-
1
-
-
77955970259
-
Antibody-based proteomics: fast-tracking molecular diagnostics in oncology
-
Brennan DJ, O'Connor DP, Rexhepaj E, Ponten F, Gallagher WM, (2010) Antibody-based proteomics: fast-tracking molecular diagnostics in oncology. Nat Rev Cancer 10: 605-617.
-
(2010)
Nat Rev Cancer
, vol.10
, pp. 605-617
-
-
Brennan, D.J.1
O'Connor, D.P.2
Rexhepaj, E.3
Ponten, F.4
Gallagher, W.M.5
-
2
-
-
0031822837
-
Tissue microarrays for high-throughput molecular profiling of tumor specimens
-
Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, et al. (1998) Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 4: 844-847.
-
(1998)
Nat Med
, vol.4
, pp. 844-847
-
-
Kononen, J.1
Bubendorf, L.2
Kallioniemi, A.3
Barlund, M.4
Schraml, P.5
-
3
-
-
57149110826
-
The Human Protein Atlas - a tool for pathology
-
Ponten F, Jirstrom K, Uhlen M, (2008) The Human Protein Atlas - a tool for pathology. J Pathol 216: 387-393.
-
(2008)
J Pathol
, vol.216
, pp. 387-393
-
-
Ponten, F.1
Jirstrom, K.2
Uhlen, M.3
-
4
-
-
17844396912
-
Antibody-based proteomics for human tissue profiling
-
Uhlen M, Ponten F, (2005) Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics 4: 384-393.
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 384-393
-
-
Uhlen, M.1
Ponten, F.2
-
5
-
-
78650034777
-
Towards a knowledge-based Human Protein Atlas
-
Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, et al. (2010) Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 28: 1248-1250.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1248-1250
-
-
Uhlen, M.1
Oksvold, P.2
Fagerberg, L.3
Lundberg, E.4
Jonasson, K.5
-
6
-
-
77149135744
-
Review of imaging solutions for integrated quantitative immunohistochemistry in the Pathology daily practice
-
Rojo MG, Bueno G, Slodkowska J, (2009) Review of imaging solutions for integrated quantitative immunohistochemistry in the Pathology daily practice. Folia Histochem Cytobiol 47: 349-354.
-
(2009)
Folia Histochem Cytobiol
, vol.47
, pp. 349-354
-
-
Rojo, M.G.1
Bueno, G.2
Slodkowska, J.3
-
7
-
-
84856803150
-
Digital pathology in personalized cancer therapy
-
Slodkowska J, Rojo MG, (2011) Digital pathology in personalized cancer therapy. Folia Histochem Cytobiol 49: 570-578.
-
(2011)
Folia Histochem Cytobiol
, vol.49
, pp. 570-578
-
-
Slodkowska, J.1
Rojo, M.G.2
-
8
-
-
77149151892
-
AI (artificial intelligence) in histopathology - from image analysis to automated diagnosis
-
Kayser K, Gortler J, Bogovac M, Bogovac A, Goldmann T, et al. (2009) AI (artificial intelligence) in histopathology - from image analysis to automated diagnosis. Folia Histochem Cytobiol 47: 355-361.
-
(2009)
Folia Histochem Cytobiol
, vol.47
, pp. 355-361
-
-
Kayser, K.1
Gortler, J.2
Bogovac, M.3
Bogovac, A.4
Goldmann, T.5
-
9
-
-
56049114483
-
Automated image analysis in histopathology: a valuable tool in medical diagnostics
-
Mulrane L, Rexhepaj E, Penney S, Callanan JJ, Gallagher WM, (2008) Automated image analysis in histopathology: a valuable tool in medical diagnostics. Expert Rev Mol Diagn 8: 707-725.
-
(2008)
Expert Rev Mol Diagn
, vol.8
, pp. 707-725
-
-
Mulrane, L.1
Rexhepaj, E.2
Penney, S.3
Callanan, J.J.4
Gallagher, W.M.5
-
10
-
-
81055146760
-
Systematic analysis of breast cancer morphology uncovers stromal features associated with survival
-
Beck AH, Sangoi AR, Leung S, Marinelli RJ, Nielsen TO, et al. (2011) Systematic analysis of breast cancer morphology uncovers stromal features associated with survival. Sci Transl Med 3: 108ra113.
-
(2011)
Sci Transl Med
, vol.3
-
-
Beck, A.H.1
Sangoi, A.R.2
Leung, S.3
Marinelli, R.J.4
Nielsen, T.O.5
-
11
-
-
84866784798
-
Leukocyte Complexity Predicts Breast Cancer Survival and Functionally Regulates Response to Chemotherapy
-
Denardo DG, Brennan DJ, Rexhepaj E, Ruffell B, Shiao SL, et al. (2011) Leukocyte Complexity Predicts Breast Cancer Survival and Functionally Regulates Response to Chemotherapy. Cancer Discov 1: 54-67.
-
(2011)
Cancer Discov
, vol.1
, pp. 54-67
-
-
Denardo, D.G.1
Brennan, D.J.2
Rexhepaj, E.3
Ruffell, B.4
Shiao, S.L.5
-
12
-
-
79955574256
-
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, et al. (2011) Evaluation of the prognostic significance of MSMB and CRISP3 in prostate cancer using automated image analysis. Mod Pathol 24: 708-719.
-
(2011)
Mod Pathol
, vol.24
, pp. 708-719
-
-
Dahlman, A.1
Rexhepaj, E.2
Brennan, D.J.3
Gallagher, W.M.4
Gaber, A.5
-
13
-
-
0036852721
-
Automated subcellular localization and quantification of protein expression in tissue microarrays
-
Camp RL, Chung GG, Rimm DL, (2002) Automated subcellular localization and quantification of protein expression in tissue microarrays. Nature medicine 8: 1323-1327.
-
(2002)
Nature Medicine
, vol.8
, pp. 1323-1327
-
-
Camp, R.L.1
Chung, G.G.2
Rimm, D.L.3
-
14
-
-
0037382283
-
Quantitative analysis of breast cancer tissue microarrays shows that both high and normal levels of HER2 expression are associated with poor outcome
-
Camp RL, Dolled-Filhart M, King BL, Rimm DL, (2003) Quantitative analysis of breast cancer tissue microarrays shows that both high and normal levels of HER2 expression are associated with poor outcome. Cancer Res 63: 1445-1448.
-
(2003)
Cancer Res
, vol.63
, pp. 1445-1448
-
-
Camp, R.L.1
Dolled-Filhart, M.2
King, B.L.3
Rimm, D.L.4
-
15
-
-
33751290510
-
Classification of breast cancer using genetic algorithms and tissue microarrays
-
Dolled-Filhart M, Ryden L, Cregger M, Jirstrom K, Harigopal M, et al. (2006) Classification of breast cancer using genetic algorithms and tissue microarrays. Clin Cancer Res 12: 6459-6468.
-
(2006)
Clin Cancer Res
, vol.12
, pp. 6459-6468
-
-
Dolled-Filhart, M.1
Ryden, L.2
Cregger, M.3
Jirstrom, K.4
Harigopal, M.5
-
16
-
-
33746099745
-
AQUA and FISH analysis of HER-2/neu expression and amplification in a small cell lung carcinoma tissue microarray
-
Giltnane JM, Murren JR, Rimm DL, King BL, (2006) AQUA and FISH analysis of HER-2/neu expression and amplification in a small cell lung carcinoma tissue microarray. Histopathology 49: 161-169.
-
(2006)
Histopathology
, vol.49
, pp. 161-169
-
-
Giltnane, J.M.1
Murren, J.R.2
Rimm, D.L.3
King, B.L.4
-
17
-
-
77950595440
-
Automated Image Analysis Approaches in Histopathology
-
Foley R, DiFranco M, Bryan K, Rexhepaj E, Mulrane L, et al. (2008) Automated Image Analysis Approaches in Histopathology. Handbook of Research on Systems Biology Applications in Medicine: IGI Global Books.
-
(2008)
Handbook of Research on Systems Biology Applications in Medicine: IGI Global Books
-
-
Foley, R.1
DiFranco, M.2
Bryan, K.3
Rexhepaj, E.4
Mulrane, L.5
-
18
-
-
3042547731
-
Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections
-
Wahlby C, Sintorn IM, Erlandsson F, Borgefors G, Bengtsson E, (2004) Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections. J Microsc 215: 67-76.
-
(2004)
J Microsc
, vol.215
, pp. 67-76
-
-
Wahlby, C.1
Sintorn, I.M.2
Erlandsson, F.3
Borgefors, G.4
Bengtsson, E.5
-
19
-
-
33845792555
-
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
-
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, et al. (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7: R100.
-
(2006)
Genome Biol
, vol.7
-
-
Carpenter, A.E.1
Jones, T.R.2
Lamprecht, M.R.3
Clarke, C.4
Kang, I.H.5
-
20
-
-
78649675858
-
Pattern recognition software and techniques for biological image analysis
-
Shamir L, Delaney JD, Orlov N, Eckley DM, Goldberg IG, (2010) Pattern recognition software and techniques for biological image analysis. PLoS Comput Biol 6: e1000974.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Shamir, L.1
Delaney, J.D.2
Orlov, N.3
Eckley, D.M.4
Goldberg, I.G.5
-
21
-
-
79551519982
-
Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice
-
Elkabets M, Gifford AM, Scheel C, Nilsson B, Reinhardt F, et al. (2011) Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice. J Clin Invest 121: 784-799.
-
(2011)
J Clin Invest
, vol.121
, pp. 784-799
-
-
Elkabets, M.1
Gifford, A.M.2
Scheel, C.3
Nilsson, B.4
Reinhardt, F.5
-
22
-
-
58249106935
-
The protein expression of TRP-1 and galectin-1 in cutaneous malignant melanomas
-
Bolander A, Agnarsdottir M, Stromberg S, Ponten F, Hesselius P, et al. (2008) The protein expression of TRP-1 and galectin-1 in cutaneous malignant melanomas. Cancer Genomics Proteomics 5: 293-300.
-
(2008)
Cancer Genomics Proteomics
, vol.5
, pp. 293-300
-
-
Bolander, A.1
Agnarsdottir, M.2
Stromberg, S.3
Ponten, F.4
Hesselius, P.5
-
23
-
-
77649254440
-
The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells
-
Paavilainen L, Edvinsson A, Asplund A, Hober S, Kampf C, et al. (2010) The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells. J Histochem Cytochem 58: 237-246.
-
(2010)
J Histochem Cytochem
, vol.58
, pp. 237-246
-
-
Paavilainen, L.1
Edvinsson, A.2
Asplund, A.3
Hober, S.4
Kampf, C.5
-
24
-
-
33748752115
-
Quantification of immunohistochemistry - issues concerning methods, utility and semiquantitative assessment I
-
Walker RA, (2006) Quantification of immunohistochemistry - issues concerning methods, utility and semiquantitative assessment I. Histopathology. 49: 406-410.
-
(2006)
Histopathology
, vol.49
, pp. 406-410
-
-
Walker, R.A.1
-
25
-
-
33748269365
-
Quantification of immunohistochemistry - issues concerning methods, utility and semiquantitative assessment II
-
Taylor CR, Levenson RM, (2006) Quantification of immunohistochemistry - issues concerning methods, utility and semiquantitative assessment II. Histopathology 49: 411-424.
-
(2006)
Histopathology
, vol.49
, pp. 411-424
-
-
Taylor, C.R.1
Levenson, R.M.2
-
26
-
-
79958283183
-
Standardization in immunohistology
-
Leong AS, Leong TY, (2011) Standardization in immunohistology. Methods Mol Biol 724: 37-68.
-
(2011)
Methods Mol Biol
, vol.724
, pp. 37-68
-
-
Leong, A.S.1
Leong, T.Y.2
-
27
-
-
79954500285
-
Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
-
Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, et al. (2011) Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics 27: 1179-1180.
-
(2011)
Bioinformatics
, vol.27
, pp. 1179-1180
-
-
Kamentsky, L.1
Jones, T.R.2
Fraser, A.3
Bray, M.A.4
Logan, D.J.5
-
28
-
-
0034890852
-
Quantification of histochemical staining by color deconvolution
-
Ruifrok AC, Johnston DA, (2001) Quantification of histochemical staining by color deconvolution. Anal Quant Cytol Histol 23: 291-299.
-
(2001)
Anal Quant Cytol Histol
, vol.23
, pp. 291-299
-
-
Ruifrok, A.C.1
Johnston, D.A.2
-
29
-
-
1842372117
-
Applying watershed algorithms to the segmentation of clustered nuclei
-
Malpica N, de Solorzano CO, Vaquero JJ, Santos A, Vallcorba I, et al. (1997) Applying watershed algorithms to the segmentation of clustered nuclei. Cytometry 28: 289-297.
-
(1997)
Cytometry
, vol.28
, pp. 289-297
-
-
Malpica, N.1
de Solorzano, C.O.2
Vaquero, J.J.3
Santos, A.4
Vallcorba, I.5
-
30
-
-
0032966937
-
Segmentation of confocal microscope images of cell nuclei in thick tissue sections
-
Ortiz de Solorzano C, Garcia Rodriguez E, Jones A, Pinkel D, Gray JW, et al. (1999) Segmentation of confocal microscope images of cell nuclei in thick tissue sections. J Microsc 193: 212-226.
-
(1999)
J Microsc
, vol.193
, pp. 212-226
-
-
Ortiz de Solorzano, C.1
Garcia Rodriguez, E.2
Jones, A.3
Pinkel, D.4
Gray, J.W.5
-
31
-
-
0036139314
-
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells
-
Boland MV, Murphy RF, (2001) A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics 17: 1213-1223.
-
(2001)
Bioinformatics
, vol.17
, pp. 1213-1223
-
-
Boland, M.V.1
Murphy, R.F.2
-
33
-
-
76749092270
-
Witten The WEKA Data Mining Software: An Update
-
Mark Hall EF, Holmes G, Pfahringer B, Reutemann P, Witten IH (2009) Witten The WEKA Data Mining Software: An Update. SIGKDD Explorations 11.
-
(2009)
SIGKDD Explorations
, vol.11
-
-
Mark Hall, E.F.1
Holmes, G.2
Pfahringer, B.3
Reutemann, P.4
Witten, I.H.5
-
35
-
-
16444381830
-
Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma
-
Shi T, Seligson D, Belldegrun AS, Palotie A, Horvath S, (2005) Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma. Mod Pathol 18: 547-557.
-
(2005)
Mod Pathol
, vol.18
, pp. 547-557
-
-
Shi, T.1
Seligson, D.2
Belldegrun, A.S.3
Palotie, A.4
Horvath, S.5
-
36
-
-
0345040882
-
Support vector machine applications in bioinformatics
-
Byvatov E, Schneider G, (2003) Support vector machine applications in bioinformatics. Appl Bioinformatics 2: 67-77.
-
(2003)
Appl Bioinformatics
, vol.2
, pp. 67-77
-
-
Byvatov, E.1
Schneider, G.2
-
37
-
-
20744453541
-
Biological applications of support vector machines
-
Yang ZR, (2004) Biological applications of support vector machines. Brief Bioinform 5: 328-338.
-
(2004)
Brief Bioinform
, vol.5
, pp. 328-338
-
-
Yang, Z.R.1
-
38
-
-
79952214714
-
Robust automated tumour segmentation on histological and immunohistochemical tissue images
-
Wang CW, Fennell D, Paul I, Savage K, Hamilton P, (2011) Robust automated tumour segmentation on histological and immunohistochemical tissue images. PLoS One 6: e15818.
-
(2011)
PLoS One
, vol.6
-
-
Wang, C.W.1
Fennell, D.2
Paul, I.3
Savage, K.4
Hamilton, P.5
-
39
-
-
78349306096
-
SOX10 expression in superficial spreading and nodular malignant melanomas
-
Agnarsdottir M, Sooman L, Bolander A, Stromberg S, Rexhepaj E, et al. (2010) SOX10 expression in superficial spreading and nodular malignant melanomas. Melanoma Res 20: 468-478.
-
(2010)
Melanoma Res
, vol.20
, pp. 468-478
-
-
Agnarsdottir, M.1
Sooman, L.2
Bolander, A.3
Stromberg, S.4
Rexhepaj, E.5
-
40
-
-
77954760173
-
Biomarkers: the useful and the not so useful - an assessment of molecular prognostic markers for cutaneous melanoma
-
Gould Rothberg BE, Rimm DL, (2010) Biomarkers: the useful and the not so useful - an assessment of molecular prognostic markers for cutaneous melanoma. J Invest Dermatol 130: 1971-1987.
-
(2010)
J Invest Dermatol
, vol.130
, pp. 1971-1987
-
-
Gould Rothberg, B.E.1
Rimm, D.L.2
-
41
-
-
78650900647
-
ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67
-
Tuominen VJ, Ruotoistenmaki S, Viitanen A, Jumppanen M, Isola J, (2010) ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67. Breast Cancer Res 12: R56.
-
(2010)
Breast Cancer Res
, vol.12
-
-
Tuominen, V.J.1
Ruotoistenmaki, S.2
Viitanen, A.3
Jumppanen, M.4
Isola, J.5
-
42
-
-
73349128764
-
Melanoma prognostic model using tissue microarrays and genetic algorithms
-
Gould Rothberg BE, Berger AJ, Molinaro AM, Subtil A, Krauthammer MO, et al. (2009) Melanoma prognostic model using tissue microarrays and genetic algorithms. J Clin Oncol 27: 5772-5780.
-
(2009)
J Clin Oncol
, vol.27
, pp. 5772-5780
-
-
Gould Rothberg, B.E.1
Berger, A.J.2
Molinaro, A.M.3
Subtil, A.4
Krauthammer, M.O.5
-
43
-
-
78549255596
-
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, et al. (2010) Validation of cytoplasmic-to-nuclear ratio of survivin as an indicator of improved prognosis in breast cancer. BMC Cancer 10: 639.
-
(2010)
BMC Cancer
, vol.10
, pp. 639
-
-
Rexhepaj, E.1
Jirstrom, K.2
O'Connor, D.P.3
O'Brien, S.L.4
Landberg, G.5
-
44
-
-
59449103707
-
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, et al. (2008) 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. Breast Cancer Res 10: R89.
-
(2008)
Breast Cancer Res
, vol.10
-
-
Rexhepaj, E.1
Brennan, D.J.2
Holloway, P.3
Kay, E.W.4
McCann, A.H.5
-
45
-
-
80053458657
-
Practical considerations of image analysis and quantification of signal transduction IHC staining
-
Grunkin M, Raundahl J, Foged NT, (2011) Practical considerations of image analysis and quantification of signal transduction IHC staining. Methods Mol Biol 717: 143-154.
-
(2011)
Methods Mol Biol
, vol.717
, pp. 143-154
-
-
Grunkin, M.1
Raundahl, J.2
Foged, N.T.3
-
46
-
-
73849145104
-
A global view of protein expression in human cells, tissues, and organs
-
Ponten F, Gry M, Fagerberg L, Lundberg E, Asplund A, et al. (2009) A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol 5: 337.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 337
-
-
Ponten, F.1
Gry, M.2
Fagerberg, L.3
Lundberg, E.4
Asplund, A.5
|