system

GeneQuery is a new computational tool for finding related phenotypes using ad hoc transcriptional signatures. Unlike earlier analogues, the service works with primary, uncurated data from the open Gene Expression Omnibus (GEO) expression data repository. GeneQuery has already proved itself from the biological point of view, showing the ability to find fundamentally new and biologically significant information in a huge volume of expression data.

Antibody repertoire construction from Ion Torrent reads

Antibody repertoire is defined as an entire set of antibodies in an organism. It describes adaptive immune system, and thus serves as an input to most immunoinformatics studies. This makes antibody repertoire construction a fundamental problem of immunoinformatics.

Hardware-effective Tool for Genome Mappability Score Estimation

Our project is devoted to a development of an effective and accurate tool for a genome mappability evaluation. Mappability is a genome-wide function showing if a region in a genome could be identified unambiguously using a read of a particular length. This function typically ranges between 0 and 100. If exact genome subsequence may be found in more than one location, then the mappability in that location of the genome is set to zero. Otherwise, if the subsequence is unique, mappabity is close to 100.

Time course data enrichment analysis

In the cases of description of time-course expression data, there is a need for accurate methods that allow finding regulated pathways. While commonly used for comparison of two conditions, gene set enrichment is not straightforward for time-course and multiple-condition experiments.

GSEA is a commonly used method for comparing two conditions and is based on comparing metric for pathway with metric for random gene sets of the same size.

TwoPaCo for fragmented genomes

The de Bruijn graphs are the key algorithmic technique in genome assembly and metagenomic analysis. The construction of a de Bruijn graph is one of the most resource intensive steps of many algorithms in bioinformatics. A de Bruijn graph can be compacted by collapsing non-branching paths into single edges. Building and storing the ordinary graph takes lots of space, so it is an interesting question if is it possible to construct the compacted graph directly and in more optimal way.

Pipeline for target sequencing analysis

Next-Generation Sequencing(NGS) is used worldwide in many different applications, such as scientific investigations, medical analyses and forensic expertises. Volume of data generated by NGS is increasing daily and its manual processing is becoming impossible. To cope with this problem workflow automatization is performed.

Searching for RNA polymerase II promoter regions responsible for transcription on lampbrush chromosomes in chicken (Gallus gallus)

Lampbrush chromosomes (LBCs) are specific form of chromosomes during meiosis in oocytes of most vertebrates, including birds. They appear as half-bivalent with chromomere-loop organization. The prominent structure of the LBCs loops is maintained by a high density of transcripts mainly produced by RNA polymerase II. Despite years of research, the reason of such an intense transcription in the meiotic diplotene I is unknown and most transcribed sequences themselves and their biological role still need to be clarified.


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