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2026
Lecture Notes in Computer Science
2026
Lecture Notes in Computer Science
2025
Lecture Notes in Computer Science
2025
GreedyMini: generating low-density DNA minimizers
Bioinformatics
2025
Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
Genome Research
2025
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap
Nature Biotechnology
2025
ASVBM: Structural variant benchmarking with local joint analysis for multiple callsets
Computational and Structural Biotechnology Journal
2025
Taming large-scale genomic analyses via sparsified genomics
Nature Communications
2025
The open-closed mod-minimizer algorithm
Algorithms for Molecular Biology
2025
A survey of sequence-to-graph mapping algorithms in the pangenome era
Genome Biology
2025
Lecture Notes in Computer Science
2025
Fast and flexible minimizer digestion with digest
Bioinformatics
2025
Lecture Notes in Computer Science
2025
Oatk: a de novo assembly tool for complex plant organelle genomes
Genome Biology
2025
Efficient seeding for error-prone sequences with SubseqHash2
Bioinformatics
2025
De novo clustering of large long-read transcriptome datasets with isONclust3
Bioinformatics
2025
Deep learning neural network development for the classification of bacteriocin sequences produced by lactic acid bacteria
F1000Research
2024
Deep learning neural network development for the classification of bacteriocin sequences produced by lactic acid bacteria
F1000Research
2024
k-nonical space: sketching with reverse complements
Bioinformatics
2024
The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches
Journal of Computational Biology
2024
Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme
Journal of Computational Biology
2024
When less is more: sketching with minimizers in genomics
Genome Biology
2024
Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
Genome Research
2024
A near-tight lower bound on the density of forward sampling schemes
Bioinformatics
2024
ESKEMAP: exact sketch-based read mapping
Algorithms for Molecular Biology
2024
Phylogenomics
2024
A simple refined DNA minimizer operator enables 2-fold faster computation
Bioinformatics
2024
Genome assembly in the telomere-to-telomere era
Nature Reviews Genetics
2024
Haplotype-aware sequence alignment to pangenome graphs
Genome Research
2024
2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2024
DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms
BMC Bioinformatics
2024
Lecture Notes in Computer Science
2024
Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets
Journal of Computational Biology
2024
On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis
Journal of Computational Biology
2024
A survey of k-mer methods and applications in bioinformatics
Computational and Structural Biotechnology Journal
2024
Designing efficient randstrobes for sequence similarity analyses
Bioinformatics
2023
Navigating bottlenecks and trade-offs in genomic data analysis
Nature Reviews Genetics
2023
A survey of mapping algorithms in the long-reads era
Genome Biology
2023
LexicHash: sequence similarity estimation via lexicographic comparison of hashes
Bioinformatics
2023
Seeding with minimized subsequence
Bioinformatics
2023
Creating and Using Minimizer Sketches in Computational Genomics
Journal of Computational Biology
2023
How to optimally sample a sequence for rapid analysis
Bioinformatics
2023
isONform: reference-free transcriptome reconstruction from Oxford Nanopore data
Bioinformatics
2023
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic
Genome Research
2023
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Nature Biotechnology
2023
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
Bioinformatics
2023
Bidirectional String Anchors for Improved Text Indexing and Top-$K$ Similarity Search
IEEE Transactions on Knowledge and Data Engineering
2023
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries
Genome Biology
2023
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
Bioinformatics
2022
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
Computational and Structural Biotechnology Journal
2022
Strobealign: flexible seed size enables ultra-fast and accurate read alignment
Genome Biology
2022
Theory of local k-mer selection with applications to long-read alignment
Bioinformatics
2022
Multiple genome alignment in the telomere-to-telomere assembly era
Genome Biology
2022
A closed formula relevant to ‘Theory of local k-mer selection with applications to long-read alignment’ by Jim Shaw and Yun William Yu
Bioinformatics
2022
Parameterized syncmer schemes improve long-read mapping
PLOS Computational Biology
2021
Sequence-specific minimizers via polar sets
Bioinformatics
2021
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
Cell Systems
2021
Effective sequence similarity detection with strobemers
Genome Research
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