-
1
-
-
0034948896
-
A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
-
Baldi P, Long AD. 2001. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17:509-519.
-
(2001)
Bioinformatics
, vol.17
, pp. 509-519
-
-
Baldi, P.1
Long, A.D.2
-
2
-
-
0042838381
-
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes
-
Bar-Joseph Z, Gerber GK, Simon I, Gifford DK, Jaakkola TS. 2003a. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci USA 100:10146-10151.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 10146-10151
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Simon, I.3
Gifford, D.K.4
Jaakkola, T.S.5
-
3
-
-
0041346457
-
Continuous representations of time series gene expression
-
Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. 2003b. Continuous representations of time series gene expression. J Comput Biol 10:341-356.
-
(2003)
J Comput Biol
, vol.10
, pp. 341-356
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Gifford, D.K.3
Jaakkola, T.S.4
Simon, I.5
-
5
-
-
84984932472
-
Exploring the new world of the genome with DNA microarrays
-
Brown PO, Botstsein D. 1999. Exploring the new world of the genome with DNA microarrays. Nat Genet 21:33-37.
-
(1999)
Nat Genet
, vol.21
, pp. 33-37
-
-
Brown, P.O.1
Botstsein, D.2
-
8
-
-
35048884971
-
-
Chu G, Narasimhan B, Tibshirani R, Tusher V. SAM User guide and Technical Document [http://www-stat.stanford.edu/~tibs/SAM/]. Downloaded September 2006.
-
Chu G, Narasimhan B, Tibshirani R, Tusher V. SAM User guide and Technical Document [http://www-stat.stanford.edu/~tibs/SAM/]. Downloaded September 2006.
-
-
-
-
9
-
-
24144445705
-
Improved statistical tests for differential gene expression by shrinking variance components estimates
-
Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA. 2005. Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6:59-75.
-
(2005)
Biostatistics
, vol.6
, pp. 59-75
-
-
Cui, X.1
Hwang, J.T.2
Qiu, J.3
Blades, N.J.4
Churchill, G.A.5
-
10
-
-
0042093637
-
Noise sampling method: An ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays
-
Draghici S, Kulaeva O, Hoff B, Petrov A, Shams S, Tainsky MA. 2003. Noise sampling method: An ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays. Bioinformatics 19:1348-1359.
-
(2003)
Bioinformatics
, vol.19
, pp. 1348-1359
-
-
Draghici, S.1
Kulaeva, O.2
Hoff, B.3
Petrov, A.4
Shams, S.5
Tainsky, M.A.6
-
12
-
-
28644452470
-
Clustering short time series gene expression data
-
Ernst J, Nau GJ, Bar-Joseph Z. 2005. Clustering short time series gene expression data. Bioinformatics Suppl 1:i159-i168.
-
(2005)
Bioinformatics
, Issue.SUPPL. 1
-
-
Ernst, J.1
Nau, G.J.2
Bar-Joseph, Z.3
-
13
-
-
0033667460
-
Mining of biological data. I. Identifying discriminating features via mean hypothesis testing
-
Kamimura RT, Bicciato S, Shimizu H, Alford J, Stephanopoulos G. 2000. Mining of biological data. I. Identifying discriminating features via mean hypothesis testing. Metab Eng 2:218-227.
-
(2000)
Metab Eng
, vol.2
, pp. 218-227
-
-
Kamimura, R.T.1
Bicciato, S.2
Shimizu, H.3
Alford, J.4
Stephanopoulos, G.5
-
14
-
-
35048854505
-
2 - Case study
-
Nikolaou BJ, Wurtele ES, editors, New York: Springer. p
-
2 - Case study. In: Nikolaou BJ, Wurtele ES, editors. Concepts in Plant Metabolomics. New York: Springer. p 93-110.
-
(2007)
Concepts in Plant Metabolomics
, pp. 93-110
-
-
Kanani, H.1
Dutta, B.2
Quackenbush, J.3
Klapa, M.I.4
-
16
-
-
0037350568
-
Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray
-
Kim H, Snesrud EC, Haas B, Cheung F, Town CD, Quackenbush J. 2003. Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res 13:327-340.
-
(2003)
Genome Res
, vol.13
, pp. 327-340
-
-
Kim, H.1
Snesrud, E.C.2
Haas, B.3
Cheung, F.4
Town, C.D.5
Quackenbush, J.6
-
18
-
-
35048860256
-
-
Korn EL, Troendle JF, McShane LM, Simon R. 2001. Controlling the number of false discoveries: Application to high-dimensional genomic data Technical report 003, Biometrie Research Branch, National Cancer Institute. http://linus.nci.nih.gov/~brb/TechReport.htm.
-
Korn EL, Troendle JF, McShane LM, Simon R. 2001. Controlling the number of false discoveries: Application to high-dimensional genomic data Technical report 003, Biometrie Research Branch, National Cancer Institute. http://linus.nci.nih.gov/~brb/TechReport.htm.
-
-
-
-
19
-
-
25444458298
-
Considerations when using the significance analysis of microarrays (SAM) algorithm
-
Larsson O, Wahlestedt C, Timmons JA. 2005. Considerations when using the significance analysis of microarrays (SAM) algorithm. BMC Bioinform 6:129.
-
(2005)
BMC Bioinform
, vol.6
, pp. 129
-
-
Larsson, O.1
Wahlestedt, C.2
Timmons, J.A.3
-
20
-
-
20444462441
-
Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis
-
Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J. 2005. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol 137:1115-1129.
-
(2005)
Plant Physiol
, vol.137
, pp. 1115-1129
-
-
Liu, F.1
Vantoai, T.2
Moy, L.P.3
Bock, G.4
Linford, L.D.5
Quackenbush, J.6
-
21
-
-
3042587319
-
Measurement of somatostatin receptor subtype 2 mRNA in breast cancer and corresponding normal tissue
-
Orlando C, Raggi CC, Bianchi S, Distante V, Simi L, Vezzosi V, Gelmini S, Pinzani P, Smith MC, Buonamano A, Lazzeri E, Pazzagli M, Cataliotti L, Maggi M, Serio M. 2004. Measurement of somatostatin receptor subtype 2 mRNA in breast cancer and corresponding normal tissue. Endocr Relat Cancer 11:323-332.
-
(2004)
Endocr Relat Cancer
, vol.11
, pp. 323-332
-
-
Orlando, C.1
Raggi, C.C.2
Bianchi, S.3
Distante, V.4
Simi, L.5
Vezzosi, V.6
Gelmini, S.7
Pinzani, P.8
Smith, M.C.9
Buonamano, A.10
Lazzeri, E.11
Pazzagli, M.12
Cataliotti, L.13
Maggi, M.14
Serio, M.15
-
22
-
-
0035999977
-
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
-
Pan W. 2002. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18:546-554.
-
(2002)
Bioinformatics
, vol.18
, pp. 546-554
-
-
Pan, W.1
-
23
-
-
0037433769
-
Statistical tests for identifying differentially expressed genes in time-course microarray experiments
-
Park T, Yi SG, Lee S, Lee SY, Yoo DH, Ahn JI, Lee YS. 2003. Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics 19:694-703.
-
(2003)
Bioinformatics
, vol.19
, pp. 694-703
-
-
Park, T.1
Yi, S.G.2
Lee, S.3
Lee, S.Y.4
Yoo, D.H.5
Ahn, J.I.6
Lee, Y.S.7
-
24
-
-
0037311919
-
T M4: A free, open-source system for microarray data management and analysis
-
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. 2003. T M4: A free, open-source system for microarray data management and analysis. Biotechniques 34:374-378.
-
(2003)
Biotechniques
, vol.34
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
Sturn, A.11
Snuffin, M.12
Rezantsev, A.13
Popov, D.14
Ryltsov, A.15
Kostukovich, E.16
Borisovsky, I.17
Liu, Z.18
Vinsavich, A.19
Trush, V.20
Quackenbush, J.21
more..
-
25
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
26
-
-
24644519314
-
Significance analysis of time course microarray experiments
-
Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW. 2005. Significance analysis of time course microarray experiments. Proc Natl Acad Sci USA 102:12837-12842.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12837-12842
-
-
Storey, J.D.1
Xiao, W.2
Leek, J.T.3
Tompkins, R.G.4
Davis, R.W.5
-
27
-
-
0036856209
-
Nonparametric methods for identifying differentially expressed genes in microarray data
-
Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. 2002. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18:1454-1461.
-
(2002)
Bioinformatics
, vol.18
, pp. 1454-1461
-
-
Troyanskaya, O.G.1
Garber, M.E.2
Brown, P.O.3
Botstein, D.4
Altman, R.B.5
-
28
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci 98:5116-5121.
-
(2001)
Proc Natl Acad Sci
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
29
-
-
4544298732
-
Sample size for identifying differentially expressed genes in microarray experiments
-
Wang S, Chen JJ. 2004. Sample size for identifying differentially expressed genes in microarray experiments. J Comput Biol 11:714-726.
-
(2004)
J Comput Biol
, vol.11
, pp. 714-726
-
-
Wang, S.1
Chen, J.J.2
-
30
-
-
17444374677
-
Differential gene expression detection using penalized linear regression models: The improved SAM statistics
-
Wu B. 2005. Differential gene expression detection using penalized linear regression models: The improved SAM statistics. Bioinformatics 21:1565-1571.
-
(2005)
Bioinformatics
, vol.21
, pp. 1565-1571
-
-
Wu, B.1
-
32
-
-
0037180744
-
Improved significance test for DNA microarray data: Temporal effects of shear stress on endothelial genes
-
Zhao Y, Chen BP, Miao H, Yuan S, Li YS, Hu Y, Rocke DM, Chien S. 2002. Improved significance test for DNA microarray data: Temporal effects of shear stress on endothelial genes. Physiol Genom 12:1-11.
-
(2002)
Physiol Genom
, vol.12
, pp. 1-11
-
-
Zhao, Y.1
Chen, B.P.2
Miao, H.3
Yuan, S.4
Li, Y.S.5
Hu, Y.6
Rocke, D.M.7
Chien, S.8
|