-
1
-
-
48349141827
-
Using microarrays to study the microenvironment in tumor biology: the crucial role of statistics
-
Baker SG (2008) Using microarrays to study the microenvironment in tumor biology: the crucial role of statistics. Semin Cancer Biol 18: 305-310.
-
(2008)
Semin Cancer Biol
, vol.18
, pp. 305-310
-
-
Baker, S.G.1
-
2
-
-
0034610257
-
The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies
-
Belcher CE, Drenkow J, Kehoe B, Gingeras TR, McNamara N, Lemjabbar H, Basbaum C, Relman DA (2000) The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proc Natl Acad Sci USA 97: 13847-13852
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 13847-13852
-
-
Belcher, C.E.1
Drenkow, J.2
Kehoe, B.3
Gingeras, T.R.4
McNamara, N.5
Lemjabbar, H.6
Basbaum, C.7
Relman, D.A.8
-
3
-
-
13244289933
-
Optimized LOWESS normalization parameter selection for DNA microarray data
-
Berger JA, Hautaniemi S, Järvinen AK, Edgren H, Mitra SK, Astola J (2004) Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5: 194.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 194
-
-
Berger, J.A.1
Hautaniemi, S.2
Järvinen, A.K.3
Edgren, H.4
Mitra, S.K.5
Astola, J.6
-
4
-
-
33645505591
-
A novel normalization method for effective removal of systematic variation in microarray data
-
Chua S, Vijayakumar, P, Nissom P, Yang H (2006) A novel normalization method for effective removal of systematic variation in microarray data. Nucleic Acids Res 34: e38.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Chua, S.1
Vijayakumar, P.2
Nissom, P.3
Yang, H.4
-
5
-
-
0036900895
-
Fundamentals of experimental design for cDNA microarrays
-
Churchill G A (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32: 490-495.
-
(2002)
Nat Genet
, vol.32
, pp. 490-495
-
-
Churchill, G.A.1
-
6
-
-
33847261476
-
The application of microarray technology to the analysis of the cancer genome
-
Cowell JK, Hawthorn L (2007) The application of microarray technology to the analysis of the cancer genome. Curr Mol Med 7: 103-120.
-
(2007)
Curr Mol Med
, vol.7
, pp. 103-120
-
-
Cowell, J.K.1
Hawthorn, L.2
-
7
-
-
40849114757
-
In vitro evaluation of the probiotic properties of human intestinal Bifidobacterium species and selection of new probiotic candidates
-
Delgado S, O'Sullivan E, Fitzgerald G, Mayo B (2008) In vitro evaluation of the probiotic properties of human intestinal Bifidobacterium species and selection of new probiotic candidates. J Appl Microbiol 104: 1119-1127.
-
(2008)
J Appl Microbiol
, vol.104
, pp. 1119-1127
-
-
Delgado, S.1
O'Sullivan, E.2
Fitzgerald, G.3
Mayo, B.4
-
8
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiment
-
Dudoit S, Yang YH, Callow MJ, Speed TP (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiment. Statistica Sinica 12: 111-139.
-
(2002)
Statistica Sinica
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
9
-
-
0034640417
-
Analysis by high density cDNA arrays of altered gene expression in human intestinal epithelial cells in response to infection with the invasive enteric bacteria Salmonella
-
Eckmann L, Smith JR, Housley MP, Dwinell MB, Kagnoff MF (2000) Analysis by high density cDNA arrays of altered gene expression in human intestinal epithelial cells in response to infection with the invasive enteric bacteria Salmonella. J Biol Chem 275: 14084-14094.
-
(2000)
J Biol Chem
, vol.275
, pp. 14084-14094
-
-
Eckmann, L.1
Smith, J.R.2
Housley, M.P.3
Dwinell, M.B.4
Kagnoff, M.F.5
-
10
-
-
0038649968
-
Non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice
-
Fukushima K, Ogawa H, Takahashi K, Naito H, Funayama Y, Kitayama T, Yonezawa H, Sasaki I (2003) Non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice. Scand J Gastroenterol 38: 626-634.
-
(2003)
Scand J Gastroenterol
, vol.38
, pp. 626-634
-
-
Fukushima, K.1
Ogawa, H.2
Takahashi, K.3
Naito, H.4
Funayama, Y.5
Kitayama, T.6
Yonezawa, H.7
Sasaki, I.8
-
11
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman R, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
12
-
-
33645756545
-
-
Springer, New York
-
Gentleman R, Irizarry RA, Carey VJ, Dudoit S, Hubrer W (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, New York.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
-
-
Gentleman, R.1
Irizarry, R.A.2
Carey, V.J.3
Dudoit, S.4
Hubrer, W.5
-
13
-
-
0035812167
-
In vitro adherence properties of Lactobacillus rhamnosus DR20 and Bifidobacterium lactis DR10 strains and their antagonistic activity against an enterotoxigenic Escherichia coli
-
Gopal PK, Prasad J, Smart J, Gill HS (2001) In vitro adherence properties of Lactobacillus rhamnosus DR20 and Bifidobacterium lactis DR10 strains and their antagonistic activity against an enterotoxigenic Escherichia coli. Int J Food Microbiol 67: 207-216.
-
(2001)
Int J Food Microbiol
, vol.67
, pp. 207-216
-
-
Gopal, P.K.1
Prasad, J.2
Smart, J.3
Gill, H.S.4
-
14
-
-
33748495591
-
Rat toxicogenomic study reveals analytical consistency across microarray platforms
-
Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng XT, Sun YMA, Tong WD, Dragan YP, Shi LM (2006) Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nature Biotechnology 24: 1162-1169.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1162-1169
-
-
Guo, L.1
Lobenhofer, E.K.2
Wang, C.3
Shippy, R.4
Harris, S.C.5
Zhang, L.6
Mei, N.7
Chen, T.8
Herman, D.9
Goodsaid, F.M.10
Hurban, P.11
Phillips, K.L.12
Xu, J.13
Deng, X.T.14
Sun, Y.M.A.15
Tong, W.D.16
Dragan, Y.P.17
Shi, L.M.18
-
16
-
-
34147132358
-
Critical evaluation of probiotic activity of lactic acid bacteria and their effects
-
Heczko PB, Strus M, Kochan P (2006) Critical evaluation of probiotic activity of lactic acid bacteria and their effects. J Physiol Pharmacol 57 (Suppl 9): 5-12.
-
(2006)
J Physiol Pharmacol
, vol.57
, Issue.SUPPL. 9
, pp. 5-12
-
-
Heczko, P.B.1
Strus, M.2
Kochan, P.3
-
17
-
-
0037674681
-
Developments in microarray technologies
-
Howbrook DN, van der Valk AM, O'Shaugnessy MC, Sarker DK, Baker SC, Lloyd AW (2003) Developments in microarray technologies. Drug Discov Today 8: 642-651.
-
(2003)
Drug Discov Today
, vol.8
, pp. 642-651
-
-
Howbrook, D.N.1
van der Valk, A.M.2
O'Shaugnessy, M.C.3
Sarker, D.K.4
Baker, S.C.5
Lloyd, A.W.6
-
18
-
-
67549095125
-
Feature Selection for Cancer Classification on Microarray Expression Data. Eighth International Conference on Intelligent Systems Design and Applications
-
Hsu HH, Lu MD (2008) Feature Selection for Cancer Classification on Microarray Expression Data. Eighth International Conference on Intelligent Systems Design and Applications, IEEE 2008: 153-158.
-
(2008)
IEEE 2008
, pp. 153-158
-
-
Hsu, H.H.1
Lu, M.D.2
-
19
-
-
33747344944
-
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
-
Jeffery IB, Higgins DG, Culhane AC (2006) Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 7: 359.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 359
-
-
Jeffery, I.B.1
Higgins, D.G.2
Culhane, A.C.3
-
20
-
-
25444528447
-
Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes
-
Jirapech-Umpai T, Aitken S (2005) Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes. BMC Bioinformatics 6: 148-158.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 148-158
-
-
Jirapech-Umpai, T.1
Aitken, S.2
-
21
-
-
79955766601
-
Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes
-
Jung K, Becker B, Brunner E, Beissbarth T (2011) Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes. Bioinformatics 27: 1377-1383.
-
(2011)
Bioinformatics
, vol.27
, pp. 1377-1383
-
-
Jung, K.1
Becker, B.2
Brunner, E.3
Beissbarth, T.4
-
22
-
-
67549090128
-
Best practices for hybridization design in two-colour microarray analysis
-
Knapen D, Vergauwen L, Laukens K, Blust R (2009) Best practices for hybridization design in two-colour microarray analysis. Trends Biotechnol 27: 406-414.
-
(2009)
Trends Biotechnol
, vol.27
, pp. 406-414
-
-
Knapen, D.1
Vergauwen, L.2
Laukens, K.3
Blust, R.4
-
23
-
-
36248950699
-
Microarray analysis: basic strategies for successful experiments
-
Ness SA (2007) Microarray analysis: basic strategies for successful experiments. Mol Biotechnol 36: 205-219.
-
(2007)
Mol Biotechnol
, vol.36
, pp. 205-219
-
-
Ness, S.A.1
-
24
-
-
37649013438
-
Probiotic bacteria change Escherichia coli-induced gene expression in cultured colonocytes: Implications in intestinal pathophysiology
-
Panigrahi P, Braileanu GT, Chen H, Stine OC (2007) Probiotic bacteria change Escherichia coli-induced gene expression in cultured colonocytes: Implications in intestinal pathophysiology. World J Gastroenterol 13: 6370-6378.
-
(2007)
World J Gastroenterol
, vol.13
, pp. 6370-6378
-
-
Panigrahi, P.1
Braileanu, G.T.2
Chen, H.3
Stine, O.C.4
-
25
-
-
0141668891
-
The invasive phenotype of Shigella flexneri directs a distinct gene expression pattern in the human intestinal epithelial cell line Caco-2
-
Pedron T, Thibault C, Sansonetti PJ (2003) The invasive phenotype of Shigella flexneri directs a distinct gene expression pattern in the human intestinal epithelial cell line Caco-2. J Biol Chem 278: 33878- 33886.
-
(2003)
J Biol Chem
, vol.278
, pp. 33878-33886
-
-
Pedron, T.1
Thibault, C.2
Sansonetti, P.J.3
-
26
-
-
0036898577
-
Microarray data normalization and transformation
-
Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32 (Suppl): 496-501.
-
(2002)
Nat Genet
, vol.32
, Issue.SUPPL.
, pp. 496-501
-
-
Quackenbush, J.1
-
27
-
-
70149113077
-
-
R., Development Core Team R Foundation for Statistical Computing, Vienna. URL
-
R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. URL http://www.r-project.org.
-
(2009)
R: A language and environment for statistical computing
-
-
-
28
-
-
0034040799
-
Salmonella typhimurium infection and lipopolysaccharide stimulation induce similar changes in macrophage gene expression
-
Rosenberger CM, Scott MG, Gold MR, Hancock RE, Finlay BB (2000) Salmonella typhimurium infection and lipopolysaccharide stimulation induce similar changes in macrophage gene expression. J Immunol 164: 5894-5904.
-
(2000)
J Immunol
, vol.164
, pp. 5894-5904
-
-
Rosenberger, C.M.1
Scott, M.G.2
Gold, M.R.3
Hancock, R.E.4
Finlay, B.B.5
-
29
-
-
20044371666
-
The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics
-
Sambuy Y, De Angelis I, Ranaldi G, Scarino ML, Stammati A, Zucco F (2005) The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics. Cell Biol Toxicol 21: 1-26.
-
(2005)
Cell Biol Toxicol
, vol.21
, pp. 1-26
-
-
Sambuy, Y.1
De Angelis, I.2
Ranaldi, G.3
Scarino, M.L.4
Stammati, A.5
Zucco, F.6
-
30
-
-
27644528185
-
Cross-platform comparability of microarray technology: Intraplatform consistency and appropriate data analysis procedures are essential
-
Shi LM, Tong WD, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Guo L, Su ZQ, Han T, Fuscoe JC, Xu ZA, Patterson TA, Hong HX, Xie Q, Perkins RG, Chen JJ, Casciano DA (2005) Cross-platform comparability of microarray technology: Intraplatform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 6: S12.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Shi, L.M.1
Tong, W.D.2
Fang, H.3
Scherf, U.4
Han, J.5
Puri, R.K.6
Frueh, F.W.7
Goodsaid, F.M.8
Guo, L.9
Su, Z.Q.10
Han, T.11
Fuscoe, J.C.12
Xu, Z.A.13
Patterson, T.A.14
Hong, H.X.15
Xie, Q.16
Perkins, R.G.17
Chen, J.J.18
Casciano, D.A.19
-
31
-
-
2942608807
-
-
. Springer, New York
-
Simon RM, Korn EL, McShane LM, Radmacher MD, Wright GW, Zhao Y (2007) Design and Analysis of DNA Microarray Investigations. Springer, New York.
-
(2007)
Design and Analysis of DNA Microarray Investigations
-
-
Simon, R.M.1
Korn, E.L.2
McShane, L.M.3
Radmacher, M.D.4
Wright, G.W.5
Zhao, Y.6
-
32
-
-
33644872577
-
Limma: linear models for microarray data
-
Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, eds.Springer New York
-
Smyth GK (2005) Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, eds. pp 397-420. Springer, New York.
-
(2005)
Bioinformatics and Computational Biology Solutions using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
33
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth GK, Speed TP (2003) Normalization of cDNA microarray data. Methods 31: 265-273.
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.P.2
-
34
-
-
35348853238
-
DNA microarrays: a powerful genomic tool for biomedical and clinical research
-
Trevino V, Falciani F, Barrera-Saldana HA (2007) DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol Med 13: 527-541.
-
(2007)
Mol Med
, vol.13
, pp. 527-541
-
-
Trevino, V.1
Falciani, F.2
Barrera-Saldana, H.A.3
-
35
-
-
8144226244
-
Microarrays - status and prospects
-
Venkatasubbarao S (2004) Microarrays - status and prospects. Trends Biotechnol 22: 630-637.
-
(2004)
Trends Biotechnol
, vol.22
, pp. 630-637
-
-
Venkatasubbarao, S.1
-
36
-
-
0034869983
-
Normalization for cDNA microarray data
-
Bittner ML, Chen Y, Dorsel AN, Dougherty ER eds
-
Yang YH, Dudoit S, Luu P, Speed TP (2001) Normalization for cDNA microarray data. In Microarrays: Optical Technologies and Informatics. Bittner ML, Chen Y, Dorsel AN, Dougherty ER eds. Proceedings of SPIE 4266: 141-152.
-
(2001)
Microarrays: Optical Technologies and InformaticsProceedings of SPIE
, vol.4266
, pp. 141-152
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Speed, T.P.4
-
37
-
-
1342294092
-
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
-
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucl Acids Res 30: e15.
-
(2002)
Nucl Acids Res
, vol.30
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
Speed, T.P.7
|