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Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.

Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q.

Genome Med. 2013 Mar 28;5(3):29. doi: 10.1186/gm433.


ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC.

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.


A robust tool for discriminative analysis and feature selection in paired samples impacts the identification of the genes essential for reprogramming lung tissue to adenocarcinoma.

Toh SH, Prathipati P, Motakis E, Kwoh CK, Yenamandra SP, Kuznetsov VA.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S24. doi: 10.1186/1471-2164-12-S3-S24. Epub 2011 Nov 30.


Gene expression anti-profiles as a basis for accurate universal cancer signatures.

Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT.

BMC Bioinformatics. 2012 Oct 22;13:272. doi: 10.1186/1471-2105-13-272.


Robust multi-tissue gene panel for cancer detection.

Irgon J, Huang CC, Zhang Y, Talantov D, Bhanot G, Szalma S.

BMC Cancer. 2010 Jun 22;10:319. doi: 10.1186/1471-2407-10-319.


Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy.

Erho N, Crisan A, Vergara IA, Mitra AP, Ghadessi M, Buerki C, Bergstralh EJ, Kollmeyer T, Fink S, Haddad Z, Zimmermann B, Sierocinski T, Ballman KV, Triche TJ, Black PC, Karnes RJ, Klee G, Davicioni E, Jenkins RB.

PLoS One. 2013 Jun 24;8(6):e66855. doi: 10.1371/journal.pone.0066855. Print 2013.


Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis.

Dinalankara W, Bravo HC.

Cancer Inform. 2015 Jun 7;14:71-81. doi: 10.4137/CIN.S23862. eCollection 2015.


Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures.

Fan C, Prat A, Parker JS, Liu Y, Carey LA, Troester MA, Perou CM.

BMC Med Genomics. 2011 Jan 9;4:3. doi: 10.1186/1755-8794-4-3.


Using logistic regression to improve the prognostic value of microarray gene expression data sets: application to early-stage squamous cell carcinoma of the lung and triple negative breast carcinoma.

Mount DW, Putnam CW, Centouri SM, Manziello AM, Pandey R, Garland LL, Martinez JD.

BMC Med Genomics. 2014 Jun 10;7:33. doi: 10.1186/1755-8794-7-33.


Molecular signatures in biopsy specimens of lung cancer.

Borczuk AC, Shah L, Pearson GD, Walter KL, Wang L, Austin JH, Friedman RA, Powell CA.

Am J Respir Crit Care Med. 2004 Jul 15;170(2):167-74. Epub 2004 Apr 15.


Gene profiling of clinical routine biopsies and prediction of survival in non-small cell lung cancer.

Baty F, Facompré M, Kaiser S, Schumacher M, Pless M, Bubendorf L, Savic S, Marrer E, Budach W, Buess M, Kehren J, Tamm M, Brutsche MH.

Am J Respir Crit Care Med. 2010 Jan 15;181(2):181-8. doi: 10.1164/rccm.200812-1807OC. Epub 2009 Oct 15.


Gene expression-based classification of non-small cell lung carcinomas and survival prediction.

Hou J, Aerts J, den Hamer B, van Ijcken W, den Bakker M, Riegman P, van der Leest C, van der Spek P, Foekens JA, Hoogsteden HC, Grosveld F, Philipsen S.

PLoS One. 2010 Apr 22;5(4):e10312. doi: 10.1371/journal.pone.0010312.


Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens.

Sadi AM, Wang DY, Youngson BJ, Miller N, Boerner S, Done SJ, Leong WL.

BMC Cancer. 2011 Jun 16;11:253:1-13. doi: 10.1186/1471-2407-11-25.


Identifying cancer biomarkers by network-constrained support vector machines.

Chen L, Xuan J, Riggins RB, Clarke R, Wang Y.

BMC Syst Biol. 2011 Oct 12;5:161. doi: 10.1186/1752-0509-5-161.


Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study.

Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, Erho N, Dunning MJ, Halim S, Lamb AD, Moon NC, Zafarana G, Warren AY, Meng X, Thoms J, Grzadkowski MR, Berlin A, Have CL, Ramnarine VR, Yao CQ, Malloff CA, Lam LL, Xie H, Harding NJ, Mak DY, Chu KC, Chong LC, Sendorek DH, P'ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG.

Lancet Oncol. 2014 Dec;15(13):1521-32. doi: 10.1016/S1470-2045(14)71021-6. Epub 2014 Nov 13.


A novel method for finding non-small cell lung cancer diagnosis biomarkers.

Tran QN.

BMC Med Genomics. 2013;6 Suppl 1:S11. doi: 10.1186/1755-8794-6-S1-S11. Epub 2013 Jan 23.


Robust prognostic gene expression signatures in bladder cancer and lung adenocarcinoma depend on cell cycle related genes.

Dancik GM, Theodorescu D.

PLoS One. 2014 Jan 22;9(1):e85249. doi: 10.1371/journal.pone.0085249. eCollection 2014.


Computational dissection of tissue contamination for identification of colon cancer-specific expression profiles.

Türeci O, Ding J, Hilton H, Bian H, Ohkawa H, Braxenthaler M, Seitz G, Raddrizzani L, Friess H, Buchler M, Sahin U, Hammer J.

FASEB J. 2003 Mar;17(3):376-85.


Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes.

Winter C, Kristiansen G, Kersting S, Roy J, Aust D, Knösel T, Rümmele P, Jahnke B, Hentrich V, Rückert F, Niedergethmann M, Weichert W, Bahra M, Schlitt HJ, Settmacher U, Friess H, Büchler M, Saeger HD, Schroeder M, Pilarsky C, Grützmann R.

PLoS Comput Biol. 2012;8(5):e1002511. doi: 10.1371/journal.pcbi.1002511. Epub 2012 May 17.


Nuclear receptor expression defines a set of prognostic biomarkers for lung cancer.

Jeong Y, Xie Y, Xiao G, Behrens C, Girard L, Wistuba II, Minna JD, Mangelsdorf DJ.

PLoS Med. 2010 Dec 14;7(12):e1000378. doi: 10.1371/journal.pmed.1000378.

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