Nature Search

A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

Nik-Zainal and colleagues leverage CRISPR–Cas9 and whole-genome sequencing to examine mutational patterns following knockout of 42 human DNA repair genes. They further develop and validate a clinically relevant tool to detect mismatch repair-deficient tumors.

Xueqing Zou
Gene Ching Chiek Koh
Serena Nik-Zainal
Research26 Apr 2021
Nature Cancer

Volume: 2, P: 643-657
A redefined InDel taxonomy provides insights into mutational signatures

This paper describes a framework for classifying small insertions and deletions from genomic data and applies it to a large dataset comprising seven tumor types. The analysis highlights new insertion and deletion signatures and a classifier of postreplicative repair dysfunction.

Gene Ching Chiek Koh
Arjun Scott Nanda
Serena Nik-Zainal
ResearchOpen Access10 Apr 2025
Nature Genetics

Volume: 57, P: 1132-1141
A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies

Degasperi et al. introduce a practical framework and Signal, an online tool, to analyze mutational signatures. They find evidence of tissue-specific variability in mutational signatures, which may impact tumor classification and clinical application.

Andrea Degasperi
Tauanne Dias Amarante
Serena Nik-Zainal
Research17 Feb 2020
Nature Cancer

Volume: 1, P: 249-263
Author Correction: A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies

Andrea Degasperi
Tauanne Dias Amarante
Serena Nik-Zainal
Amendments and Corrections17 Jun 2020
Nature Cancer

Volume: 1, P: 748
Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility

Formalin fixation is commonly used in tissue storage; however, this process has traditionally limited downstream whole genome sequencing usage. Here, the authors identify artefactual signatures in FFPE-derived sequencing data and demonstrate the preservation of clinical utility, thus enabling FFPE whole genome sequencing when required.

Shadi Basyuni
Laura Heskin
Serena Nik-Zainal
ResearchOpen Access04 Sept 2024
Nature Communications

Volume: 15, P: 1-12
Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner

Efforts to treat heart failure with antioxidants have failed. Here, authors reveal a robust sex-dependent endogenous defense against oxidative damage and demonstrate antioxidative treatment’s efficacy solely in subjects with inadequate redox capacity.

Zaher ElBeck
Mohammad Bakhtiar Hossain
Christer Betsholtz
ResearchOpen Access20 Mar 2024
Nature Communications

Volume: 15, P: 1-23
Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer

Defects in homologous recombination (HR) are found in some triple negative breast cancers, suggesting they may be sensitive to PARP inhibitors. In this phase II clinical trial of the PARP inhibitor rucaparib, changes in Ki67 levels did not correlate with markers of HR deficiency but HR deficiency was detected in 69% of tumours, indicating that PARP inhibitors may be a useful treatment.

Neha Chopra
Holly Tovey
Nicholas C. Turner
ResearchOpen Access29 May 2020
Nature Communications

Volume: 11, P: 1-12
A practical guide for mutational signature analysis in hematological malignancies

Mutational signature analysis provides important information about the mutational processes underpinning different stages of tumorigenesis. Here, the authors compare publicly available signature extraction tools and suggest a framework for the generation of accurate and reproducible signature data.

Francesco Maura
Andrea Degasperi
Niccolò Bolli
ResearchOpen Access05 Jul 2019
Nature Communications

Volume: 10, P: 1-12
Performance of objective functions and optimisation procedures for parameter estimation in system biology models

Andrea Degasperi
Dirk Fey
Boris N. Kholodenko
ResearchOpen Access08 Aug 2017
npj Systems Biology and Applications

Volume: 3, P: 1-9
Author Correction: A practical guide for mutational signature analysis in hematological malignancies

Francesco Maura
Andrea Degasperi
Niccolò Bolli
Amendments and CorrectionsOpen Access25 Jul 2019
Nature Communications

Volume: 10, P: 1
Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

Whole-genome sequencing in triple-negative breast cancer supports the prognostic value of the HRDetect mutational-signature-based algorithm for improving patient stratification in a real-world, population-based clinical diagnostic setting.

Johan Staaf
Dominik Glodzik
Serena Nik-Zainal
Research30 Sept 2019
Nature Medicine

Volume: 25, P: 1526-1533
A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer

Marine Inglebert
Martina Dettwiler
Sven Rottenberg
ResearchOpen Access27 Oct 2022
Scientific Reports

Volume: 12, P: 1-14
Mutational signatures: emerging concepts, caveats and clinical applications

Mutational signatures can provide insights into the origins and vulnerabilities of specific cancers, and have potential for clinical utility. This Review highlights recent developments in the field, providing insights into practical issues and challenges in mutational signature analysis.

Gene Koh
Andrea Degasperi
Serena Nik-Zainal
Reviews27 Jul 2021
Nature Reviews Cancer

Volume: 21, P: 619-637
Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma

Christine L. Jones
Andrea Degasperi
Sean J. Whittaker
ResearchOpen Access17 Feb 2021
Scientific Reports

Volume: 11, P: 1-13
DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks

Lan K. Nguyen
Andrea Degasperi
Boris N. Kholodenko
ResearchOpen Access29 Jul 2015
Scientific Reports

Volume: 5, P: 1-17

Search

Filter By:

Search

Quick links