-
1
-
-
0035375137
-
Computational analysis of microarray data
-
Quackenbush J. Computational analysis of microarray data. Nature Rev. Genet. 2(6), 418-427 (2001).
-
(2001)
Nature Rev. Genet.
, vol.2
, Issue.6
, pp. 418-427
-
-
Quackenbush, J.1
-
3
-
-
22244458625
-
Applications of DNA microarrays in biology
-
Stoughton RB. Applications of DNA microarrays in biology. Ann. Rev. Biochem. 74, 53-82 (2005).
-
(2005)
Ann. Rev. Biochem.
, vol.74
, pp. 53-82
-
-
Stoughton, R.B.1
-
4
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang YH, Speed T. Design issues for cDNA microarray experiments. Nature Rev. Genet. 3(8), 579-588 (2002).
-
(2002)
Nature Rev. Genet.
, vol.3
, Issue.8
, pp. 579-588
-
-
Yang, Y.H.1
Speed, T.2
-
5
-
-
0036900895
-
Fundamentals of experimental design for cDNA microarrays
-
Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nature Genet. 32(Suppl.), 490-495 (2002).
-
(2002)
Nature Genet.
, vol.32
, Issue.SUPPL.
, pp. 490-495
-
-
Churchill, G.A.1
-
6
-
-
0038048164
-
Statistical issues in cDNA microarray data analysis
-
Smyth GK, Yang YH, Speed T. Statistical issues in cDNA microarray data analysis. Methods Mol. Biol. 224, 111-136 (2003).
-
(2003)
Methods Mol. Biol.
, vol.224
, pp. 111-136
-
-
Smyth, G.K.1
Yang, Y.H.2
Speed, T.3
-
8
-
-
1342294092
-
Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
-
Yang YH, Dudoit S, Luu P et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30(4), e15 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, Issue.4
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
-
9
-
-
0037076772
-
Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis
-
RESEARCH0033
-
Hoffmann R, Seidl T, Dugas M. Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol. 3(7), RESEARCH0033 (2002).
-
(2002)
Genome Biol.
, vol.3
, Issue.7
-
-
Hoffmann, R.1
Seidl, T.2
Dugas, M.3
-
10
-
-
0037177855
-
Transcript abundance in yeast varies over six orders of magnitude
-
Holland MJ. Transcript abundance in yeast varies over six orders of magnitude. J. Biol. Chem, 277(17), 14363-14366 (2002).
-
(2002)
J. Biol. Chem
, vol.277
, Issue.17
, pp. 14363-14366
-
-
Holland, M.J.1
-
11
-
-
2442691827
-
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
-
Mecham BH, Klus GT, Strovel J et al. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 32(9), e74 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.9
-
-
Mecham, B.H.1
Klus, G.T.2
Strovel, J.3
-
12
-
-
13844256710
-
Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach
-
Zhang J, Finney RP, Clifford RJ, Derr LK, Buetow KH. Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach. Genomics 85(3), 297-308 (2005).
-
(2005)
Genomics
, vol.85
, Issue.3
, pp. 297-308
-
-
Zhang, J.1
Finney, R.P.2
Clifford, R.J.3
Derr, L.K.4
Buetow, K.H.5
-
13
-
-
33846563409
-
Why most published research findings are false
-
Ioannidis JP. Why most published research findings are false. PLoS Med. 2(8), e124 (2005).
-
(2005)
PLoS Med.
, vol.2
, Issue.8
-
-
Ioannidis, J.P.1
-
14
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van't Veer LJ, Dai H, van de Vijver MJ et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871), 530-536 (2002).
-
(2002)
Nature
, vol.415
, Issue.6871
, pp. 530-536
-
-
Van't Veer, L.J.1
Dai, H.2
Van De Vijver, M.J.3
-
15
-
-
0037245772
-
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data
-
Ooi CH, Tan P. Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. Bioinformatics 19(1), 37-44 (2003). Introduces a classification method in which evolutionary algorithm (EA)-based gene selection is combined with maximum likelihood Bayesian classification of gene expression data.
-
(2003)
Bioinformatics
, vol.19
, Issue.1
, pp. 37-44
-
-
Ooi, C.H.1
Tan, P.2
-
16
-
-
20744448405
-
Multiclass cancer classification and biomarker discovery using GA-based algorithms
-
Liu JJ, Cutler G, Li W et al. Multiclass cancer classification and biomarker discovery using GA-based algorithms. Bioinformatics 21(11), 2691-2697 (2005). Considers multiclass cancer classification, achieving 88.52% leave-one-out cross-validation (LOOCV) accuracy on the NCI60 data set.
-
(2005)
Bioinformatics
, vol.21
, Issue.11
, pp. 2691-2697
-
-
Liu, J.J.1
Cutler, G.2
Li, W.3
-
17
-
-
0003684449
-
-
Springer, NY, USA
-
Hastie T, Tibshirani R, Friedman JH. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. 14, Springer, NY, USA (2001).
-
(2001)
The Elements of Statistical Learning: Data Mining, Inference, and Prediction
, pp. 14
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.H.3
-
18
-
-
0035845511
-
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
-
Sorlie T, Perou CM, Tibshirani R et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98(19), 10869-10874 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, Issue.19
, pp. 10869-10874
-
-
Sorlie, T.1
Perou, C.M.2
Tibshirani, R.3
-
19
-
-
13444249852
-
Prediction of cancer outcome with microarrays: A multiple random validation strategy
-
Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365(9458), 488-492 (2005).
-
(2005)
Lancet
, vol.365
, Issue.9458
, pp. 488-492
-
-
Michiels, S.1
Koscielny, S.2
Hill, C.3
-
20
-
-
13844310310
-
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
-
Wang Y, Klijn JG, Zhang T et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365(9460), 671-679 (2005).
-
(2005)
Lancet
, vol.365
, Issue.9460
, pp. 671-679
-
-
Wang, Y.1
Klijn, J.G.2
Zhang, T.3
-
22
-
-
0037076322
-
Selection bias in gene extraction on the basis of microarray gene-expression data
-
Ambroise C, McLachlan GJ. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc. Natl Acad. Sci. USA 99(10), 6562-6566 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, Issue.10
, pp. 6562-6566
-
-
Ambroise, C.1
McLachlan, G.J.2
-
23
-
-
15844413351
-
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
-
Statnikov A, Aliferis CF, Tsamardinos I, Hardin D, Levy S. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics 21(5), 631-643 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.5
, pp. 631-643
-
-
Statnikov, A.1
Aliferis, C.F.2
Tsamardinos, I.3
Hardin, D.4
Levy, S.5
-
25
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
Brown MP, Grundy WN, Lin D et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA 97(1), 262-267 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, Issue.1
, pp. 262-267
-
-
Brown, M.P.1
Grundy, W.N.2
Lin, D.3
-
26
-
-
0022471098
-
Learning representations by backjpropagating errors
-
Rumelhart DE, Hinton GE, Williams RJ. Learning representations by backjpropagating errors. Nature 323, 533-536 (1986).
-
(1986)
Nature
, vol.323
, pp. 533-536
-
-
Rumelhart, D.E.1
Hinton, G.E.2
Williams, R.J.3
-
27
-
-
0034954414
-
Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
-
Khan J, Wei JS, Ringner M et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nature Med. 7(6), 673-679 (2001).
-
(2001)
Nature Med.
, vol.7
, Issue.6
, pp. 673-679
-
-
Khan, J.1
Wei, J.S.2
Ringner, M.3
-
28
-
-
22944458389
-
Computational analysis of leukemia microarray expression data using the GA/KNN method
-
Li L, Pedersen LG, Darden TA, Weinberg C. Computational analysis of leukemia microarray expression data using the GA/KNN method. Proceedings of the First Conference on Critical Assessment of Microarray Data Analysis, CAMDA2000 (2000). Introduces the genetic algorithm (GA)/k-nearest neighbour (KNN) method, which combines EA-based gene selection with the KNN classification method.
-
(2000)
Proceedings of the First Conference on Critical Assessment of Microarray Data Analysis, CAMDA2000
-
-
Li, L.1
Pedersen, L.G.2
Darden, T.A.3
Weinberg, C.4
-
29
-
-
0036139278
-
Gene selection for sample classification based on gene expression data: Study of sensitivity to choice of parameters of the GA/KNN method
-
Li L, Pedersen LG, Darden TA, Weinberg C. Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinfarmatics 17(12), 1131-1142 (2001).
-
(2001)
Bioinfarmatics
, vol.17
, Issue.12
, pp. 1131-1142
-
-
Li, L.1
Pedersen, L.G.2
Darden, T.A.3
Weinberg, C.4
-
30
-
-
0035664710
-
Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method
-
Li L, Darden TA, Weinberg CR, Levine AJ, Pedersen LG. Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. Comb. Chem. High Throughput Screen. 4(8), 727-739 (2001).
-
(2001)
Comb. Chem. High Throughput Screen.
, vol.4
, Issue.8
, pp. 727-739
-
-
Li, L.1
Darden, T.A.2
Weinberg, C.R.3
Levine, A.J.4
Pedersen, L.G.5
-
31
-
-
0037255041
-
Evolutionary algorithms for finding optimal gene sets in microarray prediction
-
Deutsch JM. Evolutionary algorithms for finding optimal gene sets in microarray prediction. Bioinformatics 19(1), 45-52 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.1
, pp. 45-52
-
-
Deutsch, J.M.1
-
32
-
-
0034863834
-
Classification of microarray data with penalized logistic regression
-
Eilers P, Boer J, Van Ommen GJ, Van Houwelingen H. Classification of microarray data with penalized logistic regression. In: Proceedings of SPIE, Progress in Biomedical Optics and Images, 4266, 187-198 (2001).
-
(2001)
Proceedings of SPIE, Progress in Biomedical Optics and Images
, vol.4266
, pp. 187-198
-
-
Eilers, P.1
Boer, J.2
Van Ommen, G.J.3
Van Houwelingen, H.4
-
35
-
-
33645350756
-
Analyzing gene expression data using classification rules
-
Pavlovic V, Garg A, Kasif S (Eds). Washington, DC, USA
-
Livingston G, Li X, Li G, Hao L, Zhou J. Analyzing gene expression data using classification rules. In: The Twentieth International Conference on Machine Learning Pavlovic V, Garg A, Kasif S (Eds). Washington, DC, USA (2003).
-
(2003)
The Twentieth International Conference on Machine Learning
-
-
Livingston, G.1
Li, X.2
Li, G.3
Hao, L.4
Zhou, J.5
-
36
-
-
0035478854
-
-
Machine Learning
-
Breiman L. Random Forests. Machine Learning, 45, 5-32 (2001).
-
(2001)
Random Forests
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
37
-
-
0033692876
-
Tissue classification with gene expression profiles
-
Ben-Dor A, Bruhn L, Friedman et al. Tissue classification with gene expression profiles. J. Comput. Biol. 7(3-4), 559-583 (2000).
-
(2000)
J. Comput. Biol.
, vol.7
, Issue.3-4
, pp. 559-583
-
-
Ben-Dor, A.1
Bruhn, L.2
Friedman3
-
38
-
-
33645373158
-
The analysis of cancer-associated gene expression matrices
-
Kitano H (Ed.), MIT Press, MA, USA
-
Wahde M, Szallasi Z. The analysis of cancer-associated gene expression matrices. In: Foundations of Systems Biology. Kitano H (Ed.), MIT Press, MA, USA (2001).
-
(2001)
Foundations of Systems Biology
-
-
Wahde, M.1
Szallasi, Z.2
-
40
-
-
18244409933
-
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning
-
Shipp, MA, Ross KN, Tamayo P et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nature Med. 8(1), 68-74 (2002).
-
(2002)
Nature Med.
, vol.8
, Issue.1
, pp. 68-74
-
-
Shipp, M.A.1
Ross, K.N.2
Tamayo, P.3
-
41
-
-
0037142053
-
The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma
-
Rosenwald A, Wright G, Chan WC et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346(25), 1937-1947 (2002).
-
(2002)
N. Engl. J. Med.
, vol.346
, Issue.25
, pp. 1937-1947
-
-
Rosenwald, A.1
Wright, G.2
Chan, W.C.3
-
46
-
-
0035748446
-
Selecting informative genes with parallel genetic algorithms in tissue classification
-
Liu J, Iba H, Ishizuka M. Selecting informative genes with parallel genetic algorithms in tissue classification. Genome Inform. Ser. Workshop Genome Inform. 12, 14-23 (2001).
-
(2001)
Genome Inform. Ser. Workshop Genome Inform.
, vol.12
, pp. 14-23
-
-
Liu, J.1
Iba, H.2
Ishizuka, M.3
-
47
-
-
33645361560
-
Improving the prediction of the clinical outcome of breast cancer using evolutionary algorithms
-
Wahde M, Szallasi Z. Improving the prediction of the clinical outcome of breast cancer using evolutionary algorithms. Soft Computing (2005). Completely EA-based method for binary (two-class) gene expression data classification, a method that uses an EA not only for gene selection but also for classification.
-
(2005)
Soft Computing
-
-
Wahde, M.1
Szallasi, Z.2
-
48
-
-
0033569406
-
Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
-
5439
-
Golub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (5439).
-
Science
, vol.286
, pp. 531-537
-
-
Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
-
49
-
-
0033536012
-
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
-
Alon U, Barkai N, Notterman DA et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci. USA 96(12), 6745-6750 (1999).
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, Issue.12
, pp. 6745-6750
-
-
Alon, U.1
Barkai, N.2
Notterman, D.A.3
-
50
-
-
84863049823
-
Genetic algorithms and silhouette measures applied to microarray data classification
-
Imperial College Press, London, UK
-
Lin TC, Liu RC, Chen SY, Liu CC, Chen CY. Genetic algorithms and silhouette measures applied to microarray data classification. Proceedings of the 3rd Asia-Pacific Bioinformatics Conference. Imperial College Press, London, UK 229-238 (2005). Used EA-based gene selection combined with the silhouette statistic for classification and achieved 90.3% LOOCV accuracy on the NCI60 data set.
-
(2005)
Proceedings of the 3rd Asia-Pacific Bioinformatics Conference
, pp. 229-238
-
-
Lin, T.C.1
Liu, R.C.2
Chen, S.Y.3
Liu, C.C.4
Chen, C.Y.5
-
51
-
-
0034050902
-
Systematic variation in gene expression patterns in human cancer cell lines
-
Ross DT, Scherf U, Eisen ME et al. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genet. 24(3), 227-235 (2000).
-
(2000)
Nature Genet.
, vol.24
, Issue.3
, pp. 227-235
-
-
Ross, D.T.1
Scherf, U.2
Eisen, M.E.3
-
52
-
-
0344872506
-
Molecular classification of cancer types from microarray data using the combination of genetic algorithms and support vector machines
-
Peng S, Xu Q, Ling XB et al. Molecular classification of cancer types from microarray data using the combination of genetic algorithms and support vector machines. FEBS Lett. 555(2), 358-362 (2003). Introduces a classification method in which gene selection is performed by a GA, the results of which are classified using support vector machines.
-
(2003)
FEBS Lett.
, vol.555
, Issue.2
, pp. 358-362
-
-
Peng, S.1
Xu, Q.2
Ling, X.B.3
-
53
-
-
1542577328
-
Comparing cDNA and oligonucleotide array data: Concordance of gene expression across platforms for the NCI-60 cancer cells
-
Lee JK, Bussey KJ, Gwadry FG et al. Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol. 4(12), R82 (2003).
-
(2003)
Genome Biol.
, vol.4
, Issue.12
-
-
Lee, J.K.1
Bussey, K.J.2
Gwadry, F.G.3
-
55
-
-
0345724886
-
Reliable classification of two-class cancer data using evolutionary algorithms
-
Deb K, Raji Reddy A. Reliable classification of two-class cancer data using evolutionary algorithms. Biosystems 72(1-2), 111-129 (2003).
-
(2003)
Biosystems
, vol.72
, Issue.1-2
, pp. 111-129
-
-
Deb, K.1
Raji Reddy, A.2
|