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Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.

Halabi NM, Martinez A, Al-Farsi H, Mery E, Puydenus L, Pujol P, Khalak HG, McLurcan C, Ferron G, Querleu D, Al-Azwani I, Al-Dous E, Mohamoud YA, Malek JA, Rafii A.

PLoS Genet. 2016 Jan 6;12(1):e1005755. doi: 10.1371/journal.pgen.1005755. eCollection 2016 Jan. Erratum in: PLoS Genet. 2016 Feb;12(2):e1005892.


High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer.

Tan IB, Malik S, Ramnarayanan K, McPherson JR, Ho DL, Suzuki Y, Ng SB, Yan S, Lim KH, Koh D, Hoe CM, Chan CY, Ten R, Goh BK, Chung AY, Tan J, Chan CX, Tay ST, Alexander L, Nagarajan N, Hillmer AM, Tang CL, Chua C, Teh BT, Rozen S, Tan P.

Genome Biol. 2015 Feb 12;16:32. doi: 10.1186/s13059-015-0589-1.


Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data.

Zhang J, Zhang S, Wang Y, Zhang XS.

BMC Syst Biol. 2013;7 Suppl 2:S4. doi: 10.1186/1752-0509-7-S2-S4. Epub 2013 Oct 14.


Mutated genes and driver pathways involved in myelodysplastic syndromes—a transcriptome sequencing based approach.

Liu L, Wang H, Wen J, Tseng CE, Zu Y, Chang CC, Zhou X.

Mol Biosyst. 2015 Aug;11(8):2158-66. doi: 10.1039/c4mb00663a.


Verifying the markers of ovarian cancer using RNA-seq data.

Liu T, Yu N, Ding F, Wang S, Li S, Zhang X, Sun X, Chen Y, Liu P.

Mol Med Rep. 2015 Jul;12(1):1125-30. doi: 10.3892/mmr.2015.3489. Epub 2015 Mar 13.


Integrated analysis of recurrent properties of cancer genes to identify novel drivers.

D'Antonio M, Ciccarelli FD.

Genome Biol. 2013 May 29;14(5):R52. doi: 10.1186/gb-2013-14-5-r52.


Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.

LaFramboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML.

PLoS Genet. 2010 Sep 2;6(9):e1001086. doi: 10.1371/journal.pgen.1001086.


Marked allelic imbalance on chromosome 5q31 does not explain alpha-catenin expression in epithelial ovarian cancer.

Tuhkanen H, Anttila M, Kosma VM, Puolakka J, Juhola M, Heinonen S, Mannermaa A.

Gynecol Oncol. 2004 Aug;94(2):416-21.


Gene expression profiling of ovarian carcinomas and prognostic analysis of outcome.

Cai SY, Yang T, Chen Y, Wang JW, Li L, Xu MJ.

J Ovarian Res. 2015 Jul 31;8:50. doi: 10.1186/s13048-015-0176-9.


Analysis of gene expression in stage I serous tumors identifies critical pathways altered in ovarian cancer.

Chien J, Fan JB, Bell DA, April C, Klotzle B, Ota T, Lingle WL, Gonzalez Bosquet J, Shridhar V, Hartmann LC.

Gynecol Oncol. 2009 Jul;114(1):3-11. doi: 10.1016/j.ygyno.2009.04.002. Epub 2009 May 1.


A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome.

Reinartz S, Finkernagel F, Adhikary T, Rohnalter V, Schumann T, Schober Y, Nockher WA, Nist A, Stiewe T, Jansen JM, Wagner U, Müller-Brüsselbach S, Müller R.

Genome Biol. 2016 May 23;17(1):108. doi: 10.1186/s13059-016-0956-6.


Differential gene expression identifies subgroups of ovarian carcinoma.

Skubitz AP, Pambuccian SE, Argenta PA, Skubitz KM.

Transl Res. 2006 Nov;148(5):223-48.


Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

Hoogstraat M, de Pagter MS, Cirkel GA, van Roosmalen MJ, Harkins TT, Duran K, Kreeftmeijer J, Renkens I, Witteveen PO, Lee CC, Nijman IJ, Guy T, van 't Slot R, Jonges TN, Lolkema MP, Koudijs MJ, Zweemer RP, Voest EE, Cuppen E, Kloosterman WP.

Genome Res. 2014 Feb;24(2):200-11. doi: 10.1101/gr.161026.113. Epub 2013 Nov 12.


Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures.

Ow GS, Ivshina AV, Fuentes G, Kuznetsov VA.

Cell Cycle. 2014;13(14):2262-80. doi: 10.4161/cc.29271. Epub 2014 May 30.


Tumor evolution and intratumor heterogeneity of an epithelial ovarian cancer investigated using next-generation sequencing.

Lee JY, Yoon JK, Kim B, Kim S, Kim MA, Lim H, Bang D, Song YS.

BMC Cancer. 2015 Feb 26;15:85. doi: 10.1186/s12885-015-1077-4.


Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome.

Gao C, Devarajan K, Zhou Y, Slater CM, Daly MB, Chen X.

BMC Genomics. 2012 Oct 30;13:570. doi: 10.1186/1471-2164-13-570.


Evaluation of allele-specific somatic changes of genome-wide association study susceptibility alleles in human colorectal cancers.

Gerber MM, Hampel H, Schulz NP, Fernandez S, Wei L, Zhou XP, de la Chapelle A, Ewart Toland A.

PLoS One. 2012;7(5):e37672. doi: 10.1371/journal.pone.0037672. Epub 2012 May 21.


Identification of ovarian cancer subtype-specific network modules and candidate drivers through an integrative genomics approach.

Zhang D, Chen P, Zheng CH, Xia J.

Oncotarget. 2016 Jan 26;7(4):4298-309. doi: 10.18632/oncotarget.6774.


Analyzing allele specific RNA expression using mixture models.

Lu R, Smith RM, Seweryn M, Wang D, Hartmann K, Webb A, Sadee W, Rempala GA.

BMC Genomics. 2015 Aug 1;16:566. doi: 10.1186/s12864-015-1749-0.

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