-
1
-
-
84922448166
-
Methods and advances in metabolic flux analysis: a mini-review
-
Antoniewicz M.R. Methods and advances in metabolic flux analysis: a mini-review. J Ind Microbiol Biotechnol 2015, 42:317-325.
-
(2015)
J Ind Microbiol Biotechnol
, vol.42
, pp. 317-325
-
-
Antoniewicz, M.R.1
-
2
-
-
84860009126
-
LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine
-
(Chapter 14: Unit 14)
-
Clasquin M.F., Melamud E., Rabinowitz J.D. LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr Protoc Bioinformat 2012, 11. (Chapter 14: Unit 14).
-
(2012)
Curr Protoc Bioinformat
, pp. 11
-
-
Clasquin, M.F.1
Melamud, E.2
Rabinowitz, J.D.3
-
3
-
-
77957869474
-
MetaP-server: a web-based metabolomics data analysis tool
-
Kastenmüller G., Römisch-Margl W., Wägele B., Altmaier E., Suhre K. metaP-server: a web-based metabolomics data analysis tool. J Biomed Biotechnol 2011, 2011. 7 pages, Article ID 839862. 10.1155/2011/839862.
-
(2011)
J Biomed Biotechnol
, vol.2011
, pp. 7
-
-
Kastenmüller, G.1
Römisch-Margl, W.2
Wägele, B.3
Altmaier, E.4
Suhre, K.5
-
4
-
-
25444526868
-
Processing methods for differential analysis of LC/MS profile data
-
Katajamaa M., Oresic M. Processing methods for differential analysis of LC/MS profile data. BMC Bioinformat 2005, 6:179.
-
(2005)
BMC Bioinformat
, vol.6
, pp. 179
-
-
Katajamaa, M.1
Oresic, M.2
-
5
-
-
84864071589
-
MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware
-
Lommen A., Kools H.J. MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware. Metabolomics 2012, 8:719-726.
-
(2012)
Metabolomics
, vol.8
, pp. 719-726
-
-
Lommen, A.1
Kools, H.J.2
-
6
-
-
78649695759
-
Metabolomic analysis and visualization engine for LC-MS data
-
Melamud E., Vastag L., Rabinowitz J.D. Metabolomic analysis and visualization engine for LC-MS data. Anal Chem 2010, 82:9818-9826.
-
(2010)
Anal Chem
, vol.82
, pp. 9818-9826
-
-
Melamud, E.1
Vastag, L.2
Rabinowitz, J.D.3
-
7
-
-
84930181342
-
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
-
Tsugawa H., Cajka T., Kind T., Ma Y., Higgins B., Ikeda K., Kanazawa M., VanderGheynst J., Fiehn O., Arita M. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods 2015, 12:523-526.
-
(2015)
Nat Methods
, vol.12
, pp. 523-526
-
-
Tsugawa, H.1
Cajka, T.2
Kind, T.3
Ma, Y.4
Higgins, B.5
Ikeda, K.6
Kanazawa, M.7
VanderGheynst, J.8
Fiehn, O.9
Arita, M.10
-
8
-
-
84872187695
-
XMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data
-
Uppal K., Soltow Q.A., Strobel F.H., Pittard W.S., Gernert K.M., Yu T., Jones D.P. xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data. BMC Bioinformat 2013, 14:15.
-
(2013)
BMC Bioinformat
, vol.14
, pp. 15
-
-
Uppal, K.1
Soltow, Q.A.2
Strobel, F.H.3
Pittard, W.S.4
Gernert, K.M.5
Yu, T.6
Jones, D.P.7
-
9
-
-
84979865433
-
MetaboAnalyst 3.0-making metabolomics more meaningful
-
Xia J., Sinelnikov I.V., Han B., Wishart D.S. MetaboAnalyst 3.0-making metabolomics more meaningful. Nucleic Acids Res 2015, 43:W251-W257.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. W251-W257
-
-
Xia, J.1
Sinelnikov, I.V.2
Han, B.3
Wishart, D.S.4
-
10
-
-
84916898719
-
Discovery of a class of endogenous mammalian lipids with anti-diabetic and anti-inflammatory effects
-
Yore M.M., Syed I., Moraes-Vieira P.M., Zhang T., Herman M.A., Homan E.A., Patel R.T., Lee J., Chen S., Peroni O.D., et al. Discovery of a class of endogenous mammalian lipids with anti-diabetic and anti-inflammatory effects. Cell 2014, 159:318-332.
-
(2014)
Cell
, vol.159
, pp. 318-332
-
-
Yore, M.M.1
Syed, I.2
Moraes-Vieira, P.M.3
Zhang, T.4
Herman, M.A.5
Homan, E.A.6
Patel, R.T.7
Lee, J.8
Chen, S.9
Peroni, O.D.10
-
11
-
-
84924765378
-
LC-MS alignment in theory and practice: a comprehensive algorithmic review
-
Smith R., Ventura D., Prince J.T. LC-MS alignment in theory and practice: a comprehensive algorithmic review. Brief Bioinformat 2015, 16:104-117.
-
(2015)
Brief Bioinformat
, vol.16
, pp. 104-117
-
-
Smith, R.1
Ventura, D.2
Prince, J.T.3
-
12
-
-
84915809442
-
Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis
-
Rafiei A., Sleno L. Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis. Rapid Commun Mass Spectrom 2015, 29:119-127.
-
(2015)
Rapid Commun Mass Spectrom
, vol.29
, pp. 119-127
-
-
Rafiei, A.1
Sleno, L.2
-
13
-
-
32444446805
-
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
-
Smith C.A., Want E.J., O'Maille G., Abagyan R., Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 2006, 78:779-787.
-
(2006)
Anal Chem
, vol.78
, pp. 779-787
-
-
Smith, C.A.1
Want, E.J.2
O'Maille, G.3
Abagyan, R.4
Siuzdak, G.5
-
14
-
-
60649089559
-
Highly sensitive feature detection for high resolution LC/MS
-
Tautenhahn R., Bottcher C., Neumann S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformat 2008, 9:504.
-
(2008)
BMC Bioinformat
, vol.9
, pp. 504
-
-
Tautenhahn, R.1
Bottcher, C.2
Neumann, S.3
-
15
-
-
33748490271
-
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping
-
Prince J.T., Marcotte E.M. Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem 2006, 78:6140-6152.
-
(2006)
Anal Chem
, vol.78
, pp. 6140-6152
-
-
Prince, J.T.1
Marcotte, E.M.2
-
16
-
-
84921653824
-
GridMass: a fast two-dimensional feature detection method for LC/MS
-
Trevino V., Yanez-Garza I.L., Rodriguez-Lopez C.E., Urrea-Lopez R., Garza-Rodriguez M.L., Barrera-Saldana H.A., Tamez-Pena J.G., Winkler R., Diaz de-la-Garza R.I. GridMass: a fast two-dimensional feature detection method for LC/MS. J Mass Spectrom 2015, 50:165-174.
-
(2015)
J Mass Spectrom
, vol.50
, pp. 165-174
-
-
Trevino, V.1
Yanez-Garza, I.L.2
Rodriguez-Lopez, C.E.3
Urrea-Lopez, R.4
Garza-Rodriguez, M.L.5
Barrera-Saldana, H.A.6
Tamez-Pena, J.G.7
Winkler, R.8
Diaz de-la-Garza, R.I.9
-
17
-
-
84904306550
-
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses
-
Gowda H., Ivanisevic J., Johnson C.H., Kurczy M.E., Benton H.P., Rinehart D., Nguyen T., Ray J., Kuehl J., Arevalo B., et al. Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem 2014, 86:6931-6939.
-
(2014)
Anal Chem
, vol.86
, pp. 6931-6939
-
-
Gowda, H.1
Ivanisevic, J.2
Johnson, C.H.3
Kurczy, M.E.4
Benton, H.P.5
Rinehart, D.6
Nguyen, T.7
Ray, J.8
Kuehl, J.9
Arevalo, B.10
-
18
-
-
77956586799
-
Optimization and evaluation of metabolite extraction protocols for untargeted metabolic profiling of liver samples by UPLC-MS
-
Masson P., Alves A.C., Ebbels T.M., Nicholson J.K., Want E.J. Optimization and evaluation of metabolite extraction protocols for untargeted metabolic profiling of liver samples by UPLC-MS. Anal Chem 2010, 82:7779-7786.
-
(2010)
Anal Chem
, vol.82
, pp. 7779-7786
-
-
Masson, P.1
Alves, A.C.2
Ebbels, T.M.3
Nicholson, J.K.4
Want, E.J.5
-
19
-
-
79954582170
-
Expanding coverage of the metabolome for global metabolite profiling
-
Yanes O., Tautenhahn R., Patti G.J., Siuzdak G. Expanding coverage of the metabolome for global metabolite profiling. Anal Chem 2011, 83:2152-2161.
-
(2011)
Anal Chem
, vol.83
, pp. 2152-2161
-
-
Yanes, O.1
Tautenhahn, R.2
Patti, G.J.3
Siuzdak, G.4
-
20
-
-
84875123279
-
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database
-
Zhu Z.J., Schultz A.W., Wang J., Johnson C.H., Yannone S.M., Patti G.J., Siuzdak G. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc 2013, 8:451-460.
-
(2013)
Nat Protoc
, vol.8
, pp. 451-460
-
-
Zhu, Z.J.1
Schultz, A.W.2
Wang, J.3
Johnson, C.H.4
Yannone, S.M.5
Patti, G.J.6
Siuzdak, G.7
-
21
-
-
84907903688
-
Credentialing features: a platform to benchmark and optimize untargeted metabolomic methods
-
Mahieu N.G., Huang X., Chen Y.J., Patti G.J. Credentialing features: a platform to benchmark and optimize untargeted metabolomic methods. Anal Chem 2014, 86:9583-9589.
-
(2014)
Anal Chem
, vol.86
, pp. 9583-9589
-
-
Mahieu, N.G.1
Huang, X.2
Chen, Y.J.3
Patti, G.J.4
-
22
-
-
84890503012
-
Isotopic ratio outlier analysis global metabolomics of Caenorhabditis elegans
-
Stupp G.S., Clendinen C.S., Ajredini R., Szewc M.A., Garrett T., Menger R.F., Yost R.A., Beecher C., Edison A.S. Isotopic ratio outlier analysis global metabolomics of Caenorhabditis elegans. Anal Chem 2013, 85:11858-11865.
-
(2013)
Anal Chem
, vol.85
, pp. 11858-11865
-
-
Stupp, G.S.1
Clendinen, C.S.2
Ajredini, R.3
Szewc, M.A.4
Garrett, T.5
Menger, R.F.6
Yost, R.A.7
Beecher, C.8
Edison, A.S.9
-
23
-
-
84929672388
-
Defining the metabolome: size, flux, and regulation
-
Zamboni N., Saghatelian A., Patti G.J. Defining the metabolome: size, flux, and regulation. Mol Cell 2015, 58:699-706.
-
(2015)
Mol Cell
, vol.58
, pp. 699-706
-
-
Zamboni, N.1
Saghatelian, A.2
Patti, G.J.3
-
24
-
-
84922463714
-
Autonomous metabolomics for rapid metabolite identification in global profiling
-
Benton H.P., Ivanisevic J., Mahieu N.G., Kurczy M.E., Johnson C.H., Franco L., Rinehart D., Valentine E., Gowda H., Ubhi B.K., et al. Autonomous metabolomics for rapid metabolite identification in global profiling. Anal Chem 2015, 87:884-891.
-
(2015)
Anal Chem
, vol.87
, pp. 884-891
-
-
Benton, H.P.1
Ivanisevic, J.2
Mahieu, N.G.3
Kurczy, M.E.4
Johnson, C.H.5
Franco, L.6
Rinehart, D.7
Valentine, E.8
Gowda, H.9
Ubhi, B.K.10
-
25
-
-
50049096775
-
XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization
-
Benton H.P., Wong D.M., Trauger S.A., Siuzdak G. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem 2008, 80:6382-6389.
-
(2008)
Anal Chem
, vol.80
, pp. 6382-6389
-
-
Benton, H.P.1
Wong, D.M.2
Trauger, S.A.3
Siuzdak, G.4
-
26
-
-
51249118496
-
Interferences and contaminants encountered in modern mass spectrometry
-
Keller B.O., Sui J., Young A.B., Whittal R.M. Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta 2008, 627:71-81.
-
(2008)
Anal Chim Acta
, vol.627
, pp. 71-81
-
-
Keller, B.O.1
Sui, J.2
Young, A.B.3
Whittal, R.M.4
-
27
-
-
84858790233
-
Innovation: metabolomics: the apogee of the omics trilogy
-
Patti G.J., Yanes O., Siuzdak G. Innovation: metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012, 13:263-269.
-
(2012)
Nat Rev Mol Cell Biol
, vol.13
, pp. 263-269
-
-
Patti, G.J.1
Yanes, O.2
Siuzdak, G.3
-
28
-
-
84855402302
-
CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets
-
Kuhl C., Tautenhahn R., Bottcher C., Larson T.R., Neumann S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem 2012, 84:283-289.
-
(2012)
Anal Chem
, vol.84
, pp. 283-289
-
-
Kuhl, C.1
Tautenhahn, R.2
Bottcher, C.3
Larson, T.R.4
Neumann, S.5
-
29
-
-
77749327663
-
A statistically rigorous test for the identification of parent-fragment pairs in LC-MS datasets
-
Ipsen A., Want E.J., Lindon J.C., Ebbels T.M. A statistically rigorous test for the identification of parent-fragment pairs in LC-MS datasets. Anal Chem 2010, 82:1766-1778.
-
(2010)
Anal Chem
, vol.82
, pp. 1766-1778
-
-
Ipsen, A.1
Want, E.J.2
Lindon, J.C.3
Ebbels, T.M.4
-
30
-
-
84949454389
-
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis
-
Mahieu N.G., Spalding J., Patti G.J. Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis. Bioinformatics 2015, 10.1093/bioinformatics/btv564.
-
(2015)
Bioinformatics
-
-
Mahieu, N.G.1
Spalding, J.2
Patti, G.J.3
-
31
-
-
84904383851
-
Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension
-
Patti G.J., Tautenhahn R., Johannsen D., Kalisiak E., Ravussin E., Bruning J.C., Dillin A., Siuzdak G. Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension. Metabolomics 2014, 10:737-743.
-
(2014)
Metabolomics
, vol.10
, pp. 737-743
-
-
Patti, G.J.1
Tautenhahn, R.2
Johannsen, D.3
Kalisiak, E.4
Ravussin, E.5
Bruning, J.C.6
Dillin, A.7
Siuzdak, G.8
-
32
-
-
79952124278
-
MetaXCMS: second-order analysis of untargeted metabolomics data
-
Tautenhahn R., Patti G.J., Kalisiak E., Miyamoto T., Schmidt M., Lo F.Y., McBee J., Baliga N.S., Siuzdak G. metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem 2011, 83:696-700.
-
(2011)
Anal Chem
, vol.83
, pp. 696-700
-
-
Tautenhahn, R.1
Patti, G.J.2
Kalisiak, E.3
Miyamoto, T.4
Schmidt, M.5
Lo, F.Y.6
McBee, J.7
Baliga, N.S.8
Siuzdak, G.9
-
33
-
-
84858764020
-
Meta-analysis of untargeted metabolomic data from multiple profiling experiments
-
Patti G.J., Tautenhahn R., Siuzdak G. Meta-analysis of untargeted metabolomic data from multiple profiling experiments. Nat Protoc 2012, 7:508-516.
-
(2012)
Nat Protoc
, vol.7
, pp. 508-516
-
-
Patti, G.J.1
Tautenhahn, R.2
Siuzdak, G.3
-
34
-
-
84904383851
-
Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension
-
Patti G.J., Tautenhahn R., Johannsen D., Kalisiak E., Ravussin E., Bruning J.C., Dillin A., Siuzdak G. Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension. Metabolomics 2014, 10:7.
-
(2014)
Metabolomics
, vol.10
, pp. 7
-
-
Patti, G.J.1
Tautenhahn, R.2
Johannsen, D.3
Kalisiak, E.4
Ravussin, E.5
Bruning, J.C.6
Dillin, A.7
Siuzdak, G.8
-
35
-
-
84858414020
-
Cellular metabolism and disease: what do metabolic outliers teach us?
-
DeBerardinis R.J., Thompson C.B. Cellular metabolism and disease: what do metabolic outliers teach us?. Cell 2012, 148:1132-1140.
-
(2012)
Cell
, vol.148
, pp. 1132-1140
-
-
DeBerardinis, R.J.1
Thompson, C.B.2
-
36
-
-
84923596826
-
A roadmap for interpreting C metabolite labeling patterns from cells
-
Buescher J.M., Antoniewicz M.R., Boros L.G., Burgess S.C., Brunengraber H., Clish C.B., DeBerardinis R.J., Feron O., Frezza C., Ghesquiere B., et al. A roadmap for interpreting C metabolite labeling patterns from cells. Curr Opin Biotechnol 2015, 34:189-201.
-
(2015)
Curr Opin Biotechnol
, vol.34
, pp. 189-201
-
-
Buescher, J.M.1
Antoniewicz, M.R.2
Boros, L.G.3
Burgess, S.C.4
Brunengraber, H.5
Clish, C.B.6
DeBerardinis, R.J.7
Feron, O.8
Frezza, C.9
Ghesquiere, B.10
-
37
-
-
84869425686
-
Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation
-
Creek D.J., Chokkathukalam A., Jankevics A., Burgess K.E., Breitling R., Barrett M.P. Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation. Anal Chem 2012, 84:8442-8447.
-
(2012)
Anal Chem
, vol.84
, pp. 8442-8447
-
-
Creek, D.J.1
Chokkathukalam, A.2
Jankevics, A.3
Burgess, K.E.4
Breitling, R.5
Barrett, M.P.6
-
38
-
-
84904985062
-
Differential incorporation of glucose into biomass during Warburg metabolism
-
Chen Y.J., Huang X., Mahieu N.G., Cho K., Schaefer J., Patti G.J. Differential incorporation of glucose into biomass during Warburg metabolism. Biochemistry 2014, 53:4755-4757.
-
(2014)
Biochemistry
, vol.53
, pp. 4755-4757
-
-
Chen, Y.J.1
Huang, X.2
Mahieu, N.G.3
Cho, K.4
Schaefer, J.5
Patti, G.J.6
-
39
-
-
84912088491
-
Estimating relative changes of metabolic fluxes
-
Huang L., Kim D., Liu X., Myers C.R., Locasale J.W. Estimating relative changes of metabolic fluxes. PLoS Comput Biol 2014, 10:e1003958.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003958
-
-
Huang, L.1
Kim, D.2
Liu, X.3
Myers, C.R.4
Locasale, J.W.5
-
40
-
-
84893633670
-
X13CMS: global tracking of isotopic labels in untargeted metabolomics
-
Huang X., Chen Y.J., Cho K., Nikolskiy I., Crawford P.A., Patti G.J. X13CMS: global tracking of isotopic labels in untargeted metabolomics. Anal Chem 2014, 86:1632-1639.
-
(2014)
Anal Chem
, vol.86
, pp. 1632-1639
-
-
Huang, X.1
Chen, Y.J.2
Cho, K.3
Nikolskiy, I.4
Crawford, P.A.5
Patti, G.J.6
-
41
-
-
84859223223
-
IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data
-
Creek D.J., Jankevics A., Burgess K.E., Breitling R., Barrett M.P. IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. Bioinformatics 2012, 28:1048-1049.
-
(2012)
Bioinformatics
, vol.28
, pp. 1048-1049
-
-
Creek, D.J.1
Jankevics, A.2
Burgess, K.E.3
Breitling, R.4
Barrett, M.P.5
-
42
-
-
84928011252
-
IPO: a tool for automated optimization of XCMS parameters
-
Libiseller G., Dvorzak M., Kleb U., Gander E., Eisenberg T., Madeo F., Neumann S., Trausinger G., Sinner F., Pieber T., et al. IPO: a tool for automated optimization of XCMS parameters. BMC Bioinformat 2015, 16:118.
-
(2015)
BMC Bioinformat
, vol.16
, pp. 118
-
-
Libiseller, G.1
Dvorzak, M.2
Kleb, U.3
Gander, E.4
Eisenberg, T.5
Madeo, F.6
Neumann, S.7
Trausinger, G.8
Sinner, F.9
Pieber, T.10
-
43
-
-
84861915827
-
XCMS Online: a web-based platform to process untargeted metabolomic data
-
Tautenhahn R., Patti G.J., Rinehart D., Siuzdak G. XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem 2012, 84:5035-5039.
-
(2012)
Anal Chem
, vol.84
, pp. 5035-5039
-
-
Tautenhahn, R.1
Patti, G.J.2
Rinehart, D.3
Siuzdak, G.4
-
44
-
-
84866123900
-
An accelerated workflow for untargeted metabolomics using the METLIN database
-
Tautenhahn R., Cho K., Uritboonthai W., Zhu Z., Patti G.J., Siuzdak G. An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol 2012, 30:826-828.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 826-828
-
-
Tautenhahn, R.1
Cho, K.2
Uritboonthai, W.3
Zhu, Z.4
Patti, G.J.5
Siuzdak, G.6
|