Biology subjects

Kusmirek, W.

Publications and source records attributed to Kusmirek, W..

3 recordsLinked to original sources

bioRxiv2024

Direct RNA Oxford Nanopore sequencing distinguishes between modifications in tRNA at the U34 position

The measurement of tRNA modifications with single transcript resolution has been feasible for only a few modifications due to the lack of available methods. This limitation does not allow to advance basic research studies on the dynamic nature of tRNA modification and its cellular function in time and space, neither to develop modern diagnostic tools for several already known tRNA-dependent human diseases. Nanopore is a well-established sequencing method that has proven to be efficient for the study of RNA. The analysis of tRNA modifications by Nanopore is still under development. We have investigated the efficacy of nanopore technology to discriminate between complex modifications of uridine 34 in tRNA, which affect the base-calling properties of neighbouring bases and are therefore difficult to accurately predict. We have developed new methods to chemically and enzymatically synthesise single modified tRNA molecules with modifications at the anticodon loop. Nanopore technology captures the features produced by uridine with and without a thiol group when present on synthetic tRNA molecules. Thus, Oxford Nanopore Technology (ONT) has great potential for developing strategies to accurately identify the modification status of the tRNA anticodon loop (ACL), which encompasses the most complex modifications on uridine-containing RNA motifs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/630739v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@4317baorg.highwire.dtl.DTLVardef@caf204org.highwire.dtl.DTLVardef@1d7249dorg.highwire.dtl.DTLVardef@1a4f8c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2018

SeQuiLa-cov: A fast and scalable library for depth of coverage calculations

BackgroundDepth of coverage calculation is an important and computationally intensive preprocessing step in a variety of next generation sequencing pipelines, including the analyses of RNA-seq data, detection of copy number variants, or quality control procedures.\n\nResultsBuilding upon big data technologies, we have developed SeQuiLa-cov, an extension to the recently released SeQuiLa platform, which provides efficient depth of coverage calculations, reaching more than 100x speedup over the state-of-the-art tools. Performance and scalability of our solution allows for exome and genome-wide calculations running locally or on a cluster while hiding the complexity of the distributed computing with Structured Query Language Application Programming Interface.\n\nConclusionsSeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.

bioinformatics↗

bioRxiv2018

Clustering-based optimization method of reference set selection for improved CNV callers performance

BackgroundThere are over 25 tools dedicated for the detection of Copy Number Variants (CNVs) using Whole Exome Sequencing (WES) data based on read depth analysis.\n\nThe tools reported consist of several steps, including: (i) calculation of read depth for each sequencing target, (ii) normalization, (iii) segmentation and (iv) actual CNV calling. The essential aspect of the entire process is the normalization stage, in which systematic errors and biases are removed and the reference sample set is used to increase the signal-to-noise ratio.\n\nAlthough some CNV calling tools use dedicated algorithms to obtain the optimal reference sample set, most of the advanced CNV callers do not include this feature.\n\nTo our knowledge, this work is the first attempt to assess the impact of reference sample set selection on CNV detection performance.\n\nMethodsWe used WES data from the 1000 Genomes project to evaluate the impact of various methods of reference sample set selection on CNV calling performance of three chosen state-of-the-art tools: CODEX, CNVkit and exomeCopy. Two naive solutions (all samples as reference set and random selection) as well as two clustering methods (k-means and k nearest neighbours with a variable number of clusters or group sizes) have been evaluated to discover the best performing sample selection method.\n\nResults and ConclusionsThe performed experiments have shown that the appropriate selection of the reference sample set may greatly improve the CNV detection rate. In particular, we found that smart reduction of reference sample size may significantly increase the algorithms precision while having negligible negative effect on sensitivity. We observed that a complete CNV calling process with the k-means algorithm as the selection method has significantly better time complexity than kNN-based solution.

bioinformatics↗