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Bioinformatics (Oxford, England)|September 11, 2015
RNF: a general framework to evaluate NGS read mappersKarel Břinda, Valentina Boeva, Gregory Kucherov
Genome Biology|April 7, 2021
Simplitigs as an efficient and scalable representation of de Bruijn graphsKarel Břinda, Michael Baym, Gregory Kucherov
Bioinformatics (Oxford, England)|July 26, 2015
Spaced seeds improve k-mer-based metagenomic classificationKarel Břinda, Maciej Sykulski, Gregory Kucherov
Bioinformatics Advances|January 16, 2026
FroM Superstring to Indexing: a space-efficient index for unconstrained <i>k</i>-mer sets using the Masked Burrows-Wheeler Transform (MBWT)Ondřej Sladký, Pavel Veselý, Karel Břinda
Biorxiv : the Preprint Server for Biology|January 16, 2026
Novel genes arise from genomic deletions across the bacterial tree of lifeArya Kaul, Fernando Rossine, Karel Břinda, et al.
Microbiome|January 26, 2022
High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteriaYou Che, Xiaoqing Xu, Yu Yang, et al.
Proceedings of the National Academy of Sciences of the United States of America|February 2, 2021
Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genesYou Che, Yu Yang, Xiaoqing Xu, et al.
Biorxiv : the Preprint Server for Biology|May 3, 2023
Efficient and Robust Search of Microbial Genomes via Phylogenetic CompressionKarel Břinda, Leandro Lima, Simone Pignotti, et al.
Nature Methods|April 9, 2025
Efficient and robust search of microbial genomes via phylogenetic compressionKarel Břinda, Leandro Lima, Simone Pignotti, et al.
Antimicrobial Agents and Chemotherapy|March 11, 2020
Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in <i>Escherichia coli</i>Derek R MacFadden, Bryan Coburn, Karel Břinda, et al.
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