Publications

* Shared first-author contribution. † Joint senior authorship.

Preprints

  1. V. Hendrychová and K. Břinda.

    Why phylogenies compress so well: combinatorial guarantees under the infinite sites model.

    bioRxiv 2026.03.18.712055, 2026.

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  2. J. Plachý, O. Sladký, K. Břinda†, and P. Veselý†.

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

    bioRxiv 2026.03.18.712440, 2026.

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  3. A. Kaul, F. W. Rossine, K. Břinda, and M. Baym.

    Novel genes arise from genomic deletions across the bacterial tree of life.

    bioRxiv 2026.01.05.697752, 2026.

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  4. F. Brunetti and K. Břinda.

    Optimized k-mer search across millions of bacterial genomes on laptops.

    bioRxiv 2025.11.23.690050, 2025.

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  5. M. Budia-Silva, A. C. Carroll, H. Ghosh, A. McGeer, T. Giani, G. M. Rossolini, K. Břinda, W. P. Hanage, H. Grundmann, D. R. MacFadden, and S. Reuter.

    Neighbour typing using long read sequencing provides rapid prediction of sequence type and antimicrobial susceptibility of Klebsiella pneumoniae.

    bioRxiv 2025.09.03.673989, 2025.

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Journal Articles

  1. O. Sladký, P. Veselý, and K. Břinda.

    From superstring to indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT).

    Bioinformatics Advances 6(1), vbaf290, 2026.

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  2. A. C. Carroll, L. Mortimer, H. Ghosh, S. Reuter, H. Grundmann, K. Břinda, W. P. Hanage, A. Li, A. Paterson, A. Purssell, A. M. Rooney, N. R. Yee, B. Coburn, S. Able-Thomas, M. Antonio, A. McGeer, and D. R. MacFadden.

    Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection.

    Antimicrobial Agents and Chemotherapy, e01071-25, 2026.

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  3. K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov, R. Chikhi, G. Kucherov, Z. Iqbal, and M. Baym.

    Efficient and robust search of microbial genomes via phylogenetic compression.

    Nature Methods 22, 692–697, 2025.

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  4. A. C. Carroll, L. Mortimer, H. Ghosh, S. Reuter, H. Grundmann, K. Břinda, W. P. Hanage, A. Li, A. Paterson, A. Purssell, A. Rooney, N. R. Yee, B. Coburn, S. Able-Thomas, M. Antoni, A. McGeer, and D. R. MacFadden.

    Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbour typing.

    Microbiology Spectrum 13(1), e01366-24, 2025.

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  5. N. B. Wikle*, T. N.-A. Tran*, B. Gentilesco, S. Leighow, J. Albert, E. R. Strong, K. Břinda, H. Inam, F. Yang, S. Hossain, P. Chan, W. P. Hanage, M. Messick, J. Pritchard, E. Hanks, and M. F. Boni.

    SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics.

    Science Advances 8(4), 2022.

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  6. Y. Che, X. Xu, Y. Yang, K. Břinda, W. P. Hanage, C. Yang, and T. Zhang.

    High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria.

    Microbiome 10(1), 2022.

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  7. K. Břinda, M. Baym†, and G. Kucherov†.

    Simplitigs as an efficient and scalable representation of de Bruijn graphs.

    Genome Biology 22(96), 2021.

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  8. Y. Che, Y. Yang, X. Xu, K. Břinda, M. F. Polz, W. P. Hanage, and T. Zhang.

    Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.

    Proceedings of the National Academy of Sciences 118(6), 2021.

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  9. T. N.-A. Tran, N. Wikle, E. Albert, H. Inam, E. R. Strong, K. Břinda, S. M. Leighow, F. Yang, S. Hossain, J. R. Pritchard, P. Chan, W. P. Hanage, E. M. Hanks, and M. F. Boni.

    Optimal SARS-CoV-2 vaccine allocation using real-time attack-rate estimates in Rhode Island and Massachusetts.

    BMC Medicine 19(162), 2021.

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  10. K. Břinda, A. Callendrello, K. C. Ma, D. R. MacFadden, T. Charalampous, R. S. Lee, L. Cowley, C. B. Wadsworth, Y. H. Grad, G. Kucherov, J. O’Grady, M. Baym, and W. P. Hanage.

    Rapid inference of antibiotic resistance and susceptibility by Genomic Neighbour Typing.

    Nature Microbiology 5, 455–464, 2020.

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  11. D. R. MacFadden, B. Coburn, K. Břinda, A. Corbeil, N. Daneman, D. Fisman, R. Lee, M. Lipsitch, A. McGeer, R. Melano, S. Mubareka, and W. P. Hanage.

    Using genetic distance from archived samples for the prediction of antibiotic resistance in Escherichia coli.

    Antimicrobial Agents and Chemotherapy 64(5), 2020.

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  12. B. Grüning*, R. Dale*, A. Sjödin, B. A. Chapman, J. Rowe, C. H. Tomkins-Tinch, R. Valieris, J. Köster, and The Bioconda Team (incl. K. Břinda).

    Bioconda: sustainable and comprehensive software distribution for the life sciences.

    Nature Methods 15(7), 475–476, 2018.

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  13. K. Břinda, V. Boeva, and G. Kucherov.

    RNF: a general framework to evaluate NGS read mappers.

    Bioinformatics 32(1), 136–139, 2016.

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  14. K. Břinda*, M. Sykulski*, and G. Kucherov.

    Spaced seeds improve k-mer-based metagenomic classification.

    Bioinformatics 31(22), 3584–3592, 2015.

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  15. K. Břinda, E. Pelantová, and O. Turek.

    Balances of m-bonacci words.

    Fundamenta Informaticae 132(1), 33–61, 2014.

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  16. L. Balková, K. Břinda, and O. Turek.

    Abelian complexity of infinite words associated with quadratic Parry numbers.

    Theoretical Computer Science 412(45), 6252–6260, 2011.

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Peer-Reviewed Conference Articles

  1. O. Sladký, P. Veselý, and K. Břinda.

    Towards efficient k-mer set operations via function-assigned masked superstrings.

    In Proceedings of the Prague Stringology Conference 2025 (PSC 2025), pp. 26–40, 2025. Available from bioRxiv 2024.03.06.583483.

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  2. O. Sladký, P. Veselý, and K. Břinda.

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

    RECOMB-Seq 2023, 2023. Available from bioRxiv 2023.02.01.526717.

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  3. P. Červenka, K. Břinda, M. Hanousková, P. Hofman, and R. Seifert.

    Blind friendly maps: tactile maps for the blind as a part of the public map portal (mapy.cz).

    In Proceedings of 15th International Conference on Computers Helping People with Special Needs (ICCHP 2016), Lecture Notes in Computer Science 9759, pp. 131–138, 2016.

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  4. K. Břinda.

    Languages of lossless seeds.

    In Proceedings of 14th International Conference on Automata and Formal Languages (AFL 2014), Electronic Proceedings in Theoretical Computer Science 151, pp. 139–150, 2014.

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Technical Reports

  1. K. Břinda, V. Boeva, and G. Kucherov.

    Ococo: an online variant and consensus caller.

    arXiv 1712.01146 [q-bio.GN], 2018.

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  2. K. Břinda, V. Boeva, and G. Kucherov.

    Dynamic read mapping and online consensus calling for better variant detection.

    arXiv 1605.09070 [q-bio.GN], 2016.

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Patents

  1. W. P. Hanage, K. Břinda, and M. Baym.

    Rapid identification of strains from sequence data.

    United States Patent Application 17/251,343, US 2021/0246502 A1, 2021.

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Theses

  1. K. Břinda.

    Novel computational techniques for mapping and classification of Next-Generation Sequencing data.

    PhD thesis, University of Paris-Est, 2016.

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  2. K. Břinda.

    Lossless seeds for approximate string matching.

    MSc thesis, Czech Technical University, 2013.

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  3. K. Břinda.

    Abelian complexity of infinite words.

    BSc thesis, Czech Technical University, 2011.

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