ArticleBioinformatics (Oxford, England)2023
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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142 citing papers in PubMed, 146 citations in OpenAlex.
- Efficacy, safety, and predictive biomarkers of neoadjuvant nab-paclitaxel and pembrolizumab in hormone receptor-positive breast cancer: A randomized pilot trial.Nature communications · 2025Trial
- FGFR4-associated APOBEC3 mutagenesis characterizes HER2-enriched subtype of human breast cancer.British journal of cancer · 2026Article
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- Chronic Cigarette Smoke Extract Exposure Promotes Genomic and Phenotypic Reprogramming in Lung Cancer Cells.Thoracic cancer · 2026Article
- Different primary thyroid B-cell lymphomas show overlapping mutation profiles, suggesting involvement of a common pathogenic process.Haematologica · 2026Article
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- Impact of Tumor Genomic Profile on Adjuvant Chemotherapy Efficacy in Resected Pancreatic Adenocarcinoma: Results From the PRODIGE-24/CCTG PA6 Study.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026Article
- Distinct mutational landscapes for germline and somatic cancer variants in forty tumor suppressor genes.American journal of human genetics · 2026Article
- Motif-centered analyses reveal universal and tissue-specific mutagenic mechanisms operating in the human body.NAR cancer · 2026Article
- Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.Nature biotechnology · 2026Article
- Immune pathway activation in gastric cancers with LINE-1 retrotransposon overexpression and homologous recombination deficiency.Experimental & molecular medicine · 2026Article
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- Clonotypic characterization defines B-cell drivers of clonal expansion and intratumor heterogeneity in IgM monoclonal gammopathies.HemaSphere · 2026Article
- Identifying multigenic modules under selection in the tumor genome.Bioinformatics (Oxford, England) · 2026Article
- Identification and validation of a previously missed mutational signature in colorectal cancer.Nature communications · 2026Article
- 'AnbioRxiv : the preprint server for biology · 2026Article
- Two Faces of UV Mutagenesis: Independent and Collateral Mutagenesis in Skin Cancers.Life (Basel, Switzerland) · 2026Article
82 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors at 3 institutions in 3 countries.
Funding
Abstract
motivationAnalysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. To evaluate the mutational signatures operative in a cancer genome, one first needs to quantify their activities by estimating the number of mutations imprinted by each signature.
resultsHere we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures. AVAILABILITY AND IMPLEMENTATION: SigProfilerAssignment is available under the BSD 2-clause license at https://github.com/AlexandrovLab/SigProfilerAssignment with a web implementation at https://cancer.sanger.ac.uk/signatures/assignment/.
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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.