Acharya, D., & Mukhopadhyay, A. (2024). A comprehensive review of machine learning techniques for multi-omics data integration: Challenges and applications in precision oncology.
Briefings in Functional Genomics,
23(5), 549-560.
https://doi.org/10.1093/bfgp/elae013
Agnello, A., Amorisco, N.C., Keats, A., Holt, G.K., Buchanan, J., Pamela, S., Vincent, C., & McArdle, G. (2024). Emulation techniques for scenario and classical control design of tokamak plasmas.
Physics of Plasmas,
31(4), 1-12.
https://doi.org/10.1063/5.0187822
Ali, H. (2023). Artificial intelligence in multi-omics data integration: Advancing precision medicine, biomarker discovery and genomic-driven disease interventions. International Journal of Science and Research Archive, 8(1), 1012-1030. https://doi.org/10.30574/ijsra.2023.8.1.0189
Alkim, E., Dowst, H., DiCarlo, J., Dobrolecki, L.E., Hernández-Herrera, A., Hormuth, D.A., Liao, Y., McOwiti, A., Pautler, R., & Rimawi, M. (2023). Toward practical integration of omic and imaging data in co-clinical trials.
Tomography,
9(2), 810-828.
https://doi.org/10.3390/tomography9020066
Altrock, P.M., Liu, L.L., & Michor, F. (2015). The mathematics of cancer: Integrating quantitative models. Nature Reviews Cancer, 15(12), 730-745. https://doi.org/10.1038/nrc4029
Anderson, A.R., & Quaranta, V. (2008). Integrative mathematical oncology. Nature Reviews Cancer, 8(3), 227-234. https://doi.org/10.1038/nrc2329
Baião, A., Cai, Z., Poulos, R., Robinson, P., Reddel, R., Zhong, Q., Vinga, S., & Gonçalves, E. (2025). A technical review of multi-omics data integration methods: From classical statistical to deep generative approaches.
Briefings in Bioinformatics, 26(4), bbaf355.
https://doi.org/10.1093/bib/bbaf355
Barabasi, A.L., & Oltvai, Z.N. (2004). Network biology: understanding the cell's functional organization. Nature Reviews Genetics, 5(2), 101-113. https://doi.org/10.1038/nrg1272
Brunton, S.L., & Kutz, J.N. (2022).
Data-driven science and engineering: Machine learning, dynamical systems, and control.
Cambridge University Press.
https://doi.org/10.1017/9781108380690
Butner, J.D., Dogra, P., Chung, C., Koay, E.J., Welsh, J.W., Hong, D.S., Cristini, V., & Wang, Z. (2024). Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy. npj Systems Biology and Applications, 10, 88. https://doi.org/10.1038/s41540-024-00415-8
Byrne, H.M. (2010). Dissecting cancer through mathematics: from the cell to the animal model. Nature Reviews Cancer, 10(3), 221-230. https://doi.org/10.1038/nrc2808
Camacho, D.M., Collins, K.M., Powers, R.K., Costello, J.C., & Collins, J.J. (2018). Next-generation machine learning for biological networks.
Cell,
173(7), 1581-1592.
https://doi.org/10.1016/j.cell.2018.05.015
Chamseddine, I.M., & Rejniak, K.A. (2020). Hybrid modeling frameworks of tumor development and treatment.
Wiley Interdisciplinary Reviews Systems Biology and Medicine,
12(1), e1461.
https://doi.org/10.1002/wsbm.1461
Chaudhuri, A., Pash, G., Hormuth, D.A., Lorenzo, G., Kapteyn, M., Wu, C., Lima, E.A.B.F., Yankeelov, T.E., & Willcox, K. (2023). Predictive digital twin for optimizing patient-specific radiotherapy regimens under uncertainty in high-grade gliomas.
Frontiers in Artificial Intelligence,
6, 1222612.
https://doi.org/10.3389/frai.2023.1222612
Clarke, R., Tyson, J.J., Tan, M., Baumann, W.T., Jin, L., Xuan, J., & Wang, Y. (2019). Systems biology: Perspectives on multiscale modeling in research on endocrine-related cancers.
Endocrine-Related Cancer,
26(6), R345-R368.
https://doi.org/10.1530/ERC-18-0309
Croatti, A., Gabellini, M., Montagna, S., & Ricci, A. (2020). On the integration of agents and digital twins in healthcare. Journal of Medical Systems, 44(9), 161. https://doi.org/10.1007/s10916-020-01623-5
Farhadizadeh, M., Weymann, M., Blaß, M., Kraus, J., Gundler, C., Walter, S., Hempen, N., Binder, H., & Binder, N. (2025). A systematic review of challenges and proposed solutions in modeling multimodal data.
arXiv, 1-49.
https://doi.org/10.48550/arXiv.2505.06945
Fumia, H.F., & Martins, M.L. (2013). Boolean network model for cancer pathways: Predicting carcinogenesis and targeted therapy outcomes. PloS One, 8(7), e69008. https://doi.org/10.1371/journal.pone.0069008
Gatenby, R.A., & Vincent, T.L. (2003a). Application of quantitative models from population biology and evolutionary game theory to tumor therapeutic strategies. Molecular Cancer Therapeutics, 2(9), 919-927.
Gatenby, R.A., & Vincent, T.L. (2003b). An evolutionary model of carcinogenesis. Cancer Research, 63(19), 6212-6220.
Ghassemi, M., Naumann, T., Schulam, P., Beam, A.L., Chen, I.Y., & Ranganath, R. (2020). A review of challenges and opportunities in machine learning for health. AMIA Summits on Translational Science Proceedings, 2020, 191-200.
Gherman, I.M., Abdallah, Z.S., Pang, W., Gorochowski, T.E., Grierson, C.S., & Marucci, L. (2023). Bridging the gap between mechanistic biological models and machine learning surrogates. PLos Computational Biology, 19(4), e1010988. https://doi.org/10.1371/journal.pcbi.1010988
Gonçalves, I.G., & García-Aznar, J.M. (2023). Hybrid computational models of multicellular tumour growth considering glucose metabolism.
Computational and Structural Biotechnology Journal,
21, 1262-1271.
https://doi.org/10.1016/j.csbj.2023.01.044
Gong, C., Milberg, O., Wang, B., Vicini, P., Narwal, R., Roskos, L., & Popel, A.S. (2017). A computational multiscale agent-based model for simulating spatio-temporal tumour immune response to PD1 and PDL1 inhibition.
Journal of the Royal Society Interface,
14(134), 20170320.
https://doi.org/10.1098/rsif.2017.0320
Grimm, V., Revilla, E., Berger, U., Jeltsch, F., Mooij, W.M., Railsback, S.F., Thulke, H.H., Weiner, J., Wiegand, T., & DeAngelis, D.L. (2005). Pattern-oriented modeling of agent-based complex systems: Lessons from ecology.
Science,
310(5750), 987-991.
https://doi.org/10.1126/science.1116681
Hallek, M. (2025). Chronic Lymphocytic Leukemia: 2025 update on the epidemiology, pathogenesis, diagnosis, and therapy.
American Journal of Hematology,
100(3), 450–480.
https://doi.org/10.1002/ajh.27546
Hanahan, D. (2022). Hallmarks of cancer: New dimensions. Cancer Discovery, 12(1), 31-46. https://doi.org/10.1158/2159-8290.CD-21-1059
Hickey, J.W., Agmon, E., Horowitz, N., Lamore, M., Sunwoo, J., Covert, M., & Nolan, G.P. (2023). Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype transformation as a critical component of therapeutic T cell efficacy. BioRxiv, 12.06.570168. https://doi.org/10.1101/2023.12.06.570168
Hsu, C.Y., Askar, S., Alshkarchy, S.S., Nayak, P.P., Attabi, K.A., Khan, M.A., Mayan, J.A., Sharma, M., Islomov, S., & Soleimani Samarkhazan, H. (2026). AI-driven multi-omics integration in precision oncology: bridging the data deluge to clinical decisions. Clinical and Experimental Medicine, 26, 29. https://doi.org/10.1007/s10238-025-01965-9
Huang, S., Ernberg, I., & Kauffman, S. (2009). Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective.
Seminars in Cell & Developmental Biology, 20(7), 869-876.
https://doi.org/10.1016/j.semcdb.2009.07.003
Jarrett, A.M., Lima, E.A.B.F., Hormuth, D.A., McKenna, M.T., Feng, X., Ekrut, D.A., Resende, A.C.M., Brock, A., & Yankeelov, T.E. (2018). Mathematical models of tumor cell proliferation: A review of the literature.
Expert Review of Anticancer Therapy,
18(12), 1271-1286.
https://doi.org/10.1080/14737140.2018.1527689
Kansal, A.R., Torquato, S., Harsh, G.R., Chiocca, E.A., & Deisboeck, T.S. (2000). Simulated brain tumor growth dynamics using a three-dimensional cellular automaton. Journal of Theoretical Biology, 203(4), 367-382. https://doi.org/10.1006/jtbi.2000
Katsaounis, D., Harbour, N., Williams, T., Chaplain, M.A., & Sfakianakis, N. (2024). A genuinely hybrid, multiscale 3d cancer invasion and metastasis modelling framework. Bulletin of Mathematical Biology, 86(6), 64. https://doi.org/10.1007/s11538-024-01286-0
Kaul, R., Ossai, C., Forkan, A.R.M., Jayaraman, P.P., Zelcer, J., Vaughan, S., & Wickramasinghe, N. (2023). The role of AI for developing digital twins in healthcare: The case of cancer care.
WIREs Data Mining and Knowledge Discovery, 13(1), e1480.
https://doi.org/10.1002/widm.1480
Kreeger, P.K., & Lauffenburger, D.A. (2010). Cancer systems biology: a network modeling perspective. Carcinogenesis, 31(1), 2-8. https://doi.org/10.1093/carcin/bgp261
Metzcar, J., Jutzeler, C.R., Macklin, P., Köhn-Luque, A., & Brüningk, S.C. (2024). A review of mechanistic learning in mathematical oncology. Frontiers in Immunology, 15, 1363144. https://doi.org/10.3389/fimmu.2024.1363144
Metzcar, J., Wang, Y., Heiland, R., & Macklin, P. (2019). A review of cell-based computational modeling in cancer biology.
JCO Clinical Cancer Informatics,
3, 1-13.
https://doi.org/10.1200/CCI.18.00069
Mirzaei, N.M., & Shahriyari, L. (2024). Modeling cancer progression: An integrated workflow extending data-driven kinetic models to bio-mechanical PDE models.
Physical Biology,
21(2), 022001.
https://doi.org/10.1088/1478-3975/ad2777
Nardini, J.T., Baker, R.E., Simpson, M.J., & Flores, K.B. (2021). Learning differential equation models from stochastic agent-based model simulations.
Journal of the Royal Society Interface,
18(176), 20200987.
https://doi.org/10.1098/rsif.2020.0987
Norton, K.A., Gong, C., Jamalian, S., & Popel, A.S. (2019). Multiscale agent-based and hybrid modeling of the tumor immune microenvironment. Processes, 7(1), 37. https://doi.org/10.3390/pr7010037
Poleszczuk, J., Macklin, P., & Enderling, H. (2016). Agent-based modeling of cancer stem cell driven solid tumor growth. In Methods in Molecular Biology, 1516, 335-346. https://doi.org/10.1007/7651-2016-346
Rackauckas, C., Ma, Y., Martensen, J., Warner, C., Zubov, K., Supekar, R., Skinner, D., Ramadhan, A., & Edelman, A. (2020). Universal differential equations for scientific machine learning.
arXiv, 1-55.
https://doi.org/10.48550/arXiv.2001.04385
Ramis-Conde, I., Chaplain, M.A., & Anderson, A.R. (2008). Mathematical modelling of cancer cell invasion of tissue. Mathematical and Computer Modelling, 47(5-6), 533-545. https://doi.org/10.1016/j.mcm.2007.02.034
Ran, D., Li, J., Zhao, M., Du, L., Zhang, Y., & Zhu, J. (2025). Artificial intelligence integrates multi-omics data for precision stratification and drug resistance prediction in breast cancer. Frontiers in Oncology, 15, 1612474. https://doi.org/10.3389/fonc.2025.1612474
Rikard, S.M., Athey, T.L., Nelson, A.R., Christiansen, S.L., Lee, J.J., Holmes, J.W., Peirce, S.M., & Saucerman, J.J. (2019). Multiscale coupling of an agent-based model of tissue fibrosis and a logic-based model of intracellular signaling. Frontiers in Physiology, 10, 1481. https://doi.org/10.3389/fphys.2019.01481
Rubanova, Y., Chen, R.T.Q., & Duvenaud, D. (2019). Latent ordinary differential equations for irregularly-sampled time series. arXiv, 1-21. https://doi.org/10.48550/arXiv.1907.03907
Ruiz-Martinez, A., Gong, C., Wang, H., Sove, R.J., Mi, H., Kimko, H., & Popel, A.S. (2022). Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model. PLos Computational Biology, 18(7), e1010254. https://doi.org/10.1371/journal.pcbi.1010254
Sancho-Araiz, A., Mangas-Sanjuan, V., & Trocóniz, I.F. (2021). The role of mathematical models in immuno-oncology: challenges and future perspectives. Pharmaceutics, 13(7), 1016. https://doi.org/10.3390/pharmaceutics13071016
Seoni, S., Jahmunah, V., Salvi, M., Barua, P.D., Molinari, F., & Acharya, U.R. (2023). Application of uncertainty quantification to artificial intelligence in healthcare: A review of last decade (2013-2023). Computers in Biology and Medicine, 165, 107441. https://doi.org/10.1016/j.compbiomed.2023.107441
Si, H., Kumar, S., Lata, S., Ahmad, A., Ghosh, S., Stephansen, K., Nagarkar, D., Zhou, E., & Higgs, B.W. (2025). Mechanistically explainable AI model for predicting synergistic cancer therapy combinations. Current Oncology, 32(10), 548. https://doi.org/10.3390/curroncol32100548
Stéphanou, A., Fanchon, E., Innominato, P.F., & Ballesta, A. (2018). Systems biology, systems medicine, systems pharmacology: The what and the why. Acta Biotheoretica, 66, 345-365. https://doi.org/10.1007/s10441-018-9330-2
Sun, X., & Hu, B. (2018). Mathematical modeling and computational prediction of cancer drug resistance. Briefings in Bioinformatics, 19(6), 1382-1399. https://doi.org/10.1093/bib/bbx065
Tomlinson, I., & Bodmer, W. (1997). Modelling the consequences of interactions between tumour cells. British Journal of Cancer, 75(2), 157-160. https://doi.org/10.1038/bjc.1997.26
Villa, C., Maini, P.K., Browning, A.P., Jenner, A.L., Hamis, S., & Cassidy, T. (2025). Reducing phenotype-structured partial differential equations models of cancer evolution to systems of ordinary differential equations: A generalised moment dynamics approach. Journal of Mathematical Biology, 91(2), 22. https://doi.org/10.1007/s00285-025-02246-5
Wang, L.S., Yu, J., Li, S., & Liu, Z. (2025). Analysis and mean-field limit of a hybrid PDE-ABM modeling angiogenesis-regulated resistance evolution. Mathematics, 13(17), 2898. https://doi.org/10.3390/math13172898
Wolfram, S., & Gad-el-Hak, M. (2003). A new kind of science. Applied Mechanics Reviews, 56(2), B18-B19. https://doi.org/10.1115/1.1553433
Wysocka, M., Wysocki, O., Zufferey, M., Landers, D., & Freitas, A. (2023). A systematic review of biologically-informed deep learning models for cancer: Fundamental trends for encoding and interpreting oncology data. BMC Bioinformatics, 24, 198. https://doi.org/10.1186/s12859-023-05262-8
Yankeelov, T.E., An, G., Saut, O., Luebeck, E.G., Popel, A.S., Ribba, B., Vicini, P., Zhou, X., Weis, J.A., & Ye, K. (2016). Multi-scale modeling in clinical oncology: Opportunities and barriers to success. Annals of Biomedical Engineering, 44(9), 2626-2641. https://doi.org/10.1007/s10439-016-1691-6
Zahir, N., Sun, R., Gallahan, D., Gatenby, R.A., & Curtis, C. (2020). Characterizing the ecological and evolutionary dynamics of cancer. Nature Genetics, 52(8), 759-767. https://doi.org/10.1038/s41588-020-0668-4
Zangooei, M.H., & Habibi, J. (2017). Hybrid multiscale modeling and prediction of cancer cell behavior. PloS One, 12(8), e0183810. https://doi.org/10.1371/journal.pone.0183810
Zou, J., Huss, M., Abid, A., Mohammadi, P., Torkamani, A., & Telenti, A. (2019). A primer on deep learning in genomics. Nature genetics, 51(1), 12-18. https://doi.org/10.1038/s41588-018-0295-5