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2024Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.
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2023Comparing methods for constructing and representing human pangenome graphs., Genome Biol 2023 Nov; 24(1): 274.
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2023aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets., iScience 2023 Nov; 26(11): 108057.
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2023decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods., Microbiome 2023 Nov; 11(1): 243.
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2023Efficient mapping of accurate long reads in minimizer space with mapquik., Genome Res 2023 Jun; (): .
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2022SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads., Nat Methods 2022 Dec; (): .
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2022Mapping-friendly sequence reductions: Going beyond homopolymer compression., iScience 2022 Nov; 25(11): 105305.
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2022The K-mer File Format: a standardized and compact disk representation of sets of k-mers., Bioinformatics 2022 Jul; (): .
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2021Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer., Cell Syst 2021 Sep; (): .
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2021Strainberry: automated strain separation in low-complexity metagenomes using long reads., Nat Commun 2021 07; 12(1): 4485.
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