-
1
-
-
77958478375
-
Bioinformatic strategies for cDNA-microarray data processing
-
John Wiley & Sons, Scherer A
-
Fahlén J, Landfors M, Freyhult E, Trygg J, Hvidsten TR, Rydén P. Bioinformatic strategies for cDNA-microarray data processing. Batch Effects and Noise in Microarray Experiments: Sources and Solutions 2009, John Wiley & Sons, Scherer A.
-
(2009)
Batch Effects and Noise in Microarray Experiments: Sources and Solutions
-
-
Fahlén, J.1
Landfors, M.2
Freyhult, E.3
Trygg, J.4
Hvidsten, T.R.5
Rydén, P.6
-
2
-
-
35748949257
-
A comparison of background correction methods for two-colour microarrays
-
10.1093/bioinformatics/btm412, 17720982
-
Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007, 23(20):2700-2707. 10.1093/bioinformatics/btm412, 17720982.
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2700-2707
-
-
Ritchie, M.E.1
Silver, J.2
Oshlack, A.3
Holmes, M.4
Diyagama, D.5
Holloway, A.6
Smyth, G.K.7
-
3
-
-
0036898577
-
Microarray data normalization and transformation
-
Quackenbush J. Microarray data normalization and transformation. Nat Genet 2002, 32(Suppl):496-501.
-
(2002)
Nat Genet
, vol.32
, Issue.SUPPL
, pp. 496-501
-
-
Quackenbush, J.1
-
4
-
-
33746994071
-
Evaluation of microarray data normalization procedures using spike-in experiments
-
10.1186/1471-2105-7-300, 1526761, 16774679
-
Ryden P, Andersson H, Landfors M, Naslund L, Hartmanova B, Noppa L, Sjostedt A. Evaluation of microarray data normalization procedures using spike-in experiments. BMC Bioinformatics 2006, 7:300. 10.1186/1471-2105-7-300, 1526761, 16774679.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 300
-
-
Ryden, P.1
Andersson, H.2
Landfors, M.3
Naslund, L.4
Hartmanova, B.5
Noppa, L.6
Sjostedt, A.7
-
5
-
-
9144268360
-
Empirical evaluation of data transformations and ranking statistics for microarray analysis
-
10.1093/nar/gkh866, 524279, 15479783
-
Qin LX, Kerr KF. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32(18):5471-5479. 10.1093/nar/gkh866, 524279, 15479783.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.18
, pp. 5471-5479
-
-
Qin, L.X.1
Kerr, K.F.2
-
6
-
-
33645552696
-
Effect of data normalization on fuzzy clustering of DNA microarray data
-
10.1186/1471-2105-7-134, 1431564, 16533412
-
Kim SY, Lee JW, Bae JS. Effect of data normalization on fuzzy clustering of DNA microarray data. BMC Bioinformatics 2006, 7:134. 10.1186/1471-2105-7-134, 1431564, 16533412.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 134
-
-
Kim, S.Y.1
Lee, J.W.2
Bae, J.S.3
-
7
-
-
77957674888
-
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
-
Freyhult E, Landfors M, Onskog J, Hvidsten TR, Ryden P. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering. BMC Bioinformatics 11:503.
-
BMC Bioinformatics
, vol.11
, pp. 503
-
-
Freyhult, E.1
Landfors, M.2
Onskog, J.3
Hvidsten, T.R.4
Ryden, P.5
-
8
-
-
35748932917
-
A review of feature selection techniques in bioinformatics
-
10.1093/bioinformatics/btm344, 17720704
-
Saeys Y, Inza I, Larranaga P. A review of feature selection techniques in bioinformatics. Bioinformatics 2007, 23(19):2507-2517. 10.1093/bioinformatics/btm344, 17720704.
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2507-2517
-
-
Saeys, Y.1
Inza, I.2
Larranaga, P.3
-
9
-
-
77950356812
-
Advances in metaheuristics for gene selection and classification of microarray data
-
Duval B, Hao JK. Advances in metaheuristics for gene selection and classification of microarray data. Brief Bioinform 11(1):127-141.
-
Brief Bioinform
, vol.11
, Issue.1
, pp. 127-141
-
-
Duval, B.1
Hao, J.K.2
-
10
-
-
33748849648
-
Machine learning in bioinformatics
-
10.1093/bib/bbk007, 16761367
-
Larranaga P, Calvo B, Santana R, Bielza C, Galdiano J, Inza I, Lozano JA, Armananzas R, Santafe G, Perez A, et al. Machine learning in bioinformatics. Brief Bioinform 2006, 7(1):86-112. 10.1093/bib/bbk007, 16761367.
-
(2006)
Brief Bioinform
, vol.7
, Issue.1
, pp. 86-112
-
-
Larranaga, P.1
Calvo, B.2
Santana, R.3
Bielza, C.4
Galdiano, J.5
Inza, I.6
Lozano, J.A.7
Armananzas, R.8
Santafe, G.9
Perez, A.10
-
11
-
-
44449145580
-
A comparative study of different machine learning methods on microarray gene expression data
-
10.1186/1471-2164-9-S1-S13, 2559877, 18831778
-
Pirooznia M, Yang JY, Yang MQ, Deng Y. A comparative study of different machine learning methods on microarray gene expression data. BMC Genomics 2008, 9(Suppl 1):S13. 10.1186/1471-2164-9-S1-S13, 2559877, 18831778.
-
(2008)
BMC Genomics
, vol.9
, Issue.SUPPL. 1
-
-
Pirooznia, M.1
Yang, J.Y.2
Yang, M.Q.3
Deng, Y.4
-
12
-
-
0037447386
-
Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification
-
10.1093/hmg/ddg093, 12668606
-
Romualdi C, Campanaro S, Campagna D, Celegato B, Cannata N, Toppo S, Valle G, Lanfranchi G. Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification. Hum Mol Genet 2003, 12(8):823-836. 10.1093/hmg/ddg093, 12668606.
-
(2003)
Hum Mol Genet
, vol.12
, Issue.8
, pp. 823-836
-
-
Romualdi, C.1
Campanaro, S.2
Campagna, D.3
Celegato, B.4
Cannata, N.5
Toppo, S.6
Valle, G.7
Lanfranchi, G.8
-
13
-
-
10444280144
-
An extensive comparison of recent classification tools applied to microarray data
-
10.1016/j.csda.2004.03.017, 3186933, 22013401
-
Lee JW, Lee JB, Park M, Song SH. An extensive comparison of recent classification tools applied to microarray data. Computational Statistics & Data Analysis 2005, 48(4):869-885. 10.1016/j.csda.2004.03.017, 3186933, 22013401.
-
(2005)
Computational Statistics & Data Analysis
, vol.48
, Issue.4
, pp. 869-885
-
-
Lee, J.W.1
Lee, J.B.2
Park, M.3
Song, S.H.4
-
14
-
-
7244248755
-
A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
-
10.1093/bioinformatics/bth267, 15087314
-
Li T, Zhang C, Ogihara M. A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. Bioinformatics 2004, 20(15):2429-2437. 10.1093/bioinformatics/bth267, 15087314.
-
(2004)
Bioinformatics
, vol.20
, Issue.15
, pp. 2429-2437
-
-
Li, T.1
Zhang, C.2
Ogihara, M.3
-
15
-
-
15844413351
-
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
-
10.1093/bioinformatics/bti033, 15374862
-
Statnikov A, Aliferis CF, Tsamardinos I, Hardin D, Levy S. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics 2005, 21(5):631-643. 10.1093/bioinformatics/bti033, 15374862.
-
(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
-
16
-
-
50349090268
-
Cross-validation and bootstrapping are unreliable in small sample classification
-
Isaksson A, Wallman M, Goransson H, Gustafsson M. Cross-validation and bootstrapping are unreliable in small sample classification. Pattern Recognition Letters 2008, 29(14):1960-1965.
-
(2008)
Pattern Recognition Letters
, vol.29
, Issue.14
, pp. 1960-1965
-
-
Isaksson, A.1
Wallman, M.2
Goransson, H.3
Gustafsson, M.4
-
17
-
-
67049095607
-
Impossibility of successful classification when useful features are rare and weak
-
10.1073/pnas.0903931106, 2682944, 19447927
-
Jin J. Impossibility of successful classification when useful features are rare and weak. Proc Natl Acad Sci USA 2009, 106(22):8859-8864. 10.1073/pnas.0903931106, 2682944, 19447927.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.22
, pp. 8859-8864
-
-
Jin, J.1
-
18
-
-
1842420581
-
General conditions for predictivity in learning theory
-
10.1038/nature02341, 15042089
-
Poggio T, Rifkin R, Mukherjee S, Niyogi P. General conditions for predictivity in learning theory. Nature 2004, 428(6981):419-422. 10.1038/nature02341, 15042089.
-
(2004)
Nature
, vol.428
, Issue.6981
, pp. 419-422
-
-
Poggio, T.1
Rifkin, R.2
Mukherjee, S.3
Niyogi, P.4
-
19
-
-
64549112122
-
Outcome prediction based on microarray analysis: a critical perspective on methods
-
10.1186/1471-2105-10-53, 2667512, 19200394
-
Zervakis M, Blazadonakis ME, Tsiliki G, Danilatou V, Tsiknakis M, Kafetzopoulos D. Outcome prediction based on microarray analysis: a critical perspective on methods. BMC Bioinformatics 2009, 10:53. 10.1186/1471-2105-10-53, 2667512, 19200394.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 53
-
-
Zervakis, M.1
Blazadonakis, M.E.2
Tsiliki, G.3
Danilatou, V.4
Tsiknakis, M.5
Kafetzopoulos, D.6
-
20
-
-
0004089660
-
Engineering statistics
-
Hoboken, N.J.: Weily, 4
-
Montgomery DC, Runger GC, Hubele NF. Engineering statistics. 2007, Hoboken, N.J.: Weily, 4.
-
(2007)
-
-
Montgomery, D.C.1
Runger, G.C.2
Hubele, N.F.3
-
21
-
-
0004255908
-
Machine learning
-
Singapore: McGraw-Hill, First
-
Mitchell TM. Machine learning. 1997, Singapore: McGraw-Hill, First.
-
(1997)
-
-
Mitchell, T.M.1
-
22
-
-
0037076322
-
Selection bias in gene extraction on the basis of microarray gene-expression data
-
10.1073/pnas.102102699, 124442, 11983868
-
Ambroise C, McLachlan GJ. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci USA 2002, 99(10):6562-6566. 10.1073/pnas.102102699, 124442, 11983868.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.10
, pp. 6562-6566
-
-
Ambroise, C.1
McLachlan, G.J.2
-
23
-
-
0036855402
-
Comparison of microarray designs for class comparison and class discovery
-
10.1093/bioinformatics/18.11.1438, 12424114
-
Dobbin K, Simon R. Comparison of microarray designs for class comparison and class discovery. Bioinformatics 2002, 18(11):1438-1445. 10.1093/bioinformatics/18.11.1438, 12424114.
-
(2002)
Bioinformatics
, vol.18
, Issue.11
, pp. 1438-1445
-
-
Dobbin, K.1
Simon, R.2
-
24
-
-
0034598746
-
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
-
10.1038/35000501, 10676951
-
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403(6769):503-511. 10.1038/35000501, 10676951.
-
(2000)
Nature
, vol.403
, Issue.6769
, pp. 503-511
-
-
Alizadeh, A.A.1
Eisen, M.B.2
Davis, R.E.3
Ma, C.4
Lossos, I.S.5
Rosenwald, A.6
Boldrick, J.C.7
Sabet, H.8
Tran, T.9
Yu, X.10
-
25
-
-
33751312857
-
Gene expression signatures of morphologically normal breast tissue identify basal-like tumors
-
10.1186/bcr1608, 1779486, 17054791
-
Finak G, Sadekova S, Pepin F, Hallett M, Meterissian S, Halwani F, Khetani K, Souleimanova M, Zabolotny B, Omeroglu A, et al. Gene expression signatures of morphologically normal breast tissue identify basal-like tumors. Breast Cancer Res 2006, 8(5):R58. 10.1186/bcr1608, 1779486, 17054791.
-
(2006)
Breast Cancer Res
, vol.8
, Issue.5
-
-
Finak, G.1
Sadekova, S.2
Pepin, F.3
Hallett, M.4
Meterissian, S.5
Halwani, F.6
Khetani, K.7
Souleimanova, M.8
Zabolotny, B.9
Omeroglu, A.10
-
26
-
-
77953548553
-
Differential gene expression profiles of invasive and non-invasive non-functioning pituitary adenomas based on microarray analysis
-
Galland F, Lacroix L, Saulnier P, Dessen P, Meduri G, Bernier M, Gaillard S, Guibourdenche J, Fournier T, Evain-Brion D, et al. Differential gene expression profiles of invasive and non-invasive non-functioning pituitary adenomas based on microarray analysis. Endocr Relat Cancer 17(2):361-371.
-
Endocr Relat Cancer
, vol.17
, Issue.2
, pp. 361-371
-
-
Galland, F.1
Lacroix, L.2
Saulnier, P.3
Dessen, P.4
Meduri, G.5
Bernier, M.6
Gaillard, S.7
Guibourdenche, J.8
Fournier, T.9
Evain-Brion, D.10
-
27
-
-
34548863946
-
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
-
10.1186/gb-2007-8-5-r76, 1929138, 17493263
-
Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, et al. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 2007, 8(5):R76. 10.1186/gb-2007-8-5-r76, 1929138, 17493263.
-
(2007)
Genome Biol
, vol.8
, Issue.5
-
-
Herschkowitz, J.I.1
Simin, K.2
Weigman, V.J.3
Mikaelian, I.4
Usary, J.5
Hu, Z.6
Rasmussen, K.E.7
Jones, L.P.8
Assefnia, S.9
Chandrasekharan, S.10
-
28
-
-
1542375346
-
Two prognostically significant subtypes of high-grade lung neuroendocrine tumours independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles
-
10.1016/S0140-6736(04)15693-6, 15016488
-
Jones MH, Virtanen C, Honjoh D, Miyoshi T, Satoh Y, Okumura S, Nakagawa K, Nomura H, Ishikawa Y. Two prognostically significant subtypes of high-grade lung neuroendocrine tumours independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. Lancet 2004, 363(9411):775-781. 10.1016/S0140-6736(04)15693-6, 15016488.
-
(2004)
Lancet
, vol.363
, Issue.9411
, pp. 775-781
-
-
Jones, M.H.1
Virtanen, C.2
Honjoh, D.3
Miyoshi, T.4
Satoh, Y.5
Okumura, S.6
Nakagawa, K.7
Nomura, H.8
Ishikawa, Y.9
-
29
-
-
0035845511
-
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
-
10.1073/pnas.191367098, 58566, 11553815
-
Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98(19):10869-10874. 10.1073/pnas.191367098, 58566, 11553815.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.19
, pp. 10869-10874
-
-
Sorlie, T.1
Perou, C.M.2
Tibshirani, R.3
Aas, T.4
Geisler, S.5
Johnsen, H.6
Hastie, T.7
Eisen, M.B.8
van de Rijn, M.9
Jeffrey, S.S.10
-
30
-
-
0037391756
-
Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning
-
10.1038/nm843, 12640447
-
Ye QH, Qin LX, Forgues M, He P, Kim JW, Peng AC, Simon R, Li Y, Robles AI, Chen Y, et al. Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 2003, 9(4):416-423. 10.1038/nm843, 12640447.
-
(2003)
Nat Med
, vol.9
, Issue.4
, pp. 416-423
-
-
Ye, Q.H.1
Qin, L.X.2
Forgues, M.3
He, P.4
Kim, J.W.5
Peng, A.C.6
Simon, R.7
Li, Y.8
Robles, A.I.9
Chen, Y.10
-
31
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
-
Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002, 12:111-140.
-
(2002)
Statistica Sinica
, vol.12
, pp. 111-140
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
32
-
-
1342294092
-
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
-
10.1093/nar/30.4.e15, 100354, 11842121
-
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30(4):e15. 10.1093/nar/30.4.e15, 100354, 11842121.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.4
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
Speed, T.P.7
-
33
-
-
0004278772
-
ScanAlyze. User manual
-
Eisen MB. ScanAlyze. User manual. 1999,
-
(1999)
-
-
Eisen, M.B.1
-
34
-
-
82555167236
-
Bioinformatic Strategies for cDNA-Microarray Data Processing
-
John Wiley & Sons, Ltd, (ed.)
-
Scherer A, . (ed.) Bioinformatic Strategies for cDNA-Microarray Data Processing. 2009, John Wiley & Sons, Ltd, (ed.).
-
(2009)
-
-
Scherer, A.1
-
35
-
-
77950949307
-
Dealing with missing values in large-scale studies: microarray data imputation and beyond
-
Aittokallio T. Dealing with missing values in large-scale studies: microarray data imputation and beyond. Brief Bioinform 11(2):253-264.
-
Brief Bioinform
, vol.11
, Issue.2
, pp. 253-264
-
-
Aittokallio, T.1
-
36
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
10.1093/bioinformatics/17.6.520, 11395428
-
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17(6):520-525. 10.1093/bioinformatics/17.6.520, 11395428.
-
(2001)
Bioinformatics
, vol.17
, Issue.6
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
Tibshirani, R.6
Botstein, D.7
Altman, R.B.8
-
37
-
-
0004172718
-
Pattern recognition
-
San Diego, Calif.: Academic Press
-
Theodoridis S, Koutroumbas K. Pattern recognition. 1999, San Diego, Calif.: Academic Press.
-
(1999)
-
-
Theodoridis, S.1
Koutroumbas, K.2
-
38
-
-
0003684449
-
The elements of statistical learning: data mining, inference, and prediction
-
New York: Springer
-
Hastie T, Tibshirani R, Friedman JH. The elements of statistical learning: data mining, inference, and prediction. 2001, New York: Springer.
-
(2001)
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.H.3
-
39
-
-
0003594381
-
Statistical inference
-
Pacific Grove, Calif.: Duxbury, 2
-
Casella G, Berger RL. Statistical inference. 2002, Pacific Grove, Calif.: Duxbury, 2.
-
(2002)
-
-
Casella, G.1
Berger, R.L.2
-
41
-
-
55449125185
-
Support vector machines and kernels for computational biology
-
10.1371/journal.pcbi.1000173, 2547983, 18974822
-
Ben-Hur A, Ong CS, Sonnenburg S, Scholkopf B, Ratsch G. Support vector machines and kernels for computational biology. PLoS Comput Biol 2008, 4(10):e1000173. 10.1371/journal.pcbi.1000173, 2547983, 18974822.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.10
-
-
Ben-Hur, A.1
Ong, C.S.2
Sonnenburg, S.3
Scholkopf, B.4
Ratsch, G.5
-
43
-
-
33846148245
-
Extending the linear model with R: generalized linear, mixed effects and nonparametric regression models
-
Boca Raton: Chapman & Hall/CRC
-
Faraway JJ. Extending the linear model with R: generalized linear, mixed effects and nonparametric regression models. 2006, Boca Raton: Chapman & Hall/CRC.
-
(2006)
-
-
Faraway, J.J.1
-
44
-
-
0004255908
-
Machine learning
-
New York: McGraw-Hill
-
Mitchell TM. Machine learning. 1997, New York: McGraw-Hill.
-
(1997)
-
-
Mitchell, T.M.1
-
45
-
-
33846148245
-
Extending the Linear Model with R
-
United State of America: Chapman & Hall/CRC, First
-
Faraway JJ. Extending the Linear Model with R. 2006, United State of America: Chapman & Hall/CRC, First.
-
(2006)
-
-
Faraway, J.J.1
|