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For: Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F. A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol 2012;8:e1002337. [PMID: 22241976 PMCID: PMC3252265 DOI: 10.1371/journal.pcbi.1002337] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/17/2011] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Weller J, Potthoff A, Zeyen T, Schaub C, Duffy C, Schneider M, Herrlinger U. Current status of precision oncology in adult glioblastoma. Mol Oncol 2024;18:2927-2950. [PMID: 38899374 PMCID: PMC11619805 DOI: 10.1002/1878-0261.13678] [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: 11/16/2023] [Revised: 04/05/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]  Open
2
Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023;15:1958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023]  Open
3
Rajabi A, Kayedi M, Rahimi S, Dashti F, Mirazimi SMA, Homayoonfal M, Mahdian SMA, Hamblin MR, Tamtaji OR, Afrasiabi A, Jafari A, Mirzaei H. Non-coding RNAs and glioma: Focus on cancer stem cells. Mol Ther Oncolytics 2022;27:100-123. [PMID: 36321132 PMCID: PMC9593299 DOI: 10.1016/j.omto.2022.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
4
Lin B, Ziebro J, Smithberger E, Skinner KR, Zhao E, Cloughesy TF, Binder ZA, O’Rourke DM, Nathanson DA, Furnari FB, Miller CR. EGFR, the Lazarus target for precision oncology in glioblastoma. Neuro Oncol 2022;24:2035-2062. [PMID: 36125064 PMCID: PMC9713527 DOI: 10.1093/neuonc/noac204] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
5
Xiao Y, Wang Z, Zhao M, Deng Y, Yang M, Su G, Yang K, Qian C, Hu X, Liu Y, Geng L, Xiao Y, Zou Y, Tang X, Liu H, Xiao H, Fan R. Single-Cell Transcriptomics Revealed Subtype-Specific Tumor Immune Microenvironments in Human Glioblastomas. Front Immunol 2022;13:914236. [PMID: 35669791 PMCID: PMC9163377 DOI: 10.3389/fimmu.2022.914236] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022]  Open
6
Diaz-Colunga J, Diaz-Uriarte R. Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next? PLoS Comput Biol 2021;17:e1009055. [PMID: 34932572 PMCID: PMC8730404 DOI: 10.1371/journal.pcbi.1009055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/05/2022] [Accepted: 11/25/2021] [Indexed: 12/13/2022]  Open
7
Nicol PB, Coombes KR, Deaver C, Chkrebtii O, Paul S, Toland AE, Asiaee A. Oncogenetic network estimation with disjunctive Bayesian networks. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
8
Wang M, Yu T, Liu J, Chen L, Stromberg AJ, Villano JL, Arnold SM, Liu C, Wang C. A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. BMC Bioinformatics 2019;20:620. [PMID: 31791231 PMCID: PMC6889196 DOI: 10.1186/s12859-019-3218-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 11/12/2019] [Indexed: 12/02/2022]  Open
9
Khakabimamaghani S, Ding D, Snow O, Ester M. Uncovering the subtype-specific temporal order of cancer pathway dysregulation. PLoS Comput Biol 2019;15:e1007451. [PMID: 31710622 PMCID: PMC6872169 DOI: 10.1371/journal.pcbi.1007451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/21/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022]  Open
10
Motion, fixation probability and the choice of an evolutionary process. PLoS Comput Biol 2019;15:e1007238. [PMID: 31381556 PMCID: PMC6746388 DOI: 10.1371/journal.pcbi.1007238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/16/2019] [Accepted: 07/02/2019] [Indexed: 11/21/2022]  Open
11
Diaz-Uriarte R, Vasallo C. Every which way? On predicting tumor evolution using cancer progression models. PLoS Comput Biol 2019;15:e1007246. [PMID: 31374072 PMCID: PMC6693785 DOI: 10.1371/journal.pcbi.1007246] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 08/14/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022]  Open
12
In silico learning of tumor evolution through mutational time series. Proc Natl Acad Sci U S A 2019;116:9501-9510. [PMID: 31015295 PMCID: PMC6510994 DOI: 10.1073/pnas.1901695116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
13
Zhang W, Wang SL. An Integrated Framework for Identifying Mutated Driver Pathway and Cancer Progression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:455-464. [PMID: 29990286 DOI: 10.1109/tcbb.2017.2788016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
14
Tirosh I, Suvà ML. Dissecting human gliomas by single-cell RNA sequencing. Neuro Oncol 2019;20:37-43. [PMID: 29016805 DOI: 10.1093/neuonc/nox126] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
15
Single-Cell RNA-Sequencing in Glioma. Curr Oncol Rep 2018;20:42. [PMID: 29637300 DOI: 10.1007/s11912-018-0673-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
16
De S, Ganesan S. Looking beyond drivers and passengers in cancer genome sequencing data. Ann Oncol 2018;28:938-945. [PMID: 27998972 DOI: 10.1093/annonc/mdw677] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
17
Hainke K, Szugat S, Fried R, Rahnenführer J. Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV. BMC Bioinformatics 2017;18:358. [PMID: 28764644 PMCID: PMC5539896 DOI: 10.1186/s12859-017-1762-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 07/14/2017] [Indexed: 12/12/2022]  Open
18
Schwartz R, Schäffer AA. The evolution of tumour phylogenetics: principles and practice. Nat Rev Genet 2017;18:213-229. [PMID: 28190876 PMCID: PMC5886015 DOI: 10.1038/nrg.2016.170] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
19
Dimitrakopoulos CM, Beerenwinkel N. Computational approaches for the identification of cancer genes and pathways. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016;9. [PMID: 27863091 PMCID: PMC5215607 DOI: 10.1002/wsbm.1364] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/26/2016] [Accepted: 08/23/2016] [Indexed: 12/27/2022]
20
Zhou J, Lin Y, Rajan V, Hoskins W, Feng B, Tang J. Analysis of gene copy number changes in tumor phylogenetics. Algorithms Mol Biol 2016;11:26. [PMID: 27688796 PMCID: PMC5034472 DOI: 10.1186/s13015-016-0088-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 09/08/2016] [Indexed: 02/04/2023]  Open
21
Altrock PM, Liu LL, Michor F. The mathematics of cancer: integrating quantitative models. Nat Rev Cancer 2015;15:730-45. [PMID: 26597528 DOI: 10.1038/nrc4029] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
22
Lecca P, Casiraghi N, Demichelis F. Defining order and timing of mutations during cancer progression: the TO-DAG probabilistic graphical model. Front Genet 2015;6:309. [PMID: 26528329 PMCID: PMC4602157 DOI: 10.3389/fgene.2015.00309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/24/2015] [Indexed: 01/08/2023]  Open
23
Lathia JD, Mack SC, Mulkearns-Hubert EE, Valentim CLL, Rich JN. Cancer stem cells in glioblastoma. Genes Dev 2015;29:1203-17. [PMID: 26109046 PMCID: PMC4495393 DOI: 10.1101/gad.261982.115] [Citation(s) in RCA: 1201] [Impact Index Per Article: 120.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
24
Wangsa D, Chowdhury SA, Ryott M, Gertz EM, Elmberger G, Auer G, Åvall Lundqvist E, Küffer S, Ströbel P, Schäffer AA, Schwartz R, Munck-Wikland E, Ried T, Heselmeyer-Haddad K. Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis. Int J Cancer 2015;138:98-109. [PMID: 26175310 DOI: 10.1002/ijc.29691] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/21/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022]
25
Ramazzotti D, Caravagna G, Olde Loohuis L, Graudenzi A, Korsunsky I, Mauri G, Antoniotti M, Mishra B. CAPRI: efficient inference of cancer progression models from cross-sectional data. Bioinformatics 2015;31:3016-26. [DOI: 10.1093/bioinformatics/btv296] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/04/2015] [Indexed: 12/27/2022]  Open
26
Furnari FB, Cloughesy TF, Cavenee WK, Mischel PS. Heterogeneity of epidermal growth factor receptor signalling networks in glioblastoma. Nat Rev Cancer 2015;15:302-10. [PMID: 25855404 PMCID: PMC4875778 DOI: 10.1038/nrc3918] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
27
Turajlic S, McGranahan N, Swanton C. Inferring mutational timing and reconstructing tumour evolutionary histories. BIOCHIMICA ET BIOPHYSICA ACTA 2015;1855:264-75. [PMID: 25827356 DOI: 10.1016/j.bbcan.2015.03.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/28/2022]
28
Raphael BJ, Vandin F. Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data. J Comput Biol 2015;22:510-27. [PMID: 25785493 DOI: 10.1089/cmb.2014.0161] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
29
Diaz-Uriarte R. Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. BMC Bioinformatics 2015;16:41. [PMID: 25879190 PMCID: PMC4339747 DOI: 10.1186/s12859-015-0466-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/15/2015] [Indexed: 11/29/2022]  Open
30
Sakoparnig T, Fried P, Beerenwinkel N. Identification of constrained cancer driver genes based on mutation timing. PLoS Comput Biol 2015;11:e1004027. [PMID: 25569148 PMCID: PMC4287396 DOI: 10.1371/journal.pcbi.1004027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/05/2014] [Indexed: 12/18/2022]  Open
31
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Cancer evolution: mathematical models and computational inference. Syst Biol 2015;64:e1-25. [PMID: 25293804 PMCID: PMC4265145 DOI: 10.1093/sysbio/syu081] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 09/26/2014] [Indexed: 12/12/2022]  Open
32
Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC. Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. Cancer Cell 2014;26:288-300. [PMID: 25117714 PMCID: PMC4143139 DOI: 10.1016/j.ccr.2014.06.005] [Citation(s) in RCA: 301] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 02/20/2014] [Accepted: 06/11/2014] [Indexed: 01/16/2023]
33
Zadeh G, Aldape K. RESICstance is futile-but not in glioblastoma. Cancer Cell 2014;26:156-7. [PMID: 25117706 DOI: 10.1016/j.ccr.2014.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
34
The role of targeted therapies in the management of progressive glioblastoma. J Neurooncol 2014;118:557-99. [DOI: 10.1007/s11060-013-1339-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 12/28/2013] [Indexed: 12/28/2022]
35
Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R. Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinformatics 2013;29:i189-98. [PMID: 23812984 PMCID: PMC3694640 DOI: 10.1093/bioinformatics/btt205] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
36
Shahrabi Farahani H, Lagergren J. Learning oncogenetic networks by reducing to mixed integer linear programming. PLoS One 2013;8:e65773. [PMID: 23799047 PMCID: PMC3683041 DOI: 10.1371/journal.pone.0065773] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/28/2013] [Indexed: 12/22/2022]  Open
37
Winslow RL, Trayanova N, Geman D, Miller MI. Computational medicine: translating models to clinical care. Sci Transl Med 2013;4:158rv11. [PMID: 23115356 DOI: 10.1126/scitranslmed.3003528] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
38
Czibula G, Bocicor IM, Czibula IG. Temporal ordering of cancer microarray data through a reinforcement learning based approach. PLoS One 2013;8:e60883. [PMID: 23565283 PMCID: PMC3614992 DOI: 10.1371/journal.pone.0060883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 03/04/2013] [Indexed: 11/19/2022]  Open
39
Gu Y, Wang H, Qin Y, Zhang Y, Zhao W, Qi L, Zhang Y, Wang C, Guo Z. Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma. MOLECULAR BIOSYSTEMS 2013;9:467-77. [PMID: 23344900 DOI: 10.1039/c2mb25528f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
40
Raffel C. Editorial: glioblastoma subtype. J Neurosurg 2012;117:474; discussion 475. [PMID: 22725980 DOI: 10.3171/2012.1.jns112254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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