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Items: 28


Compound Functional Prediction Using Multiple Unrelated Morphological Profiling Assays.

Rose F, Basu S, Rexhepaj E, Chauchereau A, Del Nery E, Genovesio A.

SLAS Technol. 2018 Jun;23(3):243-251. doi: 10.1177/2472630317740831. Epub 2017 Nov 3.


Smooth 2D manifold extraction from 3D image stack.

Shihavuddin A, Basu S, Rexhepaj E, Delestro F, Menezes N, Sigoillot SM, Del Nery E, Selimi F, Spassky N, Genovesio A.

Nat Commun. 2017 May 31;8:15554. doi: 10.1038/ncomms15554.


Tumour islet Foxp3+ T-cell infiltration predicts poor outcome in nonsmall cell lung cancer.

O'Callaghan DS, Rexhepaj E, Gately K, Coate L, Delaney D, O'Donnell DM, Kay E, O'Connell F, Gallagher WM, O'Byrne KJ.

Eur Respir J. 2015 Dec;46(6):1762-72. doi: 10.1183/13993003.00176-2014. Epub 2015 Nov 5.


A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.

Rexhepaj E, Agnarsdóttir M, Bergman J, Edqvist PH, Bergqvist M, Uhlén M, Gallagher WM, Lundberg E, Ponten F.

PLoS One. 2013 May 17;8(5):e62070. doi: 10.1371/journal.pone.0062070. Print 2013.


Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.

Danielsson F, Skogs M, Huss M, Rexhepaj E, O'Hurley G, Klevebring D, Pontén F, Gad AK, Uhlén M, Lundberg E.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6853-8. doi: 10.1073/pnas.1216436110. Epub 2013 Apr 8. Erratum in: Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7158.


Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer.

O Leary PC, Penny SA, Dolan RT, Kelly CM, Madden SF, Rexhepaj E, Brennan DJ, McCann AH, Pontén F, Uhlén M, Zagozdzon R, Duffy MJ, Kell MR, Jirström K, Gallagher WM.

BMC Cancer. 2013 Apr 2;13:175. doi: 10.1186/1471-2407-13-175.


Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, Murphy RF, Pepperkok R, Uhlén M, Simpson JC, Lundberg E.

Nat Methods. 2013 Apr;10(4):315-23. doi: 10.1038/nmeth.2377. Epub 2013 Feb 24.


The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ERα, and is an independent prognostic factor in node-negative breast cancer.

Brennan DJ, O'Connor DP, Laursen H, McGee SF, McCarthy S, Zagozdzon R, Rexhepaj E, Culhane AC, Martin FM, Duffy MJ, Landberg G, Ryden L, Hewitt SM, Kuhar MJ, Bernards R, Millikan RC, Crown JP, Jirström K, Gallagher WM.

Oncogene. 2012 Jul 26;31(30):3483-94. doi: 10.1038/onc.2011.519. Epub 2011 Dec 5.


Leukocyte complexity predicts breast cancer survival and functionally regulates response to chemotherapy.

DeNardo DG, Brennan DJ, Rexhepaj E, Ruffell B, Shiao SL, Madden SF, Gallagher WM, Wadhwani N, Keil SD, Junaid SA, Rugo HS, Hwang ES, Jirström K, West BL, Coussens LM.

Cancer Discov. 2011 Jun;1(1):54-67. doi: 10.1158/2159-8274.CD-10-0028. Epub 2011 Jun 1.


Identification of a myometrial molecular profile for dystocic labor.

Brennan DJ, McGee SF, Rexhepaj E, O'Connor DP, Robson M, O'Herlihy C.

BMC Pregnancy Childbirth. 2011 Oct 16;11:74. doi: 10.1186/1471-2393-11-74.


The tumour suppressor SOX11 is associated with improved survival among high grade epithelial ovarian cancers and is regulated by reversible promoter methylation.

Sernbo S, Gustavsson E, Brennan DJ, Gallagher WM, Rexhepaj E, Rydnert F, Jirström K, Borrebaeck CA, Ek S.

BMC Cancer. 2011 Sep 24;11:405. doi: 10.1186/1471-2407-11-405.


RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.

Ehlén Å, Nodin B, Rexhepaj E, Brändstedt J, Uhlén M, Alvarado-Kristensson M, Pontén F, Brennan DJ, Jirström K.

Transl Oncol. 2011 Aug;4(4):212-21. Epub 2011 Aug 1.


Interleukin-6 as a therapeutic target in human ovarian cancer.

Coward J, Kulbe H, Chakravarty P, Leader D, Vassileva V, Leinster DA, Thompson R, Schioppa T, Nemeth J, Vermeulen J, Singh N, Avril N, Cummings J, Rexhepaj E, Jirström K, Gallagher WM, Brennan DJ, McNeish IA, Balkwill FR.

Clin Cancer Res. 2011 Sep 15;17(18):6083-96. doi: 10.1158/1078-0432.CCR-11-0945. Epub 2011 Jul 27.


SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.

Magnusson K, de Wit M, Brennan DJ, Johnson LB, McGee SF, Lundberg E, Naicker K, Klinger R, Kampf C, Asplund A, Wester K, Gry M, Bjartell A, Gallagher WM, Rexhepaj E, Kilpinen S, Kallioniemi OP, Belt E, Goos J, Meijer G, Birgisson H, Glimelius B, Borrebaeck CA, Navani S, Uhlén M, O'Connor DP, Jirström K, Pontén F.

Am J Surg Pathol. 2011 Jul;35(7):937-48. doi: 10.1097/PAS.0b013e31821c3dae.


Evaluation of the prognostic significance of MSMB and CRISP3 in prostate cancer using automated image analysis.

Dahlman A, Rexhepaj E, Brennan DJ, Gallagher WM, Gaber A, Lindgren A, Jirström K, Bjartell A.

Mod Pathol. 2011 May;24(5):708-19. doi: 10.1038/modpathol.2010.238. Epub 2011 Jan 14.


Validation of cytoplasmic-to-nuclear ratio of survivin as an indicator of improved prognosis in breast cancer.

Rexhepaj E, Jirstrom K, O'Connor DP, O'Brien SL, Landberg G, Duffy MJ, Brennan DJ, Gallagher WM.

BMC Cancer. 2010 Nov 23;10:639. doi: 10.1186/1471-2407-10-639.


Tissue microarrays and digital image analysis.

Ryan D, Mulrane L, Rexhepaj E, Gallagher WM.

Methods Mol Biol. 2011;691:97-112. doi: 10.1007/978-1-60761-849-2_6.


Receptor tyrosine kinase signaling favors a protumorigenic state in breast cancer cells by inhibiting the adaptive immune response.

Ursini-Siegel J, Cory S, Zuo D, Hardy WR, Rexhepaj E, Lam S, Schade B, Jirstrom K, Bjur E, Piccirillo CA, Denardo D, Coussens LM, Brennan DJ, Gallagher WM, Park M, Pawson T, Hallett M, Muller WJ.

Cancer Res. 2010 Oct 15;70(20):7776-87. doi: 10.1158/0008-5472.CAN-10-2229. Epub 2010 Oct 5.


SOX10 expression in superficial spreading and nodular malignant melanomas.

Agnarsdóttir M, Sooman L, Bolander A, Strömberg S, Rexhepaj E, Bergqvist M, Ponten F, Gallagher W, Lennartsson J, Ekman S, Uhlen M, Hedstrand H.

Melanoma Res. 2010 Dec;20(6):468-78. doi: 10.1097/CMR.0b013e3283403ccd.


Antibody-based proteomics: fast-tracking molecular diagnostics in oncology.

Brennan DJ, O'Connor DP, Rexhepaj E, Ponten F, Gallagher WM.

Nat Rev Cancer. 2010 Sep;10(9):605-17. doi: 10.1038/nrc2902. Epub 2010 Aug 19. Review.


Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer.

Brennan DJ, Brändstedt J, Rexhepaj E, Foley M, Pontén F, Uhlén M, Gallagher WM, O'Connor DP, O'Herlihy C, Jirstrom K.

BMC Cancer. 2010 Apr 1;10:125. doi: 10.1186/1471-2407-10-125.


Selective expression of Syntaxin-7 protein in benign melanocytes and malignant melanoma.

Strömberg S, Agnarsdóttir M, Magnusson K, Rexhepaj E, Bolander A, Lundberg E, Asplund A, Ryan D, Rafferty M, Gallagher WM, Uhlen M, Bergqvist M, Ponten F.

J Proteome Res. 2009 Apr;8(4):1639-46. doi: 10.1021/pr800745e.


Automated image analysis in histopathology: a valuable tool in medical diagnostics.

Mulrane L, Rexhepaj E, Penney S, Callanan JJ, Gallagher WM.

Expert Rev Mol Diagn. 2008 Nov;8(6):707-25. doi: 10.1586/14737159.8.6.707. Review.


Novel image analysis approach for quantifying expression of nuclear proteins assessed by immunohistochemistry: application to measurement of oestrogen and progesterone receptor levels in breast cancer.

Rexhepaj E, Brennan DJ, Holloway P, Kay EW, McCann AH, Landberg G, Duffy MJ, Jirstrom K, Gallagher WM.

Breast Cancer Res. 2008;10(5):R89. doi: 10.1186/bcr2187. Epub 2008 Oct 23.


Creation of a digital slide and tissue microarray resource from a multi-institutional predictive toxicology study in the rat: an initial report from the PredTox group.

Mulrane L, Rexhepaj E, Smart V, Callanan JJ, Orhan D, Eldem T, Mally A, Schroeder S, Meyer K, Wendt M, O'Shea D, Gallagher WM.

Exp Toxicol Pathol. 2008 Aug;60(4-5):235-45. doi: 10.1016/j.etp.2007.12.004. Epub 2008 May 13.


Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer.

Brennan DJ, Rexhepaj E, O'Brien SL, McSherry E, O'Connor DP, Fagan A, Culhane AC, Higgins DG, Jirstrom K, Millikan RC, Landberg G, Duffy MJ, Hewitt SM, Gallagher WM.

Clin Cancer Res. 2008 May 1;14(9):2681-9. doi: 10.1158/1078-0432.CCR-07-1760.


Contribution of DNA and tissue microarray technology to the identification and validation of biomarkers and personalised medicine in breast cancer.

Brennan DJ, Kelly C, Rexhepaj E, Dervan PA, Duffy MJ, Gallagher WM.

Cancer Genomics Proteomics. 2007 May-Jun;4(3):121-34. Review.


Combination of SELDI-TOF-MS and data mining provides early-stage response prediction for rectal tumors undergoing multimodal neoadjuvant therapy.

Smith FM, Gallagher WM, Fox E, Stephens RB, Rexhepaj E, Petricoin EF 3rd, Liotta L, Kennedy MJ, Reynolds JV.

Ann Surg. 2007 Feb;245(2):259-66.

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