-
1
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
10.1038/nbt1296-1675, 9634850
-
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 1996, 14. 10.1038/nbt1296-1675, 9634850.
-
(1996)
Nature Biotechnology
, vol.14
-
-
Lockhart, D.J.1
Dong, H.2
Byrne, M.C.3
Follettie, M.T.4
Gallo, M.V.5
Chee, M.S.6
Mittmann, M.7
Wang, C.8
Kobayashi, M.9
Horton, H.10
Brown, E.L.11
-
2
-
-
33747343754
-
The developmental competence of bovine nuclear transfer embryos derived from cow versus heifer cytoplasts
-
10.1016/j.anireprosci.2005.10.011, 16324805
-
Aston KI, Li GP, Hicks BA, Sessions BR, Pate BJ, Hammon DS, Bunch TD, White KL. The developmental competence of bovine nuclear transfer embryos derived from cow versus heifer cytoplasts. Animal Reproduction Science 2006, 95:234-243. 10.1016/j.anireprosci.2005.10.011, 16324805.
-
(2006)
Animal Reproduction Science
, vol.95
, pp. 234-243
-
-
Aston, K.I.1
Li, G.P.2
Hicks, B.A.3
Sessions, B.R.4
Pate, B.J.5
Hammon, D.S.6
Bunch, T.D.7
White, K.L.8
-
3
-
-
32544443763
-
Effect of the time interval between fusion and activation on nuclear state and development in vitro and in vivo of bovine somatic cell nuclear transfer embryos
-
10.1530/rep.1.00714, 16388008
-
Aston KI, Li GP, Hicks BA, Sessions BR, Pate BJ, Hammon DS, Bunch TD, White KL. Effect of the time interval between fusion and activation on nuclear state and development in vitro and in vivo of bovine somatic cell nuclear transfer embryos. Reproduction 2006, 131:45-51. 10.1530/rep.1.00714, 16388008.
-
(2006)
Reproduction
, vol.131
, pp. 45-51
-
-
Aston, K.I.1
Li, G.P.2
Hicks, B.A.3
Sessions, B.R.4
Pate, B.J.5
Hammon, D.S.6
Bunch, T.D.7
White, K.L.8
-
4
-
-
65249166312
-
Global Gene Expression Analysis of Bovine Somatic Cell Nuclear Transfer Blastocysts and Cotyledons
-
10.1002/mrd.20962, 19062181
-
Aston KI, Li GP, Sessions BR, Davis AP, Winger QA, Rickords LF, Stevens JR, White KL. Global Gene Expression Analysis of Bovine Somatic Cell Nuclear Transfer Blastocysts and Cotyledons. Molecular Reproduction and Development 2009, 76:471-482. 10.1002/mrd.20962, 19062181.
-
(2009)
Molecular Reproduction and Development
, vol.76
, pp. 471-482
-
-
Aston, K.I.1
Li, G.P.2
Sessions, B.R.3
Davis, A.P.4
Winger, Q.A.5
Rickords, L.F.6
Stevens, J.R.7
White, K.L.8
-
5
-
-
33645756545
-
-
New York, Springer
-
Gentleman R, Huber W, Carey VJ, Irizarry RA, Dudoit S. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, New York, Springer.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
-
-
Gentleman, R.1
Huber, W.2
Carey, V.J.3
Irizarry, R.A.4
Dudoit, S.5
-
6
-
-
84874655904
-
Latin Square Data for Expression Algorithm Assessment
-
Affymetrix
-
Affymetrix Latin Square Data for Expression Algorithm Assessment. Affymetrix., http://www.affymetrix.com/support/technical/sample_data/datasets.affx
-
-
-
-
7
-
-
33847288899
-
A distribution free summarization method for Affymetrix GeneChip arrays
-
10.1093/bioinformatics/btl609, 17148508
-
Chen Z, McGee M, Liu Q, Scheuermann RH. A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics 2007, 23(3):321-327. 10.1093/bioinformatics/btl609, 17148508.
-
(2007)
Bioinformatics
, vol.23
, Issue.3
, pp. 321-327
-
-
Chen, Z.1
McGee, M.2
Liu, Q.3
Scheuermann, R.H.4
-
8
-
-
22144461265
-
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
-
551536, 15693945
-
Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biology 2005, 6(R16). 551536, 15693945.
-
(2005)
Genome Biology
, vol.6
, Issue.16 R
-
-
Choe, S.E.1
Boutros, M.2
Michelson, A.M.3
Church, G.M.4
Halfon, M.S.5
-
9
-
-
33845562634
-
Feature-level expoloration of a published Affymetrix GeneChip control dataset
-
1779590, 16953902
-
Irizarry RA, Cope LM, Wu Z. Feature-level expoloration of a published Affymetrix GeneChip control dataset. Genome Biology 2006, 7(404). 1779590, 16953902.
-
(2006)
Genome Biology
, vol.7
, Issue.404
-
-
Irizarry, R.A.1
Cope, L.M.2
Wu, Z.3
-
10
-
-
42449144718
-
A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
-
2324099, 18366762
-
Pearson RD. A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods. BMC Bioinformatics 2008, 9(164). 2324099, 18366762.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.164
-
-
Pearson, R.D.1
-
11
-
-
12344280017
-
Summaries of Affymetrix GeneChip probe level data
-
e15, 150247, 12582260
-
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 2003, 31(4 e15). 150247, 12582260.
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.4
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
12
-
-
10844290766
-
A model-based background adjustment for oligonucleotide expression arrays
-
Wu ZJ, Irizarry RA, Gentleman R, Martinez Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 2004, 99(468):909-917.
-
(2004)
Journal of the American Statistical Association
, vol.99
, Issue.468
, pp. 909-917
-
-
Wu, Z.J.1
Irizarry, R.A.2
Gentleman, R.3
Martinez Murillo, F.4
Spencer, F.5
-
13
-
-
70149113077
-
-
R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team
-
R Development Core Team R: A Language and Environment for Statistical Computing 2009, R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team., http://www.R-project.org
-
(2009)
R: A Language and Environment for Statistical Computing
-
-
-
14
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
10.1186/gb-2004-5-10-r80, 545600, 15461798
-
Gentleman RC, 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 JYH, Zhang J. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
-
(2004)
Genome Biology
, vol.5
-
-
Gentleman, R.C.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.H.24
Zhang, J.25
more..
-
15
-
-
21444460810
-
Unconstrained Parameterizations for Variance-Covariance Matrices
-
Pinheiro JC, Bates DM. Unconstrained Parameterizations for Variance-Covariance Matrices. Statistics and Computing 1996, 6:289-296.
-
(1996)
Statistics and Computing
, vol.6
, pp. 289-296
-
-
Pinheiro, J.C.1
Bates, D.M.2
-
17
-
-
77954621418
-
Probe-level model based test statistics for detecting differential expression
-
University of California, Berkeley
-
Bolstad B. Probe-level model based test statistics for detecting differential expression. PhD thesis 2004, University of California, Berkeley.
-
(2004)
PhD thesis
-
-
Bolstad, B.1
-
18
-
-
4544341015
-
Linear models and empirical Bayes Methods for assessing differential expression in microarray experiments
-
Smyth GK. Linear models and empirical Bayes Methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3(1):3.
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
, Issue.1
, pp. 3
-
-
Smyth, G.K.1
-
19
-
-
33749326335
-
Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression
-
1579233, 16934150
-
Lemieux S. Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression. BMC Bioinformatics 2006, 7(391). 1579233, 16934150.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.391
-
-
Lemieux, S.1
-
20
-
-
0035998835
-
Model-based clustering, discriminant analysis, and density estimation
-
Fraley C, Raftery AE. Model-based clustering, discriminant analysis, and density estimation. Journal of the American Statistical Association 2002, 97:611-631.
-
(2002)
Journal of the American Statistical Association
, vol.97
, pp. 611-631
-
-
Fraley, C.1
Raftery, A.E.2
-
21
-
-
37049031005
-
Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data
-
10.1089/cmb.2007.0078, 18052774
-
Astrand M, Mostad P, Rudemo M. Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data. Journal of Computational Biology 2007, 14(10):1353-1367. 10.1089/cmb.2007.0078, 18052774.
-
(2007)
Journal of Computational Biology
, vol.14
, Issue.10
, pp. 1353-1367
-
-
Astrand, M.1
Mostad, P.2
Rudemo, M.3
-
22
-
-
42949149103
-
Empirical Bayes models for multiple probe type microarrays at the probe level
-
2358895, 18366694
-
Astrand M, Mostad P, Rudemo M. Empirical Bayes models for multiple probe type microarrays at the probe level. BMC Bioinformatics 2008, 9(156). 2358895, 18366694.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.156
-
-
Astrand, M.1
Mostad, P.2
Rudemo, M.3
-
23
-
-
41949124937
-
Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays
-
10.1093/bioinformatics/btn053, 18316342
-
Xu J, Cui X. Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays. Bioinformatics 2008, 24(8):1056-1062. 10.1093/bioinformatics/btn053, 18316342.
-
(2008)
Bioinformatics
, vol.24
, Issue.8
, pp. 1056-1062
-
-
Xu, J.1
Cui, X.2
-
24
-
-
74249098883
-
A first principles approach to differential expression in microarray data analysis
-
2749840, 19758448
-
Rubin RA. A first principles approach to differential expression in microarray data analysis. BMC Bioinformatics 2009, 10(292). 2749840, 19758448.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.292
-
-
Rubin, R.A.1
-
25
-
-
24644460573
-
A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
-
10.1093/bioinformatics/bti583, 16020470
-
Liu X, Milo M, Lawrence ND, Rattray M. A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips. Bioinformatics 2005, 21(18):3637-3644. 10.1093/bioinformatics/bti583, 16020470.
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3637-3644
-
-
Liu, X.1
Milo, M.2
Lawrence, N.D.3
Rattray, M.4
-
26
-
-
33748644662
-
Probe-level measurement error improves accuracy in detecting differential gene expression
-
10.1093/bioinformatics/btl361, 16820429
-
Liu X, Milo M, Lawrence ND, Rattray M. Probe-level measurement error improves accuracy in detecting differential gene expression. Bioinformatics 2006, 22(17):2107-2113. 10.1093/bioinformatics/btl361, 16820429.
-
(2006)
Bioinformatics
, vol.22
, Issue.17
, pp. 2107-2113
-
-
Liu, X.1
Milo, M.2
Lawrence, N.D.3
Rattray, M.4
-
27
-
-
34147152900
-
Including probe-level uncertainty in model-based gene expression clustering
-
Liu X, Lin KK, Andersen B, Rattray M. Including probe-level uncertainty in model-based gene expression clustering. BMC Bioinformatics 2007, 8(98).
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.98
-
-
Liu, X.1
Lin, K.K.2
Andersen, B.3
Rattray, M.4
-
28
-
-
67949098968
-
Puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis
-
10.1186/1471-2105-10-211, 2714555, 19589155
-
Pearson RD, Liu X, Sanguinetti G, Milo M, Lawrence ND, Rattray M. puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis. BMC Bioinformatics 2009, 10:211. 10.1186/1471-2105-10-211, 2714555, 19589155.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 211
-
-
Pearson, R.D.1
Liu, X.2
Sanguinetti, G.3
Milo, M.4
Lawrence, N.D.5
Rattray, M.6
-
31
-
-
33644922417
-
Multiple Testing Procedures: the multtest Package and Applications to Genomics
-
Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S
-
Pollard KS, Dudoit S, Laan MJ. Multiple Testing Procedures: the multtest Package and Applications to Genomics. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 249-271. Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 249-271
-
-
Pollard, K.S.1
Dudoit, S.2
Laan, M.J.3
-
32
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 1995, 57:289-300.
-
(1995)
Journal of the Royal Statistical Society, Series B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
35
-
-
38749086405
-
Analysis of Differential Gene Expression Studies
-
Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S
-
Scholtens D, von Heydebreck A. Analysis of Differential Gene Expression Studies. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 229-248. Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 229-248
-
-
Scholtens, D.1
von Heydebreck, A.2
-
36
-
-
63449142392
-
Filtering for Increased Power for Microarray Data Analysis
-
2661050, 19133141
-
Hackstadt AJ, Hess AM. Filtering for Increased Power for Microarray Data Analysis. BMC Bioinformatics 2009, 10(11). 2661050, 19133141.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.11
-
-
Hackstadt, A.J.1
Hess, A.M.2
-
37
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
10.1038/75556, 10802651, The Gene Ontology Consortium
-
The Gene Ontology Consortium Gene Ontology: tool for the unification of biology. Nature Genetics 2000, 25:25-29. 10.1038/75556, 10802651, The Gene Ontology Consortium.
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
-
38
-
-
33749539291
-
Case Studies Using Graphs on Biological Data
-
Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S
-
Gentleman R, Scholtens D, Ding B, Carey VJ, Huber W. Case Studies Using Graphs on Biological Data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 369-394. Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 369-394
-
-
Gentleman, R.1
Scholtens, D.2
Ding, B.3
Carey, V.J.4
Huber, W.5
-
39
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
10.1093/bioinformatics/btl140, 16606683
-
Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006, 22(13):1600-1607. 10.1093/bioinformatics/btl140, 16606683.
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
40
-
-
0042871633
-
Cloning adult farm animals: a review of the possibilities and problems associated with somatic cell nuclear transfer
-
10.1034/j.1600-0897.2003.00064.x, 12846674
-
Edwards JL, Schrick FN, McCracken MD, van Amstel SR, Hopkins FM, Welborn MG, Davies CJ. Cloning adult farm animals: a review of the possibilities and problems associated with somatic cell nuclear transfer. American Journal of Reproductive Immunology 2003, 50:113-123. 10.1034/j.1600-0897.2003.00064.x, 12846674.
-
(2003)
American Journal of Reproductive Immunology
, vol.50
, pp. 113-123
-
-
Edwards, J.L.1
Schrick, F.N.2
McCracken, M.D.3
van Amstel, S.R.4
Hopkins, F.M.5
Welborn, M.G.6
Davies, C.J.7
-
41
-
-
0036136468
-
Frequency and occurrence of late-gestation losses from cattle cloned embryos
-
10.1095/biolreprod66.1.6, 11751257
-
Heyman Y, Chavatte-Palmer P, LeBourhis D, Camous S, Vignon X, Renard JP. Frequency and occurrence of late-gestation losses from cattle cloned embryos. Biology of Reproduction 2002, 66:6-13. 10.1095/biolreprod66.1.6, 11751257.
-
(2002)
Biology of Reproduction
, vol.66
, pp. 6-13
-
-
Heyman, Y.1
Chavatte-Palmer, P.2
LeBourhis, D.3
Camous, S.4
Vignon, X.5
Renard, J.P.6
-
42
-
-
0033150614
-
Clinical and pathological features of cloned transgenic calves and fetuses (13 case studies)
-
10.1016/S0093-691X(99)00089-8, 10729073
-
Hill JR, Roussel AJ, Cibelli JB, Edwards JF, Hooper NL, Miller MW, Thompson JA, Looney CR, Westhusin ME, Robl JM, Stice SL. Clinical and pathological features of cloned transgenic calves and fetuses (13 case studies). Theriogenology 1999, 51:1451-1465. 10.1016/S0093-691X(99)00089-8, 10729073.
-
(1999)
Theriogenology
, vol.51
, pp. 1451-1465
-
-
Hill, J.R.1
Roussel, A.J.2
Cibelli, J.B.3
Edwards, J.F.4
Hooper, N.L.5
Miller, M.W.6
Thompson, J.A.7
Looney, C.R.8
Westhusin, M.E.9
Robl, J.M.10
Stice, S.L.11
-
43
-
-
0033693416
-
Evidence for placental abnormality as the major cause of mortality in first-trimester somatic cell cloned bovine fetuses
-
10.1095/biolreprod63.6.1787, 11090450
-
Hill JR, Burghardt RC, Jones K, Long CR, Looney CR, Shin T, Spencer TE, Thompson JA, Winger QA, Westhusin ME. Evidence for placental abnormality as the major cause of mortality in first-trimester somatic cell cloned bovine fetuses. Biology of Reproduction 2000, 63:1787-1794. 10.1095/biolreprod63.6.1787, 11090450.
-
(2000)
Biology of Reproduction
, vol.63
, pp. 1787-1794
-
-
Hill, J.R.1
Burghardt, R.C.2
Jones, K.3
Long, C.R.4
Looney, C.R.5
Shin, T.6
Spencer, T.E.7
Thompson, J.A.8
Winger, Q.A.9
Westhusin, M.E.10
|