ArticleBMC genomics2018
Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Two Faces of UV Mutagenesis: Independent and Collateral Mutagenesis in Skin Cancers.Life (Basel, Switzerland) · 2026Article
- A signature-agnostic test for differences between tumor mutation spectra reveals carcinogen and ancestry effects.Communications biology · 2026Article
- A signature-agnostic test for differences between tumor mutation spectra reveals carcinogen and ancestry effects.bioRxiv : the preprint server for biology · 2025Article
- Diffsig: Associating Risk Factors with Mutational Signatures.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2024Article
- Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia.Nature cancer · 2023Article
- Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing.Zoological research · 2023Article
- Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications.Cancers · 2023Review
- Accuracy of mutational signature software on correlated signatures.Scientific reports · 2022Article
- Mutational Signatures of Replication Timing and Epigenetic Modification Persist through the Global Divergence of Mutation Spectra across the Great Ape Phylogeny.Genome biology and evolution · 2022Article
- Different members of the APOBEC3 family of DNA mutators have opposing associations with the landscape of breast cancer.American journal of cancer research · 2021Article
- Lymphovascular invasion in breast cancer is associated with gene expression signatures of cell proliferation but not lymphangiogenesis or immune response.Breast cancer research and treatment · 2020Article
- SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events.BMC genomics · 2019Article
- Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance.PloS one · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundThe spectrum of somatic single-nucleotide variants in cancer genomes often reflects the signatures of multiple distinct mutational processes, which can provide clinically actionable insights into cancer etiology. Existing software tools for identifying and evaluating these mutational signatures do not scale to analyze large datasets containing thousands of individuals or millions of variants.
resultsWe introduce Helmsman, a program designed to perform mutation signature analysis on arbitrarily large sequencing datasets. Helmsman is up to 300 times faster than existing software. Helmsman's memory usage is independent of the number of variants, resulting in a small enough memory footprint to analyze datasets that would otherwise exceed the memory limitations of other programs.
conclusionsHelmsman is a computationally efficient tool that enables users to evaluate mutational signatures in massive sequencing datasets that are otherwise intractable with existing software. Helmsman is freely available at https://github.com/carjed/helmsman .
Indexed as
Identifiers
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.