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data.bib
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@article{Cancer2012,
title={The cancer genome atlas pan-cancer analysis project},
author={Weinstein, John N and Collisson, Eric A and Mills, Gordon B and Shaw, Kenna R Mills and Ozenberger, Brad A and Ellrott, Kyle and Shmulevich, Ilya and Sander, Chris and Stuart, Joshua M and Cancer Genome Atlas Research Network and others},
journal={Nature genetics},
volume={45},
number={10},
pages={1113},
year={2013},
publisher={Nature Publishing Group}
}
@article{Curtis2012,
author = {Curtis, Christina and Shah, Sohrab P. and Chin, Suet Feung and Turashvili, Gulisa and Rueda, Oscar M. and Dunning, Mark J. and Speed, Doug and Lynch, Andy G. and Samarajiwa, Shamith and Yuan, Yinyin and Gr{\"{a}}f, Stefan and Ha, Gavin and Haffari, Gholamreza and Bashashati, Ali and Russell, Roslin and McKinney, Steven and Aparicio, Samuel and Brenton, James D. and Ellis, Ian and Huntsman, David and Pinder, Sarah and Murphy, Leigh and Bardwell, Helen and Ding, Zhihao and Jones, Linda and Liu, Bin and Papatheodorou, Irene and Sammut, Stephen J. and Wishart, Gordon and Chia, Steven and Gelmon, Karen and Speers, Caroline and Watson, Peter and Blamey, Roger and Green, Andrew and MacMillan, Douglas and Rakha, Emad and Gillett, Cheryl and Grigoriadis, Anita and {De Rinaldis}, Emanuele and Tutt, Andy and Parisien, Michelle and Troup, Sandra and Chan, Derek and Fielding, Claire and Maia, Ana Teresa and McGuire, Sarah and Osborne, Michelle and Sayalero, Sara M. and Spiteri, Inmaculada and Hadfield, James and Bell, Lynda and Chow, Katie and Gale, Nadia and Kovalik, Maria and Ng, Ying and Prentice, Leah and Tavar{\'{e}}, Simon and Markowetz, Florian and Langer{\o}d, Anita and Provenzano, Elena and Purushotham, Arnie and B{\o}rresen-Dale, Anne Lise and Caldas, Carlos},
doi = {10.1038/nature10983},
eprint = {NIHMS150003},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {00280836},
journal = {Nature},
number = {7403},
pages = {346--352},
pmid = {22522925},
title = {{The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups}},
volume = {486},
year = {2012}
}
@article{Bekhouche2011,
author = {Bekhouche, Ismahane and Finetti, Pascal and Adela{\"{i}}de, Jos{\'{e}} and Ferrari, Anthony and Tarpin, Carole and Charafe-Jauffret, Emmanuelle and Charpin, Colette and Houvenaeghel, Gilles and Jacquemier, Jocelyne and Bidaut, Ghislain and Birnbaum, Daniel and Viens, Patrice and Chaffanet, Max and Bertucci, Fran{\c{c}}ois},
doi = {10.1371/journal.pone.0016950},
issn = {19326203},
journal = {PLoS ONE},
number = {2},
pmid = {21339811},
title = {{High-resolution comparative genomic hybridization of Inflammatory breast cancer and identification of candidate genes}},
volume = {6},
year = {2011}
}
@article{Wang2005,
author = {Wang, Yixin and Klijn, Jan G.M. and Zhang, Yi and Sieuwerts, Anieta M. and Look, Maxime P. and Yang, Fei and Talantov, Dmitri and Timmermans, Mieke and {Meijer-Van Gelder}, Marion E. and Yu, Jack and Jatkoe, Tim and Berns, Els M.J.J. and Atkins, David and Foekens, John A.},
doi = {10.1016/S0140-6736(05)17947-1},
isbn = {1474-547X (Electronic)$\backslash$r0140-6736 (Linking)},
issn = {01406736},
journal = {Lancet},
number = {9460},
pages = {671--679},
pmid = {15721472},
title = {{Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer}},
volume = {365},
year = {2005}
}
@article{Kanehisa2000,
author = {Kanehisa, M and Goto, S},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {1},
pages = {27--30},
pmid = {10592173},
title = {{KEGG: kyoto encyclopedia of genes and genomes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10592173 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC102409},
volume = {28},
year = {2000}
}
@article{JoshiTope2004,
author = {Joshi-Tope, G. and Gillespie, M and Vastrik, I and D'Eustachio, P and Schmidt, E and de Bono, B and Jassal, B and Gopinath, G R and Wu, G R and Matthews, L and Lewis, S and Birney, E and Stein, L},
doi = {10.1093/nar/gki072},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {Database issue},
pages = {D428--D432},
pmid = {15608231},
title = {{Reactome: a knowledgebase of biological pathways}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15608231 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC540026 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gki072},
volume = {33},
year = {2004}
}
@article{Szklarczyk2017,
author = {Szklarczyk, Damian and Morris, John H and Cook, Helen and Kuhn, Michael and Wyder, Stefan and Simonovic, Milan and Santos, Alberto and Doncheva, Nadezhda T and Roth, Alexander and Bork, Peer and Jensen, Lars J. and von Mering, Christian},
doi = {10.1093/nar/gkw937},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {D1},
pages = {D362--D368},
pmid = {27924014},
title = {{The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27924014 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5210637 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw937},
volume = {45},
year = {2017}
}
@article{KeshavaPrasad2009,
author = {{Keshava Prasad}, T. S. and Goel, R. and Kandasamy, K. and Keerthikumar, S. and Kumar, S. and Mathivanan, S. and Telikicherla, D. and Raju, R. and Shafreen, B. and Venugopal, A. and Balakrishnan, L. and Marimuthu, A. and Banerjee, S. and Somanathan, D. S. and Sebastian, A. and Rani, S. and Ray, S. and {Harrys Kishore}, C. J. and Kanth, S. and Ahmed, M. and Kashyap, M. K. and Mohmood, R. and Ramachandra, Y. L. and Krishna, V. and Rahiman, B. A. and Mohan, S. and Ranganathan, P. and Ramabadran, S. and Chaerkady, R. and Pandey, A.},
doi = {10.1093/nar/gkn892},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {Database},
pages = {D767--D772},
pmid = {18988627},
title = {{Human Protein Reference Database--2009 update}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18988627 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2686490 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkn892},
volume = {37},
year = {2009}
}
@article{Brunk2018,
author = {Brunk, Elizabeth and Sahoo, Swagatika and Zielinski, Daniel C and Altunkaya, Ali and Dr{\"{a}}ger, Andreas and Mih, Nathan and Gatto, Francesco and Nilsson, Avlant and {Preciat Gonzalez}, German Andres and Aurich, Maike Kathrin and Prli{\'{c}}, Andreas and Sastry, Anand and Danielsdottir, Anna D and Heinken, Almut and Noronha, Alberto and Rose, Peter W and Burley, Stephen K and Fleming, Ronan M T and Nielsen, Jens and Thiele, Ines and Palsson, Bernhard O},
doi = {10.1038/nbt.4072},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {3},
pages = {272--281},
pmid = {29457794},
title = {{Recon3D enables a three-dimensional view of gene variation in human metabolism}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/29457794 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5840010 http://www.nature.com/doifinder/10.1038/nbt.4072},
volume = {36},
year = {2018}
}
@Book{ggplot2,
author = {Hadley Wickham},
title = {ggplot2: Elegant Graphics for Data Analysis},
publisher = {Springer-Verlag New York},
year = {2016},
isbn = {978-3-319-24277-4},
url = {http://ggplot2.org},
}
@Manual{plotly,
title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
year = {2017},
note = {R package version 4.7.1},
url = {https://CRAN.R-project.org/package=plotly},
}
@Manual{pheatmap,
title = {pheatmap: Pretty Heatmaps},
author = {Raivo Kolde},
year = {2018},
note = {R package version 1.0.10},
url = {https://CRAN.R-project.org/package=pheatmap},
}
@Manual{gridExtra,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2017},
note = {R package version 2.3},
url = {https://CRAN.R-project.org/package=gridExtra},
}
@Book{lattice,
title = {Lattice: Multivariate Data Visualization with R},
author = {Deepayan Sarkar},
publisher = {Springer},
address = {New York},
year = {2008},
note = {ISBN 978-0-387-75968-5},
url = {http://lmdvr.r-forge.r-project.org},
}