ref.bib

@article{macintyre2018copy,
  title={Copy number signatures and mutational processes in ovarian carcinoma},
  author={Macintyre, Geoff and Goranova, Teodora E and De Silva, Dilrini and Ennis, Darren and Piskorz, Anna M and Eldridge, Matthew and Sie, Daoud and Lewsley, Liz-Anne and Hanif, Aishah and Wilson, Cheryl and others},
  journal={Nature genetics},
  volume={50},
  number={9},
  pages={1262--1270},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{alexandrov2020repertoire,
  title={The repertoire of mutational signatures in human cancer},
  author={Alexandrov, Ludmil B and Kim, Jaegil and Haradhvala, Nicholas J and Huang, Mi Ni and Ng, Alvin Wei Tian and Wu, Yang and Boot, Arnoud and Covington, Kyle R and Gordenin, Dmitry A and Bergstrom, Erik N and others},
  journal={Nature},
  volume={578},
  number={7793},
  pages={94--101},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{mayakonda2018maftools,
  title={Maftools: efficient and comprehensive analysis of somatic variants in cancer},
  author={Mayakonda, Anand and Lin, De-Chen and Assenov, Yassen and Plass, Christoph and Koeffler, H Phillip},
  journal={Genome research},
  volume={28},
  number={11},
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  year={2018},
  publisher={Cold Spring Harbor Lab}
}

@article{gaujoux2010flexible,
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@article{tan2012automatic,
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@article{kim2016somatic,
  title={Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors},
  author={Kim, Jaegil and Mouw, Kent W and Polak, Paz and Braunstein, Lior Z and Kamburov, Atanas and Tiao, Grace and Kwiatkowski, David J and Rosenberg, Jonathan E and Van Allen, Eliezer M and D D'Andrea, Alan and others},
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}s

@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.org/knitr/},
}


@article {WangSX2020,
	author = {Wang, Shixiang and Li, Huimin and Song, Minfang and He, Zaoke and Wu, Tao and Wang, Xuan and Tao, Ziyu and Wu, Kai and Liu, Xue-Song},
	title = {Copy number signature analyses in prostate cancer reveal distinct etiologies and clinical outcomes},
	elocation-id = {2020.04.27.20082404},
	year = {2020},
	doi = {10.1101/2020.04.27.20082404},
	publisher = {Cold Spring Harbor Laboratory Press},
	abstract = {Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer, however, signatures of cancer genome copy number alteration (CNA) are still elusive in most cancer types, especially in prostate cancer (PC), which is particularly driven by complex genome alterations. Here, a user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization. Five copy number signatures are identified from human PC genome with this tool. The underlying driving forces for each signature have been illustrated. Sample clustering based on copy number signature exposure revealed considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. Copy number signature analyses provide distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis work was supported in part by The National Natural Science Foundation of China (31771373), and startup funding from ShanghaiTech University.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll code required to reproduce the analysis outlined in this manuscript are freely available at https://github.com/ShixiangWang/prad_signature. Analyses can be read online at https://shixiangwang.github.io/prad_signature/.},
	URL = {https://www.medrxiv.org/content/early/2020/04/29/2020.04.27.20082404},
	eprint = {https://www.medrxiv.org/content/early/2020/04/29/2020.04.27.20082404.full.pdf},
	journal = {medRxiv}
}



@article{hanahanHallmarksCancerNext2011,
  title = {Hallmarks of {{Cancer}}: {{The Next Generation}}},
  author = {Hanahan, Douglas},
  date = {2011-03-04},
  journaltitle = {Cell},
  shortjournal = {Cell},
  pages = {29},
  doi = {10.1016/j.cell.2011.02.013},
  file = {/Users/wsx/Nutstore Files/zotero-tablet/hanahan_hallmarks_of_cancer.pdf},
  langid = {english}
}