A5030676152- Algorithms and Data Compression
- Network Packet Processing and Optimization
- Natural Language Processing Techniques
- Genomics and Phylogenetic Studies
- semigroups and automata theory
- DNA and Biological Computing
- Data Management and Algorithms
- Advanced Database Systems and Queries
- Web Data Mining and Analysis
- Diverse Musicological Studies
- Advanced Data Compression Techniques
- RNA and protein synthesis mechanisms
- Musicology and Musical Analysis
- Error Correcting Code Techniques
- Information Technology Governance and Strategy
- Fractal and DNA sequence analysis
- Music and Audio Processing
- Music Technology and Sound Studies
- Plant and Fungal Interactions Research
- Data Mining Algorithms and Applications
- Cellular Automata and Applications
- Plant Virus Research Studies
- Urbanization and City Planning
- Cancer-related molecular mechanisms research
- Evolutionary Algorithms and Applications
Czech Technical University in Prague
2014-2023
Jan Evangelista Purkyně University in Ústí nad Labem
2019
Research Institute of Inorganic Chemistry
2019
The constant advances in sequencing technology have redefined the way genome is performed. They are able to produce tens of millions short sequences (reads), during a single experiment, and with much lower cost than previously possible. Due this massive amount data, efficient algorithms for mapping these reads reference great demand, recently, there has been ample work publishing such algorithms. In paper, we study different version problem: dynamically changing genomic sequence. We propose...
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) genomic databases. Given string S, it produces dictionary D and parse P overlapping phrases such that BWT(S) can be computed from in time workspace bounded terms their combined size |PFP(S)|. In practice are significantly smaller than S computing them is more efficient directly, at least when concatenation many genomes. this paper, we consider...
DCA (Data Compression using Antidictionaries) is a novel lossless data compression method working on bit streams presented by Crochemore et al. takes advantage of words that do not occur as factors in the text, i.e. are forbidden. Due to these forbidden (antiwords), some symbols text can be predicted. We build antidictionary suffix array time O(k * N log N), where k maximal antiword length. Length and LCP constructed over binary alphabet will 8 times length input text. Still memory...
Abstract Motivation The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such scenario is online search over collection similar texts, problem with surprisingly few solutions presented so far. Results We present SOPanG, simple tool exact pattern matching an elastic-degenerate string, recently proposed simplified model the pan-genome. Thanks bit-parallelism, it achieves speeds above 400...
Nowadays, decreasing cost and better accessibility of sequencing methods have enabled studies genetic variation between individuals the same species also two related species. This has led to a rapid increase in biological data consisting sequences that are very similar each other, these usually being stored together one database. We propose compression method based on Wavelet Tree FM-index optimized for set sequences. The is tracking single changes (together with their context) every...
Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect yield and quality. Utilizing high-throughput sequencing (HTS), we identified novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct plants. This study provides comprehensive characterization RaEV1, focusing on its genomic structure, phylogeny, possible transmission routes. Analysis nearly complete genomes from 14 RaEV1 isolates highlighted regions variance,...
We introduce quasi suffix arrays as a generalization of for character strings. show that array encodes enough the structure string to be useful construct many applications where full power is not necessary, notably in problems do require lexicographical order, example, pattern-matching or calculation repeating substrings. are interested arrays, we believe they can calculated by simple, fast, and space efficient algorithms. As first step towards this goal, describe family DIST algorithms...
Covid-19 related restrictions bring new challenges to all aspects and phases of higher education. At universities, remote formats are deployed or even developed both for lectures laboratory exercises. This article addresses describes the experience with lessons during pandemic time at Department Measurement Czech Technical University in Prague, Faculty Electrical Engineering. It introduces best practices exercised using Home Lab, which helps distance teaching practical electronic classes....
A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections flower stalks, and the complete genome sequence novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), determined verified using high-throughput sequencing. The genomic organization BCRV2 characteristic cytorhabdoviruses (family Rhabdoviridae) included seven genes: 3 ́- N-P´-P-P3-M-G-L -5 ́. BLASTP analysis revealed...