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% =====================================================================
% TCGA-KIRC molecular characterization
% =====================================================================
@article{ricketts2018tcgakirc,
author = {Ricketts, Christopher J. and De Cubas, Aguirre A. and Fan, Huihui and Smith, Christof C. and Lang, Martin and Reznik, Ed and Bowlby, Reanne and Gibb, Ewan A. and Akbani, Rehan and Beroukhim, Rameen and Bottaro, Donald P. and Choueiri, Toni K. and Gibbs, Richard A. and Godwin, Andrew K. and Haake, Scott and Hakimi, A. Ari and Henske, Elizabeth P. and Hsieh, James J. and Ho, Thai H. and Kanchi, Rupa S. and Krishnan, Bhavani and Kwiatkowski, David J. and Lui, Wembin and Merino, Maria J. and Mills, Gordon B. and Myers, Jerome and Nickerson, Michael L. and Reuter, Victor E. and Schmidt, Laura S. and Shelley, C. Simon and Shen, Hui and Shuch, Brian and Signoretti, Sabina and Srinivasan, Ramaprasad and Tamboli, Pheroze and Thomas, George and Vincent, Benjamin G. and Vocke, Cathy D. and Wheeler, David A. and Yang, Lixing and Kim, William Y. and Robertson, A. Gordon and Spellman, Paul T. and Rathmell, W. Kimryn and Linehan, W. Marston},
title = {The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma},
journal = {Cell Reports},
volume = {23},
number = {1},
pages = {313--326.e5},
year = {2018},
doi = {10.1016/j.celrep.2018.03.075}
}
% =====================================================================
% Radiogenomics — TCGA-KIRC / clear cell RCC
% =====================================================================
@article{karlo2014ccrcc,
author = {Karlo, Christoph A. and Di Paolo, Pier Luigi and Chaim, Joshua and Hakimi, A. Ari and Ostrovnaya, Irina and Russo, Paul and Hricak, Hedvig and Motzer, Robert and Hsieh, James J. and Akin, Oguz},
title = {Radiogenomics of Clear Cell Renal Cell Carcinoma: Associations Between CT Imaging Features and Mutations},
journal = {Radiology},
volume = {270},
number = {2},
pages = {464--471},
year = {2014},
doi = {10.1148/radiol.13130663}
}
@article{shinagare2015ccrcc,
author = {Shinagare, Atul B. and Vikram, Raghunandan and Jaffe, Carl and Akin, Oguz and Kirby, Justin and Huang, Erich and Freymann, John and Sainani, Nisha I. and Sadow, Cheryl A. and Bathala, Tharakeshwara K. and Rubin, Daniel L. and Oto, Aytekin and Heller, Matthew T. and Surabhi, Venkateswar R. and Katabathina, Venkata and Silverman, Stuart G.},
title = {Radiogenomics of Clear Cell Renal Cell Carcinoma: Preliminary Findings of The Cancer Genome Atlas--Renal Cell Carcinoma (TCGA-RCC) Imaging Research Group},
journal = {Abdominal Imaging},
volume = {40},
number = {6},
pages = {1684--1692},
year = {2015},
doi = {10.1007/s00261-015-0386-z}
}
@article{udayakumar2024radiogenomic,
author = {Udayakumar, Durga and Zhang, Zhang and Xi, Yin and Dwivedi, Durgesh K. and Fulkerson, Michael and Haldeman, Shannon and Yuan, Qing and Bagrodia, Aditya and Margulis, Vitaly and Brugarolas, James and Madhuranthakam, Ananth J. and Pedrosa, Ivan},
title = {Radiogenomic Associations of Clear Cell Renal Cell Carcinoma},
journal = {Oncology},
volume = {101},
number = {6},
pages = {375--388},
year = {2023},
doi = {10.1159/000529733}
}
@article{shao2025hypoxia,
author = {Shao, Yijun and Cen, Harmony S. and Dhananjay, Anu and Pawan, S. J. and Lei, Xiaomeng and Gill, Inderbir S. and D'souza, Anishka and Duddalwar, Vinay A.},
title = {Radiogenomic Correlation of Hypoxia-Related Biomarkers in Clear Cell Renal Cell Carcinoma},
journal = {Journal of Cancer Research and Clinical Oncology},
volume = {151},
number = {6},
pages = {186},
year = {2025},
doi = {10.1007/s00432-025-06240-8}
}
@article{jamshidi2015ccrcc,
author = {Jamshidi, Neema and Jonasch, Eric and Zapala, Matthew and Korn, R. Lee and Aganovic, Lejla and Zhao, Hongjuan and Sitaram, Raja T. and Tibshirani, Robert J. and Banerjee, Sourav and Brooks, James D. and Ljungberg, B{\"o}rje and Kuo, Michael D.},
title = {The Radiogenomic Risk Score: Construction of a Prognostic Quantitative, Noninvasive Image-based Molecular Assay for Renal Cell Carcinoma},
journal = {Radiology},
volume = {277},
number = {1},
pages = {114--123},
year = {2015},
doi = {10.1148/radiol.2015150800}
}
% =====================================================================
% Information theory: information bottleneck, deep learning, foundations
% =====================================================================
@article{tishby2015deep,
author = {Tishby, Naftali and Zaslavsky, Noga},
title = {Deep Learning and the Information Bottleneck Principle},
journal = {arXiv preprint arXiv:1503.02406},
year = {2015},
url = {https://arxiv.org/abs/1503.02406}
}
@inproceedings{tishby1999ib,
author = {Tishby, Naftali and Pereira, Fernando C. and Bialek, William},
title = {The Information Bottleneck Method},
booktitle = {Proceedings of the 37th Annual Allerton Conference on Communication, Control, and Computing},
pages = {368--377},
year = {1999}
}
@book{cover2006elements,
author = {Cover, Thomas M. and Thomas, Joy A.},
title = {Elements of Information Theory},
edition = {2nd},
publisher = {Wiley-Interscience},
year = {2006}
}
@article{shannon1948mathematical,
author = {Shannon, Claude E.},
title = {A Mathematical Theory of Communication},
journal = {Bell System Technical Journal},
volume = {27},
number = {3},
pages = {379--423},
year = {1948}
}
@article{kraskov2004mi,
author = {Kraskov, Alexander and St{\"o}gbauer, Harald and Grassberger, Peter},
title = {Estimating Mutual Information},
journal = {Physical Review E},
volume = {69},
number = {6},
pages = {066138},
year = {2004},
doi = {10.1103/PhysRevE.69.066138}
}
@inproceedings{belghazi2018mine,
author = {Belghazi, Mohamed Ishmael and Baratin, Aristide and Rajeshwar, Sai and Ozair, Sherjil and Bengio, Yoshua and Courville, Aaron and Hjelm, Devon},
title = {Mutual Information Neural Estimation},
booktitle = {International Conference on Machine Learning (ICML)},
pages = {531--540},
year = {2018}
}
% =====================================================================
% Radiomics / imaging feature extraction
% =====================================================================
@article{vangriethuysen2017pyradiomics,
author = {van Griethuysen, Joost J. M. and Fedorov, Andriy and Parmar, Chintan and Hosny, Ahmed and Aucoin, Nicole and Narayan, Vivek and Beets-Tan, Regina G. H. and Fillion-Robin, Jean-Christophe and Pieper, Steve and Aerts, Hugo J. W. L.},
title = {Computational Radiomics System to Decode the Radiographic Phenotype},
journal = {Cancer Research},
volume = {77},
number = {21},
pages = {e104--e107},
year = {2017},
doi = {10.1158/0008-5472.CAN-17-0339}
}
@article{mei2022radimagenet,
author = {Mei, Xueyan and Liu, Zelong and Robson, Philip M. and Marinelli, Brett and Huang, Mingqian and Doshi, Amish and Jacobi, Adam and Cao, Chendi and Link, Katherine E. and Yang, Thomas and Wang, Ying and Greenspan, Hayit and Deyer, Timothy and Fayad, Zahi A. and Yang, Yang},
title = {{RadImageNet}: An Open Radiologic Deep Learning Research Dataset for Effective Transfer Learning},
journal = {Radiology: Artificial Intelligence},
volume = {4},
number = {5},
pages = {e210315},
year = {2022},
doi = {10.1148/ryai.210315}
}
@article{aerts2014radiomics,
author = {Aerts, Hugo J. W. L. and Velazquez, Emmanuel Rios and Leijenaar, Ralph T. H. and Parmar, Chintan and Grossmann, Patrick and Carvalho, Sara and Bussink, Johan and Monshouwer, Ren{\'e} and Haibe-Kains, Benjamin and Rietveld, Derek and Hoebers, Frank and Rietbergen, Michelle M. and Leemans, C. Ren{\'e} and Dekker, Andre and Quackenbush, John and Gillies, Robert J. and Lambin, Philippe},
title = {Decoding Tumour Phenotype by Noninvasive Imaging Using a Quantitative Radiomics Approach},
journal = {Nature Communications},
volume = {5},
pages = {4006},
year = {2014},
doi = {10.1038/ncomms5006}
}
@article{lambin2012radiomics,
author = {Lambin, Philippe and Rios-Velazquez, Emmanuel and Leijenaar, Ralph and Carvalho, Sara and van Stiphout, Ruud G. P. M. and Granton, Patrick and Zegers, Catharina M. L. and Gillies, Robert and Boellard, Ronald and Dekker, Andr{\'e} and Aerts, Hugo J. W. L.},
title = {Radiomics: Extracting More Information from Medical Images Using Advanced Feature Analysis},
journal = {European Journal of Cancer},
volume = {48},
number = {4},
pages = {441--446},
year = {2012},
doi = {10.1016/j.ejca.2011.11.036}
}
% =====================================================================
% TCGA / cancer imaging archive
% =====================================================================
@article{clark2013tcia,
author = {Clark, Kenneth and Vendt, Bruce and Smith, Kirk and Freymann, John and Kirby, Justin and Koppel, Paul and Moore, Stephen and Phillips, Stanley and Maffitt, David and Pringle, Michael and Tarbox, Lawrence and Prior, Fred},
title = {The Cancer Imaging Archive ({TCIA}): Maintaining and Operating a Public Information Repository},
journal = {Journal of Digital Imaging},
volume = {26},
number = {6},
pages = {1045--1057},
year = {2013},
doi = {10.1007/s10278-013-9622-7}
}
@article{tcgakirc_tcia,
author = {Akin, Oguz and Elnajjar, P. and Heller, M. and Jarosz, R. and Erickson, B. J. and Kirk, S. and Lee, Y. and Linehan, M. W. and Gautam, R. and Vikram, R. and Garcia, K. M. and Roche, C. and Bonaccio, E. and Filippini, J.},
title = {Radiology Data from The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma {[TCGA-KIRC]} Collection},
journal = {The Cancer Imaging Archive},
year = {2016},
doi = {10.7937/K9/TCIA.2016.V6PBVTDR}
}
% =====================================================================
% Rate--distortion and statistical estimation
% =====================================================================
@article{berger1971rate,
author = {Berger, Toby},
title = {Rate Distortion Theory: A Mathematical Basis for Data Compression},
journal = {Prentice-Hall},
year = {1971}
}
@article{chechik2005gaussianib,
author = {Chechik, Gal and Globerson, Amir and Tishby, Naftali and Weiss, Yair},
title = {Information Bottleneck for Gaussian Variables},
journal = {Journal of Machine Learning Research},
volume = {6},
pages = {165--188},
year = {2005}
}
@article{paninski2003entropy,
author = {Paninski, Liam},
title = {Estimation of Entropy and Mutual Information},
journal = {Neural Computation},
volume = {15},
number = {6},
pages = {1191--1253},
year = {2003},
doi = {10.1162/089976603321780272}
}
% =====================================================================
% Radiogenomics — foundations and reviews
% =====================================================================
@article{rutman2009radiogenomics,
author = {Rutman, Aaron M. and Kuo, Michael D.},
title = {Radiogenomics: Creating a Link Between Molecular Diagnostics and Diagnostic Imaging},
journal = {European Journal of Radiology},
volume = {70},
number = {2},
pages = {232--241},
year = {2009},
doi = {10.1016/j.ejrad.2009.01.050}
}
@article{gevaert2012nsclc,
author = {Gevaert, Olivier and Xu, Jiajing and Hoang, Chuong D. and Leung, Ann N. and Xu, Yue and Quon, Andrew and Rubin, Daniel L. and Napel, Sandy and Plevritis, Sylvia K.},
title = {Non--Small Cell Lung Cancer: Identifying Prognostic Imaging Biomarkers by Leveraging Public Gene Expression Microarray Data---Methods and Preliminary Results},
journal = {Radiology},
volume = {264},
number = {2},
pages = {387--396},
year = {2012},
doi = {10.1148/radiol.12111607}
}
@article{bodalal2019radiogenomics,
author = {Bodalal, Zuhir and Trebeschi, Stefano and Nguyen-Kim, Thi Dan Linh and Schats, Winnie and Beets-Tan, Regina},
title = {Radiogenomics: Bridging Imaging and Genomics},
journal = {Abdominal Radiology},
volume = {44},
number = {6},
pages = {1960--1984},
year = {2019},
doi = {10.1007/s00261-019-02028-w}
}
% =====================================================================
% Radiomics and AI in imaging — reviews
% =====================================================================
@article{gillies2016radiomics,
author = {Gillies, Robert J. and Kinahan, Paul E. and Hricak, Hedvig},
title = {Radiomics: Images Are More than Pictures, They Are Data},
journal = {Radiology},
volume = {278},
number = {2},
pages = {563--577},
year = {2016},
doi = {10.1148/radiol.2015151169}
}
@article{lambin2017radiomics,
author = {Lambin, Philippe and Leijenaar, Ralph T. H. and Deist, Timo M. and Peerlings, Jurgen and de Jong, Evelyn E. C. and van Timmeren, Janita and Sanduleanu, Sebastian and Larue, Ruben T. H. M. and Even, Aniek J. G. and Jochems, Arthur and van Wijk, Yvonka and Woodruff, Henry and van Soest, Johan and Lustberg, Tim and Roelofs, Erik and van Elmpt, Wouter and Dekker, Andre and Mottaghy, Felix M. and Wildberger, Joachim E. and Walsh, Sean},
title = {Radiomics: The Bridge Between Medical Imaging and Personalized Medicine},
journal = {Nature Reviews Clinical Oncology},
volume = {14},
number = {12},
pages = {749--762},
year = {2017},
doi = {10.1038/nrclinonc.2017.141}
}
@article{mayerhoefer2020radiomics,
author = {Mayerhoefer, Marius E. and Materka, Andrzej and Langs, Georg and H{\"a}ggstr{\"o}m, Ida and Szczypi{\'n}ski, Piotr and Gibbs, Peter and Cook, Gary},
title = {Introduction to Radiomics},
journal = {Journal of Nuclear Medicine},
volume = {61},
number = {4},
pages = {488--495},
year = {2020},
doi = {10.2967/jnumed.118.222893}
}
@article{hosny2018ai,
author = {Hosny, Ahmed and Parmar, Chintan and Quackenbush, John and Schwartz, Lawrence H. and Aerts, Hugo J. W. L.},
title = {Artificial Intelligence in Radiology},
journal = {Nature Reviews Cancer},
volume = {18},
number = {8},
pages = {500--510},
year = {2018},
doi = {10.1038/s41568-018-0016-5}
}
@article{bi2019ai,
author = {Bi, Wenya Linda and Hosny, Ahmed and Schabath, Matthew B. and Giger, Maryellen L. and Birkbak, Nicolai J. and Mehrtash, Alireza and Allison, Tavis and Arnaout, Omar and Abbosh, Christopher and Dunn, Ian F. and Mak, Raymond H. and Tamimi, Rulla M. and Tempany, Clare M. and Swanton, Charles and Hoffmann, Udo and Schwartz, Lawrence H. and Gillies, Robert J. and Huang, Raymond Y. and Aerts, Hugo J. W. L.},
title = {Artificial Intelligence in Cancer Imaging: Clinical Challenges and Applications},
journal = {CA: A Cancer Journal for Clinicians},
volume = {69},
number = {2},
pages = {127--157},
year = {2019},
doi = {10.3322/caac.21552}
}
% =====================================================================
% Information bottleneck — deep learning theory
% =====================================================================
@article{saxe2019ib,
author = {Saxe, Andrew M. and Bansal, Yamini and Dapello, Joel and Advani, Madhu and Kolchinsky, Artemy and Tracey, Brendan D. and Cox, David D.},
title = {On the Information Bottleneck Theory of Deep Learning},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
volume = {2019},
number = {12},
pages = {124020},
year = {2019},
doi = {10.1088/1742-5468/ab3985}
}
@article{achille2018infodropout,
author = {Achille, Alessandro and Soatto, Stefano},
title = {Information Dropout: Learning Optimal Representations Through Noisy Computation},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
volume = {40},
number = {12},
pages = {2897--2905},
year = {2018},
doi = {10.1109/TPAMI.2017.2784440}
}
@article{kolchinsky2019nonlinearib,
author = {Kolchinsky, Artemy and Tracey, Brendan D. and Wolpert, David H.},
title = {Nonlinear Information Bottleneck},
journal = {Entropy},
volume = {21},
number = {12},
pages = {1181},
year = {2019},
doi = {10.3390/e21121181}
}
% =====================================================================
% Estimation methods, high-dimensional CCA, and software
% =====================================================================
@article{ledoit2004shrinkage,
author = {Ledoit, Olivier and Wolf, Michael},
title = {A Well-Conditioned Estimator for Large-Dimensional Covariance Matrices},
journal = {Journal of Multivariate Analysis},
volume = {88},
number = {2},
pages = {365--411},
year = {2004},
doi = {10.1016/S0047-259X(03)00096-4}
}
@article{higham2002nearcorr,
author = {Higham, Nicholas J.},
title = {Computing the Nearest Correlation Matrix---A Problem from Finance},
journal = {IMA Journal of Numerical Analysis},
volume = {22},
number = {3},
pages = {329--343},
year = {2002},
doi = {10.1093/imanum/22.3.329}
}
@article{wachter1980limiting,
author = {Wachter, Kenneth W.},
title = {The Limiting Empirical Measure of Multiple Discriminant Ratios},
journal = {The Annals of Statistics},
volume = {8},
number = {5},
pages = {937--957},
year = {1980},
doi = {10.1214/aos/1176345134}
}
@article{yang2015independence,
author = {Yang, Yanrong and Pan, Guangming},
title = {Independence Test for High Dimensional Data Based on Regularized Canonical Correlation Coefficients},
journal = {The Annals of Statistics},
volume = {43},
number = {2},
pages = {467--500},
year = {2015},
doi = {10.1214/14-AOS1284}
}
@article{wasserthal2023totalsegmentator,
author = {Wasserthal, Jakob and Breit, Hanns-Christian and Meyer, Manfred T. and Pradella, Maurice and Hinck, Daniel and Sauter, Alexander W. and Heye, Tobias and Boll, Daniel T. and Cyriac, Joshy and Yang, Shan and Bach, Michael and Segeroth, Martin},
title = {{TotalSegmentator}: Robust Segmentation of 104 Anatomic Structures in CT Images},
journal = {Radiology: Artificial Intelligence},
volume = {5},
number = {5},
pages = {e230024},
year = {2023},
doi = {10.1148/ryai.230024}
}
@article{wolf2018scanpy,
author = {Wolf, F. Alexander and Angerer, Philipp and Theis, Fabian J.},
title = {{SCANPY}: Large-Scale Single-Cell Gene Expression Data Analysis},
journal = {Genome Biology},
volume = {19},
number = {1},
pages = {15},
year = {2018},
doi = {10.1186/s13059-017-1382-0}
}
@article{bakr2018nsclcradiogenomics,
title={A radiogenomic dataset of non-small cell lung cancer},
volume={5},
ISSN={2052-4463},
url={http://dx.doi.org/10.1038/sdata.2018.202},
DOI={10.1038/sdata.2018.202},
number={1},
journal={Scientific Data},
publisher={Springer Science and Business Media LLC},
author={Bakr, Shaimaa and Gevaert, Olivier and Echegaray, Sebastian and Ayers, Kelsey and Zhou, Mu and Shafiq, Majid and Zheng, Hong and Benson, Jalen Anthony and Zhang, Weiruo and Leung, Ann N. C. and Kadoch, Michael and Hoang, Chuong D. and Shrager, Joseph and Quon, Andrew and Rubin, Daniel L. and Plevritis, Sylvia K. and Napel, Sandy},
year={2018},
month=Oct
}
@article{henschel2020fastsurfer, title={FastSurfer - A fast and accurate deep learning based neuroimaging pipeline}, volume={219}, ISSN={1053-8119}, url={http://dx.doi.org/10.1016/j.neuroimage.2020.117012}, DOI={10.1016/j.neuroimage.2020.117012}, journal={NeuroImage}, publisher={Elsevier BV}, author={Henschel, Leonie and Conjeti, Sailesh and Estrada, Santiago and Diers, Kersten and Fischl, Bruce and Reuter, Martin}, year={2020}, month=Oct, pages={117012} }
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