references.bib

@article{hutter2018TCGA, 
 title={The Cancer Genome Atlas: creating lasting value beyond its data}, 
 author={Hutter, Carolyn and Zenklusen, Jean Claude}, 
 journal={Cell}, 
 volume={173}, 
 number={2}, 
 pages={283--285}, 
 year={2018}, 
 publisher={Elsevier} 
}

@article{ramos2020curatedTCGAData,
  title={Multiomic integration of public oncology databases in bioconductor},
  author={Ramos, Marcel and Geistlinger, Ludwig and Oh, Sehyun and Schiffer, Lucas and Azhar, Rimsha and Kodali, Hanish and de Bruijn, Ino and Gao, Jianjiong and Carey, Vincent J and Morgan, Martin and others},
  journal={JCO Clinical Cancer Informatics},
  volume={1},
  pages={958--971},
  year={2020},
  publisher={American Society of Clinical Oncology}
}

@article{ramos2017MultiAssayExperiment,
  title={Software for the integration of multiomics experiments in bioconductor},
  author={Ramos, Marcel and Schiffer, Lucas and Re, Angela and Azhar, Rimsha and Basunia, Azfar and Rodriguez, Carmen and Chan, Tiffany and Chapman, Phil and Davis, Sean R and Gomez-Cabrero, David and others},
  journal={Cancer research},
  volume={77},
  number={21},
  pages={e39--e42},
  year={2017},
  publisher={AACR}
}

@article{gliozzo2020pnet,
  title={Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction},
  author={Gliozzo, Jessica and Perlasca, Paolo and Mesiti, Marco and Casiraghi, Elena and Vallacchi, Viviana and Vergani, Elisabetta and Frasca, Marco and Grossi, Giuliano and Petrini, Alessandro and Re, Matteo and others},
  journal={Scientific Reports},
  volume={10},
  number={1},
  pages={3612},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{zhu2002label.prop,
  title={Learning from labeled and unlabeled data with label propagation},
  author={Zhu, Xiaojin and Ghahramani, Zoubin},
  year={2002},
  publisher={Citeseer}
}

@article{bengio2006labelprop,
  title={11 label propagation and quadratic criterion},
  author={Bengio, Yoshua and Delalleau, Olivier and Le Roux, Nicolas},
  journal={located at: https://www. researchgate. net/profile/Y\_Bengio/publication/238675708\_Label\_Propagation\_and\_Quadratic\_Criterion/links/0f3175320aae4ada34000000/Label-Propagation-and-Quadratic-Criterion. pdf},
  year={2006}
}

@article{oliver2000GBA,
  title={Guilt-by-association goes global},
  author={Oliver, Stephen},
  journal={Nature},
  volume={403},
  number={6770},
  pages={601--602},
  year={2000},
  publisher={Nature Publishing Group UK London}
}

@article{liu2018TCGA-CDR,
  title={An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics},
  author={Liu, Jianfang and Lichtenberg, Tara and Hoadley, Katherine A and Poisson, Laila M and Lazar, Alexander J and Cherniack, Andrew D and Kovatich, Albert J and Benz, Christopher C and Levine, Douglas A and Lee, Adrian V and others},
  journal={Cell},
  volume={173},
  number={2},
  pages={400--416},
  year={2018},
  publisher={Elsevier}
}

@article{re2012fast,
  title={A fast ranking algorithm for predicting gene functions in biomolecular networks},
  author={Re, Matteo and Mesiti, Marco and Valentini, Giorgio},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  volume={9},
  number={6},
  pages={1812--1818},
  year={2012},
  publisher={IEEE}
}

@article{valentini2016ranks,
  title={RANKS: a flexible tool for node label ranking and classification in biological networks},
  author={Valentini, Giorgio and Armano, Giuliano and Frasca, Marco and Lin, Jianyi and Mesiti, Marco and Re, Matteo},
  journal={Bioinformatics},
  volume={32},
  number={18},
  pages={2872--2874},
  year={2016},
  publisher={Oxford University Press}
}

@article{gliozzo2022heterogeneous,
  title={Heterogeneous data integration methods for patient similarity networks},
  author={Gliozzo, Jessica and Mesiti, Marco and Notaro, Marco and Petrini, Alessandro and Patak, Alex and Puertas-Gallardo, Antonio and Paccanaro, Alberto and Valentini, Giorgio and Casiraghi, Elena},
  journal={Briefings in Bioinformatics},
  volume={23},
  number={4},
  pages={bbac207},
  year={2022},
  publisher={Oxford University Press}
}

@article{golub1999molecular,
  title={Molecular classification of cancer: class discovery and class prediction by gene expression monitoring},
  author={Golub, Todd R and Slonim, Donna K and Tamayo, Pablo and Huard, Christine and Gaasenbeek, Michelle and Mesirov, Jill P and Coller, Hilary and Loh, Mignon L and Downing, James R and Caligiuri, Mark A and others},
  journal={science},
  volume={286},
  number={5439},
  pages={531--537},
  year={1999},
  publisher={American Association for the Advancement of Science}
}

@misc{falcon2007introduction,
  title={An introduction to bioconductor’s expressionset class},
  author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
  year={2007}
}

@misc{wiki:DNA_microarray,
   author = "Wikipedia",
   title = "{DNA microarray} --- {W}ikipedia{,} The Free Encyclopedia",
   year = "2023",
   howpublished = {\url{http://en.wikipedia.org/w/index.php?title=DNA\%20microarray&oldid=1136268850}},
   note = "[Online; accessed 27-March-2023]"
 }
 
 @misc{wiki:Leukemia,
   author = "Wikipedia",
   title = "{Leukemia} --- {W}ikipedia{,} The Free Encyclopedia",
   year = "2023",
   howpublished = {\url{http://en.wikipedia.org/w/index.php?title=Leukemia&oldid=1144681167}},
   note = "[Online; accessed 27-March-2023]"
 }
 
 @article{wang2014similarity,
  title={Similarity network fusion for aggregating data types on a genomic scale},
  author={Wang, Bo and Mezlini, Aziz M and Demir, Feyyaz and Fiume, Marc and Tu, Zhuowen and Brudno, Michael and Haibe-Kains, Benjamin and Goldenberg, Anna},
  journal={Nature methods},
  volume={11},
  number={3},
  pages={333--337},
  year={2014},
  publisher={Nature Publishing Group US New York}
}

@article{saria2015subtyping,
  title={Subtyping: What it is and its role in precision medicine},
  author={Saria, Suchi and Goldenberg, Anna},
  journal={IEEE Intelligent Systems},
  volume={30},
  number={4},
  pages={70--75},
  year={2015},
  publisher={IEEE}
}

@misc{BiologicalPathways,
	author = {{National Human Genome Research Institute (NIH)}},
	title = {{B}iological {P}athways {F}act {S}heet --- genome.gov},
	howpublished = {\url{https://www.genome.gov/about-genomics/fact-sheets/Biological-Pathways-Fact-Sheet#:~:text=A%20biological%20pathway%20is%20a,spur%20a%20cell%20to%20move.}},
	year = {2020},
	note = {[Accessed 29-Mar-2023]},
}

@inbook{PAM,
  publisher = {John Wiley & Sons, Ltd},
  isbn = {9780470316801},
  title = {Partitioning Around Medoids (Program PAM)},
  booktitle = {Finding Groups in Data},
  chapter = {2},
  pages = {68-125},
  doi = {https://doi.org/10.1002/9780470316801.ch2},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470316801.ch2},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470316801.ch2},
  year = {1990},
  keywords = {medoids, representative objects, central memory, partitioning around       medoids, graphical representation},
  abstract = {Summary The prelims comprise: Short Description of the Method How to Use   the Program PAM Examples More on the Algorithm and the Program Related Methods and     References}
}

@article{von2007SP,
  title={A tutorial on spectral clustering},
  author={Von Luxburg, Ulrike},
  journal={Statistics and computing},
  volume={17},
  pages={395--416},
  year={2007},
  publisher={Springer}
}

@article{parker2009PAM50,
  title={Supervised risk predictor of breast cancer based on intrinsic subtypes},
  author={Parker, Joel S and Mullins, Michael and Cheang, Maggie CU and Leung, Samuel and Voduc, David and Vickery, Tammi and Davies, Sherri and Fauron, Christiane and He, Xiaping and Hu, Zhiyuan and others},
  journal={Journal of clinical oncology},
  volume={27},
  number={8},
  pages={1160},
  year={2009},
  publisher={American Society of Clinical Oncology}
}

@article{momeni2020survey,
  title={A survey on single and multi omics data mining methods in cancer data classification},
  author={Momeni, Zahra and Hassanzadeh, Esmail and Abadeh, Mohammad Saniee and Bellazzi, Riccardo},
  journal={Journal of Biomedical Informatics},
  volume={107},
  pages={103466},
  year={2020},
  publisher={Elsevier}
}

@article{venkat2018curse,
  title={The curse of dimensionality: Inside out},
  author={Venkat, Naveen},
  journal={Pilani (IN): Birla Institute of Technology and Science, Pilani, Department of Computer Science and Information Systems},
  volume={10},
  year={2018}
}

@article{schettini2022perspective,
  title={A perspective on the development and lack of interchangeability of the breast cancer intrinsic subtypes},
  author={Schettini, Francesco and Bras{\'o}-Maristany, Fara and Kuderer, Nicole M and Prat, Aleix},
  journal={NPJ Breast Cancer},
  volume={8},
  number={1},
  pages={85},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

@book{wagner2007comparing,
  title={Comparing clusterings: an overview},
  author={Wagner, Silke and Wagner, Dorothea},
  year={2007},
  publisher={Universit{\"a}t Karlsruhe, Fakult{\"a}t f{\"u}r Informatik Karlsruhe}
}

@article{abeshouse2015molecularPRAD,
  title={The molecular taxonomy of primary prostate cancer},
  author={Abeshouse, Adam and Ahn, Jaeil and Akbani, Rehan and Ally, Adrian and Amin, Samirkumar and Andry, Christopher D and Annala, Matti and Aprikian, Armen and Armenia, Joshua and Arora, Arshi and others},
  journal={Cell},
  volume={163},
  number={4},
  pages={1011--1025},
  year={2015},
  publisher={Elsevier}
}

@article{shen2009integrative,
  title={Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis},
  author={Shen, Ronglai and Olshen, Adam B and Ladanyi, Marc},
  journal={Bioinformatics},
  volume={25},
  number={22},
  pages={2906--2912},
  year={2009},
  publisher={Oxford University Press}
}

@article{rappoport2019nemo,
  title={NEMO: cancer subtyping by integration of partial multi-omic data},
  author={Rappoport, Nimrod and Shamir, Ron},
  journal={Bioinformatics},
  volume={35},
  number={18},
  pages={3348--3356},
  year={2019},
  publisher={Oxford University Press}
}