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For: Drier Y, Domany E. Do two machine-learning based prognostic signatures for breast cancer capture the same biological processes? PLoS One 2011;6:e17795. [PMID: 21423753 DOI: 10.1371/journal.pone.0017795] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 02/14/2011] [Indexed: 01/16/2023]  Open
Number Cited by Other Article(s)
1
Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024;74:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
2
Zapperi S, La Porta CAM. The Response of Triple-Negative Breast Cancer to Neoadjuvant Chemotherapy and the Epithelial–Mesenchymal Transition. Int J Mol Sci 2023;24:ijms24076422. [PMID: 37047393 PMCID: PMC10094549 DOI: 10.3390/ijms24076422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]  Open
3
La Porta CAM, Zapperi S. Artificial intelligence in breast cancer diagnostics. Cell Rep Med 2022;3:100851. [PMID: 36543102 PMCID: PMC9798018 DOI: 10.1016/j.xcrm.2022.100851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022]
4
Classification of triple negative breast cancer by epithelial mesenchymal transition and the tumor immune microenvironment. Sci Rep 2022;12:9651. [PMID: 35688895 PMCID: PMC9187759 DOI: 10.1038/s41598-022-13428-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022]  Open
5
Narykov O, Johnson NT, Korkin D. Predicting protein interaction network perturbation by alternative splicing with semi-supervised learning. Cell Rep 2021;37:110045. [PMID: 34818539 DOI: 10.1016/j.celrep.2021.110045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/21/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]  Open
6
Tran KA, Kondrashova O, Bradley A, Williams ED, Pearson JV, Waddell N. Deep learning in cancer diagnosis, prognosis and treatment selection. Genome Med 2021;13:152. [PMID: 34579788 PMCID: PMC8477474 DOI: 10.1186/s13073-021-00968-x] [Citation(s) in RCA: 301] [Impact Index Per Article: 100.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 09/12/2021] [Indexed: 12/13/2022]  Open
7
Albaradei S, Thafar M, Alsaedi A, Van Neste C, Gojobori T, Essack M, Gao X. Machine learning and deep learning methods that use omics data for metastasis prediction. Comput Struct Biotechnol J 2021;19:5008-5018. [PMID: 34589181 PMCID: PMC8450182 DOI: 10.1016/j.csbj.2021.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/16/2021] [Accepted: 09/02/2021] [Indexed: 12/14/2022]  Open
8
Manjang K, Yli-Harja O, Dehmer M, Emmert-Streib F. Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer. Front Genet 2021;12:649429. [PMID: 34367234 PMCID: PMC8340016 DOI: 10.3389/fgene.2021.649429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/01/2021] [Indexed: 11/28/2022]  Open
9
Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition. Cell Syst 2021;12:457-462.e4. [PMID: 33961788 DOI: 10.1016/j.cels.2021.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 12/29/2022]
10
Seifert S, Gundlach S, Junge O, Szymczak S. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. Bioinformatics 2021;36:4301-4308. [PMID: 32399562 PMCID: PMC7520048 DOI: 10.1093/bioinformatics/btaa483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022]  Open
11
Yoosuf N, Navarro JF, Salmén F, Ståhl PL, Daub CO. Identification and transfer of spatial transcriptomics signatures for cancer diagnosis. Breast Cancer Res 2020;22:6. [PMID: 31931856 PMCID: PMC6958738 DOI: 10.1186/s13058-019-1242-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/27/2019] [Indexed: 12/21/2022]  Open
12
DeepCC: a novel deep learning-based framework for cancer molecular subtype classification. Oncogenesis 2019;8:44. [PMID: 31420533 PMCID: PMC6697729 DOI: 10.1038/s41389-019-0157-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/13/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022]  Open
13
Wang W, Kandimalla R, Huang H, Zhu L, Li Y, Gao F, Goel A, Wang X. Molecular subtyping of colorectal cancer: Recent progress, new challenges and emerging opportunities. Semin Cancer Biol 2019;55:37-52. [PMID: 29775690 PMCID: PMC6240404 DOI: 10.1016/j.semcancer.2018.05.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
14
Giraud P, Giraud P, Gasnier A, El Ayachy R, Kreps S, Foy JP, Durdux C, Huguet F, Burgun A, Bibault JE. Radiomics and Machine Learning for Radiotherapy in Head and Neck Cancers. Front Oncol 2019;9:174. [PMID: 30972291 PMCID: PMC6445892 DOI: 10.3389/fonc.2019.00174] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/28/2019] [Indexed: 12/13/2022]  Open
15
Degenhardt F, Seifert S, Szymczak S. Evaluation of variable selection methods for random forests and omics data sets. Brief Bioinform 2019;20:492-503. [PMID: 29045534 PMCID: PMC6433899 DOI: 10.1093/bib/bbx124] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/06/2017] [Indexed: 12/28/2022]  Open
16
La Porta CAM, Zapperi S. Explaining the dynamics of tumor aggressiveness: At the crossroads between biology, artificial intelligence and complex systems. Semin Cancer Biol 2018;53:42-47. [PMID: 30017637 DOI: 10.1016/j.semcancer.2018.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/09/2018] [Indexed: 01/08/2023]
17
Dorman SN, Baranova K, Knoll JHM, Urquhart BL, Mariani G, Carcangiu ML, Rogan PK. Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning. Mol Oncol 2015;10:85-100. [PMID: 26372358 DOI: 10.1016/j.molonc.2015.07.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/31/2015] [Indexed: 12/21/2022]  Open
18
Veytsman B, Wang L, Cui T, Bruskin S, Baranova A. Distance-based classifiers as potential diagnostic and prediction tools for human diseases. BMC Genomics 2015;15 Suppl 12:S10. [PMID: 25563076 PMCID: PMC4303935 DOI: 10.1186/1471-2164-15-s12-s10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
19
Kourou K, Exarchos TP, Exarchos KP, Karamouzis MV, Fotiadis DI. Machine learning applications in cancer prognosis and prediction. Comput Struct Biotechnol J 2014;13:8-17. [PMID: 25750696 PMCID: PMC4348437 DOI: 10.1016/j.csbj.2014.11.005] [Citation(s) in RCA: 1160] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
20
Rivas-Perea P, Baker E, Hamerly G, Shaw BF. Detection of leukocoria using a soft fusion of expert classifiers under non-clinical settings. BMC Ophthalmol 2014;14:110. [PMID: 25204762 PMCID: PMC4167153 DOI: 10.1186/1471-2415-14-110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/21/2014] [Indexed: 11/10/2022]  Open
21
Endesfelder D, Burrell R, Kanu N, McGranahan N, Howell M, Parker PJ, Downward J, Swanton C, Kschischo M. Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer. Cancer Res 2014;74:4853-4863. [PMID: 24970479 PMCID: PMC4167338 DOI: 10.1158/0008-5472.can-13-2664] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
22
Domany E. Using High-Throughput Transcriptomic Data for Prognosis: A Critical Overview and Perspectives. Cancer Res 2014;74:4612-21. [DOI: 10.1158/0008-5472.can-13-3338] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
23
Tian F, Wang Y, Seiler M, Hu Z. Functional characterization of breast cancer using pathway profiles. BMC Med Genomics 2014;7:45. [PMID: 25041817 PMCID: PMC4113668 DOI: 10.1186/1755-8794-7-45] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 07/09/2014] [Indexed: 02/05/2023]  Open
24
Zhao X, Rødland EA, Sørlie T, Vollan HKM, Russnes HG, Kristensen VN, Lingjærde OC, Børresen-Dale AL. Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status. BMC Cancer 2014;14:211. [PMID: 24645668 PMCID: PMC4000128 DOI: 10.1186/1471-2407-14-211] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 02/21/2014] [Indexed: 11/06/2022]  Open
25
Pathway-based personalized analysis of cancer. Proc Natl Acad Sci U S A 2013;110:6388-93. [PMID: 23547110 DOI: 10.1073/pnas.1219651110] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
26
Shi M, Beauchamp RD, Zhang B. A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients. PLoS One 2012;7:e41292. [PMID: 22844451 PMCID: PMC3402487 DOI: 10.1371/journal.pone.0041292] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 06/19/2012] [Indexed: 01/08/2023]  Open
27
Mefford D, Mefford J. Stromal genes add prognostic information to proliferation and histoclinical markers: a basis for the next generation of breast cancer gene signatures. PLoS One 2012;7:e37646. [PMID: 22719844 PMCID: PMC3377707 DOI: 10.1371/journal.pone.0037646] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Accepted: 04/26/2012] [Indexed: 12/12/2022]  Open
28
Cun Y, Fröhlich HF. Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. BMC Bioinformatics 2012;13:69. [PMID: 22548963 PMCID: PMC3436770 DOI: 10.1186/1471-2105-13-69] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 05/01/2012] [Indexed: 01/17/2023]  Open
29
Yeung KY, Gooley TA, Zhang A, Raftery AE, Radich JP, Oehler VG. Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data. ACTA ACUST UNITED AC 2012;28:823-30. [PMID: 22296787 DOI: 10.1093/bioinformatics/bts059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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