-
2
-
-
33644874718
-
Metabolomic identification of novel biomarkers of myocardial ischemia
-
• A wonderful example of thoughtful experimental design and data analysis using metabolomics to identify novel markers of myocardial ischemia
-
Sabatine MS, Liu E, Morrow DA, et al. Metabolomic identification of novel biomarkers of myocardial ischemia. Circulation 2005; 112:3868-3875. • A wonderful example of thoughtful experimental design and data analysis using metabolomics to identify novel markers of myocardial ischemia.
-
(2005)
Circulation
, vol.112
, pp. 3868-3875
-
-
Sabatine, M.S.1
Liu, E.2
Morrow, D.A.3
-
4
-
-
22544463675
-
Focused metabolomic profiling in the drug development process: Advances from lipid profiling
-
Morris M, Watkins SM. Focused metabolomic profiling in the drug development process: advances from lipid profiling. Curr Opin Chem Biol 2005; 4:407-412.
-
(2005)
Curr Opin Chem Biol
, vol.4
, pp. 407-412
-
-
Morris, M.1
Watkins, S.M.2
-
5
-
-
22144478635
-
The emerging field of lipidomics
-
Wenk MR. The emerging field of lipidomics. Nat Rev Drug Discov 2005; 4:594-610.
-
(2005)
Nat Rev Drug Discov
, vol.4
, pp. 594-610
-
-
Wenk, M.R.1
-
6
-
-
20444419500
-
A comprehensive classification system for lipids
-
E-pub 16 February
-
Fahy E, Subramaniam S, Brown HA, et al. A comprehensive classification system for lipids. J Lipid Res 2005; 46:839-861; E-pub 16 February 2005.
-
(2005)
J Lipid Res 2005
, vol.46
, pp. 839-861
-
-
Fahy, E.1
Subramaniam, S.2
Brown, H.A.3
-
7
-
-
0038013967
-
Novel docosatrienes and 17S-resolvins generated from docosahexaenoic acid in murine brain, human blood, and glial cells. Autacoids in antiinflammation
-
Hong S, Gronert K, Devchand PR, et al. Novel docosatrienes and 17S-resolvins generated from docosahexaenoic acid in murine brain, human blood, and glial cells. Autacoids in antiinflammation. J Biol Chem 2003; 278:14677-14687.
-
(2003)
J Biol Chem
, vol.278
, pp. 14677-14687
-
-
Hong, S.1
Gronert, K.2
Devchand, P.R.3
-
8
-
-
33746401106
-
Targeted lipidomics: Discovery of new fatty acyl amides
-
Tan B, Bradshaw HB, Rimmerman N, et al. Targeted lipidomics: discovery of new fatty acyl amides. AAPS J 2006; 8:E461-E465.
-
AAPS
, vol.J 2006
, Issue.8
-
-
Tan, B.1
Bradshaw, H.B.2
Rimmerman, N.3
-
9
-
-
18344393519
-
Shotgun lipidomics: Electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples
-
Han X, Gross RW. Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 2005; 24:367-412.
-
(2005)
Mass Spectrom Rev
, vol.24
, pp. 367-412
-
-
Han, X.1
Gross, R.W.2
-
10
-
-
17244377704
-
Shotgun lipidomics: Multidimensional MS analysis of cellular lipidomes
-
Han X, Gross RW. Shotgun lipidomics: multidimensional MS analysis of cellular lipidomes. Expert Rev Proteomics 2005; 2:253-264.
-
(2005)
Expert Rev Proteomics
, vol.2
, pp. 253-264
-
-
Han, X.1
Gross, R.W.2
-
11
-
-
0141457601
-
Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry
-
Lee SH, Williams MV, DuBois RN, Blair IA. Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry. Rapid Commun Mass Spectrom 2003; 17:2168-2176.
-
(2003)
Rapid Commun Mass Spectrom
, vol.17
, pp. 2168-2176
-
-
Lee, S.H.1
Williams, M.V.2
DuBois, R.N.3
Blair, I.A.4
-
12
-
-
20444423814
-
A multiplex quantitation method for eicosanoids and platelet-activating factor using column-switching reversedphase liquid chromatography-tandem mass spectrometry
-
Kita Y, Takahashi T, Uozumi N, Shimizu T. A multiplex quantitation method for eicosanoids and platelet-activating factor using column-switching reversedphase liquid chromatography-tandem mass spectrometry. Anal Biochem 2005; 342:134-143.
-
(2005)
Anal Biochem
, vol.342
, pp. 134-143
-
-
Kita, Y.1
Takahashi, T.2
Uozumi, N.3
Shimizu, T.4
-
13
-
-
0036740840
-
The simultaneous quantification of cytochrome P450 dependent linoleate and arachidonate metabolites in urine by HPLC-MS/MS
-
Newman JW, Watanabe T, Hammock BD. The simultaneous quantification of cytochrome P450 dependent linoleate and arachidonate metabolites in urine by HPLC-MS/MS. J Lipid Res 2002; 43:1563-1578.
-
(2002)
J Lipid Res
, vol.43
, pp. 1563-1578
-
-
Newman, J.W.1
Watanabe, T.2
Hammock, B.D.3
-
14
-
-
1542327636
-
-
Moran FM, Hendrickx AG, Shideler S, et al. Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on fatty acid availability and neural tube formation in cynomolgus macaque, Macaca fascicularis. Birth Defects Res B Dev Reprod Toxicol 2004; 71:37-46.
-
Moran FM, Hendrickx AG, Shideler S, et al. Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on fatty acid availability and neural tube formation in cynomolgus macaque, Macaca fascicularis. Birth Defects Res B Dev Reprod Toxicol 2004; 71:37-46.
-
-
-
-
15
-
-
0242577796
-
Phosphatidylethanolamine-N- methyltransferase activity and dietary choline regulate liver-plasma lipid flux and essential fatty acid metabolism in mice
-
Watkins SM, Zhu X, Zeisel SH. Phosphatidylethanolamine-N- methyltransferase activity and dietary choline regulate liver-plasma lipid flux and essential fatty acid metabolism in mice. J Nutr 2003; 133:3386-3391.
-
(2003)
J Nutr
, vol.133
, pp. 3386-3391
-
-
Watkins, S.M.1
Zhu, X.2
Zeisel, S.H.3
-
16
-
-
0036846241
-
Lipid metabolome-wide effects of the PPARgamma agonist rosiglitazone
-
Watkins SM, Reifsnyder PR, Pan HJ, et al. Lipid metabolome-wide effects of the PPARgamma agonist rosiglitazone. J Lipid Res 2002; 43:1809-1817.
-
(2002)
J Lipid Res
, vol.43
, pp. 1809-1817
-
-
Watkins, S.M.1
Reifsnyder, P.R.2
Pan, H.J.3
-
17
-
-
5444275263
-
Matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry in lipid and phospholipid research
-
Schiller J, Suss R, Arnhold J, et al. Matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry in lipid and phospholipid research. Prog Lipid Res 2004; 43:449-488.
-
(2004)
Prog Lipid Res
, vol.43
, pp. 449-488
-
-
Schiller, J.1
Suss, R.2
Arnhold, J.3
-
18
-
-
0035970197
-
-
Sullards MC, Merrill AH. Analysis of sphingosine 1-phosphate, ceramides, and other bioactive sphingolipids by high-performance liquid chromatography-tandem mass spectrometry. Sci STKE 2001; 67:pl1.
-
Sullards MC, Merrill AH. Analysis of sphingosine 1-phosphate, ceramides, and other bioactive sphingolipids by high-performance liquid chromatography-tandem mass spectrometry. Sci STKE 2001; 67:pl1.
-
-
-
-
19
-
-
33746271951
-
Simultaneous quantitative analysis of bioactive sphingolipids by high-performance liquid chromatography-tandem mass spectrometry
-
Bielawski J, Szulc ZM, Hannun YA, Bielawska A. Simultaneous quantitative analysis of bioactive sphingolipids by high-performance liquid chromatography-tandem mass spectrometry. Methods 2006; 39:82-91.
-
(2006)
Methods
, vol.39
, pp. 82-91
-
-
Bielawski, J.1
Szulc, Z.M.2
Hannun, Y.A.3
Bielawska, A.4
-
20
-
-
1842834377
-
Validation of an ESI-MS/MS screening method for acylcarnitine profiling in urine specimens of neonates, children, adolescents and adults
-
Mueller P, Schulze A, Schindler I, et al. Validation of an ESI-MS/MS screening method for acylcarnitine profiling in urine specimens of neonates, children, adolescents and adults. Clin Chim Acta 2003; 327:47-57.
-
(2003)
Clin Chim Acta
, vol.327
, pp. 47-57
-
-
Mueller, P.1
Schulze, A.2
Schindler, I.3
-
21
-
-
30744460897
-
Large-scale human metabolomics studies: A strategy for data (pre) processing and validation
-
•• An excellent paper illustrating a practical protocol for processing metabolomics data from a large sample set
-
Bijlsma S, Bobeldijk I, Verheij ER, et al. Large-scale human metabolomics studies: a strategy for data (pre) processing and validation. Anal Chem 2006; 78:567-574. •• An excellent paper illustrating a practical protocol for processing metabolomics data from a large sample set.
-
(2006)
Anal Chem
, vol.78
, pp. 567-574
-
-
Bijlsma, S.1
Bobeldijk, I.2
Verheij, E.R.3
-
22
-
-
33947101603
-
-
Westgard JO. Basic QC practices: training in statistical quality control for healthcare laboratories. 2nd ed. Madison: Westgard QC, Inc.; 2002.
-
Westgard JO. Basic QC practices: training in statistical quality control for healthcare laboratories. 2nd ed. Madison: Westgard QC, Inc.; 2002.
-
-
-
-
23
-
-
33746065295
-
Transforming omics data into context: Bioinformatics on genomics and proteomics raw data
-
• A good review of computational procedures for the analysis of genomic and proteomic data that is also relevant to metabolomic data
-
Perco P, Rapberger R, Siehs C, et al. Transforming omics data into context: bioinformatics on genomics and proteomics raw data. Electrophoresis 2006; 27:2659-2675. • A good review of computational procedures for the analysis of genomic and proteomic data that is also relevant to metabolomic data.
-
(2006)
Electrophoresis
, vol.27
, pp. 2659-2675
-
-
Perco, P.1
Rapberger, R.2
Siehs, C.3
-
24
-
-
0142008803
-
A data-analytic strategy for protein biomarker discovery: Profiling of high-dimensional proteomic data for cancer detection
-
Yasui Y, Pepe M, Thompson ML, et al. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics 2003; 4:449-463.
-
(2003)
Biostatistics
, vol.4
, pp. 449-463
-
-
Yasui, Y.1
Pepe, M.2
Thompson, M.L.3
-
25
-
-
0036846241
-
Lipid metabolome-wide effects of the PPARγ agonist rosiglitazone
-
Watkins SM, Reifsnyder PR, Pan H, et al. Lipid metabolome-wide effects of the PPARγ agonist rosiglitazone. J Lipid Res 2002; 43:1809-1817.
-
(2002)
J Lipid Res
, vol.43
, pp. 1809-1817
-
-
Watkins, S.M.1
Reifsnyder, P.R.2
Pan, H.3
-
26
-
-
33645523238
-
Agpat6 - a novel lipid biosynthetic gene required for triacylglycerol production in mammary epithelium
-
Beigneux AP, Vergnes L, Qiao X, et al. Agpat6 - a novel lipid biosynthetic gene required for triacylglycerol production in mammary epithelium. J Lipid Res 2006; 47:734-744.
-
(2006)
J Lipid Res
, vol.47
, pp. 734-744
-
-
Beigneux, A.P.1
Vergnes, L.2
Qiao, X.3
-
27
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya O, Cantor M, Sherlock G, et al. Missing value estimation methods for DNA microarrays. Bioinformatics 2001; 17:520-525.
-
(2001)
Bioinformatics
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
-
28
-
-
10944250544
-
Epidemiologic evaluation of measurement data in the presence of detection limits
-
Lubin JH, Colt JS, Camann D, et al. Epidemiologic evaluation of measurement data in the presence of detection limits. Environ Health Perspect 2004; 112:1691-1696.
-
(2004)
Environ Health Perspect
, vol.112
, pp. 1691-1696
-
-
Lubin, J.H.1
Colt, J.S.2
Camann, D.3
-
29
-
-
17844365855
-
Modelling skewed data with many zeros: A simple approach combining ordinary and logistic regression
-
Stat, • A paper introducing a method of analyzing data with missing values
-
Fletcher D, Mackensie D, Villouta E. Modelling skewed data with many zeros: a simple approach combining ordinary and logistic regression. Environmen Ecol Stat 2005; 12:45-54. • A paper introducing a method of analyzing data with missing values.
-
(2005)
Environmen Ecol
, vol.12
, pp. 45-54
-
-
Fletcher, D.1
Mackensie, D.2
Villouta, E.3
-
30
-
-
26844479547
-
-
Meleth S, Deshane J, Kim H. The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins. BMC Biotechnol 2005; 5:7. • A paper examining the effects of data pre-processing on 2D gel electrophoresis. Results indicate statistical results aredependent upon the methodof pre-processing.
-
Meleth S, Deshane J, Kim H. The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins. BMC Biotechnol 2005; 5:7. • A paper examining the effects of data pre-processing on 2D gel electrophoresis. Results indicate statistical results aredependent upon the methodof pre-processing.
-
-
-
-
32
-
-
21344479527
-
An interpretation of partial least squares
-
Garthwaite PH. An interpretation of partial least squares. JASA 1994; 89:122-127.
-
(1994)
JASA
, vol.89
, pp. 122-127
-
-
Garthwaite, P.H.1
-
33
-
-
0036166439
-
Tumor classification by partial least squares using microarray gene expression data
-
Nguyen DV, Rocke DM. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 2002; 18:39-50.
-
(2002)
Bioinformatics
, vol.18
, pp. 39-50
-
-
Nguyen, D.V.1
Rocke, D.M.2
-
34
-
-
0041592555
-
On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression
-
Pan W. On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression. Bioinformatics 2003; 19:1333-1340.
-
(2003)
Bioinformatics
, vol.19
, pp. 1333-1340
-
-
Pan, W.1
-
35
-
-
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. J R Stat Soc 1995; 57:289-300.
-
(1995)
J R Stat Soc
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
36
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
This paper illustrates how incorporating biological knowledge into data analysis results in an increased ability to detect relevant changes in gene expression
-
Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005; 102:15545-15550. •• An introduction to gene set enrichment analysis. This paper illustrates how incorporating biological knowledge into data analysis results in an increased ability to detect relevant changes in gene expression.
-
Proc Natl Acad Sci U S A 2005; 102:15545-15550. •• An introduction to gene set enrichment analysis
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
-
37
-
-
0347513219
-
Characterizing gene sets with funcassociate
-
Berriz GF, King OD, Bryant B, et al. Characterizing gene sets with funcassociate. Bioinformatics 2003; 19:2502-2504.
-
(2003)
Bioinformatics
, vol.19
, pp. 2502-2504
-
-
Berriz, G.F.1
King, O.D.2
Bryant, B.3
-
38
-
-
84934379606
-
Choosing between logistic regression and discriminant analysis
-
Press SJ, Wilson S. Choosing between logistic regression and discriminant analysis. JASA 1978; 73:699-705.
-
(1978)
JASA
, vol.73
, pp. 699-705
-
-
Press, S.J.1
Wilson, S.2
-
39
-
-
9244261068
-
Evaluating methods for classifying expression data
-
Man MZ, Dyson G, Johnson K, et al. Evaluating methods for classifying expression data. J Biopharm Stat 2004; 14:1065-1084.
-
(2004)
J Biopharm Stat
, vol.14
, pp. 1065-1084
-
-
Man, M.Z.1
Dyson, G.2
Johnson, K.3
-
40
-
-
84950461478
-
Estimating the error rate of a prediction rule: Improvement on crossvalidation
-
Efron B. Estimating the error rate of a prediction rule: improvement on crossvalidation. JASA 1983; 78:316-331.
-
(1983)
JASA
, vol.78
, pp. 316-331
-
-
Efron, B.1
-
41
-
-
0000629975
-
Cross-validatory choice and assessment of statistical predictors
-
Stone M. Cross-validatory choice and assessment of statistical predictors. J R Stat Soc 1974; 36:111-147.
-
(1974)
J R Stat Soc
, vol.36
, pp. 111-147
-
-
Stone, M.1
|