Results 21 to 30 of about 77,245 (318)

A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures [PDF]

BMC Bioinformatics
Background Mutational processes of diverse origin leave their imprints in the genome during tumour evolution. These imprints are called mutational signatures and they have been characterised for point mutations, structural variants and copy number ...
Lena Morrill Gavarró, Dominique-Laurent Couturier, Florian Markowetz   +2 more
doaj   +3 more sources

SomaticSiMu: a mutational signature simulator [PDF]

Bioinformatics, 2021
Abstract Summary SomaticSiMu is an in silico simulator of single and double base substitutions, and single base insertions and deletions in an input genomic sequence to mimic mutational signatures.
David Chen, Gurjit S Randhawa, Maximillian P M Soltysiak, Camila P E de Souza, Lila Kari, Shiva M Singh, Kathleen A Hill   +6 more
openaire   +2 more sources

Pan-Cancer Analysis for Immune Cell Infiltration and Mutational Signatures Using Non-Negative Canonical Correlation Analysis

Applied Sciences, 2022
Mutational signatures indicate the mutational processes and substitution patterns in cancer cell genomes. However, the functional consequences of mutational signatures remain unclear, and there have been no comprehensive systematic studies to examine the
Je-Keun Rhee
doaj   +1 more source

Unveiling the interplay between mutational signatures and tumor microenvironment: a pan-cancer analysis

Frontiers in Immunology, 2023
BackgroundWhile recent studies have separately explored mutational signatures and the tumor microenvironment (TME), there is limited research on the associations of both factors in a pan-cancer context.Materials and methodsWe performed a pan-cancer ...
Li-Zhi Luo, Sheng Li, Chen Wei, Jiao Ma, Li-Mei Qian, Yan-Xing Chen, Shi-Xiang Wang, Qi Zhao   +7 more
doaj   +1 more source

Mutational Signatures in Salivary Gland Carcinomas. [PDF]

Cancer Diagn Progn, 2023
Salivary gland carcinomas belong to the head and neck carcinoma super category of malignancies. They are characterized by histopathological diversity and comprise a variety of entities and subtypes. Mucoepidermoid, adenoid cystic and salivary duct carcinomas represent the most prominent malignancies. Concerning their corresponding genetic background, a
Chrysovergis A, Papanikolaou V, Spyropoulou D, Roukas D, Asimakopoulos AD, Papanastasiou G, Mastronikoli S, Falidas E, Papouliakos S, Tsiambas E, Pantos P, Ragos V, Peschos D, Mastronikolis N, Kyrodimos E.   +14 more
europepmc   +4 more sources

Mutational Signatures: From Methods to Mechanisms [PDF]

Annual Review of Biomedical Data Science, 2021
Mutations are the driving force of evolution, yet they underlie many diseases, in particular, cancer. They are thought to arise from a combination of stochastic errors in DNA processing, naturally occurring DNA damage (e.g., the spontaneous deamination of methylated CpG sites), replication errors, and dysregulation of DNA repair mechanisms.
Yoo-Ah, Kim, Mark D M, Leiserson, Priya, Moorjani, Roded, Sharan, Damian, Wojtowicz, Teresa M, Przytycka   +5 more
openaire   +2 more sources

Regional mutational signature activities in cancer genomes [PDF]

PLOS Computational Biology, 2022
Cancer genomes harbor a catalog of somatic mutations. The type and genomic context of these mutations depend on their causes and allow their attribution to particular mutational signatures. Previous work has shown that mutational signature activities change over the course of tumor development, but investigations of genomic region variability in ...
Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan   +2 more
openaire   +3 more sources

Divergent mutational processes distinguish hypoxic and normoxic tumours. [PDF]

, 2020
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific ...
Bhandari, Vinayak, Boutros, Paul C, Bristow, Robert G, Li, Constance H, PCAWG Consortium   +4 more
core   +1 more source

Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator

BMC Bioinformatics, 2020
Background Performing a statistical test requires a null hypothesis. In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis for making biological discoveries ...
Erik N. Bergstrom, Mark Barnes, Iñigo Martincorena, Ludmil B. Alexandrov   +3 more
doaj   +1 more source

Mutational spectra are associated with bacterial niche

Nature Communications, 2023
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells.
Christopher Ruis, Aaron Weimann, Gerry Tonkin-Hill, Arun Prasad Pandurangan, Marta Matuszewska, Gemma G. R. Murray, Roger C. Lévesque, Tom L. Blundell, R. Andres Floto, Julian Parkhill   +9 more
doaj   +1 more source