@Article{Gaujoux2010,
author="Gaujoux, Renaud
and Seoighe, Cathal",
title="A flexible R package for nonnegative matrix factorization",
journal="BMC Bioinformatics",
year="2010",
volume="11",
number="1",
pages="367",
abstract="Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. Developments in NMF theory and applications have resulted in a variety of algorithms and methods. However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community.",
issn="1471-2105",
doi="10.1186/1471-2105-11-367",
url="http://dx.doi.org/10.1186/1471-2105-11-367"
}

@Article{Blokzijl2016,
author="Blokzijl, Francis
and de Ligt, Joep
and Jager, Myrthe
and Sasselli, Valentina
and Roerink, Sophie
and Sasaki, Nobuo
and Huch, Meritxell
and Boymans, Sander
and Kuijk, Ewart
and Prins, Pjotr
and Nijman, Isaac J.
and Martincorena, Inigo
and Mokry, Michal
and Wiegerinck, Caroline L.
and Middendorp, Sabine
and Sato, Toshiro
and Schwank, Gerald
and Nieuwenhuis, Edward E. S.
and Verstegen, Monique M. A.
and van der Laan, Luc J. W.
and de Jonge, Jeroen
and IJzermans, Jan N. M.
and Vries, Robert G.
and van de Wetering, Marc
and Stratton, Michael R.
and Clevers, Hans
and Cuppen, Edwin
and van Boxtel, Ruben",
title="Tissue-specific mutation accumulation in human adult stem cells during life",
journal="Nature",
year="2016",
month="Oct",
day="13",
publisher="Macmillan Publishers Limited, part of Springer Nature. All rights reserved.",
volume="538",
number="7624",
pages="260--264",
note="Letter",
issn="0028-0836",
url="http://dx.doi.org/10.1038/nature19768"
}

@Article{Alexandrov2013,
author="Alexandrov, Ludmil B.
and Nik-Zainal, Serena
and Wedge, David C.
and Aparicio, Samuel A. J. R.
and Behjati, Sam
and Biankin, Andrew V.
and Bignell, Graham R.
and Bolli, Niccolo
and Borg, Ake
and Borresen-Dale, Anne-Lise
and Boyault, Sandrine
and Burkhardt, Birgit
and Butler, Adam P.
and Caldas, Carlos
and Davies, Helen R.
and Desmedt, Christine
and Eils, Roland
and Eyfjord, Jorunn Erla
and Foekens, John A.
and Greaves, Mel
and Hosoda, Fumie
and Hutter, Barbara
and Ilicic, Tomislav
and Imbeaud, Sandrine
and Imielinsk, Marcin
and Jager, Natalie
and Jones, David T. W.
and Jones, David
and Knappskog, Stian
and Kool, Marcel
and Lakhani, Sunil R.
and Lopez-Otin, Carlos
and Martin, Sancha
and Munshi, Nikhil C.
and Nakamura, Hiromi
and Northcott, Paul A.
and Pajic, Marina
and Papaemmanuil, Elli
and Paradiso, Angelo
and Pearson, John V.
and Puente, Xose S.
and Raine, Keiran
and Ramakrishna, Manasa
and Richardson, Andrea L.
and Richter, Julia
and Rosenstiel, Philip
and Schlesner, Matthias
and Schumacher, Ton N.
and Span, Paul N.
and Teague, Jon W.
and Totoki, Yasushi
and Tutt, Andrew N. J.
and Valdes-Mas, Rafael
and van Buuren, Marit M.
and van /'t Veer, Laura
and Vincent-Salomon, Anne
and Waddell, Nicola
and Yates, Lucy R.
and Initiative, Australian Pancreatic Cancer Genome
and Consortium, ICGC Breast Cancer
and Consortium, ICGC MMML-Seq
and PedBrain, I. C. G. C.
and Zucman-Rossi, Jessica
and Andrew Futreal, P.
and McDermott, Ultan
and Lichter, Peter
and Meyerson, Matthew
and Grimmond, Sean M.
and Siebert, Reiner
and Campo, Elias
and Shibata, Tatsuhiro
and Pfister, Stefan M.
and Campbell, Peter J.
and Stratton, Michael R.",
title="Signatures of mutational processes in human cancer",
journal="Nature",
year="2013",
month="Aug",
day="22",
publisher="Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.",
volume="500",
number="7463",
pages="415--421",
note="Article",
issn="0028-0836",
url="http://dx.doi.org/10.1038/nature12477"
}

@Article{Durinck2005,
author="Durinck, Steffen
and Moreau, Yves
and Kasprzyk, Arek
and Davis, Sean
and De Moor, Bart
and Brazma, Alvis
and Huber, Wolfgang",
title="BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis",
journal="Bioinformatics",
year="2005",
month="Aug",
day="15",
volume="21",
number="16",
pages="3439--3440",
abstract="Summary:biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.Availability:http://www.bioconductor.org. LGPLContact:steffen.durinck@esat.kuleuven.ac.be",
issn="1367-4803",
doi="10.1093/bioinformatics/bti525",
url="http://dx.doi.org/10.1093/bioinformatics/bti525"
}

@article{Osorio2018,
author = {Osorio, Fernando G and Huber, Axel Rosendahl and Oka, Rurika and Varela, Ignacio and Camargo, Fernando D and Boxtel, Ruben Van and Osorio, Fernando G and Huber, Axel Rosendahl and Oka, Rurika and Verheul, Mark and Patel, Sachin H and Hasaart, Karlijn},
doi = {10.1016/j.celrep.2018.11.014},
file = {:Users/freekmanders/Library/Application Support/Mendeley Desktop/Downloaded/Osorio et al. - 2018 - Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Report Somatic Mutations Reve.pdf:pdf},
issn = {2211-1247},
journal = {CellReports},
number = {9},
pages = {2308--2316.e4},
publisher = {ElsevierCompany.},
title = {{Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Report Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis}},
url = {https://doi.org/10.1016/j.celrep.2018.11.014},
volume = {25},
year = {2018}
}

@article{Alexandrov2020,
abstract = {Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses3–15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated—but distinct—DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.},
author = {Alexandrov, Ludmil B and Kim, Jaegil and Haradhvala, Nicholas J and Huang, Mi Ni and {Tian Ng}, Alvin Wei and Wu, Yang and Boot, Arnoud and Covington, Kyle R and Gordenin, Dmitry A and Bergstrom, Erik N and Islam, S M Ashiqul and Lopez-Bigas, Nuria and Klimczak, Leszek J and McPherson, John R and Morganella, Sandro and Sabarinathan, Radhakrishnan and Wheeler, David A and Mustonen, Ville and Alexandrov, Ludmil B and Bergstrom, Erik N and Boot, Arnoud and Boutros, Paul and Chan, Kin and Covington, Kyle R and Fujimoto, Akihiro and Getz, Gad and Gordenin, Dmitry A and Haradhvala, Nicholas J and Huang, Mi Ni and Islam, S M Ashiqul and Kazanov, Marat and Kim, Jaegil and Klimczak, Leszek J and Lopez-Bigas, Nuria and Lawrence, Michael and Martincorena, I{\~{n}}igo and McPherson, John R and Morganella, Sandro and Mustonen, Ville and Nakagawa, Hidewaki and {Tian Ng}, Alvin Wei and Polak, Paz and Prokopec, Stephenie and Roberts, Steven A and Rozen, Steven G and Sabarinathan, Radhakrishnan and Saini, Natalie and Shibata, Tatsuhiro and Shiraishi, Yuichi and Stratton, Michael R and Teh, Bin Tean and V{\'{a}}zquez-Garc{\'{i}}a, Ignacio and Wheeler, David A and Wu, Yang and Yousif, Fouad and Yu, Willie and Getz, Gad and Rozen, Steven G and Stratton, Michael R and Group, PCAWG Mutational Signatures Working and Consortium, PCAWG},
doi = {10.1038/s41586-020-1943-3},
issn = {1476-4687},
journal = {Nature},
number = {7793},
pages = {94--101},
title = {{The repertoire of mutational signatures in human cancer}},
url = {https://doi.org/10.1038/s41586-020-1943-3},
volume = {578},
year = {2020}
}

@article{Huang2018,
abstract = {MOTIVATION: Cancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as carcinogenic exposures or cancer related aberrations of DNA maintenance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. The decomposition of a cancer genome's mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology. However, the results from different decomposition methods are not always consistent. Hence, one needs to be able to not only decompose a patient's mutational profile into signatures but also establish the accuracy of such decomposition. RESULTS: We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes. We identified both very stable and highly unstable signatures, as well as signatures that previously have not been associated with breast cancer. We also provided additional support for the novel signatures. Our results emphasize the importance of assessing the confidence and stability of inferred signature contributions. AVAILABILITY AND IMPLEMENTATION: All tools developed in this paper have been implemented in an R package, called SignatureEstimation, which is available from https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi$\backslash${\#}signatureestimation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
author = {Huang, Xiaoqing and Wojtowicz, Damian and Przytycka, Teresa M},
doi = {10.1093/bioinformatics/btx604},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
language = {eng},
month = {jan},
number = {2},
pages = {330--337},
publisher = {Oxford University Press},
title = {{Detecting presence of mutational signatures in cancer with confidence}},
url = {https://pubmed.ncbi.nlm.nih.gov/29028923 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860213/},
volume = {34},
year = {2018}
}

@Book{Wickham2016,
author = {Hadley Wickham},
title = {ggplot2: Elegant Graphics for Data Analysis},
publisher = {Springer-Verlag New York},
year = {2016},
isbn = {978-3-319-24277-4},
url = {https://ggplot2.tidyverse.org},
 }
 
@article{Aitken2020,
abstract = {Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion1,2. Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterize this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. The phasing of lesions enables accurate measurement of strand-biased repair processes, quantification of oncogenic selection and fine mapping of sister-chromatid-exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes.},
author = {Aitken, Sarah J and Anderson, Craig J and Connor, Frances and Pich, Oriol and Sundaram, Vasavi and Feig, Christine and Rayner, Tim F and Lukk, Margus and Aitken, Stuart and Luft, Juliet and Kentepozidou, Elissavet and Arnedo-Pac, Claudia and Beentjes, Sjoerd V and Davies, Susan E and Drews, Ruben M and Ewing, Ailith and Kaiser, Vera B and Khamseh, Ava and L{\'{o}}pez-Arribillaga, Erika and Redmond, Aisling M and Santoyo-Lopez, Javier and Sent{\'{i}}s, In{\'{e}}s and Talmane, Lana and Yates, Andrew D and Aitken, Sarah J and Aitken, Stuart and Anderson, Craig J and Arnedo-Pac, Claudia and Connor, Frances and Drews, Ruben M and Ewing, Ailith and Feig, Christine and Flicek, Paul and Kaiser, Vera B and Kentepozidou, Elissavet and L{\'{o}}pez-Arribillaga, Erika and L{\'{o}}pez-Bigas, N{\'{u}}ria and Luft, Juliet and Lukk, Margus and Odom, Duncan T and Pich, Oriol and Rayner, Tim F and Semple, Colin A and Sent{\'{i}}s, In{\'{e}}s and Sundaram, Vasavi and Talmane, Lana and Taylor, Martin S and Semple, Colin A and L{\'{o}}pez-Bigas, N{\'{u}}ria and Flicek, Paul and Odom, Duncan T and Taylor, Martin S and Consortium, Liver Cancer Evolution},
doi = {10.1038/s41586-020-2435-1},
issn = {1476-4687},
journal = {Nature},
number = {7815},
pages = {265--270},
title = {{Pervasive lesion segregation shapes cancer genome evolution}},
url = {https://doi.org/10.1038/s41586-020-2435-1},
volume = {583},
year = {2020}
}


@article{Degasperi2020,
abstract = {Mutational signatures are patterns of mutations that arise during tumorigenesis. We present an enhanced, practical framework for mutational signature analyses. Applying these methods on 3,107 whole genome sequenced (WGS) primary cancers of 21 organs reveals known signatures and nine previously undescribed rearrangement signatures. We highlight inter-organ variability of signatures and present a way of visualizing that diversity, reinforcing our findings in an independent analysis of 3,096 WGS metastatic cancers. Signatures with a high level of genomic instability are dependent on TP53 dysregulation. We illustrate how uncertainty in mutational signature identification and assignment to samples affects tumor classification, reinforcing that using multiple orthogonal mutational signature data is not only beneficial, it is essential for accurate tumor stratification. Finally, we present a reference web-based tool for cancer and experimentally-generated mutational signatures, called Signal (https://signal.mutationalsignatures.com), that also supports performing mutational signature analyses.},
author = {Degasperi, Andrea and Amarante, Tauanne Dias and Czarnecki, Jan and Shooter, Scott and Zou, Xueqing and Glodzik, Dominik and Morganella, Sandro and Nanda, Arjun S and Badja, Cherif and Koh, Gene and Momen, Sophie E and Georgakopoulos-Soares, Ilias and Dias, Jo{\~{a}}o M L and Young, Jamie and Memari, Yasin and Davies, Helen and Nik-Zainal, Serena},
doi = {10.1038/s43018-020-0027-5},
edition = {2020/02/17},
issn = {2662-1347},
journal = {Nature cancer},
keywords = {Mutational signatures,homologous recombination deficiency,somatic variants,whole genome sequencing},
language = {eng},
month = {feb},
number = {2},
pages = {249--263},
title = {{A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies}},
url = {https://pubmed.ncbi.nlm.nih.gov/32118208 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048622/},
volume = {1},
year = {2020}
}

@article{Kucab2019,
annote = {doi: 10.1016/j.cell.2019.03.001},
author = {Kucab, Jill E and Zou, Xueqing and Morganella, Sandro and Joel, Madeleine and Nanda, A Scott and Nagy, Eszter and Gomez, Celine and Degasperi, Andrea and Harris, Rebecca and Jackson, Stephen P and Arlt, Volker M and Phillips, David H and Nik-Zainal, Serena},
doi = {10.1016/j.cell.2019.03.001},
issn = {0092-8674},
journal = {Cell},
month = {may},
number = {4},
pages = {821--836.e16},
publisher = {Elsevier},
title = {{A Compendium of Mutational Signatures of Environmental Agents}},
url = {https://doi.org/10.1016/j.cell.2019.03.001},
volume = {177},
year = {2019}
}