-
1
-
-
0035942271
-
Significance analysis of microarray applied to the ionizing radiation response
-
Tusher,V.G., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarray applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
2
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Article 3
-
Smyth,G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Gen. Mol. Biol, 3, Article 3.
-
(2004)
Stat. Appl. Gen. Mol. Biol
, vol.3
-
-
Smyth, G.K.1
-
3
-
-
0037438387
-
Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis
-
Akashi,K., He,X., Chen,J., Iwasaki,H., Niu,C., Steenhard,B., Zhang,J., Haug,J. and Li,L. (2003) Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood, 101, 383-389.
-
(2003)
Blood
, vol.101
, pp. 383-389
-
-
Akashi, K.1
He, X.2
Chen, J.3
Iwasaki, H.4
Niu, C.5
Steenhard, B.6
Zhang, J.7
Haug, J.8
Li, L.9
-
4
-
-
0037112047
-
Projection of an immunological self shadow within the thymus by the Aire protein
-
Anderson,M.S., Venanzi,E.S., Klein,L., Chen,Z., Berzins,S.P., Turley,S.J., von Boehmer,H., Bronson,R., Dierich,A., Benoist,C. et al. (2002) Projection of an immunological self shadow within the thymus by the Aire protein. Science, 298, 1395-1401.
-
(2002)
Science
, vol.298
, pp. 1395-1401
-
-
Anderson, M.S.1
Venanzi, E.S.2
Klein, L.3
Chen, Z.4
Berzins, S.P.5
Turley, S.J.6
von Boehmer, H.7
Bronson, R.8
Dierich, A.9
Benoist, C.10
-
5
-
-
56749105120
-
The variable immunological self: genetic variation and nongenetic noise in aire-regulated transcription
-
Venanzi,E.S., Melamed,R., Mathis,D. and Benoist,C. (2008) The variable immunological self: genetic variation and nongenetic noise in aire-regulated transcription. Proc. Natl Acad. Sci. USA, 105, 15860-15865.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 15860-15865
-
-
Venanzi, E.S.1
Melamed, R.2
Mathis, D.3
Benoist, C.4
-
6
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on bias and variance
-
Bolstad,B.M., Irizarry,R.A., Astrand,M. and Speed,T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics, 19, 185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
7
-
-
0037340843
-
Can transcriptome size be estimated from sage catalogs?
-
Stern,M.D., Anisimov,S.V. and Boheler,K.R. (2003) Can transcriptome size be estimated from sage catalogs? Bioinformatics, 19, 443-448.
-
(2003)
Bioinformatics
, vol.19
, pp. 443-448
-
-
Stern, M.D.1
Anisimov, S.V.2
Boheler, K.R.3
-
8
-
-
44349127575
-
Modeling transcriptome based on transcript-sampling data
-
Zhu,J., He,F., Wang,J. and Yu,J. (2008) Modeling transcriptome based on transcript-sampling data. PLoS ONE, 3, e1659.
-
(2008)
PLoS ONE
, vol.3
-
-
Zhu, J.1
He, F.2
Wang, J.3
Yu, J.4
-
9
-
-
77950937550
-
Detection call algorithms for high-throughput gene expression microarray data
-
Archer,K.J. and Reese,S.E. (2010) Detection call algorithms for high-throughput gene expression microarray data. Brief Bioinform, 11, 244-252.
-
(2010)
Brief Bioinform
, vol.11
, pp. 244-252
-
-
Archer, K.J.1
Reese, S.E.2
-
10
-
-
71049195324
-
-
Illumina. (16 November, 2009, date last accessed)
-
Illumina. BeadStudio Gene Expression Module User Guide, 2008. www.illumina.com (16 November, 2009, date last accessed).
-
(2008)
BeadStudio Gene Expression Module User Guide
-
-
-
11
-
-
0141966130
-
-
Affymetrix. (16 November, 2009, date last accessed)
-
Affymetrix. Statistical Algorithms Description Document, 2002. www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf (16 November, 2009, date last accessed).
-
(2002)
Statistical Algorithms Description Document
-
-
-
12
-
-
39549113189
-
Correcting for sequence biases in present/absent calls
-
Schuster,E.F., Blanc,E., Partridge,L. and Thornton,J.M. (2007) Correcting for sequence biases in present/absent calls. Genome Biol., 8, R125.
-
(2007)
Genome Biol
, vol.8
-
-
Schuster, E.F.1
Blanc, E.2
Partridge, L.3
Thornton, J.M.4
-
13
-
-
48249152355
-
A statistical framework for the analysis of mciroarray probe-level data
-
Wu,Z. and Irizarry,R.A. (2007) A statistical framework for the analysis of mciroarray probe-level data. Ann. Appl. Stat., 1, 333-357.
-
(2007)
Ann. Appl. Stat.
, vol.1
, pp. 333-357
-
-
Wu, Z.1
Irizarry, R.A.2
-
14
-
-
35748952199
-
A gene expression bar code for microarray data
-
Zilliox,M.J. and Irizarry,R.A. (2007) A gene expression bar code for microarray data. Nat. Methods, 4, 911-913.
-
(2007)
Nat. Methods
, vol.4
, pp. 911-913
-
-
Zilliox, M.J.1
Irizarry, R.A.2
-
15
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
-
MAQC Consortium
-
MAQC Consortium. (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1151-1161
-
-
-
16
-
-
74549199294
-
Analysis of FOXP3+ regulatory T cells that display apparent viral antigen specificity during chronic hepatitis C virus infection
-
Li,S., Floess,S., Hamann,A., Gaudieri,S., Lucas,A., Hellard,M., Roberts,S., Paukovic,G., Plebanski,M., Loveland,B.E. et al. (2009) Analysis of FOXP3+ regulatory T cells that display apparent viral antigen specificity during chronic hepatitis C virus infection. PLoS Pathog., 5, e1000707.
-
(2009)
PLoS Pathog
, vol.5
-
-
Li, S.1
Floess, S.2
Hamann, A.3
Gaudieri, S.4
Lucas, A.5
Hellard, M.6
Roberts, S.7
Paukovic, G.8
Plebanski, M.9
Loveland, B.E.10
-
17
-
-
68349130357
-
Aberrant luminal progenitors as the candidate target population for basal tumor development in brca1 mutation carriers
-
Lim,E., Vaillant,F., Wu,D., Forrest,N.C., Pal,B., Hart,A.H., Asselin-Labat,M.L., Gyorki,D.E., Ward,T., Partanen,A. et al. (2009) Aberrant luminal progenitors as the candidate target population for basal tumor development in brca1 mutation carriers. Nat. Med., 15, 907-913.
-
(2009)
Nat. Med.
, vol.15
, pp. 907-913
-
-
Lim, E.1
Vaillant, F.2
Wu, D.3
Forrest, N.C.4
Pal, B.5
Hart, A.H.6
Asselin-Labat, M.L.7
Gyorki, D.E.8
Ward, T.9
Partanen, A.10
-
18
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry,R.A., Hobbs,B., Collin,F., Beazer-Barclay,Y.D., Antonellis,K.J., Scherf,U. and Speed,T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 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
Speed, T.P.7
-
19
-
-
33749027459
-
Parameter estimation for the exponential-normal convolution model for background correction of Affymetrix GeneChip data
-
Article 24
-
McGee,M. and Chen,Z. (2006) Parameter estimation for the exponential-normal convolution model for background correction of Affymetrix GeneChip data. Stat. Appl. Genet. Mol. Biol., 5, Article 24.
-
(2006)
Stat. Appl. Genet. Mol. Biol.
, vol.5
-
-
McGee, M.1
Chen, Z.2
-
20
-
-
61449107655
-
Microarray background correction: maximum likelihood estimation for the normal-exponential convolution model
-
Silver,J., Ritchie,M.E. and Smyth,G.K. (2009) Microarray background correction: maximum likelihood estimation for the normal-exponential convolution model. Biostatistics, 10, 352-363.
-
(2009)
Biostatistics
, vol.10
, pp. 352-363
-
-
Silver, J.1
Ritchie, M.E.2
Smyth, G.K.3
-
21
-
-
35748949257
-
A comparison of background correction methods for two-colour microarrays
-
Ritchie,M.E., Silver,J., shlack,A.O., Holmes,M., Diyagama,D., Holloway,A. and Smyth,G.K. (2007) A comparison of background correction methods for two-colour microarrays. Bioinformatics, 23, 2700-2707.
-
(2007)
Bioinformatics
, vol.23
, pp. 2700-2707
-
-
Ritchie, M.E.1
Silver, J.2
shlack, A.O.3
Holmes, M.4
Diyagama, D.5
Holloway, A.6
Smyth, G.K.7
-
22
-
-
65449133931
-
Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype
-
Hubert,F.X., Kinkel,S.A., Crewther,P.E., Cannon,P.Z., Webster,K.E., Link,M., Uibo,R., O'Bryan,M.K., Meager,A., Forehan,S.P. et al. (2009) Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype. J. Immunol., 182, 3902-3918.
-
(2009)
J. Immunol.
, vol.182
, pp. 3902-3918
-
-
Hubert, F.X.1
Kinkel, S.A.2
Crewther, P.E.3
Cannon, P.Z.4
Webster, K.E.5
Link, M.6
Uibo, R.7
O'Bryan, M.K.8
Meager, A.9
Forehan, S.P.10
-
23
-
-
0023922373
-
Purification and characterization of mouse hematopoietic stem cells
-
Spangrude,G.J., Heimfeld,S. and Weissman,I.L. (1988) Purification and characterization of mouse hematopoietic stem cells. Science, 241, 58-62.
-
(1988)
Science
, vol.241
, pp. 58-62
-
-
Spangrude, G.J.1
Heimfeld, S.2
Weissman, I.L.3
-
24
-
-
33644872577
-
Limma: linear models for microarray data
-
Gentleman,R., Carey,V., Dudoit,S., Irizarry,R. and Huber,W. (eds), Springer, New York
-
Smyth,G.K. (2005) Limma: linear models for microarray data. In Gentleman,R., Carey,V., Dudoit,S., Irizarry,R. and Huber,W. (eds), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp. 397-420.
-
(2005)
Bioinformatics and Computational Biology Solutions using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
25
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen,T.S., Ku,M., Jaffe,D.B., Issac,B., Lieberman,E., Giannoukos,G., Alvarez,P., Brockman,W., Kim,T.K., Koche,R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.K.9
Koche, R.P.10
-
26
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein,B.E., Mikkelsen,T.S., Xie,X., Kamal,M., Huebert,D.J., Cuff,J., Fry,B., Meissner,A., Wernig,M., Plath,K. et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell, 125, 315-326.
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
Kamal, M.4
Huebert, D.J.5
Cuff, J.6
Fry, B.7
Meissner, A.8
Wernig, M.9
Plath, K.10
-
27
-
-
33846252240
-
Genome-wide atlas of gene expression in the adult mouse brain
-
Lein,E.S. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445, 168-176.
-
(2007)
Nature
, vol.445
, pp. 168-176
-
-
Lein, E.S.1
-
28
-
-
0030831130
-
Identification of clonogenic common lymphoid progenitors in mouse bone marrow
-
Kondo,M., Weissman,I.L. and Akashi,K. (1997) Identification of clonogenic common lymphoid progenitors in mouse bone marrow. Cell, 91, 661-672.
-
(1997)
Cell
, vol.91
, pp. 661-672
-
-
Kondo, M.1
Weissman, I.L.2
Akashi, K.3
-
29
-
-
0034624828
-
A clonogenic common myeloid progenitor that gives rise to all myeloid lineages
-
Akashi,K., Traver,D., Miyamoto,T. and Weissman,I.L. (2000) A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature, 404, 193-197.
-
(2000)
Nature
, vol.404
, pp. 193-197
-
-
Akashi, K.1
Traver, D.2
Miyamoto, T.3
Weissman, I.L.4
-
30
-
-
0035171545
-
Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self
-
Derbinski,J., Schulte,A., Kyewski,B. and Klein,L. (2001) Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self. Nat. Immunol., 2, 1032-1039.
-
(2001)
Nat. Immunol.
, vol.2
, pp. 1032-1039
-
-
Derbinski, J.1
Schulte, A.2
Kyewski, B.3
Klein, L.4
-
31
-
-
0942288397
-
Medullary epithelial cells of the human thymus express a highly diverse selection of tissue-specific genes colocalized in chromosomal clusters
-
Gotter,J., Brors,B., Hergenhahn,M. and Kyewski,B. (2004) Medullary epithelial cells of the human thymus express a highly diverse selection of tissue-specific genes colocalized in chromosomal clusters. J. Exp. Med., 199, 155-166.
-
(2004)
J. Exp. Med.
, vol.199
, pp. 155-166
-
-
Gotter, J.1
Brors, B.2
Hergenhahn, M.3
Kyewski, B.4
-
32
-
-
0037383758
-
Aire regulates negative selection of organ-specific t cells
-
Liston,A., Lesage,S., Wilson,J., Peltonen,L. and Goodnow,C.C. (2003) Aire regulates negative selection of organ-specific t cells. Nat. Immunol., 4, 350-354.
-
(2003)
Nat. Immunol.
, vol.4
, pp. 350-354
-
-
Liston, A.1
Lesage, S.2
Wilson, J.3
Peltonen, L.4
Goodnow, C.C.5
-
33
-
-
7244227646
-
Gene dosage-limiting role of Aire in thymic expression, clonal deletion, and organ-specific autoimmunity
-
Liston,A., Gray,D.H., Lesage,S., Fletcher,A.L., Wilson,J., Webster,K.E., Scott,H.S., Boyd,R.L., Peltonen,L. and Goodnow,C.C. (2004) Gene dosage-limiting role of Aire in thymic expression, clonal deletion, and organ-specific autoimmunity. J. Exp. Med., 200, 1015-1026.
-
(2004)
J. Exp. Med.
, vol.200
, pp. 1015-1026
-
-
Liston, A.1
Gray, D.H.2
Lesage, S.3
Fletcher, A.L.4
Wilson, J.5
Webster, K.E.6
Scott, H.S.7
Boyd, R.L.8
Peltonen, L.9
Goodnow, C.C.10
-
34
-
-
33751513054
-
Spontaneous autoimmunity prevented by thymic expression of a single self-antigen
-
DeVoss,J., Hou,Y., Johannes,K., Lu,W., Liou,G.I., Rinn,J., Chang,H., Caspi,R.R., Fong,L. and Anderson,M.S. (2006) Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. J. Exp. Med., 203, 2727-2735.
-
(2006)
J. Exp. Med.
, vol.203
, pp. 2727-2735
-
-
DeVoss, J.1
Hou, Y.2
Johannes, K.3
Lu, W.4
Liou, G.I.5
Rinn, J.6
Chang, H.7
Caspi, R.R.8
Fong, L.9
Anderson, M.S.10
-
35
-
-
22344449972
-
Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels
-
Derbinski,J., Gbler,J., Brors,B., Tierling,S., Jonnakuty,S., Hergenhahn,M., Peltonen,L., Walter,J. and Kyewski,B. (2005) Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels. J. Exp. Med., 202, 33-45.
-
(2005)
J. Exp. Med.
, vol.202
, pp. 33-45
-
-
Derbinski, J.1
Gbler, J.2
Brors, B.3
Tierling, S.4
Jonnakuty, S.5
Hergenhahn, M.6
Peltonen, L.7
Walter, J.8
Kyewski, B.9
-
36
-
-
0346599403
-
An autoimmune disease, APECED, caused by mutations in a novel gene featuring two phd-type zinc-finger domains
-
The Finnish-German APECED Consortium
-
The Finnish-German APECED Consortium. (1997) An autoimmune disease, APECED, caused by mutations in a novel gene featuring two phd-type zinc-finger domains. Nature, 17, 399-403.
-
(1997)
Nature
, vol.17
, pp. 399-403
-
-
-
37
-
-
16944367194
-
Positional cloning of the APECED gene
-
Nagamine,K., Peterson,P., Scott,H.S., Kudoh,J., Minoshima,S., Heino,M., Krohn,K.J., Lalioti,M.D., Mullis,P.E., Antonarakis,S.E. et al. (1997) Positional cloning of the APECED gene. Nat. Genet., 17, 393-398.
-
(1997)
Nat. Genet.
, vol.17
, pp. 393-398
-
-
Nagamine, K.1
Peterson, P.2
Scott, H.S.3
Kudoh, J.4
Minoshima, S.5
Heino, M.6
Krohn, K.J.7
Lalioti, M.D.8
Mullis, P.E.9
Antonarakis, S.E.10
-
38
-
-
0037084784
-
Aire deficient mice develop multiple features of APECED phenotype and show altered immune response
-
Ramsey,C., Winqvist,O., Puhakka,L., Halonen,M., Moro,A., Kmpe,O., Eskelin,P., Pelto-Huikko,M. and Peltonen,L. (2002) Aire deficient mice develop multiple features of APECED phenotype and show altered immune response. Hum. Mol. Genet., 11, 397-409.
-
(2002)
Hum. Mol. Genet.
, vol.11
, pp. 397-409
-
-
Ramsey, C.1
Winqvist, O.2
Puhakka, L.3
Halonen, M.4
Moro, A.5
Kmpe, O.6
Eskelin, P.7
Pelto-Huikko, M.8
Peltonen, L.9
-
39
-
-
63449142392
-
Filtering for increased power for microarray data analysis
-
Hackstadt,A.J. and Hess,A.M. (2009) Filtering for increased power for microarray data analysis. BMC Bioinformatics, 10, 11.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 11
-
-
Hackstadt, A.J.1
Hess, A.M.2
-
40
-
-
71049139886
-
Illumina WG-6 BeadChip strips should be normalized separately
-
Shi,W. and Smyth,G.K. (2009) Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics, 10, 372.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 372
-
-
Shi, W.1
Smyth, G.K.2
|