-
1
-
-
67650348463
-
Gene-expression profiling in rheumatic disease: Tools and therapeutic potential
-
Bauer JW, Bilgic H, Baechler EC (2009) Gene-expression profiling in rheumatic disease: tools and therapeutic potential. Nat Rev Rheumatol 5:257-265.
-
(2009)
Nat Rev Rheumatol
, vol.5
, pp. 257-265
-
-
Bauer, J.W.1
Bilgic, H.2
Baechler, E.C.3
-
3
-
-
48149083805
-
Gene expression profiling as a tool for basic analysis and clinical application of human cancer
-
Garcia-Escudero R, Paramio JM (2008) Gene expression profiling as a tool for basic analysis and clinical application of human cancer. Mol Carcinog 47:573-579.
-
(2008)
Mol Carcinog
, vol.47
, pp. 573-579
-
-
Garcia-Escudero, R.1
Paramio, J.M.2
-
4
-
-
42749095940
-
Transcriptome analysis of endocrine tumors: Clinical perspectives
-
Giordano TJ (2008) Transcriptome analysis of endocrine tumors: clinical perspectives. Ann Endocrinol (Paris) 69:130-134.
-
(2008)
Ann Endocrinol (Paris)
, vol.69
, pp. 130-134
-
-
Giordano, T.J.1
-
5
-
-
34347337394
-
Review of the literature examining the correlation among DNA microarray technologies
-
DOI 10.1002/em.20290
-
Yauk CL, Berndt ML (2007) Review of the literature examining the correlation among DNA microarray technologies. Environ Mol Mutagen 48:380-394. (Pubitemid 47011767)
-
(2007)
Environmental and Molecular Mutagenesis
, vol.48
, Issue.5
, pp. 380-394
-
-
Yauk, C.L.1
Berndt, M.L.2
-
6
-
-
33746108159
-
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
-
DOI 10.1038/nbt1217, PII NBT1217
-
Kuo WP, Liu F, Trimarchi J et al (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24:832-840. (Pubitemid 44086625)
-
(2006)
Nature Biotechnology
, vol.24
, Issue.7
, pp. 832-840
-
-
Kuo, W.P.1
Liu, F.2
Trimarchi, J.3
Punzo, C.4
Lombardi, M.5
Sarang, J.6
Whipple, M.E.7
Maysuria, M.8
Serikawa, K.9
Lee, S.Y.10
McCrann, D.11
Kang, J.12
Shearstone, J.R.13
Burke, J.14
Park, D.J.15
Wang, X.16
Rector, T.L.17
Ricciardi-Castagnoli, P.18
Perrin, S.19
Choi, S.20
Bumgarner, R.21
Kim, J.H.22
Short III, G.F.23
Freeman, M.W.24
Seed, B.25
Jensen, R.26
Church, G.M.27
Hovig, E.28
Cepko, C.L.29
Park, P.30
Ohno-Machado, L.31
Jenssen, T.-K.32
more..
-
7
-
-
67649354569
-
Minimum Information about a Microarray Experiment (MIAME)-Successes, failures, challenges
-
Brazma A (2009) Minimum Information About a Microarray Experiment (MIAME)-successes, failures, challenges. Scientific World Journal 9:420-423.
-
(2009)
Scientific World Journal
, vol.9
, pp. 420-423
-
-
Brazma, A.1
-
8
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data
-
DOI 10.1038/ng1201-365
-
Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365-371. (Pubitemid 34326681)
-
(2001)
Nature Genetics
, vol.29
, Issue.4
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
Gaasterland, T.11
Glenisson, P.12
Holstege, F.C.P.13
Kim, I.F.14
Markowitz, V.15
Matese, J.C.16
Parkinson, H.17
Robinson, A.18
Sarkans, U.19
Schulze-Kremer, S.20
Stewart, J.21
Taylor, R.22
Vilo, J.23
Vingron, M.24
more..
-
9
-
-
84860881302
-
-
MIAME. (Minimum Information About a Microarray Experiment)
-
MIAME. (Minimum Information About a Microarray Experiment) http://www.mged. org/Workgroups/MIAME/miame.html.
-
-
-
-
10
-
-
27144548491
-
The external RNA controls consortium: A progress report
-
DOI 10.1038/nmeth1005-731, PII N1005731
-
Baker SC, Bauer SR, Beyer RP et al (2005) The External RNA Controls Consortium: a progress report. Nat Methods 2:731-734. (Pubitemid 41486201)
-
(2005)
Nature Methods
, vol.2
, Issue.10
, pp. 731-734
-
-
Baker, S.C.1
Bauer, S.R.2
Beyer, R.P.3
Brenton, J.D.4
Bromley, B.5
Burrill, J.6
Causton, H.7
Conley, M.P.8
Elespuru, R.9
Fero, M.10
Foy, C.11
Fuscoe, J.12
Gao, X.13
Gerhold, D.L.14
Gilles, P.15
Goodsaid, F.16
Guo, X.17
Hackett, J.18
Hockett, R.D.19
Ikonomi, P.20
Irizarry, R.A.21
Kawasaki, E.S.22
Kaysser-Kranich, T.23
Kerr, K.24
Kiser, G.25
Koch, W.H.26
Lee, K.Y.27
Liu, C.28
Liu, Z.L.29
Lucas, A.30
Manohar, C.F.31
Miyada, G.32
Modrusan, Z.33
Parkes, H.34
Puri, R.K.35
Reid, L.36
Ryder, T.B.37
Salit, M.38
Samaha, R.R.39
Scherf, U.40
Sendera, T.J.41
Setterquist, R.A.42
Shi, L.43
Shippy, R.44
Soriano, J.V.45
Wagar, E.A.46
Warrington, J.A.47
Williams, M.48
Wilmer, F.49
Wilson, M.50
Wolber, P.K.51
Wu, X.52
Zadro, R.53
more..
-
11
-
-
84860885778
-
-
ERCC. (The External RNA Controls Consortium)
-
ERCC. (The External RNA Controls Consortium) http://www.cstl.nist.gov/ biotech/Cell&TissueMeasurements/GeneExpression/ERCC.htm.
-
-
-
-
12
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
DOI 10.1038/nbt1239, PII NBT1239
-
Shi L, Reid LH, Jones WD et al (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151-1161. (Pubitemid 44359727)
-
(2006)
Nature Biotechnology
, vol.24
, Issue.9
, pp. 1151-1161
-
-
Shi, L.1
-
13
-
-
84860885779
-
-
MAQC. (Microarray Quality Control)
-
MAQC. (Microarray Quality Control) http://www.fda.gov/nctr/science/ centers/toxicoinformatics/maqc/.
-
-
-
-
14
-
-
77950789262
-
Standards affecting the consistency of gene expression arrays in clinical applications
-
Enkemann SA (2010) Standards affecting the consistency of gene expression arrays in clinical applications. Cancer Epidemiol Biomarkers Prev 19:1000-1003.
-
(2010)
Cancer Epidemiol Biomarkers Prev
, vol.19
, pp. 1000-1003
-
-
Enkemann, S.A.1
-
15
-
-
84860881300
-
-
GEO. (Gene Expression Omnibus)
-
GEO. (Gene Expression Omnibus) http://www.ncbi.nlm.nih.gov/geo/.
-
-
-
-
16
-
-
84860881301
-
-
The Cepko Laboratory at Harvard Medical School
-
The Cepko Laboratory at Harvard Medical School (http://genetics.med. harvard.edu/-cepko/).
-
-
-
-
17
-
-
25444515422
-
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
-
Carter SL, Eklund AC, Mecham BH et al (2005) Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6:107.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 107
-
-
Carter, S.L.1
Eklund, A.C.2
Mecham, B.H.3
-
18
-
-
2442691827
-
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
-
Mecham BH, Klus GT, Strovel J et al (2004) Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 32:e74.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Mecham, B.H.1
Klus, G.T.2
Strovel, J.3
-
19
-
-
4844222268
-
Increased measurement accuracy for sequence-verified microarray probes
-
DOI 10.1152/physiolgenomics.00066.2004
-
Mecham BH, Wetmore DZ, Szallasi Z et al (2004) Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics 18:308-315. (Pubitemid 39319514)
-
(2004)
Physiological Genomics
, vol.18
, pp. 308-315
-
-
Mecham, B.H.1
Wetmore, D.Z.2
Szallasi, Z.3
Sadovsky, Y.4
Kohane, I.5
Mariani, T.J.6
-
20
-
-
0034730124
-
Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
-
Lee ML, Kuo FC, Whitmore GA et al (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A 97:9834-9839.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 9834-9839
-
-
Lee, M.L.1
Kuo, F.C.2
Whitmore, G.A.3
-
21
-
-
84860885776
-
-
The R Project for Statistical Computing
-
The R Project for Statistical Computing: http://www.r-project.org/.
-
-
-
-
22
-
-
18844447998
-
Statistical development and evaluation of microarray gene expression data filters
-
DOI 10.1089/cmb.2005.12.482
-
Pounds S, Cheng C (2005) Statistical development and evaluation of microarray gene expression data filters. J Comput Biol 12:482-495. (Pubitemid 40696483)
-
(2005)
Journal of Computational Biology
, vol.12
, Issue.4
, pp. 482-495
-
-
Pounds, S.1
Cheng, C.2
-
23
-
-
9144256854
-
Performance evaluation of commercial shortoligonucleotide microarrays and the impact of noise in making cross-platform correlations
-
Shippy R, Sendera TJ, Lockner R et al (2004) Performance evaluation of commercial shortoligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 5:61.
-
(2004)
BMC Genomics
, vol.5
, pp. 61
-
-
Shippy, R.1
Sendera, T.J.2
Lockner, R.3
-
24
-
-
13244289933
-
Optimized LOWESS normalization parameter selection for DNA microarray data
-
Berger JA, Hautaniemi S, Jarvinen AK et al (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
Jarvinen, A.K.3
-
25
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
DOI 10.1093/bioinformatics/19.2.185
-
Bolstad BM, Irizarry RA, Astrand M et al (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193. (Pubitemid 36181903)
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
26
-
-
0037200201
-
A new non-linear normalization method for reducing variability in DNA microarray experiments
-
research0048
-
Workman C, Jensen LJ, Jarmer H et al (2002) A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 3: research0048.
-
(2002)
Genome Biol
, vol.3
-
-
Workman, C.1
Jensen, L.J.2
Jarmer, H.3
-
27
-
-
0037499970
-
MatchMiner: A tool for batch navigation among gene and gene product identifiers
-
Bussey KJ, Kane D, Sunshine M et al (2003) MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol 4:R27.
-
(2003)
Genome Biol
, vol.4
-
-
Bussey, K.J.1
Kane, D.2
Sunshine, M.3
-
28
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12:656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
29
-
-
84860889385
-
-
UCSC Genome Site
-
UCSC Genome Site: http://www.genomear chive.cse.ucsc.edu/goldenPath/ mmFeb2003/bigZips/.
-
-
-
-
30
-
-
0037208157
-
NetAffx: Affymetrix probesets and annotations
-
Liu G, Loraine AE, Shigeta R et al (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31:82-86.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 82-86
-
-
Liu, G.1
Loraine, A.E.2
Shigeta, R.3
-
31
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry RA, Warren D, Spencer F et al (2005) Multiple-laboratory comparison of microarray platforms. Nat Methods 2:345-350.
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
-
32
-
-
84860885777
-
-
Ambion
-
Ambion: http://www.ambion.com/catalog/CatNum.php?6050.
-
-
-
-
33
-
-
84860881298
-
-
Stratagene
-
Stratagene: http://www.stratagene.com/manuals/740000.pdf.
-
-
-
-
34
-
-
0035977135
-
Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes
-
DOI 10.1016/S0092-8674(01)00574-8
-
Blackshaw S, Fraioli RE, Furukawa T et al (2001) Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell 107:579-589. (Pubitemid 34014860)
-
(2001)
Cell
, vol.107
, Issue.5
, pp. 579-589
-
-
Blackshaw, S.1
Fraioli, R.E.2
Furukawa, T.3
Cepko, C.L.4
|