Results 31 to 40 of about 79,548 (256)

SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events

BMC Genomics, 2019
Background Cancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying mutational processes. A plethora of
Erik N. Bergstrom, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen, Ludmil B. Alexandrov   +6 more
doaj   +1 more source

Validating the concept of mutational signatures with isogenic cell models. [PDF]

, 2018
The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy.
A Besaratinia, A Fischer, A Hirao, AR Venkitaraman, C Pilati, D Branzei, D Glodzik, D Jones, DJ Mozzherin, DT Long, F Zhang, FA Ran, FJ Rouhani, G Poulogiannis, GM Li, GM Li, H Davies, H Gad, I Garcia-Higuera, J Bartek, J Drost, J Genschel, JD Sander, JE Carette, JR Pon, JS Gehring, K Wei, K Ye, L Zannini, LA Garraway, LB Alexandrov, LB Alexandrov, LB Alexandrov, M Jasin, M Secrier, M Spies, MC Kottemann, MJ Martin, MR Stratton, N Krishnamurthy, ND Dees, P Hsieh, P Stephens, R Sabarinathan, S Behjati, S Morganella, S Nik-Zainal, S Nik-Zainal, S Nik-Zainal, S Ray, SE Liberti, T Helleday, The Cancer Genome Atlas Research, N., The Cancer Genome Atlas, N., The, E.P.C., TJ Cradick, W Niedzwiedz, X Xiao, Y Shiraishi, Z Li, Z Liu   +60 more
core   +2 more sources

SUITOR: Selecting the number of mutational signatures through cross-validation.

PLoS Computational Biology, 2022
For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses.
Donghyuk Lee, Difei Wang, Xiaohong R Yang, Jianxin Shi, Maria Teresa Landi, Bin Zhu   +5 more
doaj   +1 more source

Quantifying the pro- and antimutagenic roles of DNA damage and repair [PDF]

, 2020
Genome integrity is essential to the survival of any living organism. The genome is constantly challenged by a multitude of endogenous and exogenous mutagenic factors such as environmental exposures or replication errors.
Volkova, Nadezda
core   +1 more source

Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS-CoV-2 [PDF]

J Med Virol. 2024 Mar;96(3):e29557. PMID: 38506190, 2021
A genome, composed of a precisely ordered sequence of four nucleotides (ATCG), encompasses a multitude of specific genome features like AAA motif. Mutations occurring within a genome disrupt the sequential order and composition of these features, thereby influencing the evolutionary trajectories and yielding variants.
arxiv   +1 more source

Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization

BMC Bioinformatics, 2023
Background The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF).
Marta Pelizzola, Ragnhild Laursen, Asger Hobolth   +2 more
doaj   +1 more source

Mutational signatures among young-onset testicular cancers

BMC Medical Genomics, 2021
Background Incidence of testicular cancer is highest among young adults and has been increasing dramatically for men born since 1945. This study aimed to elucidate the factors driving this trend by investigating differences in mutational signatures by ...
Nicole E. Mealey, Dylan E. O’Sullivan, Cheryl E. Peters, Daniel Y. C. Heng, Darren R. Brenner   +4 more
doaj   +1 more source

Two subtypes of cutaneous melanoma with distinct mutational signatures and clinico-genomic characteristics

Frontiers in Genetics, 2022
Background: To decipher mutational signatures and their associations with biological implications in cutaneous melanomas (CMs), including those with a low ultraviolet (UV) signature.Materials and Methods: We applied non-negative matrix factorization (NMF)
Yoon-Seob Kim, Yoon-Seob Kim, Yoon-Seob Kim, Minho Lee, Yeun-Jun Chung, Yeun-Jun Chung, Yeun-Jun Chung, Yeun-Jun Chung   +7 more
doaj   +1 more source

Impact of cancer mutational signatures on transcription factor motifs in the human genome

BMC Medical Genomics, 2019
Background Somatic mutations in cancer genomes occur through a variety of molecular mechanisms, which contribute to different mutational patterns. To summarize these, mutational signatures have been defined using a large number of cancer genomes, and ...
Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann   +4 more
doaj   +1 more source

A flexible model-based framework for robust estimation of mutational signatures [PDF]

arXiv, 2022
Somatic mutations in cancer can be viewed as a mixture distribution of several mutational signatures, which can be inferred using non-negative matrix factorization (NMF). Mutational signatures have previously been parametrized using either simple mono-nucleotide interaction models or general tri-nucleotide interaction models. We describe a flexible and
arxiv