-
3
-
-
0036900895
-
Fundamentals of experimental design for cDNA microarrays
-
Churchill G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32:(Suppl. 2):2002;490-495.
-
(2002)
Nat. Genet.
, vol.32
, Issue.SUPPL. 2
, pp. 490-495
-
-
Churchill, G.A.1
-
4
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang Y.H., Speed T. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3:2002;579-588.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 579-588
-
-
Yang, Y.H.1
Speed, T.2
-
5
-
-
0037335024
-
Experimental design of DNA microarray experiments
-
Simon R.M., Dobbin K. Experimental design of DNA microarray experiments. Biotechniques. 2003;S16-S21.
-
(2003)
Biotechniques
-
-
Simon, R.M.1
Dobbin, K.2
-
6
-
-
0035733719
-
Show me the data!
-
Perou C.M. Show me the data! Nat. Genet. 29:2001;373.
-
(2001)
Nat. Genet.
, vol.29
, pp. 373
-
-
Perou, C.M.1
-
7
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
-
Brazma A., 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
-
8
-
-
0037179669
-
Microarray standards at last
-
Microarray standards at last. Nature. 419:2002;323.
-
(2002)
Nature
, vol.419
, pp. 323
-
-
-
9
-
-
0035751799
-
Analysis of cDNA microarray images
-
Yang Y.H., et al. Analysis of cDNA microarray images. Brief. Bioinform. 2:2001;341-349.
-
(2001)
Brief. Bioinform.
, vol.2
, pp. 341-349
-
-
Yang, Y.H.1
-
10
-
-
0036180003
-
Fully automatic quantification of microarray image data
-
Jain A.N., et al. Fully automatic quantification of microarray image data. Genome Res. 12:2002;325-332.
-
(2002)
Genome Res.
, vol.12
, pp. 325-332
-
-
Jain, A.N.1
-
11
-
-
0036898577
-
Microarray data normalization and transformation
-
Quackenbush J. Microarray data normalization and transformation. Nat. Genet. 32:(Suppl.):2002;496-501.
-
(2002)
Nat. Genet.
, vol.32
, Issue.SUPPL.
, pp. 496-501
-
-
Quackenbush, J.1
-
12
-
-
0036178995
-
Control genes and variability: Absence of ubiquitous reference transcripts in diverse mammalian expression studies
-
Lee P.D. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res. 12:2002;292-297.
-
(2002)
Genome Res.
, vol.12
, pp. 292-297
-
-
Lee, P.D.1
-
13
-
-
0035699287
-
Characterization of variability in large-scale gene expression data: Implications for study design
-
Novak J.P., et al. Characterization of variability in large-scale gene expression data: implications for study design. Genomics. 79:2002;104-113.
-
(2002)
Genomics
, vol.79
, pp. 104-113
-
-
Novak, J.P.1
-
14
-
-
0035818559
-
Project normal: Defining normal variance in mouse gene expression
-
Pritchard C.C., et al. Project normal: defining normal variance in mouse gene expression. Proc. Natl. Acad. Sci. U. S. A. 98:2001;13266-13271.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 13266-13271
-
-
Pritchard, C.C.1
-
15
-
-
0036574916
-
Statistical issues with microarrays: Processing and analysis
-
Nadon R., Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends Genet. 18:2002;265-271.
-
(2002)
Trends Genet.
, vol.18
, pp. 265-271
-
-
Nadon, R.1
Shoemaker, J.2
-
16
-
-
0034730124
-
Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
-
Lee M.L., et al. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. U. S. A. 97:2000;9834-9839.
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 9834-9839
-
-
Lee, M.L.1
-
18
-
-
0041423883
-
SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays
-
G. et al. Parmigiani. Springer
-
Storey J.D., Tibshirani R. SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. Parmigiani G., et al. The Analysis of Gene Expression Data: Methods and Software. 2003;Springer.
-
(2003)
The Analysis of Gene Expression Data: Methods and Software
-
-
Storey, J.D.1
Tibshirani, R.2
-
19
-
-
0034927555
-
Analysis of variance for gene expression microarray data
-
Kerr M.K., et al. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7:2000;819-837.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 819-837
-
-
Kerr, M.K.1
-
20
-
-
0035827588
-
Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12
-
Long A.D., et al. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276:2001;19937-19944.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 19937-19944
-
-
Long, A.D.1
-
21
-
-
0034948896
-
A Bayesian framework for the analysis of microarray expression data: Regularized t test and statistical inferences of gene changes
-
Baldi P., Long A.D. A Bayesian framework for the analysis of microarray expression data: regularized t test and statistical inferences of gene changes. Bioinformatics. 17:2001;509-519.
-
(2001)
Bioinformatics
, vol.17
, pp. 509-519
-
-
Baldi, P.1
Long, A.D.2
-
22
-
-
0034807713
-
Analysing gene expression data from DNA microarrays to identify candidate genes
-
Wu T.D. Analysing gene expression data from DNA microarrays to identify candidate genes. J. Pathol. 195:2001;53-65.
-
(2001)
J. Pathol.
, vol.195
, pp. 53-65
-
-
Wu, T.D.1
-
23
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
-
Dudoit S., et al. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sinica. 12:2002;111-139.
-
(2002)
Stat. Sinica
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
-
24
-
-
14844364789
-
Post-analysis follow-up and validation of microarray experiments
-
Chuaqui R.F., et al. Post-analysis follow-up and validation of microarray experiments. Nat. Genet. 32:(Suppl. 2):2002;509-514.
-
(2002)
Nat. Genet.
, vol.32
, Issue.SUPPL. 2
, pp. 509-514
-
-
Chuaqui, R.F.1
-
25
-
-
0037433040
-
Identifying differentially expressed genes using false discovery rate controlling procedures
-
Reiner A., et al. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 19:2003;368-375.
-
(2003)
Bioinformatics
, vol.19
, pp. 368-375
-
-
Reiner, A.1
-
26
-
-
0033657261
-
Principal components analysis to summarize microarray experiments: Application to sporulation time series
-
Raychaudhuri S. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac. Symp. Biocomput. 2000;455-466.
-
(2000)
Pac. Symp. Biocomput.
, pp. 455-466
-
-
Raychaudhuri, S.1
-
27
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
Alter O., et al. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. U. S. A. 97:2000;10101-10106.
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
-
28
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen M.B., et al. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95:1998;14863-14868.
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
-
29
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie S., et al. Systematic determination of genetic network architecture. Nat. Genet. 22:1999;281-285.
-
(1999)
Nat. Genet.
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
-
30
-
-
0033027794
-
Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
-
Tamayo P., et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. U. S. A. 96:1999;2907-2912.
-
(1999)
Proc. Natl. Acad. Sci. U. S. A.
, vol.96
, pp. 2907-2912
-
-
Tamayo, P.1
-
31
-
-
0035375137
-
Computational analysis of microarray data
-
Quackenbush J. Computational analysis of microarray data. Nat. Rev. Genet. 2:2001;418-427.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 418-427
-
-
Quackenbush, J.1
-
32
-
-
0035755549
-
Analysis of large-scale gene expression data
-
Sherlock G. Analysis of large-scale gene expression data. Brief. Bioinform. 2:2001;350-362.
-
(2001)
Brief. Bioinform.
, vol.2
, pp. 350-362
-
-
Sherlock, G.1
-
33
-
-
0036975148
-
Pattern recognition techniques in microarray data analysis: A survey
-
Valafar F. Pattern recognition techniques in microarray data analysis: a survey. Ann. N. Y. Acad. Sci. 980:2002;41-64.
-
(2002)
Ann. N. Y. Acad. Sci.
, vol.980
, pp. 41-64
-
-
Valafar, F.1
-
34
-
-
0037165140
-
Prediction of central nervous system embryonal tumour outcome based on gene expression
-
Pomeroy S.L., et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 415:2002;436-442.
-
(2002)
Nature
, vol.415
, pp. 436-442
-
-
Pomeroy, S.L.1
-
35
-
-
18244409933
-
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning
-
Shipp M.A., et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat. Med. 8:2002;68-74.
-
(2002)
Nat. Med.
, vol.8
, pp. 68-74
-
-
Shipp, M.A.1
-
36
-
-
0034954414
-
Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
-
Khan J., et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med. 7:2001;673-679.
-
(2001)
Nat. Med.
, vol.7
, pp. 673-679
-
-
Khan, J.1
-
37
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
Brown M.P. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. U. S. A. 97:2000;262-267.
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 262-267
-
-
Brown, M.P.1
-
38
-
-
0035082045
-
Neural network model of gene expression
-
Vohradsky J. Neural network model of gene expression. FASEB J. 15:2001;846-854.
-
(2001)
FASEB J.
, vol.15
, pp. 846-854
-
-
Vohradsky, J.1
-
39
-
-
0036141951
-
Finding genes in the C2C12 osteogenic pathway by k-nearest-neighbor classification of expression data
-
Theilhaber J., et al. Finding genes in the C2C12 osteogenic pathway by k-nearest-neighbor classification of expression data. Genome Res. 12:2002;165-176.
-
(2002)
Genome Res.
, vol.12
, pp. 165-176
-
-
Theilhaber, J.1
-
40
-
-
0033692876
-
Tissue classification with gene expression profiles
-
Ben-Dor A., et al. Tissue classification with gene expression profiles. J. Comput. Biol. 7:2000;559-583.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 559-583
-
-
Ben-Dor, A.1
-
41
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel Y., et al. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29:2001;153-159.
-
(2001)
Nat. Genet.
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
-
42
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes T.R., et al. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
-
43
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie S., et al. Systematic determination of genetic network architecture. Nat. Genet. 22:1999;281-285.
-
(1999)
Nat. Genet.
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
-
44
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang S., et al. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. 1998;18-29.
-
(1998)
Pac. Symp. Biocomput.
, pp. 18-29
-
-
Liang, S.1
-
45
-
-
0033677274
-
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function
-
Akutsu T., et al. Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. J. Comput. Biol. 7:2000;331-343.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 331-343
-
-
Akutsu, T.1
-
46
-
-
0035221090
-
Development of a system for the inference of large scale genetic networks
-
Maki Y., et al. Development of a system for the inference of large scale genetic networks. Pac. Symp. Biocomput. 2001;446-458.
-
(2001)
Pac. Symp. Biocomput.
, pp. 446-458
-
-
Maki, Y.1
-
47
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N., et al. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7:2000;601-620.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 601-620
-
-
Friedman, N.1
-
48
-
-
0035221560
-
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
-
Hartemink A.J., et al. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac. Symp. Biocomput. 2001;422-433.
-
(2001)
Pac. Symp. Biocomput.
, pp. 422-433
-
-
Hartemink, A.J.1
-
49
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9:2002;67-103.
-
(2002)
J. Comput. Biol.
, vol.9
, pp. 67-103
-
-
De Jong, H.1
-
50
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
D'haeseleer P. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 16:2000;707-726.
-
(2000)
Bioinformatics
, vol.16
, pp. 707-726
-
-
D'haeseleer, P.1
-
51
-
-
0036061833
-
Pathway Processor: A tool for integrating whole-genome expression results into metabolic networks
-
Grosu P., et al. Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Res. 12:2002;1121-1126.
-
(2002)
Genome Res.
, vol.12
, pp. 1121-1126
-
-
Grosu, P.1
-
52
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
-
53
-
-
84984933234
-
High density synthetic oligonucleotide arrays
-
Lipshutz R.J., et al. High density synthetic oligonucleotide arrays. Nat. Genet. 21:(Suppl. 1):1999;20-24.
-
(1999)
Nat. Genet.
, vol.21
, Issue.SUPPL. 1
, pp. 20-24
-
-
Lipshutz, R.J.1
-
54
-
-
0038119656
-
Algorithms for high-density oligonucleotide array
-
Zhou Y., Abagyan R. Algorithms for high-density oligonucleotide array. Curr. Opin. Drug Discov. Devel. 6:2003;339-345.
-
(2003)
Curr. Opin. Drug Discov. Devel.
, vol.6
, pp. 339-345
-
-
Zhou, Y.1
Abagyan, R.2
-
55
-
-
0035752668
-
Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data
-
Schadt E.E., et al. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem. 37:(Suppl.):2001;120-125.
-
(2001)
J. Cell. Biochem.
, vol.37
, Issue.SUPPL.
, pp. 120-125
-
-
Schadt, E.E.1
-
56
-
-
0034536614
-
Analyzing high-density oligonucleotide gene expression array data
-
Schadt E.E., et al. Analyzing high-density oligonucleotide gene expression array data. J. Cell. Biochem. 80:2000;192-202.
-
(2000)
J. Cell. Biochem.
, vol.80
, pp. 192-202
-
-
Schadt, E.E.1
-
57
-
-
12244298154
-
Statistical analysis of high-density oligonucleotide arrays: A multiplicative noise model
-
Sasik R., et al. Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinformatics. 18:2002;1633-1640.
-
(2002)
Bioinformatics
, vol.18
, pp. 1633-1640
-
-
Sasik, R.1
-
58
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
Li C., Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U. S. A. 98:2001;31-36.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
|