Author

Ondřej Sladký

Charles UniversityORCID 0000-0002-7465-8222Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Assay:whole-genome sequencing· 2 Research Focus:database / resource· 1 Research Focus:dimensionality reduction· 1 Approach:optimal transport· 1

Frequent Co-Authors

Karel BřindaiD· 4 shared Pavel VeselýiD· 4 shared Ján PlachýiD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

3 top collaborators · 3 mutual co-author links

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4 shared papersBioinformatics

Karel BřindaORCID

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4 papers

Recent·Most cited

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

Ján Plachý, Ondřej Sladký, Karel Břinda, Pavel Veselý

This paper introduces a Pareto optimization method for masked superstrings to improve the compression of pan-genome k-mer sets, achieving 12-19% better compressibility.

Journal of Computational Biology · Oct 8, 2026Peer-reviewedBioinformatics

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

Ondřej Sladký, Pavel Veselý, Karel Břinda

This paper introduces FMSI, a superstring-based index for k-mer sets that improves space efficiency and query performance compared to existing methods.

Bioinformatics Advances · Nov 11, 2025Peer-reviewedBioinformatics

Towards Efficient k-Mer Set Operations via Function-Assigned Masked Superstrings

Ondřej Sladký, Pavel Veselý, Karel Břinda

This paper introduces f-masked superstrings to enable efficient set operations on k-mer sets using index merging and Burrows-Wheeler Transform techniques.

bioRxiv · Mar 6, 2024 · PreprintBioinformatics

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

Ondřej Sladký, Pavel Veselý, Karel Břinda

The paper introduces masked superstrings as a unified framework for k-mer set representations, showing they are NP-hard to compute and proposing greedy heuristics for efficient implementation.

bioRxiv · Feb 1, 2023 · PreprintBioinformatics