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A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis.

Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F.

PLoS Comput Biol. 2012 Jan;8(1):e1002337. doi: 10.1371/journal.pcbi.1002337.


A mathematical framework to determine the temporal sequence of somatic genetic events in cancer.

Attolini CS, Cheng YK, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17604-9. doi: 10.1073/pnas.1009117107.


Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

Brennan C, Momota H, Hambardzumyan D, Ozawa T, Tandon A, Pedraza A, Holland E.

PLoS One. 2009 Nov 13;4(11):e7752. doi: 10.1371/journal.pone.0007752.


miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis.

Silber J, Jacobsen A, Ozawa T, Harinath G, Pedraza A, Sander C, Holland EC, Huse JT.

PLoS One. 2012;7(3):e33844. doi: 10.1371/journal.pone.0033844.


Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma.

Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC.

Cancer Cell. 2014 Aug 11;26(2):288-300. doi: 10.1016/j.ccr.2014.06.005.


IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals.

Ping Y, Zhang H, Deng Y, Wang L, Zhao H, Pang L, Fan H, Xu C, Li F, Zhang Y, Gong Y, Xiao Y, Li X.

Mol Biosyst. 2014 Aug;10(8):2031-42. doi: 10.1039/c4mb00289j.


The temporal order of genetic and pathway alterations in tumorigenesis.

Gerstung M, Eriksson N, Lin J, Vogelstein B, Beerenwinkel N.

PLoS One. 2011;6(11):e27136. doi: 10.1371/journal.pone.0027136.


Molecular and Genomic Alterations in Glioblastoma Multiforme.

Crespo I, Vital AL, Gonzalez-Tablas M, Patino Mdel C, Otero A, Lopes MC, de Oliveira C, Domingues P, Orfao A, Tabernero MD.

Am J Pathol. 2015 Jul;185(7):1820-33. doi: 10.1016/j.ajpath.2015.02.023. Review.


An integrative characterization of recurrent molecular aberrations in glioblastoma genomes.

Sintupisut N, Liu PL, Yeang CH.

Nucleic Acids Res. 2013 Oct;41(19):8803-21. doi: 10.1093/nar/gkt656.


Estimating the order of mutations during tumorigenesis from tumor genome sequencing data.

Youn A, Simon R.

Bioinformatics. 2012 Jun 15;28(12):1555-61. doi: 10.1093/bioinformatics/bts168.


Oncostatin-M differentially regulates mesenchymal and proneural signature genes in gliomas via STAT3 signaling.

Natesh K, Bhosale D, Desai A, Chandrika G, Pujari R, Jagtap J, Chugh A, Ranade D, Shastry P.

Neoplasia. 2015 Feb;17(2):225-37. doi: 10.1016/j.neo.2015.01.001.


RTVP-1 promotes mesenchymal transformation of glioma via a STAT-3/IL-6-dependent positive feedback loop.

Giladi ND, Ziv-Av A, Lee HK, Finniss S, Cazacu S, Xiang C, Waldman Ben-Asher H, deCarvalho A, Mikkelsen T, Poisson L, Brodie C.

Oncotarget. 2015 Sep 8;6(26):22680-97.


MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.

Gill BJ, Pisapia DJ, Malone HR, Goldstein H, Lei L, Sonabend A, Yun J, Samanamud J, Sims JS, Banu M, Dovas A, Teich AF, Sheth SA, McKhann GM, Sisti MB, Bruce JN, Sims PA, Canoll P.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12550-5. doi: 10.1073/pnas.1405839111.


Discovering gene-environment interactions in glioblastoma through a comprehensive data integration bioinformatics method.

Kunkle B, Yoo C, Roy D.

Neurotoxicology. 2013 Mar;35:1-14. doi: 10.1016/j.neuro.2012.11.001.


Mutual exclusivity analysis identifies oncogenic network modules.

Ciriello G, Cerami E, Sander C, Schultz N.

Genome Res. 2012 Feb;22(2):398-406. doi: 10.1101/gr.125567.111.


A high Notch pathway activation predicts response to γ secretase inhibitors in proneural subtype of glioma tumor-initiating cells.

Saito N, Fu J, Zheng S, Yao J, Wang S, Liu DD, Yuan Y, Sulman EP, Lang FF, Colman H, Verhaak RG, Yung WK, Koul D.

Stem Cells. 2014 Jan;32(1):301-12. doi: 10.1002/stem.1528.


Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma.

Gu Y, Wang H, Qin Y, Zhang Y, Zhao W, Qi L, Zhang Y, Wang C, Guo Z.

Mol Biosyst. 2013 Mar;9(3):467-77. doi: 10.1039/c2mb25528f.


Expression signature of IFN/STAT1 signaling genes predicts poor survival outcome in glioblastoma multiforme in a subtype-specific manner.

Duarte CW, Willey CD, Zhi D, Cui X, Harris JJ, Vaughan LK, Mehta T, McCubrey RO, Khodarev NN, Weichselbaum RR, Gillespie GY.

PLoS One. 2012;7(1):e29653. doi: 10.1371/journal.pone.0029653.


Role of proto-oncogene activation in carcinogenesis.

Anderson MW, Reynolds SH, You M, Maronpot RM.

Environ Health Perspect. 1992 Nov;98:13-24. Review.


Systems biology approach to identification of biomarkers for metastatic progression in cancer.

Ptitsyn AA, Weil MM, Thamm DH.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S8. doi: 10.1186/1471-2105-9-S9-S8.

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