Biology subjects

Vesely, P.

Publications and source records attributed to Vesely, P..

8 recordsLinked to original sources

bioRxiv2026

Pareto optimization of masked superstrings improves compression of pan-genome k-mer sets

The growing interest in k-mer-based methods across bioinformatics calls for compact k-mer set representations that can be optimized for specific downstream applications. Recently, masked superstrings have provided such flexibility by moving beyond de Bruijn graph paths to general k-mer superstrings equipped with a binary mask, thereby subsuming Spectrum-Preserving String Sets and achieving compactness on arbitrary k-mer sets. However, existing methods optimize superstring length and mask properties in two separate steps, possibly missing solutions where a small increase in superstring length yields a substantial reduction in mask complexity. Here, we introduce the first method for Pareto optimization of k-mer superstrings and masks, and apply it to the problem of compressing pan-genome k-mer sets. We model the compressibility of masked superstrings using an objective that combines superstring length and the number of runs in the mask. We prove that the resulting optimization problem is NP-hard and develop a heuristic based on iterative deepening search in the Aho-Corasick automaton. Using microbial pan-genome datasets, we characterize the Pareto front in the superstring-length/mask-run space and show that the front contains points that Pareto-dominate simplitigs and matchtigs. Finally, we demonstrate that Pareto-optimized masked superstrings improve pan-genome k-mer set compressibility by 12-19% when combined with neural-network compressors, achieving less than 1.2 bits per k-mer in common scenarios.

bioinformatics↗

bioRxiv2025

Citizen science and detailed searches reveal widespread occurrence of hybrid-like Syrian x Great-spotted woodpeckers

The Syrian Woodpecker (hereafter SW) expansion into Europe since the end of the 19th century has enabled its hybridisation with the Great spotted Woodpecker (hereafter GW). This phenomenon, however, has generally been considered sporadic. Here, we examined the occurrence of mixed pairs and hybrids based on our own field observations and citizen science data. Interspecific pairs and individuals of SW and GW were found to be generally scarce but occurred in all parts of the area investigated, not only at the edges of the SWs range. The proportion of hybrid occurrence in woodpecker populations was found to be similar across the whole SWs range in Europe and in both urban and rural populations. However, on a local level, hybrids seemed to be more abundant in certain regions, for example, E Austria, Moravia, SE Poland, W Russia, S Ukraine, Bulgaria, E Greece and W Turkey. Generally, females were 1.4 times more frequent among hybrids. Three major phenotypical hybrid forms were identified: GW-like, SW-like, and intermediate, with first two forms being more frequent in the central and south of Europe respectively. Whereas proportion of the intermediate form was relatively constant across the whole range of hybrid occurrence. The results indicate that hybrids of the two species have become significant part of woodpecker populations and thus should be considered in research and nature conservation projects.

zoology↗

bioRxiv2024

FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)

The growing volumes and heterogeneity of genomic data call for scalable and versatile k-mer-set indexes. However, state-of-the-art indexes such as Spectral Burrows-Wheeler Transform (SBWT) and SSHash depend on long non-branching paths in de Bruijn graphs, which limits their efficiency for small k, sampled data, or high-diversity settings. Here, we introduce FMSI, a superstring-based index for arbitrary k-mer sets that supports efficient membership and compressed dictionary queries with strong theoretical guarantees. FMSI builds on recent advances in k-mer superstrings and uses the Masked Burrows-Wheeler Transform (MBWT), a novel extension of the classical BWT that incorporates position masking. Across a range of k values and dataset types - including genomic, pangenomic, and metagenomic - FMSI consistently achieves superior query space efficiency, using up to 2-3x less memory than state-of-the-art methods, while maintaining competitive query times. Only a space-optimized version of SBWT can match the FMSIs footprint in some cases, but then FMSI is 2-3x faster. Our results establish superstring-based indexing as a robust, scalable, and versatile framework for arbitrary k-mer sets across diverse bioinformatics applications.

bioinformatics↗

bioRxiv2024

Function-Assigned Masked Superstrings as a Versatile and Compact Data Type for ????-Mer Sets

The design of efficient dynamic data structures for large k-mer sets belongs to central challenges of sequence bioinformatics. Recent advances in compact k-mer set representations via Spectrum-Preserving String Sets (SPSS), culminating with the masked superstring framework, have provided data structures of remarkable space efficiency for wide ranges of k-mer sets. However, the possibility to perform set operations with the resulting indexes has remained limited due to the static nature of the underlying compact representations. Here, we develop f-masked superstrings, a concept combining masked superstrings with custom demasking functions f to enable k-mer set operations based on index merging. Combined with the FMSI index for masked superstrings, we obtain a memory-efficient k-mer membership index and compressed dictionary supporting set operations via Burrows-Wheeler Transform merging. The framework provides a promising theoretical solution to a pressing bioinformatics problem and highlights the potential of f-masked superstrings to become an elementary data type for k-mer sets.

bioinformatics↗

bioRxiv2023

Genome size is positively correlated with extinction risk in herbaceous angiosperms

O_LIAngiosperms with large genomes experience nuclear-, cellular- and organism-level constraints that may limit their phenotypic plasticity and ecological niche. These constraints have been documented to vary across lineages, life-history strategies, ecogeographic patterns and environmental conditions. Therefore, we test the hypotheses that extinction risk is higher in large-genomed compared to small-genomed species, and that the effect of genome size varies across three selected covariates: life form, endemism, and climatic zones. C_LIO_LIWe collated genome size and extinction risk information for a representative sample of angiosperms comprising 3,250 species, which we analyzed alongside life form, endemism and climate variables using a phylogenetic framework. C_LIO_LIAngiosperm genome size is positively correlated with extinction risk, a pattern driven by a signal in herbaceous but not woody species, regardless of climate and endemism. The influence of genome size is stronger in endemic herbaceous species, but is relatively homogenous across different climates. Beyond its indirect link via endemism and climate, genome size also influences extinction risk directly and significantly. C_LIO_LIGenome size may serve as a proxy for difficult-to-measure parameters associated with resilience and vulnerability in herbaceous angiosperms. Therefore, it merits further exploration as a useful biological attribute for understanding intrinsic extinction risk and augmenting plant conservation efforts. C_LI

plant biology↗

bioRxiv2023

Masked superstrings as a unified framework for textual ????-mer set representations

The popularity of k-mer-based methods has recently led to the development of compact k-mer-set representations, such as simplitigs/Spectrum-Preserving String Sets (SPSS), matchtigs, and eulertigs. These aim to represent k-mer sets via strings that contain individual k-mers as substrings more efficiently than the traditional unitigs. Here, we demonstrate that all such representations can be viewed as superstrings of input k-mers, and as such can be generalized into a unified framework that we call the masked superstring of k-mers. We study the complexity of masked superstring computation and prove NP-hardness for both k-mer superstrings and their masks. We then design local and global greedy heuristics for efficient computation of masked superstrings, implement them in a program called KmerCamel, and evaluate their performance using selected genomes and pan-genomes. Overall, masked superstrings unify the theory and practice of textual k-mer set representations and provide a useful framework for optimizing representations for specific bioinformatics applications.

bioinformatics↗

bioRxiv2022

The global biogeography of angiosperm genome size is shaped by climate and range size

O_LIAngiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large-genome-constraint, mutational-hazard, polyploidy-mediated, and climate-mediated hypotheses. C_LIO_LIWe compiled the largest genome size dataset to date, encompassing >5% of known angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. C_LIO_LIWe observed that angiosperms with large range sizes generally had small genomes, supporting the large-genome-constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50{degrees}N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40-50{degrees}N northwards. C_LIO_LIOur analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically-mediated purifying selection, genetic drift, relaxed selection, and environmental filtering. C_LI

evolutionary biology↗

bioRxiv2020

Loss of malate-aspartate shuttle component SLC25A12 induces pulmonary metastasis

BackgroundAspartate biosynthesis and its delivery to the cytosol can be crucial for tumor growth in vivo. However, the impact of aspartate synthesis on metastasis has not been studied. We previously described that loss-of-aspartate glutamate carrier 1 (SLC25A12 or AGC1), an important component of the malate-aspartate shuttle, impairs cytosolic aspartate levels, NAD+/NADH ratio, mitochondrial respiration, and tumor growth. Here, we report the impact of AGC1-knockdown on metastasis. ResultsAGC1 expression is positively correlated with worse patient prognosis in many cancers. AGC1-knockdown in mouse lung carcinoma and melanoma cell lines leads to increased pulmonary metastasis following subcutaneous or intravenous injections, respectively. On the other hand, conventional in vitro metastasis assays show no indication of increased metastasis capacity of AGC1-knockdown cells. ConclusionThis study highlights that certain branches of metabolism impact tumor growth and tumor metastasis differently. In addition, it also argues that commonly known metastasis indicators, including EMT genes, cell migration, or colony formation do not always reflect the metastatic capacity in vivo.

cancer biology↗