-
1
-
-
45549084475
-
Systems biology. The scale of prediction
-
N.S. Baliga Systems biology. The scale of prediction Science 320 2008 1297 1298
-
(2008)
Science
, vol.320
, pp. 1297-1298
-
-
Baliga, N.S.1
-
2
-
-
47249142778
-
Revealing the architecture of gene regulation: The promise of eQTL studies
-
Y. Gilad, S.A. Rifkin, and J.K. Pritchard Revealing the architecture of gene regulation: the promise of eQTL studies Trends Genet 24 2008 408 415
-
(2008)
Trends Genet
, vol.24
, pp. 408-415
-
-
Gilad, Y.1
Rifkin, S.A.2
Pritchard, J.K.3
-
3
-
-
66349121862
-
The HapMap and genome-wide association studies in diagnosis and therapy
-
T.A. Manolio, and F.S. Collins The HapMap and genome-wide association studies in diagnosis and therapy Annu Rev Med 60 2009 443 456
-
(2009)
Annu Rev Med
, vol.60
, pp. 443-456
-
-
Manolio, T.A.1
Collins, F.S.2
-
4
-
-
51849087593
-
Genes and networks expressed in perioperative omental adipose tissue are correlated with weight loss from Roux-en-Y gastric bypass
-
Lond
-
K. Kim, B. Perroud, G. Espinal, D. Kachinskas, I. Austrheim-Smith, B.M. Wolfe, et al. Genes and networks expressed in perioperative omental adipose tissue are correlated with weight loss from Roux-en-Y gastric bypass Int J Obes (Lond) 32 2008 1395 1406
-
(2008)
Int J Obes
, vol.32
, pp. 1395-1406
-
-
Kim, K.1
Perroud, B.2
Espinal, G.3
Kachinskas, D.4
Austrheim-Smith, I.5
Wolfe, B.M.6
-
5
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
L.J. van't Veer, H. Dai, M.J. van de Vijver, Y.D. He, A.A. Hart, M. Mao, et al. Gene expression profiling predicts clinical outcome of breast cancer Nature 415 2002 530 536
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
Van't Veer, L.J.1
Dai, H.2
Van De Vijver, M.J.3
He, Y.D.4
Hart, A.A.5
Mao, M.6
-
6
-
-
0037137519
-
A gene-expression signature as a predictor of survival in breast cancer
-
M.J. van de Vijver, Y.D. He, L.J. van't Veer, H. Dai, A.A. Hart, D.W. Voskuil, et al. A gene-expression signature as a predictor of survival in breast cancer N Engl J Med 347 2002 1999 2009
-
(2002)
N Engl J Med
, vol.347
, pp. 1999-2009
-
-
Van De Vijver, M.J.1
He, Y.D.2
Van'T Veer, L.J.3
Dai, H.4
Hart, A.A.5
Voskuil, D.W.6
-
7
-
-
20044377912
-
Molecular classification of tamoxifen-resistant breast carcinomas by gene expression profiling
-
M.P. Jansen, J.A. Foekens, I.L. van Staveren, M.M. Dirkzwager-Kiel, K. Ritstier, M.P. Look, et al. Molecular classification of tamoxifen-resistant breast carcinomas by gene expression profiling J Clin Oncol 23 2005 732 740
-
(2005)
J Clin Oncol
, vol.23
, pp. 732-740
-
-
Jansen, M.P.1
Foekens, J.A.2
Van Staveren, I.L.3
Dirkzwager-Kiel, M.M.4
Ritstier, K.5
Look, M.P.6
-
8
-
-
14544268597
-
Prediction of docetaxel response in human breast cancer by gene expression profiling
-
K. Iwao-Koizumi, R. Matoba, N. Ueno, S.J. Kim, A. Ando, Y. Miyoshi, et al. Prediction of docetaxel response in human breast cancer by gene expression profiling J Clin Oncol 23 2005 422 431
-
(2005)
J Clin Oncol
, vol.23
, pp. 422-431
-
-
Iwao-Koizumi, K.1
Matoba, R.2
Ueno, N.3
Kim, S.J.4
Ando, A.5
Miyoshi, Y.6
-
9
-
-
33646029456
-
Stability regulation of mRNA and the control of gene expression
-
C. Cheadle, J. Fan, Y.S. Cho-Chung, T. Werner, J. Ray, L. Do, et al. Stability regulation of mRNA and the control of gene expression Ann N Y Acad Sci 1058 2005 196 204
-
(2005)
Ann N Y Acad Sci
, vol.1058
, pp. 196-204
-
-
Cheadle, C.1
Fan, J.2
Cho-Chung, Y.S.3
Werner, T.4
Ray, J.5
Do, L.6
-
10
-
-
46649115515
-
Using ribosomal protein genes as reference: A tale of caution
-
L. Thorrez, K. Van Deun, L.C. Tranchevent, L. Van Lommel, K. Engelen, K. Marchal, et al. Using ribosomal protein genes as reference: a tale of caution PLoS One 3 2008 e1854
-
(2008)
PLoS One
, vol.3
, pp. 1854
-
-
Thorrez, L.1
Van Deun, K.2
Tranchevent, L.C.3
Van Lommel, L.4
Engelen, K.5
Marchal, K.6
-
11
-
-
58149379408
-
Needle and surgical biopsy techniques differentially affect adipose tissue gene expression profiles
-
D.M. Mutch, J. Tordjman, V. Pelloux, B. Hanczar, C. Henegar, C. Poitou, et al. Needle and surgical biopsy techniques differentially affect adipose tissue gene expression profiles Am J Clin Nutr 89 2009 51 57
-
(2009)
Am J Clin Nutr
, vol.89
, pp. 51-57
-
-
Mutch, D.M.1
Tordjman, J.2
Pelloux, V.3
Hanczar, B.4
Henegar, C.5
Poitou, C.6
-
12
-
-
58949095497
-
Gene expression analysis of neural cells and tissues using DNA microarrays
-
Chapter 4:Unit 4.28
-
S.L. Karsten, L.C. Kudo, and D.H. Geschwind Gene expression analysis of neural cells and tissues using DNA microarrays Curr Protoc Neurosci 2008 Chapter 4:Unit 4.28
-
(2008)
Curr Protoc Neurosci
-
-
Karsten, S.L.1
Kudo, L.C.2
Geschwind, D.H.3
-
13
-
-
13444263949
-
New insights into functional aspects of liver morphology
-
D.E. Malarkey, K. Johnson, L. Ryan, G. Boorman, and R.R. Maronpot New insights into functional aspects of liver morphology Toxicol Pathol 33 2005 27 34
-
(2005)
Toxicol Pathol
, vol.33
, pp. 27-34
-
-
Malarkey, D.E.1
Johnson, K.2
Ryan, L.3
Boorman, G.4
Maronpot, R.R.5
-
14
-
-
26044443188
-
Noncontact laser microdissection and pressure catapulting: Sample preparation for genomic, transcriptomic, and proteomic analysis
-
Y. Niyaz, M. Stich, B. Sägmüller, R. Burgemeister, G. Friedemann, U. Sauer, et al. Noncontact laser microdissection and pressure catapulting: sample preparation for genomic, transcriptomic, and proteomic analysis Methods Mol Med 114 2005 1 24
-
(2005)
Methods Mol Med
, vol.114
, pp. 1-24
-
-
Niyaz, Y.1
Stich, M.2
Sägmüller, B.3
Burgemeister, R.4
Friedemann, G.5
Sauer, U.6
-
15
-
-
59249098002
-
Gene expression profiling of neurochemically defined regions of the human brain by in situ hybridization-guided laser capture microdissection
-
R. Bernard, I.A. Kerman, F. Meng, S.J. Evans, I. Amrein, E.G. Jones, et al. Gene expression profiling of neurochemically defined regions of the human brain by in situ hybridization-guided laser capture microdissection J Neurosci Methods 178 2009 46 54
-
(2009)
J Neurosci Methods
, vol.178
, pp. 46-54
-
-
Bernard, R.1
Kerman, I.A.2
Meng, F.3
Evans, S.J.4
Amrein, I.5
Jones, E.G.6
-
16
-
-
60349108362
-
Differential gene expression profiling of laryngeal squamous cell carcinoma by laser capture microdissection and complementary DNA microarrays
-
L.J. Ma, W. Li, X. Zhang, D.H. Huang, H. Zhang, J.Y. Xiao, et al. Differential gene expression profiling of laryngeal squamous cell carcinoma by laser capture microdissection and complementary DNA microarrays Arch Med Res 40 2009 114 123
-
(2009)
Arch Med Res
, vol.40
, pp. 114-123
-
-
Ma, L.J.1
Li, W.2
Zhang, X.3
Huang, D.H.4
Zhang, H.5
Xiao, J.Y.6
-
17
-
-
37349059336
-
Tissue handling for genome-wide expression analysis: A review of the issues, evidence, and opportunities
-
F. Medeiros, C.T. Rigl, G.G. Anderson, S.H. Becker, and K.C. Halling Tissue handling for genome-wide expression analysis: a review of the issues, evidence, and opportunities Arch Pathol Lab Med 131 2007 1805 1816
-
(2007)
Arch Pathol Lab Med
, vol.131
, pp. 1805-1816
-
-
Medeiros, F.1
Rigl, C.T.2
Anderson, G.G.3
Becker, S.H.4
Halling, K.C.5
-
18
-
-
33947535404
-
Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue
-
R.A. Coudry, S.I. Meireles, R. Stoyanova, H.S. Cooper, A. Carpino, X. Wang, et al. Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue J Mol Diagn 9 2007 70 79
-
(2007)
J Mol Diagn
, vol.9
, pp. 70-79
-
-
Coudry, R.A.1
Meireles, S.I.2
Stoyanova, R.3
Cooper, H.S.4
Carpino, A.5
Wang, X.6
-
19
-
-
0036142737
-
Accurate gene expression measurement in formalin-fixed and paraffin-embedded tumor tissue
-
D. D'Orazio, M. Stumm, and C. Sieber Accurate gene expression measurement in formalin-fixed and paraffin-embedded tumor tissue Am J Pathol 160 2002 383 384
-
(2002)
Am J Pathol
, vol.160
, pp. 383-384
-
-
D'Orazio, D.1
Stumm, M.2
Sieber, C.3
-
20
-
-
33947503758
-
RNA expression analysis of formalin-fixed paraffin-embedded tumors
-
S.K. Penland, T.O. Keku, C. Torrice, X. He, J. Krishnamurthy, K.A. Hoadley, et al. RNA expression analysis of formalin-fixed paraffin-embedded tumors Lab Invest 87 2007 383 391
-
(2007)
Lab Invest
, vol.87
, pp. 383-391
-
-
Penland, S.K.1
Keku, T.O.2
Torrice, C.3
He, X.4
Krishnamurthy, J.5
Hoadley, K.A.6
-
21
-
-
20444500954
-
Technology insight: Application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer
-
S. Paik, C.Y. Kim, Y.K. Song, and W.S. Kim Technology insight: application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer Nat Clin Pract Oncol 2 2005 246 254
-
(2005)
Nat Clin Pract Oncol
, vol.2
, pp. 246-254
-
-
Paik, S.1
Kim, C.Y.2
Song, Y.K.3
Kim, W.S.4
-
22
-
-
0035134463
-
Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue
-
K. Specht, T. Richter, U. Muller, A. Walch, M. Werner, and H. Hofler Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue Am J Pathol 158 2001 419 429
-
(2001)
Am J Pathol
, vol.158
, pp. 419-429
-
-
Specht, K.1
Richter, T.2
Muller, U.3
Walch, A.4
Werner, M.5
Hofler, H.6
-
23
-
-
60749093329
-
Selecting control genes for RT-QPCR using public microarray data
-
V. Popovici, D.R. Goldstein, J. Antonov, R. Jaggi, M. Delorenzi, and P. Wirapati Selecting control genes for RT-QPCR using public microarray data BMC Bioinform 10 2009 42
-
(2009)
BMC Bioinform
, vol.10
, pp. 42
-
-
Popovici, V.1
Goldstein, D.R.2
Antonov, J.3
Jaggi, R.4
Delorenzi, M.5
Wirapati, P.6
-
25
-
-
18244378238
-
Independence and reproducibility across microarray platforms
-
J.E. Larkin, B.C. Frank, H. Gavras, R. Sultana, and J. Quackenbush Independence and reproducibility across microarray platforms Nat Methods 2 2005 337 344
-
(2005)
Nat Methods
, vol.2
, pp. 337-344
-
-
Larkin, J.E.1
Frank, B.C.2
Gavras, H.3
Sultana, R.4
Quackenbush, J.5
-
26
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
R.A. Irizarry, D. Warren, F. Spencer, I.F. Kim, S. Biswal, B.C. Frank, et al. Multiple-laboratory comparison of microarray platforms Nat Methods 2 2005 345 350
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
-
27
-
-
18244389201
-
Standardizing global gene expression analysis between laboratories and across platforms
-
Toxicogenomics Research Consortium
-
T. Bammler, R.P. Beyer, S. Bhattacharya, G.A. Boorman, A. Boyles, B.U. Bradford, et al. Toxicogenomics Research Consortium Standardizing global gene expression analysis between laboratories and across platforms Nat Methods 295 2005 351 356
-
(2005)
Nat Methods
, vol.295
, pp. 351-356
-
-
Bammler, T.1
Beyer, R.P.2
Bhattacharya, S.3
Boorman, G.A.4
Boyles, A.5
Bradford, B.U.6
-
28
-
-
33646181184
-
A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants
-
J. Bishop, S. Blair, and A.M. Chagovetz A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants Biophys J 90 2006 831 840
-
(2006)
Biophys J
, vol.90
, pp. 831-840
-
-
Bishop, J.1
Blair, S.2
Chagovetz, A.M.3
-
29
-
-
57349116088
-
An integrated reaction-transport model for DNA surface hybridization: Implications for DNA microarrays
-
R. Singh, J. Nitsche, and S.T. Andreadis An integrated reaction-transport model for DNA surface hybridization: implications for DNA microarrays Ann Biomed Eng 37 2009 255 269
-
(2009)
Ann Biomed Eng
, vol.37
, pp. 255-269
-
-
Singh, R.1
Nitsche, J.2
Andreadis, S.T.3
-
30
-
-
27244449595
-
Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
-
X. Li, Z. He, and J. Zhou Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation Nucleic Acids Res 33 2005 6114 6123
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 6114-6123
-
-
Li, X.1
He, Z.2
Zhou, J.3
-
31
-
-
39149084716
-
Probe selection for DNA microarrays using OligoWiz
-
R. Wernersson, A.S. Juncker, and H.B. Nielsen Probe selection for DNA microarrays using OligoWiz Nat Protoc 2 2007 2677 2691
-
(2007)
Nat Protoc
, vol.2
, pp. 2677-2691
-
-
Wernersson, R.1
Juncker, A.S.2
Nielsen, H.B.3
-
32
-
-
7044286287
-
Evaluation of quality-control criteria for microarray gene expression analysis
-
C.I. Dumur, S. Nasim, A.M. Best, K.J. Archer, A.C. Ladd, V.R. Mas, et al. Evaluation of quality-control criteria for microarray gene expression analysis Clin Chem 50 2004 1994 2002
-
(2004)
Clin Chem
, vol.50
, pp. 1994-2002
-
-
Dumur, C.I.1
Nasim, S.2
Best, A.M.3
Archer, K.J.4
Ladd, A.C.5
Mas, V.R.6
-
33
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
C. Li, and W.H. Wong Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection Proc Natl Acad Sci USA 98 2001 31 36
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
34
-
-
85142128487
-
Robust estimators for expression analysis
-
E. Hubbell, W.M. Liu, and R. Mei Robust estimators for expression analysis Bioinformatics 28 2002 2585 2592
-
(2002)
Bioinformatics
, vol.28
, pp. 2585-2592
-
-
Hubbell, E.1
Liu, W.M.2
Mei, R.3
-
35
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
R.A. Irizarry, B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 2003 249 264
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
-
36
-
-
17844392693
-
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data
-
K. Shedden, W. Chen, R. Kuick, D. Ghosh, J. Macdonald, K.R. Cho, et al. Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data BMC Bioinform 6 2005 26
-
(2005)
BMC Bioinform
, vol.6
, pp. 26
-
-
Shedden, K.1
Chen, W.2
Kuick, R.3
Ghosh, D.4
MacDonald, J.5
Cho, K.R.6
-
37
-
-
25444496949
-
Sources of variation in Affymetrix microarray experiments
-
S.O. Zakharkin, K. Kim, T. Mehta, L. Chen, S. Barnes, K.E. Scheirer, et al. Sources of variation in Affymetrix microarray experiments BMC Bioinform 6 2005 214
-
(2005)
BMC Bioinform
, vol.6
, pp. 214
-
-
Zakharkin, S.O.1
Kim, K.2
Mehta, T.3
Chen, L.4
Barnes, S.5
Scheirer, K.E.6
-
38
-
-
1342294092
-
Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
-
Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 30 2002 e1
-
(2002)
Nucleic Acids Res
, vol.30
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
-
39
-
-
0037188875
-
Normalization and analysis of DNA microarray data by self-consistency and local regression
-
RESEARCH0037.1-0037.12
-
T.B. Kepler, L. Crosby, and K.T. Morgan Normalization and analysis of DNA microarray data by self-consistency and local regression Genome Biol 3 2002 RESEARCH0037.1-0037.12
-
(2002)
Genome Biol
, vol.3
-
-
Kepler, T.B.1
Crosby, L.2
Morgan, K.T.3
-
40
-
-
0037620675
-
Non-linear normalization and background correction in one-channel cDNA microarray studies
-
D. Edwards Non-linear normalization and background correction in one-channel cDNA microarray studies Bioinformatics 19 2003 825 833
-
(2003)
Bioinformatics
, vol.19
, pp. 825-833
-
-
Edwards, D.1
-
41
-
-
0035875553
-
Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
-
G.C. Tseng, M.K. Oh, L. Rohlin, J.C. Liao, and W.H. Wong Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects Nucleic Acids Res 29 2001 2549 2557
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2549-2557
-
-
Tseng, G.C.1
Oh, M.K.2
Rohlin, L.3
Liao, J.C.4
Wong, W.H.5
-
42
-
-
0035684378
-
A model for measurement error for gene expression arrays
-
D.M. Rocke, and B. Durbin A model for measurement error for gene expression arrays J Comput Biol 8 2001 557 569
-
(2001)
J Comput Biol
, vol.8
, pp. 557-569
-
-
Rocke, D.M.1
Durbin, B.2
-
43
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
W. Huber, A. Von Heydebrek, H. Sültmann, A. Poustka, and M. Vingron Variance stabilization applied to microarray data calibration and to the quantification of differential expression Bioinformatics 18 2002 S96 S104
-
(2002)
Bioinformatics
, vol.18
-
-
Huber, W.1
Von Heydebrek, A.2
Sültmann, H.3
Poustka, A.4
Vingron, M.5
-
44
-
-
0043089918
-
Transformation and normalization of oligonucleotide microarray data
-
DOI 10.1093/bioinformatics/btg245
-
S.C. Geller, J.P. Gregg, P. Hagerman, and D. Rocke Transformation and normalization of oligonucleotide microarray data Bioinformatics 19 2003 1817 1823 (Pubitemid 37220474)
-
(2003)
Bioinformatics
, vol.19
, Issue.14
, pp. 1817-1823
-
-
Geller, S.C.1
Gregg, J.P.2
Hagerman, P.3
Rocke, D.M.4
-
45
-
-
1842559887
-
Variance-stabilizing transformations for two-color microarrays
-
B. Durbin, and D. Rocke Variance-stabilizing transformations for two-color microarrays Bioinformatics 20 2004 660 667
-
(2004)
Bioinformatics
, vol.20
, pp. 660-667
-
-
Durbin, B.1
Rocke, D.2
-
46
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 19 2003 185 193
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
47
-
-
0344441000
-
Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data
-
R. Simon Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data Br J Cancer 89 2003 1599 1604
-
(2003)
Br J Cancer
, vol.89
, pp. 1599-1604
-
-
Simon, R.1
-
48
-
-
29244448340
-
Microarray data analysis: From disarray to consolidation and consensus
-
D.B. Allison, C. Cui, P.G. Page, and M. Sabripour Microarray data analysis: from disarray to consolidation and consensus Nat Rev Genet 7 2005 55 65
-
(2005)
Nat Rev Genet
, vol.7
, pp. 55-65
-
-
Allison, D.B.1
Cui, C.2
Page, P.G.3
Sabripour, M.4
-
49
-
-
27644474698
-
Reproducible clusters from microarray research: Whither?
-
N.R. Garge, G.P. Page, A.P. Sprague, B.S. Gorman, and D.B. Allison Reproducible clusters from microarray research: whither? BMC Bioinform 6 suppl 2 2005 S10
-
(2005)
BMC Bioinform
, vol.6
, Issue.SUPPL. 2
, pp. 10
-
-
Garge, N.R.1
Page, G.P.2
Sprague, A.P.3
Gorman, B.S.4
Allison, D.B.5
-
50
-
-
0037342510
-
Comparisons and validation of statistical clustering techniques for microarray gene expression data
-
S. Datta, and S. Datta Comparisons and validation of statistical clustering techniques for microarray gene expression data Bioinformatics 19 2003 459 466
-
(2003)
Bioinformatics
, vol.19
, pp. 459-466
-
-
Datta, S.1
Datta, S.2
-
51
-
-
33745612095
-
Pvclust: An R package for assessing the uncertainty in hierarchical clustering
-
R. Suzuki, and H. Shimodaira Pvclust: an R package for assessing the uncertainty in hierarchical clustering Bioinformatics 22 2006 1540 1542
-
(2006)
Bioinformatics
, vol.22
, pp. 1540-1542
-
-
Suzuki, R.1
Shimodaira, H.2
-
52
-
-
0001677717
-
Controlling the false discovery data - A practical and powerful approach to multiple tests
-
Y. Benjamini, and Y. Hochberg Controlling the false discovery data - a practical and powerful approach to multiple tests J R Stat Soc Ser B 57 1995 289 300
-
(1995)
J R Stat Soc Ser B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
54
-
-
0037076322
-
Selection bias in gene extraction on the basis of microarray gene-expression data
-
C. Ambroise, and G.J. McLachlan Selection bias in gene extraction on the basis of microarray gene-expression data Proc Natl Acad Sci USA 99 2002 6562 6566
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 6562-6566
-
-
Ambroise, C.1
McLachlan, G.J.2
-
55
-
-
13444249852
-
Prediction of cancer outcome with microarrays: A multiple random validation strategy
-
DOI 10.1016/S0140-6736(05)17866-0
-
S. Michiels, S. Koscielny, and C. Hill Prediction of cancer outcome with microarrays: a multiple random validation strategy Lancet 365 2005 488 492 (Pubitemid 40215731)
-
(2005)
Lancet
, vol.365
, Issue.9458
, pp. 488-492
-
-
Michiels, S.1
Koscielny, S.2
Hill, C.3
-
56
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
A.L. Barabási, and Z.N. Oltvai Network biology: understanding the cell's functional organization Nat Rev Genet 5 2004 101 113
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
57
-
-
67449095889
-
Computational methods for discovering gene networks from expression data
-
W.P. Lee, and W.S. Tzou Computational methods for discovering gene networks from expression data Brief Bioinform 10 2009 408 423
-
(2009)
Brief Bioinform
, vol.10
, pp. 408-423
-
-
Lee, W.P.1
Tzou, W.S.2
-
58
-
-
22844446947
-
An integrative genomics approach to infer causal associations between gene expression and disease
-
E.E. Schadt, J. Lamb, X. Yang, J. Zhu, S. Edwards, D. Guhathakurta, et al. An integrative genomics approach to infer causal associations between gene expression and disease Nat Genet 37 2005 710 717
-
(2005)
Nat Genet
, vol.37
, pp. 710-717
-
-
Schadt, E.E.1
Lamb, J.2
Yang, X.3
Zhu, J.4
Edwards, S.5
Guhathakurta, D.6
-
59
-
-
49649093339
-
Data management in structural genomics: An overview
-
S. Haquin, E. Oeuillet, A. Pajon, M. Harris, A.T. Jones, H. van Tilbeurgh, et al. Data management in structural genomics: an overview Methods Mol Biol 426 2008 49 79
-
(2008)
Methods Mol Biol
, vol.426
, pp. 49-79
-
-
Haquin, S.1
Oeuillet, E.2
Pajon, A.3
Harris, M.4
Jones, A.T.5
Van Tilbeurgh, H.6
-
60
-
-
34249025772
-
The end of the microarray Tower of Babel: Will universal standards lead the way?
-
E.S. Kawasaki The end of the microarray Tower of Babel: will universal standards lead the way? J Biomol Tech 17 2006 200 206
-
(2006)
J Biomol Tech
, vol.17
, pp. 200-206
-
-
Kawasaki, E.S.1
-
61
-
-
0038005018
-
DAVID: Database for annotation, visualization, and integrated discovery
-
G. Dennis Jr., B.T. Sherman, D.A. Hosack, J. Yang, W. Gao, H.C. Lane, et al. DAVID: database for annotation, visualization, and integrated discovery Genome Biol 4 2003 P3
-
(2003)
Genome Biol
, vol.4
-
-
Dennis Jr., G.1
Sherman, B.T.2
Hosack, D.A.3
Yang, J.4
Gao, W.5
Lane, H.C.6
-
62
-
-
0038175144
-
GoMiner: A resource for biological interpretation of genomic and proteomic data
-
B.R. Zeeberg, W. Feng, G. Wang, M.D. Wang, A.T. Fojo, M. Sunshine, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data Genome Biol 4 2003 R28
-
(2003)
Genome Biol
, vol.4
-
-
Zeeberg, B.R.1
Feng, W.2
Wang, G.3
Wang, M.D.4
Fojo, A.T.5
Sunshine, M.6
-
63
-
-
2442691827
-
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
-
B.H. Mecham, G.T. Klus, J. Strovel, M. Augustus, D. Byrne, P. Bozso, 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 2004 e74
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 74
-
-
Mecham, B.H.1
Klus, G.T.2
Strovel, J.3
Augustus, M.4
Byrne, D.5
Bozso, P.6
-
64
-
-
33645877079
-
Comparison of gene coverage of mouse oligonucleotide microarray platforms
-
R.A. Verdugo, and J.F. Medrano Comparison of gene coverage of mouse oligonucleotide microarray platforms BMC Genomics 7 2006 58
-
(2006)
BMC Genomics
, vol.7
, pp. 58
-
-
Verdugo, R.A.1
Medrano, J.F.2
-
65
-
-
25444515422
-
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
-
S.L. Carter, A.C. Eklund, B.H. Mecham, I.S. Kohane, and Z. Szallasi Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements BMC Bioinform 6 2005 107
-
(2005)
BMC Bioinform
, vol.6
, pp. 107
-
-
Carter, S.L.1
Eklund, A.C.2
Mecham, B.H.3
Kohane, I.S.4
Szallasi, Z.5
-
66
-
-
0141516672
-
Microarray technology - An intellectual property retrospective
-
R. Rouse, and G. Hardiman Microarray technology - an intellectual property retrospective Pharmacogenomics 4 2003 623 632
-
(2003)
Pharmacogenomics
, vol.4
, pp. 623-632
-
-
Rouse, R.1
Hardiman, G.2
-
67
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
for the MAQC Consortium
-
L. Shi, L.H. Reid, W.D. Jones, R. Shippy, J.A. Warrington, S.C. Baker, et al. for the MAQC Consortium The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 24 2006 1151 1161
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
Baker, S.C.6
-
68
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data
-
A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data Nat Genet 29 2001 365 371
-
(2001)
Nat Genet
, vol.29
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
-
69
-
-
58149182724
-
Ncbi Geo: Archive for high-throughput functional genomic data
-
T. Barrett, D.B. Troup, S.E. Wilhite, P. Ledoux, D. Rudnev, C. Evangelista, et al. Ncbi Geo: archive for high-throughput functional genomic data Nucleic Acids Res 2008 37, Database issue D885-90
-
(2008)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE D885-90
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
-
70
-
-
33846036710
-
The Stanford Microarray Database: Implementation of new analysis tools and open source release of software
-
J. Demeter, C. Beauheim, J. Gollub, T. Hernandez-Boussard, H. Jin, D. Maier, et al. The Stanford Microarray Database: implementation of new analysis tools and open source release of software Nucleic Acids Res 35 2007 D766 D770
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Demeter, J.1
Beauheim, C.2
Gollub, J.3
Hernandez-Boussard, T.4
Jin, H.5
Maier, D.6
-
71
-
-
33846039701
-
ArrayExpress - A public database of microarray experiments and gene expression profiles
-
H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson, A. Farne, et al. ArrayExpress - a public database of microarray experiments and gene expression profiles Nucleic Acids Res 35 2007 D747 D750
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Parkinson, H.1
Kapushesky, M.2
Shojatalab, M.3
Abeygunawardena, N.4
Coulson, R.5
Farne, A.6
-
72
-
-
0347122079
-
CIBEX: Center for information biology gene expression database
-
K. Ikeo, J. Ishi-i, T. Tamura, T. Gojobori, and Y. Tateno CIBEX: center for information biology gene expression database C R Biol 326 2003 1079 1082
-
(2003)
C R Biol
, vol.326
, pp. 1079-1082
-
-
Ikeo, K.1
Ishi-I, J.2
Tamura, T.3
Gojobori, T.4
Tateno, Y.5
-
73
-
-
58149182735
-
TB database: An integrated platform for tuberculosis research
-
T.B. Reddy, R. Riley, F. Wymore, P. Montgomery, D. DeCaprio, R. Engels, et al. TB database: an integrated platform for tuberculosis research Nucleic Acids Res 37 Database issue 2009 D499 D508
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
-
-
Reddy, T.B.1
Riley, R.2
Wymore, F.3
Montgomery, P.4
DeCaprio, D.5
Engels, R.6
-
74
-
-
33846119587
-
The mouse Gene Expression Database (GXD): 2007 update
-
C.M. Smith, J.H. Finger, T.F. Hayamizu, I.J. McCright, J.T. Eppig, J.A. Kadin, et al. The mouse Gene Expression Database (GXD): 2007 update Nucleic Acids Res 35 2007 D618 D623
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Smith, C.M.1
Finger, J.H.2
Hayamizu, T.F.3
McCright, I.J.4
Eppig, J.T.5
Kadin, J.A.6
-
75
-
-
52049123121
-
SoyXpress: A database for exploring the soybean transcriptome
-
K.C. Cheng, and M.V. Strömvik SoyXpress: a database for exploring the soybean transcriptome BMC Genomics 9 2008 368
-
(2008)
BMC Genomics
, vol.9
, pp. 368
-
-
Cheng, K.C.1
Strömvik, M.V.2
-
76
-
-
59149088407
-
Repeatability of published microarray gene expression analyses
-
J.P. Ioannidis, D.B. Allison, C.A. Ball, I. Coulibaly, X. Cui, A.C. Culhane, et al. Repeatability of published microarray gene expression analyses Nat Genet 41 2009 149 155
-
(2009)
Nat Genet
, vol.41
, pp. 149-155
-
-
Ioannidis, J.P.1
Allison, D.B.2
Ball, C.A.3
Coulibaly, I.4
Cui, X.5
Culhane, A.C.6
-
77
-
-
32644439684
-
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
-
B. Harr, and C. Schlotterer Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons Nucleic Acids Res 34 2006 e8
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Harr, B.1
Schlotterer, C.2
-
78
-
-
58049141153
-
Microarray-based gene set analysis: A comparison of current methods
-
S. Song, and M.A. Black Microarray-based gene set analysis: a comparison of current methods BMC Bioinform 9 2008 502
-
(2008)
BMC Bioinform
, vol.9
, pp. 502
-
-
Song, S.1
Black, M.A.2
-
79
-
-
33750943691
-
Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers
-
O.L. Griffith, A. Melck, S.J. Jones, and S.M. Wiseman Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers J Clin Oncol 24 2006 5043 5051
-
(2006)
J Clin Oncol
, vol.24
, pp. 5043-5051
-
-
Griffith, O.L.1
Melck, A.2
Jones, S.J.3
Wiseman, S.M.4
-
80
-
-
58149185138
-
Nucleic acids research annual database issue and the NAR online molecular biology database collection in 2009
-
M.Y. Galperin, and G.R. Cochrane Nucleic acids research annual database issue and the NAR online molecular biology database collection in 2009 Nucleic Acids Res 37 Database issue 2009 D1 D4
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
-
-
Galperin, M.Y.1
Cochrane, G.R.2
-
81
-
-
63849300612
-
A data integration framework for prediction of transcription factor targets
-
M. Nykter, H. Lähdesmäki, A. Rust, V. Thorsson, and I. Shmulevich A data integration framework for prediction of transcription factor targets Ann N Y Acad Sci 1158 2009 205 214
-
(2009)
Ann N Y Acad Sci
, vol.1158
, pp. 205-214
-
-
Nykter, M.1
Lähdesmäki, H.2
Rust, A.3
Thorsson, V.4
Shmulevich, I.5
-
82
-
-
65249108056
-
Adaptable data management for systems biology investigations
-
J. Boyle, H. Rovira, C. Cavnor, D. Burdick, S. Killcoyne, and I. Shmulevich Adaptable data management for systems biology investigations BMC Bioinform 10 2009 79
-
(2009)
BMC Bioinform
, vol.10
, pp. 79
-
-
Boyle, J.1
Rovira, H.2
Cavnor, C.3
Burdick, D.4
Killcoyne, S.5
Shmulevich, I.6
-
83
-
-
54949106292
-
SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
-
R. Chari, B.P. Coe, C. Wedseltoft, M. Benetti, I.M. Wilson, E.A. Vucic, et al. SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes BMC Bioinform 9 2008 422
-
(2008)
BMC Bioinform
, vol.9
, pp. 422
-
-
Chari, R.1
Coe, B.P.2
Wedseltoft, C.3
Benetti, M.4
Wilson, I.M.5
Vucic, E.A.6
-
84
-
-
33748039756
-
MGED standards: Work in progress
-
C.A. Ball, and A. Brazma MGED standards: work in progress OMICS 10 2006 138 144
-
(2006)
OMICS
, vol.10
, pp. 138-144
-
-
Ball, C.A.1
Brazma, A.2
-
85
-
-
53749087689
-
Relationship between gene expression and enhancement in glioblastoma multiforme: Exploratory DNA microarray analysis
-
W.B. Pope, J.H. Chen, J. Dong, M.R. Carlson, A. Perlina, T.F. Cloughesy, et al. Relationship between gene expression and enhancement in glioblastoma multiforme: exploratory DNA microarray analysis Radiology 249 2008 268 277
-
(2008)
Radiology
, vol.249
, pp. 268-277
-
-
Pope, W.B.1
Chen, J.H.2
Dong, J.3
Carlson, M.R.4
Perlina, A.5
Cloughesy, T.F.6
-
86
-
-
33750633707
-
Molecular biology of malignant gliomas
-
C. Belda-Iniesta, J. de Castro Carpeño, E. Casado Sáenz, P. Cejas Guerrero, R. Perona, and M. González Barón Molecular biology of malignant gliomas Clin Transl Oncol 8 2006 635 641
-
(2006)
Clin Transl Oncol
, vol.8
, pp. 635-641
-
-
Belda-Iniesta, C.1
De Castro Carpeño, J.2
Casado Sáenz, E.3
Cejas Guerrero, P.4
Perona, R.5
González Barón, M.6
-
87
-
-
37249089420
-
Predictive data mining in clinical medicine: Current issues and guidelines
-
R. Bellazzi, and B. Zupan Predictive data mining in clinical medicine: current issues and guidelines Int J Med Inform 77 2008 81 97
-
(2008)
Int J Med Inform
, vol.77
, pp. 81-97
-
-
Bellazzi, R.1
Zupan, B.2
-
88
-
-
77951163222
-
Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology
-
Available at
-
Baggerly K, Coombes K. Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology. Ann Appl Stat V3, N4, 2009:1309-34. Available at http://www.imstat.org/aoas/ next-issue.html
-
(2009)
Ann Appl Stat
, vol.3
, Issue.4
, pp. 1309-34
-
-
Baggerly, K.1
Coombes, K.2
-
89
-
-
77955658218
-
Fatal flaws in cancer research: AOAS paper
-
J. Morris Fatal flaws in cancer research: AOAS paper IMS Bull 39 2010 5
-
(2010)
IMS Bull
, vol.39
, pp. 5
-
-
Morris, J.1
-
90
-
-
33645825183
-
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
-
L. Ein-Dor, O. Zuk, and E. Domany Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer Proc Natl Acad Sci USA 103 2006 5923 5928
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5923-5928
-
-
Ein-Dor, L.1
Zuk, O.2
Domany, E.3
|