ArticleNature biotechnology2016
Fast search of thousands of short-read sequencing experiments.
Article in Nature biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
63 citing papers in PubMed.
- Article
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- LOCALE: Local-Alignment Embeddings for Noise-Robust DNA Search at SRA Scale.bioRxiv : the preprint server for biology · 2026Article
- LCPAN: efficient variation graph construction using locally consistent parsing.Genome biology · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.bioRxiv : the preprint server for biology · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs.Nucleic acids research · 2024Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Methods for Pangenomic Core Detection.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Compression Algorithm for Colored de Bruijn Graphs.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
- Scalable sequence database search using partitioned aggregated Bloom comb trees.Bioinformatics (Oxford, England) · 2023Article
- Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.Genome biology · 2023Article
- fimpera: drastic improvement of Approximate Membership Query data-structures with counts.Bioinformatics (Oxford, England) · 2023Article
- Navigating bottlenecks and trade-offs in genomic data analysis.Nature reviews. Genetics · 2023Review
- MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants.Bioinformatics (Oxford, England) · 2023Article
- KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.Bioinformatics (Oxford, England) · 2023Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The amount of sequence information in public repositories is growing at a rapid rate. Although these data are likely to contain clinically important information that has not yet been uncovered, our ability to effectively mine these repositories is limited. Here we introduce Sequence Bloom Trees (SBTs), a method for querying thousands of short-read sequencing experiments by sequence, 162 times faster than existing approaches. The approach searches large data archives for all experiments that involve a given sequence. We use SBTs to search 2,652 human blood, breast and brain RNA-seq experiments for all 214,293 known transcripts in under 4 days using less than 239 MB of RAM and a single CPU. Searching sequence archives at this scale and in this time frame is currently not possible using existing tools.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.