-
2
-
-
0037225727
-
Contrast normalization of oligonucleotide arrays
-
Astrand M. (2003). Contrast normalization of oligonucleotide arrays. J Comput Biol 10, 95-102.
-
(2003)
J Comput Biol
, vol.10
, pp. 95-102
-
-
Astrand, M.1
-
3
-
-
84873899821
-
Bias, randomization, and ovarian proteomic data: A reply to Producers and Consumers"
-
Baggerly KA, Coombes KR, and Morris JS. (2005). Bias, randomization, and ovarian proteomic data: A reply to "Producers and Consumers". Cancer Informatics 1, 9-14.
-
(2005)
Cancer Informatics
, vol.1
, pp. 9-14
-
-
Baggerly, K.A.1
Coombes, K.R.2
Morris, J.S.3
-
4
-
-
30744460897
-
Large-scale human metabolomics studies: A strategy for data (pre-) processing and validation
-
Bijlsma S, Bobeldijk I, Verheij ER, et al. (2006). Large-scale human metabolomics studies: A strategy for data (pre-) processing and validation. Anal Chem 78, 567-574.
-
(2006)
Anal Chem
, vol.78
, pp. 567-574
-
-
Bijlsma, S.1
Bobeldijk, I.2
Verheij, E.R.3
-
5
-
-
84883720100
-
LC-MS metabolomics from study design to data-analysis: Using a versatile pathogen as a test case
-
doi: 10.5936/csbj.201301002
-
Berg M, Vanaerschot M, Jankevics A, Cuypers B, Breitling R, and Dujardin JC. (2013). LC-MS metabolomics from study design to data-analysis: Using a versatile pathogen as a test case. Comput Struct Biotechnol J 4/5 doi: 10.5936/csbj.201301002.
-
(2013)
Comput Struct Biotechnol J
, vol.4
, pp. 57-64
-
-
Berg, M.1
Vanaerschot, M.2
Jankevics, A.3
Cuypers, B.4
Breitling, R.5
Dujardin, J.C.6
Bilban, M.7
Buehler, L.K.8
Head, S.9
Desoye, G.10
Quaranta, V.11
-
6
-
-
84883702315
-
Metabolomic systems biology of protozoan parasites
-
Chapter 6 in K. Suhre (ed.) DOI 10.1007/978-1-4614-1689-0-6
-
Breitling R, Bakker BM, Barret MP, Decuypere S, and Dujardin JC. (2012). Metabolomic systems biology of protozoan parasites. Chapter 6 in K. Suhre (ed.) Genetics Meets Metabolomics: From Dxperiment to Systems Biology, DOI 10.1007/978-1-4614-1689-0-6.
-
(2012)
Genetics Meets Metabolomics: From Dxperiment to Systems Biology
-
-
Breitling, R.1
Bakker, B.M.2
Barret, M.P.3
Decuypere, S.4
Dujardin, J.C.5
-
7
-
-
0037276175
-
Statistical tests for differential expression in cDNA microarray experiments
-
Cui X, and Churchill GA. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4, 210.
-
(2003)
Genome Biol
, vol.4
, pp. 210
-
-
Cui, X.1
Churchill, G.A.2
-
8
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina highthroughput RNA sequencing data analysis
-
doi: 10.1093/bib/bbs046
-
Dillies MA, Rau A, Aubert J, et al. (2012). A comprehensive evaluation of normalization methods for Illumina highthroughput RNA sequencing data analysis. Brief Bioinform. doi: 10.1093/bib/bbs046.
-
(2012)
Brief Bioinform
-
-
Ma, D.1
Rau, A.2
Aubert, J.3
-
9
-
-
79959913950
-
Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry
-
Dunn WB, Broadhurst D, Begley P, et al. (2011). Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols 6, 1060-1083.
-
(2011)
Nature Protocols
, vol.6
, pp. 1060-1083
-
-
Dunn, W.B.1
Broadhurst, D.2
Begley, P.3
-
11
-
-
3242741850
-
Design of experiments: An efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry
-
Gullberg J, Jonsson P, Nordström A, Sjö ström M, and Moritz T. (2004). Design of experiments: An efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331, 283-295.
-
(2004)
Anal Biochem
, vol.331
, pp. 283-295
-
-
Gullberg, J.1
Jonsson, P.2
Nordström, A.3
Sjostrom, M.4
Moritz, T.5
-
12
-
-
34547572669
-
Using linear mixed models for normalization of cDNA microarrays
-
Article 19
-
Haldermans P, Shkedy Z, Van Sanden S, Burzykowski T, and Aerts M. (2007). Using linear mixed models for normalization of cDNA microarrays. Stat Appl Genet Mol Biol 6, Article 19.
-
(2007)
Stat Appl Genet Mol Biol
, vol.6
-
-
Haldermans, P.1
Shkedy, Z.2
Van Sanden, S.3
Burzykowski, T.4
Aerts, M.5
-
13
-
-
0035749210
-
Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls
-
RESEARCH0055
-
Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, and Slonim DK. (2001). Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biol 2:RESEARCH0055
-
(2001)
Genome Biol
, vol.2
-
-
Hill, A.A.1
Brown, E.L.2
Whitley, M.Z.3
Tucker-Kellogg, G.4
Hunter, C.P.5
Slonim, D.K.6
-
15
-
-
84860361428
-
Separating the wheat from the chaff: A prioritisation pipeline for the analysis of metabolomics datasets
-
Jankevics A, Merlo ME, de Vries M, Vonk RJ, Takano E, and Breitling R. (2012). Separating the wheat from the chaff: A prioritisation pipeline for the analysis of metabolomics datasets. Metabolomics 8, 29-36.
-
(2012)
Metabolomics
, vol.8
, pp. 29-36
-
-
Jankevics, A.1
Merlo, M.E.2
De Vries, M.3
Vonk, R.J.4
Takano, E.5
Breitling, R.6
-
16
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
Johnson WE, Li C, and Rabinovic A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118.
-
(2007)
Biostatistics
, vol.8
, pp. 118
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
17
-
-
84860359421
-
State-of-the-art data normalisation methods improve NMR-based metabolomic analysis
-
Kohl SM, Klein MS, Hochrein J, Oefner PJ, Spang R, and Gronwald W. (2011). State-of-the-art data normalisation methods improve NMR-based metabolomic analysis. Metabolomics 8, 146-160.
-
(2011)
Metabolomics
, vol.8
, pp. 146-160
-
-
Kohl, S.M.1
Klein, M.S.2
Hochrein, J.3
Oefner, P.J.4
Spang, R.5
Gronwald, W.6
-
18
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek JT, and Storey JD. (2007). Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics 3, e161.
-
(2007)
PLoS Genetics
, vol.3
-
-
Leek, J.T.1
Storey, J.D.2
-
19
-
-
65549139459
-
Data-driven normalization strategies for high-throughput quantitative RTPCR
-
Mar J, Kimura Y, Schroder K, et al. (2009). Data-driven normalization strategies for high-throughput quantitative RTPCR. BMC Bioinformat 10, 110.
-
(2009)
BMC Bioinformat
, vol.10
, pp. 110
-
-
Mar, J.1
Kimura, Y.2
Schroder, K.3
-
20
-
-
33748490271
-
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping
-
Prince JT, and Marcotte EM. (2006). Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem 78, 6140-6152.
-
(2006)
Anal Chem
, vol.78
, pp. 6140-6152
-
-
Prince, J.T.1
Marcotte, E.M.2
-
22
-
-
70350095897
-
Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data
-
Redestig H, Fukushima A, Stenlund H, et al. (2009). Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Anal Chem 81, 7974-7980.
-
(2009)
Anal Chem
, vol.81
, pp. 7974-7980
-
-
Redestig, H.1
Fukushima, A.2
Stenlund, H.3
-
23
-
-
0036027086
-
An improved multiple internal standard normalisation for drift in LA-ICP-MS measurements
-
Ridder FD, Pintelon R, Schoukens J, Navez J, Andre L, and Dehairs F. (2002). An improved multiple internal standard normalisation for drift in LA-ICP-MS measurements. JAAS 17, 1461-1470.
-
(2002)
JAAS
, vol.17
, pp. 1461-1470
-
-
Ridder, F.D.1
Pintelon, R.2
Schoukens, J.3
Navez, J.4
Andre, L.5
Dehairs, F.6
-
24
-
-
78049341926
-
Simple data reduction method for high-resolution LC-MS data in metabolomics
-
Scheltema RA, Decuypere S, Dujardin JC, Watson DG, Jansen RC, and Breitling R. (2009). Simple data reduction method for high-resolution LC-MS data in metabolomics. Bioanalysis 1, 1551-1557.
-
(2009)
Bioanalysis
, vol.1
, pp. 1551-1557
-
-
Scheltema, R.A.1
Decuypere, S.2
Dujardin, J.C.3
Watson, D.G.4
Jansen, R.C.5
Breitling, R.6
-
25
-
-
79953267955
-
PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis
-
Scheltema R, Jankevics A, Jansen RC, Swertz MA, and Breitling R. (2011). PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis. Anal Chem 83, 2786-2793.
-
(2011)
Anal Chem
, vol.83
, pp. 2786-2793
-
-
Scheltema, R.1
Jankevics, A.2
Jansen, R.C.3
Ma, S.4
Breitling, R.5
-
26
-
-
77952851186
-
Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
-
Schmid R, Baum P, Ittrich C, et al. (2010). Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics 11: 349.
-
(2010)
BMC Genomics
, vol.11
, pp. 349
-
-
Schmid, R.1
Baum, P.2
Ittrich, C.3
-
27
-
-
34347384910
-
Normalization method for metabolomics data using optimal selection of multiple internal standards
-
Sysi-Aho M, Katajamaa M, Yetukuri L, and Oresic M. (2007). Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformat 8, 93.
-
(2007)
BMC Bioinformat
, vol.8
, pp. 93
-
-
Sysi-Aho, M.1
Katajamaa, M.2
Yetukuri, L.3
Oresic, M.4
-
28
-
-
60649089559
-
Highly sensitive feature detection for high resolution LC/MS
-
Tautenhahn R, Bö ttcher C, and Neumann S. (2008). Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformat 9, 504.
-
(2008)
BMC Bioinformat
, vol.9
, pp. 504
-
-
Tautenhahn, R.1
Bö Ttcher, C.2
Neumann, S.3
-
29
-
-
78049351897
-
Towards an unbiased metabolic profiling of protozoan parasites: Optimization of a Leishmania sampling protocol for HILIC-orbitrap analysis
-
t'Kindt R., Jankevics A, Scheltema RA, et al. (2010a). Towards an unbiased metabolic profiling of protozoan parasites: Optimization of a Leishmania sampling protocol for HILIC-orbitrap analysis. Analyt Bioanal Chem. 398,2059-2069.
-
(2010)
Analyt Bioanal Chem.
, vol.398
, pp. 2059-2069
-
-
T'Kindt, R.1
Jankevics, A.2
Scheltema, R.A.3
-
30
-
-
78649776458
-
Metabolomics to unveil and understand phenotypic diversity between pathogen populations
-
t'Kindt R, Scheltema RA, Jankevics A, et al. (2010b). Metabolomics to unveil and understand phenotypic diversity between pathogen populations. Plos Neg Tropic Dis. 4, e904.
-
(2010)
Plos Neg Tropic Dis.
, vol.4
-
-
T'Kindt, R.1
Scheltema, R.A.2
Jankevics, A.3
-
31
-
-
65649108127
-
A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography
-
Valkenborg D, Thomas G, Krols L, Kas K, and Burzykowski T. (2009). A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography. J Mass Spectrom 44, 516-529.
-
(2009)
J Mass Spectrom
, vol.44
, pp. 516-529
-
-
Valkenborg, D.1
Thomas, G.2
Krols, L.3
Kas, K.4
Burzykowski, T.5
-
32
-
-
33747019547
-
Centering, scaling, and transformations: Improving the biological information content of metabolomics data
-
van den Berg RA, Hoefsloot HCJ, Westerhuis JA, Smilde AK, and van der werf MJ. (2006). Centering, scaling, and transformations: Improving the biological information content of metabolomics data. BMC Genom 7, 142.
-
(2006)
BMC Genom
, vol.7
, pp. 142
-
-
Van Den Berg, R.A.1
Hoefsloot, H.C.J.2
Westerhuis, J.A.3
Smilde, A.K.4
Van Der Werf, M.J.5
-
33
-
-
70449354965
-
Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping
-
van der Kloet FM, Bobeldijk I, Verheij ER, and Jellema RH. (2009). Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping. J Proteome Res 8, 5132-5141.
-
(2009)
J Proteome Res
, vol.8
, pp. 5132-5141
-
-
Van Der Kloet, F.M.1
Bobeldijk, I.2
Verheij, E.R.3
Jellema, R.H.4
-
34
-
-
0037129827
-
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
-
RESEARCH0034
-
Vandesompele J, De Preter K, Pattyn F, et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3, RESEARCH0034.
-
(2002)
Genome Biol
, vol.3
-
-
Vandesompele, J.1
De Preter, K.2
Pattyn, F.3
-
35
-
-
10744233766
-
Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
-
Wang W, Zhou H, Lin H, et al. (2003). Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75, 4818-4826.
-
(2003)
Anal Chem
, vol.75
, pp. 4818-4826
-
-
Wang, W.1
Zhou, H.2
Lin, H.3
|