-
1
-
-
3042728487
-
New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
-
Barriot, R. et al. (2004) New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Res., 32, 3581-3589.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3581-3589
-
-
Barriot, R.1
-
2
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B, 57, 289-300.
-
(1995)
J. R. Statist. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
3
-
-
0037246058
-
ArrayExpress - A public repository for microarray gene expression data at the EBI
-
Brazma, A. (2003) ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res., 31, 68-71.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 68-71
-
-
Brazma, A.1
-
4
-
-
79961176618
-
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
-
Chan, S.J. and Ji, P. (2011) Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks. Bioinformatics, 27, 2256-2262.
-
(2011)
Bioinformatics
, vol.27
, pp. 2256-2262
-
-
Chan, S.J.1
Ji, P.2
-
5
-
-
22744458472
-
Pathways to the analysis of microarray data
-
Curtis, R.K. et al. (2005) Pathways to the analysis of microarray data. Trends Biotechnol., 23, 429-435.
-
(2005)
Trends Biotechnol.
, vol.23
, pp. 429-435
-
-
Curtis, R.K.1
-
6
-
-
0036578644
-
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
-
Dahlquist, K.D. et al. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet., 31, 19-20.
-
(2002)
Nat. Genet.
, vol.31
, pp. 19-20
-
-
Dahlquist, K.D.1
-
7
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
Duarte, N.C. et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl Acad. Sci. USA, 104, 1777-1782.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 1777-1782
-
-
Duarte, N.C.1
-
8
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar, R. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 207-210
-
-
Edgar, R.1
-
9
-
-
75849164426
-
Computing the shortest elementary flux modes in genome-scale metabolic networks
-
De Figueiredo, L.F. et al. (2009a) Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics, 25, 3158-3165.
-
(2009)
Bioinformatics
, vol.25
, pp. 3158-3165
-
-
De Figueiredo, L.F.1
-
10
-
-
75849128878
-
Response to comment on "Can sugars be produced from fatty acids? A test case for pathway analysis tools"
-
De Figueiredo, L.F. et al. (2009b) Response to comment on "Can sugars be produced from fatty acids? A test case for pathway analysis tools". Bioinformatics, 25, 3330-3331.
-
(2009)
Bioinformatics
, vol.25
, pp. 3330-3331
-
-
De Figueiredo, L.F.1
-
11
-
-
38649096951
-
Universal false discovery rate estimation methodology for genome-wide association studies
-
Forner, K. et al. (2008) Universal false discovery rate estimation methodology for genome-wide association studies. Hum. Hered., 65, 183-194.
-
(2008)
Hum. Hered.
, vol.65
, pp. 183-194
-
-
Forner, K.1
-
12
-
-
84861909720
-
Identification of microRNA-regulated gene networks by expression analysis of target genes
-
Gennarino, V.A. et al. (2012) Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res., 22, 1163-1172.
-
(2012)
Genome Res.
, vol.22
, pp. 1163-1172
-
-
Gennarino, V.A.1
-
13
-
-
27844486634
-
Genomic analysis of metabolic pathway gene expression in mice
-
Ghazalpour, A. et al. (2005) Genomic analysis of metabolic pathway gene expression in mice. Genome Biol., 6, R59.
-
(2005)
Genome Biol
, vol.6
-
-
Ghazalpour, A.1
-
14
-
-
77956407882
-
HepatoNet1: A comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology
-
Gille, C. et al. (2010) HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol. Syst. Biol., 6, 411.
-
(2010)
Mol. Syst. Biol
, vol.6
, pp. 411
-
-
Gille, C.1
-
15
-
-
34547572234
-
PathExpress: A web-based tool to identify relevant pathways in gene expression data
-
Goffard, N. andWeiller, G. (2007) PathExpress: a web-based tool to identify relevant pathways in gene expression data. Nucleic Acids Res., 35, W176-W181.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Goffard, N.1
Weiller, G.2
-
16
-
-
0021246017
-
Subcellular distribution and regulation of hepatic bilirubin UDP- glucuronyltransferase
-
Hauser, S. et al. (1984) Subcellular distribution and regulation of hepatic bilirubin UDP- glucuronyltransferase. J. Biol. Chem., 259, 4527-4533.
-
(1984)
J. Biol. Chem.
, vol.259
, pp. 4527-4533
-
-
Hauser, S.1
-
17
-
-
0021192645
-
Nicotinamide methylation and its relation to NAD synthesis in rat liver tissue culture: Biochemical basis for the physiological activities of 1-methylnicotinamide
-
Hoshino, J. et al. (1984) Nicotinamide methylation and its relation to NAD synthesis in rat liver tissue culture: Biochemical basis for the physiological activities of 1-methylnicotinamide. Biochim. Biophys. Acta, 801, 250-258.
-
(1984)
Biochim. Biophys. Acta
, vol.801
, pp. 250-258
-
-
Hoshino, J.1
-
18
-
-
0027260485
-
Inherited disorders of GABA metabolism
-
Jakobs, C. et al. (1993) Inherited disorders of GABA metabolism. J. Inherit. Metab. Dis., 16, 704-715.
-
(1993)
J. Inherit. Metab. Dis.
, vol.16
, pp. 704-715
-
-
Jakobs, C.1
-
19
-
-
77956417789
-
Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
-
Jerby, L. et al. (2010) Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol., 6, 401.
-
(2010)
Mol. Syst. Biol
, vol.6
, pp. 401
-
-
Jerby, L.1
-
20
-
-
70349636598
-
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
-
Kaleta, C. et al. (2009a) Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Res., 19, 1872-1883.
-
(2009)
Genome Res.
, vol.19
, pp. 1872-1883
-
-
Kaleta, C.1
-
21
-
-
84856560417
-
EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks
-
Grosse, I. et al. (ed.), Gesellschaft f. Informatik e.V., Halle
-
Kaleta, C. et al. (2009b) EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks. In: Grosse, I. et al. (ed.) P. 14th German Conf. Bioinformatics. Gesellschaft f. Informatik e.V., Halle, pp. 180-190.
-
(2009)
P. 14th German Conf. Bioinformatics
, pp. 180-190
-
-
Kaleta, C.1
-
22
-
-
0038693981
-
The oxidation in liver of l-tyrosine to acetoacetate through p-hydroxyphenylpyruvate and homogentisic acid
-
Knox, W.E. and LeMay-Knox, M. (1951) The oxidation in liver of l-tyrosine to acetoacetate through p-hydroxyphenylpyruvate and homogentisic acid. Biochem. J., 49, 686.
-
(1951)
Biochem. J
, vol.49
, pp. 686
-
-
Knox, W.E.1
Lemay-Knox, M.2
-
23
-
-
1542366428
-
Molecular evidence for mitochondrial dysfunction in bipolar disorder
-
Konradi, C. et al. (2004) Molecular evidence for mitochondrial dysfunction in bipolar disorder. Arch. Gen. Psychiat., 61, 300-308.
-
(2004)
Arch. Gen. Psychiat.
, vol.61
, pp. 300-308
-
-
Konradi, C.1
-
24
-
-
78651271261
-
The Gene Expression Barcode: Leveraging public data repositories to begin cataloging the human and murine transcriptomes
-
McCall, M.N. et al. (2011) The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res., 39, D1011-D1015.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
McCall, M.N.1
-
25
-
-
84855388886
-
Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background
-
Menashe, I. et al. (2012) Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. PLoS One, 7, e29396.
-
(2012)
PLoS One
, vol.7
-
-
Menashe, I.1
-
26
-
-
33644877439
-
Human protein reference database-2006 update
-
Mishra, G.R. et al. (2006) Human protein reference database-2006 update. Nucleic Acids Res., 34, D411-D414.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Mishra, G.R.1
-
27
-
-
23144431919
-
PathwayExplorer: Web service for visualizing high-throughput expression data on biological pathways
-
Mlecnik, B. et al. (2005) PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res., 33, W633-W637.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Mlecnik, B.1
-
28
-
-
65649129982
-
Bile acids: Chemistry, physiology, and pathophysiology
-
Monte, M.J. (2009) Bile acids: Chemistry, physiology, and pathophysiology. World J. Gastroentero., 15, 804.
-
(2009)
World J. Gastroentero
, vol.15
, pp. 804
-
-
Monte, M.J.1
-
29
-
-
34447650761
-
High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization
-
Naylor, T.L. et al. (2005) High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization. Breast Cancer Res., 7, R1186-R1198.
-
(2005)
Breast Cancer Res
, vol.7
-
-
Naylor, T.L.1
-
30
-
-
79957473580
-
Path finding methods accounting for stoichiometry in metabolic networks
-
Pey, J. et al. (2011) Path finding methods accounting for stoichiometry in metabolic networks. Genome Biol., 12, R49.
-
(2011)
Genome Biol
, vol.12
-
-
Pey, J.1
-
31
-
-
0344052685
-
METATOOL: For studying metabolic networks
-
Pfeiffer, T. et al. (1999) METATOOL: for studying metabolic networks. Bioinformatics, 15, 251-257.
-
(1999)
Bioinformatics
, vol.15
, pp. 251-257
-
-
Pfeiffer, T.1
-
32
-
-
33747828250
-
Robust estimation of the false discovery rate
-
Pounds, S. and Cheng, C. (2006) Robust estimation of the false discovery rate. Bioinformatics, 22, 1979-1987.
-
(2006)
Bioinformatics
, vol.22
, pp. 1979-1987
-
-
Pounds, S.1
Cheng, C.2
-
33
-
-
79951528622
-
Exploring metabolic pathways in genome-scale networks via generating flux modes
-
Rezola, A. et al. (2011) Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics, 27, 534-540.
-
(2011)
Bioinformatics
, vol.27
, pp. 534-540
-
-
Rezola, A.1
-
34
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
Schuster, S. et al. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol., 18, 326-332.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 326-332
-
-
Schuster, S.1
-
35
-
-
0000029295
-
On elementary flux modes in biochemical reaction systems at steady state
-
Schuster, S. and Hilgetag, C. (1994) On elementary flux modes in biochemical reaction systems at steady state. J.f Biol. Syst., 2, 165-182.
-
(1994)
J.F Biol. Syst.
, vol.2
, pp. 165-182
-
-
Schuster, S.1
Hilgetag, C.2
-
36
-
-
39549114813
-
Observing metabolic functions at the genome scale
-
Schwartz, J.-M. et al. (2007) Observing metabolic functions at the genome scale. Genome Biol., 8, R123.
-
(2007)
Genome Biol
, vol.8
-
-
Schwartz, J.-M.1
-
37
-
-
25444515956
-
YANA - A software tool for analyzing flux modes, geneexpression and enzyme activities
-
Schwarz, R. et al. (2005) YANA - a software tool for analyzing flux modes, geneexpression and enzyme activities. BMC bioinformatics, 6, 135.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 135
-
-
Schwarz, R.1
-
38
-
-
77952312735
-
Estimating the proportion of microarray probes expressed in an RNA sample
-
Shi, W. et al. (2010) Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Res., 38, 2168-2176.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2168-2176
-
-
Shi, W.1
-
39
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
Shlomi, T. et al. (2008) Network-based prediction of human tissue-specific metabolism. Nat. Biotechnol., 26, 1003-1010.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
-
40
-
-
0347752388
-
GeneNote: Whole genome expression profiles in normal human tissues
-
Shmueli, O. et al. (2003) GeneNote: whole genome expression profiles in normal human tissues. C. R. Biol., 326, 1067-1072.
-
(2003)
C. R. Biol.
, vol.326
, pp. 1067-1072
-
-
Shmueli, O.1
-
41
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-945.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9440-9945
-
-
Storey, J.D.1
Tibshirani, R.2
-
42
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
43
-
-
0033548232
-
Evidence That a Phosphatidylinositol 3, 4, 5-Trisphosphatebinding Protein Can Function in Nucleus
-
Tanaka, K. et al. (1999) Evidence That a Phosphatidylinositol 3, 4, 5-Trisphosphatebinding Protein Can Function in Nucleus. J. Biol. Chem., 274, 3919-3922.
-
(1999)
J Biol Chem
, vol.274
, pp. 3919-3922
-
-
Tanaka, K.1
-
44
-
-
52949098408
-
Large-scale computation of elementary flux modes with bit pattern trees
-
Terzer, M. and Stelling, J. (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics, 24, 2229-2235.
-
(2008)
Bioinformatics
, vol.24
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
45
-
-
33749439331
-
D-myo-Inositol 1-phosphate as a surrogate of d-myo-inositol 1, 4, 5-tris phosphate to monitor G protein-coupled receptor activation
-
Trinquet, E. et al. (2006) d-myo-Inositol 1-phosphate as a surrogate of d-myo-inositol 1, 4, 5-tris phosphate to monitor G protein-coupled receptor activation. Anal. Biochem., 358, 126-135.
-
(2006)
Anal Biochem
, vol.358
, pp. 126-135
-
-
Trinquet, E.1
-
46
-
-
84881019919
-
Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc
-
Trupp, M. et al. (2010) Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc. Genome Biol., 11, O12.
-
(2010)
Genome Biol
, vol.11
-
-
Trupp, M.1
-
47
-
-
0024257603
-
The methylation of phosphatidylethanolamine
-
Vance, D.E. and Ridgway, N.D. (1988) The methylation of phosphatidylethanolamine. Prog. Lipid Res., 27, 61-79.
-
(1988)
Prog. Lipid Res.
, vol.27
, pp. 61-79
-
-
Vance, D.E.1
Ridgway, N.D.2
-
48
-
-
0034564487
-
Analysis of gene expression data with pathway scores
-
Zien, A. et al. (2000) Analysis of gene expression data with pathway scores. P. Int. C. Intelligent Syst. Mol. Biol. (ISMB), 8, 407-417.
-
(2000)
P. Int. C. Intelligent Syst. Mol. Biol. (ISMB)
, vol.8
, pp. 407-417
-
-
Zien, A.1
|