references.bib

@article{Mounir2019,
  title     = {New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx},
  author    = {Mounir, Mohamed AND Lucchetta, Marta AND Silva, Tiago C. AND Olsen, Catharina AND Bontempi, Gianluca AND Chen, Xi AND Noushmehr, Houtan AND Colaprico, Antonio AND Papaleo, Elena},
  year      = 2019,
  month     = {03},
  journal   = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  volume    = 15,
  number    = 3,
  pages     = {1--18},
  doi       = {10.1371/journal.pcbi.1006701},
  url       = {https://doi.org/10.1371/journal.pcbi.1006701}
}
@article{Love2014,
  title   = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author  = {Michael I. Love and Wolfgang Huber and Simon Anders},
  year    = 2014,
  journal = {Genome Biology},
  volume  = 15,
  pages   = 550,
  doi     = {10.1186/s13059-014-0550-8},
  issue   = 12
}
@article{ZhaoY2021,
  title   = {TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository},
  author  = {Zhao, Yingdong and Li, Ming-Chung and Konate, Mariam M. and Chen, Li and Das, Biswajit and Karlovich, Chris and Williams, P. Mickey and Evrard, Yvonne A. and Doroshow, James H. and McShane, Lisa M.},
  year    = 2021,
  month   = {JUN 22},
  journal = {Journal of Translational Medicine},
  volume  = 19,
  number  = 1,
  pages   = 269,
  doi     = {10.1186/s12967-021-02936-w}
}
@article{John2020,
  title     = {{M3C}: Monte Carlo reference-based consensus clustering},
  author    = {John, Christopher R and Watson, David and Russ, Dominic and Goldmann, Katriona and Ehrenstein, Michael and Pitzalis, Costantino and Lewis, Myles and Barnes, Michael},
  year      = 2020,
  month     = feb,
  journal   = {Scientific Reports},
  publisher = {Springer Science and Business Media LLC},
  volume    = 10,
  number    = 1,
  pages     = 1816,
  doi       = {10.1038/s41598-020-58766-1}
}
@article{Parker2009,
  title   = {Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes},
  author  = {Parker, Joel S. and Mullins, Michael and Cheang, Maggie C.U. and Leung, Samuel and Voduc, David and Vickery, Tammi and Davies, Sherri and Fauron, Christiane and He, Xiaping and Hu, Zhiyuan and Quackenbush, John F. and Stijleman, Inge J. and Palazzo, Juan and Marron, J.S. and Nobel, Andrew B. and Mardis, Elaine and Nielsen, Torsten O. and Ellis, Matthew J. and Perou, Charles M. and Bernard, Philip S.},
  year    = 2009,
  journal = {Journal of Clinical Oncology},
  volume  = 27,
  number  = 8,
  pages   = {1160--1167},
  doi     = {10.1200/JCO.2008.18.1370}
}
@article{Friedman2010,
  title   = {Regularization Paths for Generalized Linear Models via Coordinate Descent},
  author  = {Jerome Friedman and Trevor Hastie and Robert Tibshirani},
  year    = 2010,
  journal = {Journal of Statistical Software},
  volume  = 33,
  number  = 1,
  pages   = {1--22},
  doi     = {10.18637/jss.v033.i01},
  url     = {https://www.jstatsoft.org/v33/i01/}
}
@article{Breheny2015,
  title   = {Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors},
  author  = {Patrick Breheny and Jian Huang},
  year    = 2015,
  journal = {Statistics and Computing},
  volume  = 25,
  pages   = {173--187}
}
@article{Breheny2021,
  title   = {grpreg: Regularization Paths for Regression Models with Grouped Covariates},
  author  = {Patrick Breheny and Yaohui Zeng and Ryan Kurth},
  year    = 2021,
  journal = {R package version 3.4.0.},
  volume  = {\url{https://CRAN.R-project.org/package=grpreg} (23 January 2023, date last accessed)}
}
@article{Simon2019,
  title   = {{SGL: Fit a GLM (or Cox Model) with a Combination of Lasso and Group Lasso Regularization}},
  author  = {Noah Simon and Jerome Friedman and Trevor Hastie and Rob Tibshirani},
  year    = 2019,
  journal = {R package version 1.3.},
  volume  = {\url{https://CRAN.R-project.org/package=SGL} (23 January 2023, date last accessed)}
}
@article{Lee2021,
  title   = {{psbcGroup: Penalized Parametric and Semiparametric Bayesian Survival Models with Shrinkage and Grouping Priors}},
  author  = {Kyu Ha Lee and Sounak Chakraborty and Jianguo Sun},
  year    = 2021,
  journal = {R package version 1.5.},
  volume  = {\url{https://CRAN.R-project.org/package=psbcGroup} (23 January 2023, date last accessed)}
}
@article{Zucknick2015,
  title   = {{Nonidentical twins: Comparison of frequentist and Bayesian lasso for Cox models}},
  author  = {Zucknick, Manuela and Saadati, Maral and Benner, Axel},
  year    = 2015,
  journal = {Biometrical Journal},
  volume  = 57,
  number  = 6,
  pages   = {959--981},
  doi     = {10.1002/bimj.201400160}
}
@article{Yi2019,
  title   = {{BhGLM: Bayesian hierarchical GLMs and survival models, with applications to genomics and epidemiology}},
  author  = {Yi, Nengjun and Tang, Zaixiang and Zhang, Xinyan and Guo, Boyi},
  year    = 2019,
  month   = {09},
  journal = {Bioinformatics},
  volume  = 35,
  number  = 8,
  pages   = {1419--1421},
  doi     = {10.1093/bioinformatics/bty803},
  issn    = {1367-4803}
}
@article{Sill2014,
  title   = {{c060}: Extended Inference with Lasso and Elastic-Net Regularized Cox and Generalized Linear Models},
  author  = {Martin Sill and Thomas Hielscher and Natalia Becker and Manuela Zucknick},
  year    = 2014,
  journal = {Journal of Statistical Software},
  volume  = 62,
  number  = 5,
  pages   = {1--22},
  doi     = {10.18637/jss.v062.i05}
}
@article{Binder2008,
  title     = {Adapting Prediction Error Estimates for Biased Complexity Selection in High-Dimensional Bootstrap Samples},
  author    = {Harald Binder and Martin Schumacher},
  year      = 2008,
  month     = jan,
  journal   = {Statistical Applications in Genetics and Molecular Biology},
  publisher = {Walter de Gruyter {GmbH}},
  volume    = 7,
  number    = 1,
  doi       = {10.2202/1544-6115.1346},
  url       = {https://doi.org/10.2202/1544-6115.1346}
}
@article{Simon2011,
  title   = {{Using cross-validation to evaluate predictive accuracy of survival risk classifiers based on high-dimensional data}},
  author  = {Simon, Richard M. and Subramanian, Jyothi and Li, Ming-Chung and Menezes, Supriya},
  year    = 2011,
  month   = {02},
  journal = {Briefings in Bioinformatics},
  volume  = 12,
  number  = 3,
  pages   = {203--214},
  doi     = {10.1093/bib/bbr001}
}
@article{Mogensen2012,
  title   = {Evaluating Random Forests for Survival Analysis Using Prediction Error Curves},
  author  = {Ulla B. Mogensen and Hemant Ishwaran and Thomas A. Gerds},
  year    = 2012,
  journal = {Journal of Statistical Software},
  volume  = 50,
  number  = 11,
  pages   = {1--23},
  doi     = {10.18637/jss.v050.i11}
}
@article{Blanche2019,
  title   = {{The c-index is not proper for the evaluation of t-year predicted risks}},
  author  = {Blanche, Paul and Kattan, Michael W and Gerds, Thomas A},
  year    = 2019,
  month   = {02},
  journal = {Biostatistics},
  volume  = 20,
  number  = 2,
  pages   = {347--357},
  doi     = {10.1093/biostatistics/kxy006}
}
@article{Lang2019,
  author    = {Lang, Michel and Binder, Martin and Richter, Jakob and Schratz, Patrick and Pfisterer, Florian and Coors, Stefan and Au, Quay and Casalicchio, Giuseppe and Kotthoff, Lars and Bischl, Bernd},
  doi       = {10.21105/JOSS.01903},
  issn      = {2475-9066},
  journal   = {Journal of Open Source Software},
  month     = {dec},
  number    = {44},
  pages     = {1903},
  publisher = {The Open Journal},
  title     = {{mlr3: A modern object-oriented machine learning framework in R}},
  url       = {https://joss.theoj.org/papers/10.21105/joss.01903},
  volume    = {4},
  year      = {2019}
}

@article{Sonabend2021,
  author    = {Sonabend, Raphael and Kir{\'{a}}ly, Franz J. and Bender, Andreas and Bischl, Bernd and Lang, Michel},
  doi       = {10.1093/BIOINFORMATICS/BTAB039},
  issn      = {1367-4803},
  journal   = {Bioinformatics},
  month     = {sep},
  number    = {17},
  pages     = {2789--2791},
  publisher = {Oxford Academic},
  title     = {{mlr3proba: an R package for machine learning in survival analysis}},
  url       = {https://academic.oup.com/bioinformatics/article/37/17/2789/6125361},
  volume    = {37},
  year      = {2021}
}

@article{Sonabend2022,
  author  = {Sonabend, Raphael and Bender, Andreas and Vollmer, Sebastian},
  doi     = {10.1093/BIOINFORMATICS/BTAC451},
  editor  = {Lu, Zhiyong},
  isbn    = {451/6640155},
  issn    = {1367-4803},
  journal = {Bioinformatics},
  month   = {jul},
  title   = {{Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures}},
  url     = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac451/6640155},
  year    = {2022}
}

@article{mlr3pipelines2021,
  author  = {Martin Binder and Florian Pfisterer and Michel Lang and Lennart Schneider and Lars Kotthoff and Bernd Bischl},
  title   = {mlr3pipelines - Flexible Machine Learning Pipelines in R},
  journal = {Journal of Machine Learning Research},
  year    = {2021},
  volume  = {22},
  number  = {184},
  pages   = {1--7},
  url     = {http://jmlr.org/papers/v22/21-0281.html}
}

@inproceedings{Avati2020,
  author    = {Avati, Anand and Duan, Tony and Zhou, Sharon and Jung, Kenneth and Shah, Nigam H and Ng, Andrew Y},
  booktitle = {Proceedings of The 35th Uncertainty in Artificial Intelligence Conference},
  editor    = {Adams, Ryan P and Gogate, Vibhav},
  pages     = {145--155},
  publisher = {PMLR},
  series    = {Proceedings of Machine Learning Research},
  title     = {{Countdown Regression: Sharp and Calibrated Survival Predictions}},
  url       = {https://proceedings.mlr.press/v115/avati20a.html},
  volume    = {115},
  year      = {2020}
}

@article{Harrell1982,
  author    = {Harrell, Frank E. and Califf, Robert M. and Pryor, David B. and Lee, Kerry L. and Rosati, Robert A.},
  doi       = {10.1001/jama.1982.03320430047030},
  issn      = {15383598},
  journal   = {JAMA: The Journal of the American Medical Association},
  month     = {may},
  number    = {18},
  pages     = {2543--2546},
  pmid      = {7069920},
  publisher = {American Medical Association},
  title     = {{Evaluating the Yield of Medical Tests}},
  url       = {https://jamanetwork.com/journals/jama/fullarticle/372568},
  volume    = {247},
  year      = {1982}
}


@article{Uno2011,
  author    = {Uno, Hajime and Cai, Tianxi and Pencina, Michael J. and D'Agostino, Ralph B. and Wei, L. J.},
  doi       = {10.1002/SIM.4154},
  issn      = {1097-0258},
  journal   = {Statistics in Medicine},
  month     = {may},
  number    = {10},
  pages     = {1105--1117},
  pmid      = {21484848},
  publisher = {John Wiley & Sons, Ltd},
  title     = {{On the C-statistics for evaluating overall adequacy of risk prediction procedures with censored survival data}},
  url       = {https://onlinelibrary.wiley.com/doi/full/10.1002/sim.4154},
  volume    = {30},
  year      = {2011}
}

@article{Uno2007,
  author    = {Uno, Hajime and Cai, Tianxi and Tian, Lu and Wei, L. J.},
  doi       = {10.1198/016214507000000149},
  issn      = {01621459},
  journal   = {Journal of the American Statistical Association},
  month     = {jun},
  number    = {478},
  pages     = {527--537},
  publisher = {Taylor & Francis},
  title     = {{Evaluating Prediction Rules for t-Year Survivors With Censored Regression Models}},
  url       = {https://www.tandfonline.com/doi/abs/10.1198/016214507000000149},
  volume    = {102},
  year      = {2007}
}

@article{Graf1999,
  author  = {Graf, Erika and Schmoor, Claudia and Sauerbrei, Willi and Schumacher, Martin},
  doi     = {10.1002/(SICI)1097-0258(19990915/30)18:17/18},
  journal = {Statistics in Medicine},
  pages   = {2529--2545},
  title   = {{Assessment and comparison of prognostic classification schemes for survival data}},
  volume  = {18},
  year    = {1999}
}

@article{Andres2018,
  doi       = {10.1371/journal.pone.0193523},
  url       = {https://doi.org/10.1371/journal.pone.0193523},
  year      = {2018},
  month     = mar,
  publisher = {Public Library of Science ({PLoS})},
  volume    = {13},
  number    = {3},
  pages     = {e0193523},
  author    = {Axel Andres and Aldo Montano-Loza and Russell Greiner and Max Uhlich and Ping Jin and Bret Hoehn and David Bigam and James Andrew Mark Shapiro and Norman Mark Kneteman},
  editor    = {Yinglin Xia},
  title     = {A novel learning algorithm to predict individual survival after liver transplantation for primary sclerosing cholangitis},
  journal   = {{PLOS} {ONE}}
}

@article{Haider2020,
  author  = {Haider, Humza and Hoehn, Bret and Davis, Sarah and Greiner, Russell},
  journal = {Journal of Machine Learning Research},
  number  = {85},
  pages   = {1--63},
  title   = {{Effective Ways to Build and Evaluate Individual Survival Distributions}},
  url     = {http://jmlr.org/papers/v21/18-772.html},
  volume  = {21},
  year    = {2020}
}

@article{stabm,
  title     = {{stabm}: Stability Measures for Feature Selection},
  author    = {Andrea Bommert and Michel Lang},
  journal   = {Journal of Open Source Software},
  year      = {2021},
  doi       = {10.21105/joss.03010},
  publisher = {The Open Journal},
  volume    = {6},
  number    = {59},
  pages     = {3010}
}

@article{Nogueira2018,
  author  = {Nogueira, Sarah and Sechidis, Konstantinos and Brown, Gavin},
  issn    = {1533-7928},
  journal = {Journal of Machine Learning Research},
  number  = {174},
  pages   = {1--54},
  title   = {{On the Stability of Feature Selection Algorithms}},
  url     = {http://jmlr.org/papers/v18/17-514.html},
  volume  = {18},
  year    = {2018}
}

@article{Zucknick2008,
  url     = {https://doi.org/10.2202/1544-6115.1307},
  title   = {Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods},
  author  = {Manuela Zucknick and Sylvia Richardson and Euan A Stronach},
  volume  = {7},
  number  = {1},
  journal = {Statistical Applications in Genetics and Molecular Biology},
  doi     = {doi:10.2202/1544-6115.1307},
  year    = {2008}
}

@article{Heagerty2005,
  author    = {Heagerty, Patrick J. and Zheng, Yingye},
  doi       = {10.1111/J.0006-341X.2005.030814.X},
  issn      = {1541-0420},
  journal   = {Biometrics},
  month     = {mar},
  number    = {1},
  pages     = {92--105},
  pmid      = {15737082},
  publisher = {John Wiley & Sons, Ltd},
  title     = {{Survival Model Predictive Accuracy and ROC Curves}},
  url       = {https://onlinelibrary.wiley.com/doi/full/10.1111/j.0006-341X.2005.030814.x},
  volume    = {61},
  year      = {2005}
}

@article{Antolini2005,
  author    = {Antolini, Laura and Boracchi, Patrizia and Biganzoli, Elia and Antolini, L and Boracchi, P and Biganzoli, E},
  doi       = {10.1002/SIM.2427},
  issn      = {1097-0258},
  journal   = {Statistics in Medicine},
  month     = {dec},
  number    = {24},
  pages     = {3927--3944},
  pmid      = {16320281},
  publisher = {John Wiley & Sons, Ltd},
  title     = {{A time-dependent discrimination index for survival data}},
  url       = {https://onlinelibrary.wiley.com/doi/full/10.1002/sim.2427},
  volume    = {24},
  year      = {2005}
}

@article{Zhao2024,
annote = {https://ocbe-uio.github.io/survomics/survomics.html},
author = {Zhao, Zhi and Zobolas, John and Zucknick, Manuela and Aittokallio, Tero},
doi = {10.1093/bioinformatics/btae132},
issn = {1367-4811},
journal = {Bioinformatics},
month = {mar},
title = {{Tutorial on survival modeling with applications to omics data}},
url = {https://dx.doi.org/10.1093/bioinformatics/btae132},
year = {2024}
}

@misc{Sonabend2022,
  title         = {Scoring rules in survival analysis},
  author        = {Raphael Sonabend},
  year          = {2022},
  eprint        = {2212.05260},
  archiveprefix = {arXiv},
  primaryclass  = {math.ST}
}

@article{Zucknick2023,
  title   = {Penalized Semiparametric {Bayesian} Survival Models},
  author  = {Manuela Zucknick, Zhi Zhao, Maral Saadati, Axel Benner},
  year    = 2023,
  journal = {R package version 2.0.},
  volume  = {\url{https://github.com/ocbe-uio/psbcSpeedUp.git} (18 September 2023, date last accessed)}
}

@article{Zhao2023b,
  title   = {Penalized Semiparametric Bayesian Survival Models},
  author  = {Zhi Zhao and Manuela Zucknick and Maral Saadati and Axel Benner},
  year    = 2023,
  journal = {R package version 2.0.4.},
  volume  = {\url{https://CRAN.R-project.org/package=psbcSpeedUp}}
}

@article{Agamah2022,
  title     = {Computational approaches for network-based integrative multi-omics analysis},
  volume    = {9},
  pages           = {967205},
  issn      = {2296-889X},
  url       = {http://dx.doi.org/10.3389/fmolb.2022.967205},
  doi       = {10.3389/fmolb.2022.967205},
  journal   = {Frontiers in Molecular Biosciences},
  publisher = {Frontiers Media SA},
  author    = {Agamah,  Francis E. and Bayjanov,  Jumamurat R. and Niehues,  Anna and Njoku,  Kelechi F. and Skelton,  Michelle and Mazandu,  Gaston K. and Ederveen,  Thomas H. A. and Mulder,  Nicola and Chimusa,  Emile R. and ’t Hoen,  Peter A. C.},
  year      = {2022},
  month     = nov
}

@article{Chu2022,
  author  = {Chu, Jiadong and others},
  title   = {The Application of {B}ayesian Methods in Cancer Prognosis and Prediction},
  journal = {Cancer Genom. Proteom.},
  year    = {2022},
  volume  = {19},
  number  = {1},
  pages   = {1-11},
  month   = {JAN-FEB},
  doi     = {10.21873/cgp.20298}
}

@article{Hasin2017,
  author  = {Yehudit Hasin and Marcus Seldin and Aldons Lusis},
  title   = {Multi-omics approaches to disease},
  journal = {Genome Biol.},
  volume  = {18},
  pages   = {83},
  year    = {2017},
  month   = {08},
  doi     = {10.1186/s13059-017-1215-1}
}

@article{Herrmann2021,
  author  = {Herrmann, Moritz and others},
  title   = {Large-scale benchmark study of survival prediction methods using multi-omics data},
  journal = {Brief. Bioinform.},
  volume  = {22},
  number  = {3},
  pages   = {bbaa167},
  year    = {2021},
  month   = {08},
  issn    = {1477-4054},
  doi     = {10.1093/bib/bbaa167}
}

@article{Ickstadt2018,
  title = {Toward Integrative Bayesian Analysis in Molecular Biology},
  volume = {5},
  ISSN = {2326-831X},
  url = {http://dx.doi.org/10.1146/annurev-statistics-031017-100438},
  DOI = {10.1146/annurev-statistics-031017-100438},
  number = {1},
  journal = {Annual Review of Statistics and Its Application},
  publisher = {Annual Reviews},
  author = {Ickstadt,  Katja and Sch\"{a}fer,  Martin and Zucknick,  Manuela},
  year = {2018},
  month = mar,
  pages = {141--167}
}

@article{Kang2022,
  title     = {A roadmap for multi-omics data integration using deep learning},
  volume    = {23},
  issn      = {1477-4054},
  url       = {http://dx.doi.org/10.1093/bib/bbab454},
  doi       = {10.1093/bib/bbab454},
  number    = {1},
  pages     = {bbab454},
  journal   = {Briefings in Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author    = {Kang,  Mingon and Ko,  Euiseong and Mersha,  Tesfaye B},
  year      = {2022},
  month     = nov
}

@article{Karimi2022,
  title = {Prospects and challenges of cancer systems medicine: from genes to disease networks},
  volume = {23},
  ISSN = {1477-4054},
  url = {http://dx.doi.org/10.1093/bib/bbab343},
  DOI = {10.1093/bib/bbab343},
  number = {1},
  pages = {bbab343},
  journal = {Briefings in Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Karimi,  Mohammad Reza and Karimi,  Amir Hossein and Abolmaali,  Shamsozoha and Sadeghi,  Mehdi and Schmitz,  Ulf},
  year = {2022},
  month = sep 
}

@article{Lee2015,
  author  = {Lee, Kyu Ha and Chakraborty, Sounak and Sun, Jianguo},
  title   = {Survival prediction and variable selection with simultaneous shrinkage and grouping priors},
  journal = {Stat. Anal. Data Min.},
  volume  = {8},
  number  = {2},
  pages   = {114-127},
  doi     = {10.1002/sam.11266},
  year    = {2015}
}

@article{Madjar2021,
  author  = {Katrin Madjar and others},
  title   = {Combining heterogeneous subgroups with graph-structured variable selection priors for {C}ox regression},
  journal = {BMC Bioinformatics},
  volume  = {22},
  pages   = {586},
  year    = {2021},
  doi     = {10.1186/s12859-021-04483-z}
}

@article{Simon2013,
  doi       = {10.1080/10618600.2012.681250},
  url       = {https://doi.org/10.1080/10618600.2012.681250},
  year      = {2013},
  month     = apr,
  publisher = {Informa {UK} Limited},
  volume    = {22},
  number    = {2},
  pages     = {231--245},
  author    = {Noah Simon and others},
  title     = {A Sparse-Group Lasso},
  journal   = {J. Comput. Graph Stat.}
}

@article{Subramanian2020,
  title     = {Multi-omics Data Integration,  Interpretation,  and Its Application},
  volume    = {14},
  issn      = {1177-9322},
  url       = {http://dx.doi.org/10.1177/1177932219899051},
  doi       = {10.1177/1177932219899051},
  journal   = {Bioinformatics and Biology Insights},
  publisher = {SAGE Publications},
  author    = {Subramanian,  Indhupriya and Verma,  Srikant and Kumar,  Shiva and Jere,  Abhay and Anamika,  Krishanpal},
  year      = {2020},
  month     = jan,
  pages     = {117793221989905}
}

@article{Vandereyken2023,
  title     = {Methods and applications for single-cell and spatial multi-omics},
  volume    = {24},
  issn      = {1471-0064},
  url       = {http://dx.doi.org/10.1038/s41576-023-00580-2},
  doi       = {10.1038/s41576-023-00580-2},
  number    = {8},
  journal   = {Nature Reviews Genetics},
  publisher = {Springer Science and Business Media LLC},
  author    = {Vandereyken,  Katy and Sifrim,  Alejandro and Thienpont,  Bernard and Voet,  Thierry},
  year      = {2023},
  month     = mar,
  pages     = {494--515}
}

@article{Wissel2023,
  title = {Systematic comparison of multi-omics survival models reveals a widespread lack of noise resistance},
  volume = {3},
  ISSN = {2667-2375},
  url = {http://dx.doi.org/10.1016/j.crmeth.2023.100461},
  DOI = {10.1016/j.crmeth.2023.100461},
  number = {4},
  journal = {Cell Reports Methods},
  publisher = {Elsevier BV},
  author = {Wissel,  David and Rowson,  Daniel and Boeva,  Valentina},
  year = {2023},
  month = apr,
  pages = {100461}
}

@article{Yan2018,
  title = {Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data},
  ISSN = {1477-4054},
  url = {http://dx.doi.org/10.1093/bib/bbx066},
  DOI = {10.1093/bib/bbx066},
  journal = {Briefings in Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Yan,  Jingwen and Risacher,  Shannon L and Shen,  Li and Saykin,  Andrew J.},
  year = {2018},
  volume = {19},
number = {6},
pages = {1370–1381}
}