ArticleCell2023
SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery.
Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 18 citations in OpenAlex.
- Tools and tactics for studying alternative splicing.Nature reviews. Genetics · 2026Review
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Article
- Reference-free discovery with barcoded single-cell sequencing.Nature biotechnology · 2026Article
- A Reference-Free Algorithm Discovers Regulation in the Plant Transcriptome.Plant direct · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- Pretraining and the lasso.Journal of the Royal Statistical Society. Series B, Statistical methodology · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- Scalable and unsupervised discovery from raw sequencing reads using SPLASH2.Nature biotechnology · 2025Article
- Pseudoassembly of k-mers.bioRxiv : the preprint server for biology · 2025Article
- Viroid-like colonists of human microbiomes.Cell · 2024Article
- OASIS: An interpretable, finite-sample valid alternative to Pearson'sProceedings of the National Academy of Sciences of the United States of America · 2024Article
- SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads.bioRxiv : the preprint server for biology · 2024Article
- DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.Genome biology · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.
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What OpenQuestion holds
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.