-
1
-
-
84904810329
-
CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra
-
Allen F, Wilson M, Pon A, Greiner R, Wishart D. 2014. CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res 42(W1):W94–W99.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.W1
, pp. W94-W99
-
-
Allen, F.1
Wilson, M.2
Pon, A.3
Greiner, R.4
Wishart, D.5
-
2
-
-
84926363137
-
Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification
-
Allen F, Greiner R. 2015. Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics 11(1):98–110.
-
(2015)
Metabolomics
, vol.11
, Issue.1
, pp. 98-110
-
-
Allen, F.1
Greiner, R.2
-
3
-
-
84870918230
-
Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature
-
Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian K-D, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl H-G, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang G-L, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. 2013. Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature. Nat Prod Rep 30(1):108–160.
-
(2013)
Nat Prod Rep
, vol.30
, Issue.1
, pp. 108-160
-
-
Arnison, P.G.1
Bibb, M.J.2
Bierbaum, G.3
Bowers, A.A.4
Bugni, T.S.5
Bulaj, G.6
Camarero, J.A.7
Campopiano, D.J.8
Challis, G.L.9
Clardy, J.10
Cotter, P.D.11
Craik, D.J.12
Dawson, M.13
Dittmann, E.14
Donadio, S.15
Dorrestein, P.C.16
Entian, K.-D.17
Fischbach, M.A.18
Garavelli, J.S.19
Göransson, U.20
Gruber, C.W.21
Haft, D.H.22
Hemscheidt, T.K.23
Hertweck, C.24
Hill, C.25
Horswill, A.R.26
Jaspars, M.27
Kelly, W.L.28
Klinman, J.P.29
Kuipers, O.P.30
Link, A.J.31
Liu, W.32
Marahiel, M.A.33
Mitchell, D.A.34
Moll, G.N.35
Moore, B.S.36
Müller, R.37
Nair, S.K.38
Nes, I.F.39
Norris, G.E.40
Olivera, B.M.41
Onaka, H.42
Patchett, M.L.43
Piel, J.44
Reaney, M.J.T.45
Rebuffat, S.46
Ross, R.P.47
Sahl, H.-G.48
Schmidt, E.W.49
Selsted, M.E.50
Severinov, K.51
Shen, B.52
Sivonen, K.53
Smith, L.54
Stein, T.55
Süssmuth, R.D.56
Tagg, J.R.57
Tang, G.-L.58
Truman, A.W.59
Vederas, J.C.60
Walsh, C.T.61
Walton, J.D.62
Wenzel, S.C.63
Willey, J.M.64
van der Donk, W.A.65
more..
-
4
-
-
79551507196
-
Metabolomics: From small molecules to big ideas
-
Baker M. 2011. Metabolomics: From small molecules to big ideas. Nat Methods 8(2):117–121.
-
(2011)
Nat Methods
, vol.8
, Issue.2
, pp. 117-121
-
-
Baker, M.1
-
5
-
-
84924338899
-
A community computational challenge to predict the activity of pairs of compounds
-
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, Community NCI-DREAM, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A. 2014. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol 32(12):1213–1222.
-
(2014)
Nat Biotechnol
, vol.32
, Issue.12
, pp. 1213-1222
-
-
Bansal, M.1
Yang, J.2
Karan, C.3
Menden, M.P.4
Costello, J.C.5
Tang, H.6
Xiao, G.7
Li, Y.8
Allen, J.9
Zhong, R.10
Chen, B.11
Kim, M.12
Wang, T.13
Heiser, L.M.14
Realubit, R.15
Mattioli, M.16
Alvarez, M.J.17
Shen, Y.18
Community, N.C.I.-D.R.E.A.M.19
Gallahan, D.20
Singer, D.21
Saez-Rodriguez, J.22
Xie, Y.23
Stolovitzky, G.24
Califano, A.25
more..
-
6
-
-
49549101405
-
Towards de novo identification of metabolites by analyzing tandem mass spectra
-
Böcker S, Rasche F. 2008. Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics 24:I49–I55.
-
(2008)
Bioinformatics
, vol.24
, pp. I49-I55
-
-
Böcker, S.1
Rasche, F.2
-
7
-
-
58349086772
-
SIRIUS: Decomposing isotope patterns for metabolite identification
-
Böcker S, Letzel M, Lipták Zs, Pervukhin A. 2009. SIRIUS: Decomposing isotope patterns for metabolite identification. Bioinformatics 25(2):218–224.
-
(2009)
Bioinformatics
, vol.25
, Issue.2
, pp. 218-224
-
-
Böcker, S.1
Letzel, M.2
Lipták, Z.3
Pervukhin, A.4
-
8
-
-
84904817527
-
XTMS: Pathway design in an eXTended metabolic space
-
Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon J-L. 2014. XTMS: Pathway design in an eXTended metabolic space. Nucleic Acids Res 42:W389–W394.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W389-W394
-
-
Carbonell, P.1
Parutto, P.2
Herisson, J.3
Pandit, S.B.4
Faulon, J.-L.5
-
9
-
-
84906549588
-
A community effort to assess and improve drug sensitivity prediction algorithms
-
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi J-P, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, Community NCI-DREAM, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. 2014. A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol 32(12):1202–1212.
-
(2014)
Nat Biotechnol
, vol.32
, Issue.12
, pp. 1202-1212
-
-
Costello, J.C.1
Heiser, L.M.2
Georgii, E.3
Gönen, M.4
Menden, M.P.5
Wang, N.J.6
Bansal, M.7
Ammad-ud-din, M.8
Hintsanen, P.9
Khan, S.A.10
Mpindi, J.-P.11
Kallioniemi, O.12
Honkela, A.13
Aittokallio, T.14
Wennerberg, K.15
Community, N.C.I.-D.R.E.A.M.16
Collins, J.J.17
Gallahan, D.18
Singer, D.19
Saez-Rodriguez, J.20
Kaski, S.21
Gray, J.W.22
Stolovitzky, G.23
more..
-
11
-
-
0002629270
-
Maximum likelihood from incomplete data via the EM algorithm
-
Dempster AP, Laird NM, Rubin DB. 1977. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc 39(1):1–38.
-
(1977)
J R Stat Soc
, vol.39
, Issue.1
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
13
-
-
84930177686
-
Molecular formula identification using isotope pattern analysis and calculation of fragmentation trees
-
Dührkop K, Hufsky F, Böcker S. 2014. Molecular formula identification using isotope pattern analysis and calculation of fragmentation trees. Mass Spectrom 3(2):S0037.
-
(2014)
Mass Spectrom
, vol.3
, Issue.2
, pp. S0037
-
-
Dührkop, K.1
Hufsky, F.2
Böcker, S.3
-
14
-
-
84944201928
-
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
-
Dührkop K, Shen H, Meusel M, Rousu J, Böcker S. 2015. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci USA 112(41):12580–12585.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, Issue.41
, pp. 12580-12585
-
-
Dührkop, K.1
Shen, H.2
Meusel, M.3
Rousu, J.4
Böcker, S.5
-
15
-
-
84937761254
-
Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species
-
Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. 2015. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chem Biol 22(4):460–471.
-
(2015)
Chem Biol
, vol.22
, Issue.4
, pp. 460-471
-
-
Duncan, K.R.1
Crüsemann, M.2
Lechner, A.3
Sarkar, A.4
Li, J.5
Ziemert, N.6
Wang, M.7
Bandeira, N.8
Moore, B.S.9
Dorrestein, P.C.10
Jensen, P.R.11
-
16
-
-
0001232509
-
On the properties of bit string-based measures of chemical similarity
-
Flower DR. 1998. On the properties of bit string-based measures of chemical similarity. J Chem Inf Comput Sci 38(3):379–386.
-
(1998)
J Chem Inf Comput Sci
, vol.38
, Issue.3
, pp. 379-386
-
-
Flower, D.R.1
-
17
-
-
84875154340
-
MetFusion: integration of compound identification strategies
-
Gerlich M, Neumann S. 2013. MetFusion: integration of compound identification strategies. J Mass Spectrom 48(3):291–298.
-
(2013)
J Mass Spectrom
, vol.48
, Issue.3
, pp. 291-298
-
-
Gerlich, M.1
Neumann, S.2
-
18
-
-
77952906127
-
Ab initio prediction of molecular fragments from tandem mass spectrometry data
-
Heinonen M, Rantanen A, Mielikäinen T, Pitkänen E, Kokkonen J. 2006. Ab initio prediction of molecular fragments from tandem mass spectrometry data. In Proc. of German Conference on Bioinformatics (GCB 2006), volume P-83 of Lecture Notes in Informatics, pages 40–53.
-
(2006)
Proc. of German Conference on Bioinformatics (GCB 2006), volume P-83 of Lecture Notes in Informatics
, pp. 40-53
-
-
Heinonen, M.1
Rantanen, A.2
Mielikäinen, T.3
Pitkänen, E.4
Kokkonen, J.5
-
19
-
-
56149101337
-
FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data
-
Heinonen M, Rantanen A, Mielikäinen T, Kokkonen J, Kiuru J, Ketola RA, Rousu J. 2008. FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom 22(19):3043–3052.
-
(2008)
Rapid Commun Mass Spectrom
, vol.22
, Issue.19
, pp. 3043-3052
-
-
Heinonen, M.1
Rantanen, A.2
Mielikäinen, T.3
Kokkonen, J.4
Kiuru, J.5
Ketola, R.A.6
Rousu, J.7
-
20
-
-
84866437252
-
Metabolite identification and molecular fingerprint prediction via machine learning
-
Heinonen M, Shen H, Zamboni N, Rousu J. 2012. Metabolite identification and molecular fingerprint prediction via machine learning. Bioinformatics 28(18):2333–2341.
-
(2012)
Bioinformatics
, vol.28
, Issue.18
, pp. 2333-2341
-
-
Heinonen, M.1
Shen, H.2
Zamboni, N.3
Rousu, J.4
-
21
-
-
27544443321
-
Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach
-
Hill AW, Mortishire-Smith RJ. 2005. Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach. Rapid Commun Mass Spectrom 19(21):3111–3118.
-
(2005)
Rapid Commun Mass Spectrom
, vol.19
, Issue.21
, pp. 3111-3118
-
-
Hill, A.W.1
Mortishire-Smith, R.J.2
-
22
-
-
77954439868
-
MassBank: A public repository for sharing mass spectral data for life sciences
-
Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T. 2010. MassBank: A public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45(7):703–714.
-
(2010)
J Mass Spectrom
, vol.45
, Issue.7
, pp. 703-714
-
-
Horai, H.1
Arita, M.2
Kanaya, S.3
Nihei, Y.4
Ikeda, T.5
Suwa, K.6
Ojima, Y.7
Tanaka, K.8
Tanaka, S.9
Aoshima, K.10
Oda, Y.11
Kakazu, Y.12
Kusano, M.13
Tohge, T.14
Matsuda, F.15
Sawada, Y.16
Hirai, M.Y.17
Nakanishi, H.18
Ikeda, K.19
Akimoto, N.20
Maoka, T.21
Takahashi, H.22
Ara, T.23
Sakurai, N.24
Suzuki, H.25
Shibata, D.26
Neumann, S.27
Iida, T.28
Tanaka, K.29
Funatsu, K.30
Matsuura, F.31
Soga, T.32
Taguchi, R.33
Saito, K.34
Nishioka, T.35
more..
-
23
-
-
84864025665
-
De novo analysis of electron impact mass spectra using fragmentation trees
-
Hufsky F, Rempt M, Rasche F, Pohnert G, Böcker S. 2012. De novo analysis of electron impact mass spectra using fragmentation trees. Anal Chim Acta 739:67–76.
-
(2012)
Anal Chim Acta
, vol.739
, pp. 67-76
-
-
Hufsky, F.1
Rempt, M.2
Rasche, F.3
Pohnert, G.4
Böcker, S.5
-
24
-
-
84888191935
-
Computational mass spectrometry for small molecule fragmentation
-
Hufsky F, Scheubert K, Böcker S. 2014. Computational mass spectrometry for small molecule fragmentation. Trends Anal Chem 53:41–48.
-
(2014)
Trends Anal Chem
, vol.53
, pp. 41-48
-
-
Hufsky, F.1
Scheubert, K.2
Böcker, S.3
-
25
-
-
84900862294
-
New kids on the block: Novel informatics methods for natural product discovery
-
Hufsky F, Scheubert K, Böcker S. 2014. New kids on the block: Novel informatics methods for natural product discovery. Nat Prod Rep 31(6):807–817.
-
(2014)
Nat Prod Rep
, vol.31
, Issue.6
, pp. 807-817
-
-
Hufsky, F.1
Scheubert, K.2
Böcker, S.3
-
26
-
-
84940036737
-
MINEs: Open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
-
Jeffryes JG, Colastani RL, Elbadawi-Sidhu M, Kind T, Niehaus TD, Broadbelt LJ, Hanson AD, Fiehn O, Tyo KEJ, Henry CS. 2015. MINEs: Open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. In J Cheminform 7(44).
-
(2015)
In J Cheminform
, vol.7
, Issue.44
-
-
Jeffryes, J.G.1
Colastani, R.L.2
Elbadawi-Sidhu, M.3
Kind, T.4
Niehaus, T.D.5
Broadbelt, L.J.6
Hanson, A.D.7
Fiehn, O.8
Tyo, K.E.J.9
Henry, C.S.10
-
27
-
-
84920456840
-
Bioinformatics: The next frontier of metabolomics
-
Johnson CH, Ivanisevic J, Benton HP, Siuzdak G. 2015. Bioinformatics: The next frontier of metabolomics. Anal Chem 87(1):147–156.
-
(2015)
Anal Chem
, vol.87
, Issue.1
, pp. 147-156
-
-
Johnson, C.H.1
Ivanisevic, J.2
Benton, H.P.3
Siuzdak, G.4
-
28
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. 2006. From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res 34:D354–D357.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D354-D357
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
29
-
-
84864008587
-
In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids
-
Kangas LJ, Metz TO, Isaac G, Schrom BT, Ginovska-Pangovska B, Wang L, Tan L, Lewis RR, Miller JH. 2012. In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids. Bioinformatics 28(13):1705–1713.
-
(2012)
Bioinformatics
, vol.28
, Issue.13
, pp. 1705-1713
-
-
Kangas, L.J.1
Metz, T.O.2
Isaac, G.3
Schrom, B.T.4
Ginovska-Pangovska, B.5
Wang, L.6
Tan, L.7
Lewis, R.R.8
Miller, J.H.9
-
30
-
-
33646747122
-
MOLGEN-MS: Evaluation of low resolution electron impact mass spectra with MS classification and exhaustive structure generation
-
Kerber A, Laue R, Meringer M, Varmuza K. 2001. MOLGEN-MS: Evaluation of low resolution electron impact mass spectra with MS classification and exhaustive structure generation. Adv Mass Spectrom 15:939–940.
-
(2001)
Adv Mass Spectrom
, vol.15
, pp. 939-940
-
-
Kerber, A.1
Laue, R.2
Meringer, M.3
Varmuza, K.4
-
31
-
-
29344434218
-
Molecules in silico: The generation of structural formulae and its applications
-
Kerber A, Laue R, Meringer M, Rücker C. 2004. Molecules in silico: The generation of structural formulae and its applications. J Comput Chem Japan 3(3):85–96.
-
(2004)
J Comput Chem Japan
, vol.3
, Issue.3
, pp. 85-96
-
-
Kerber, A.1
Laue, R.2
Meringer, M.3
Rücker, C.4
-
32
-
-
33846435744
-
CASE via MS: Ranking structure candidates by mass spectra
-
Kerber A, Meringer M, Rücker C. 2006. CASE via MS: Ranking structure candidates by mass spectra. Croat Chem Acta 79(3):449–464.
-
(2006)
Croat Chem Acta
, vol.79
, Issue.3
, pp. 449-464
-
-
Kerber, A.1
Meringer, M.2
Rücker, C.3
-
33
-
-
84979586933
-
PubChem substance and compound databases
-
Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH. 2016. PubChem substance and compound databases. Nucleic Acids Res 44 (D1):D1202–D1213.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D1202-D1213
-
-
Kim, S.1
Thiessen, P.A.2
Bolton, E.E.3
Chen, J.4
Fu, G.5
Gindulyte, A.6
Han, L.7
He, J.8
He, S.9
Shoemaker, B.A.10
Wang, J.11
Yu, B.12
Zhang, J.13
Bryant, S.H.14
-
34
-
-
84881476562
-
LipidBlast in silico tandem mass spectrometry database for lipid identification
-
Kind T, Liu K-H, Lee DY, DeFelice B, Meissen JK, Fiehn O. 2013. LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat Methods 10(8):755–758.
-
(2013)
Nat Methods
, vol.10
, Issue.8
, pp. 755-758
-
-
Kind, T.1
Liu, K.-H.2
Lee, D.Y.3
DeFelice, B.4
Meissen, J.K.5
Fiehn, O.6
-
36
-
-
79251567361
-
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
-
Krumsiek J, Suhre K, Illig T, Adamski J, Theis FJ. 2011. Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst Biol 5(21).
-
(2011)
BMC Syst Biol
, vol.5
, Issue.21
-
-
Krumsiek, J.1
Suhre, K.2
Illig, T.3
Adamski, J.4
Theis, F.J.5
-
37
-
-
84888289172
-
Docking, scoring, and affinity prediction in CAPRI
-
Lensink MF, Wodak SJ. 2013. Docking, scoring, and affinity prediction in CAPRI. Proteins 81(12):2082–2095.
-
(2013)
Proteins
, vol.81
, Issue.12
, pp. 2082-2095
-
-
Lensink, M.F.1
Wodak, S.J.2
-
38
-
-
84875432479
-
MyCompoundID: Using an evidence-based metabolome library for metabolite identification
-
Li L, Li R, Zhou J, Zuniga A, Stanislaus AE, Wu Y, Huan T, Zheng J, Shi Y, Wishart DS, Lin G. 2013. MyCompoundID: Using an evidence-based metabolome library for metabolite identification. Anal Chem 85(6):3401–3408.
-
(2013)
Anal Chem
, vol.85
, Issue.6
, pp. 3401-3408
-
-
Li, L.1
Li, R.2
Zhou, J.3
Zuniga, A.4
Stanislaus, A.E.5
Wu, Y.6
Huan, T.7
Zheng, J.8
Shi, Y.9
Wishart, D.S.10
Lin, G.11
-
40
-
-
40949161450
-
In silico tools for sharing data and knowledge on toxicity and metabolism: Derek for Windows, Meteor, and Vitic
-
Marchant CA, Briggs KA, Long A. 2008. In silico tools for sharing data and knowledge on toxicity and metabolism: Derek for Windows, Meteor, and Vitic. Toxicol Mech Methods 18(2–3):177–187.
-
(2008)
Toxicol Mech Methods
, vol.18
, Issue.2-3
, pp. 177-187
-
-
Marchant, C.A.1
Briggs, K.A.2
Long, A.3
-
41
-
-
84868558116
-
MolFind: A software package enabling HPLC/MS-based identification of unknown chemical structures
-
Menikarachchi LC, Cawley S, Hill DW, Hall LM, Hall L, Lai S, Wilder J, Grant DF. 2012. MolFind: A software package enabling HPLC/MS-based identification of unknown chemical structures. Anal Chem 84(21):9388–9394.
-
(2012)
Anal Chem
, vol.84
, Issue.21
, pp. 9388-9394
-
-
Menikarachchi, L.C.1
Cawley, S.2
Hill, D.W.3
Hall, L.M.4
Hall, L.5
Lai, S.6
Wilder, J.7
Grant, D.F.8
-
42
-
-
84884555187
-
In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics
-
Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF. 2013. In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics. J Chem Inf Model 53(9):2483–2492.
-
(2013)
J Chem Inf Model
, vol.53
, Issue.9
, pp. 2483-2492
-
-
Menikarachchi, L.C.1
Hill, D.W.2
Hamdalla, M.A.3
Mandoiu, I.I.4
Grant, D.F.5
-
43
-
-
84899135483
-
Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks
-
Morreel K, Saeys Y, Dima O, Lu F, Van de Peer Y, Vanholme R, Ralph J, Vanholme B, Boerjan W. 2014. Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks. Plant Cell 26(3):929–945.
-
(2014)
Plant Cell
, vol.26
, Issue.3
, pp. 929-945
-
-
Morreel, K.1
Saeys, Y.2
Dima, O.3
Lu, F.4
Van de Peer, Y.5
Vanholme, R.6
Ralph, J.7
Vanholme, B.8
Boerjan, W.9
-
44
-
-
84893021599
-
Critical assessment of methods of protein structure prediction (CASP)-round x
-
Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. 2014. Critical assessment of methods of protein structure prediction (CASP)-round x. Proteins 82(2):1–6.
-
(2014)
Proteins
, vol.82
, Issue.2
, pp. 1-6
-
-
Moult, J.1
Fidelis, K.2
Kryshtafovych, A.3
Schwede, T.4
Tramontano, A.5
-
45
-
-
84879908779
-
MS/MS networking guided analysis of molecule and gene cluster families
-
Nguyen DD, Wu C-H, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC. 2013. MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci USA 110(28):E2611–E2620.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.28
, pp. E2611-E2620
-
-
Nguyen, D.D.1
Wu, C.-H.2
Moree, W.J.3
Lamsa, A.4
Medema, M.H.5
Zhao, X.6
Gavilan, R.G.7
Aparicio, M.8
Atencio, L.9
Jackson, C.10
Ballesteros, J.11
Sanchez, J.12
Watrous, J.D.13
Phelan, V.V.14
van de Wiel, C.15
Kersten, R.D.16
Mehnaz, S.17
De Mot, R.18
Shank, E.A.19
Charusanti, P.20
Nagarajan, H.21
Duggan, B.M.22
Moore, B.S.23
Bandeira, N.24
Palsson, B.Ø.25
Pogliano, K.26
Gutiérrez, M.27
Dorrestein, P.C.28
more..
-
46
-
-
84924051642
-
Winners of CASM I2013: Automated tools and challenge data
-
Nishioka T, Kasama T, Kinumi T, Makabe H, Matsuda F, Miura D, Miyashita M, Nakamura T, Tanaka K, Yamamoto A. 2014. Winners of CASM I2013: Automated tools and challenge data. Mass Spectrom 3(2):S0039.
-
(2014)
Mass Spectrom
, vol.3
, Issue.2
, pp. S0039
-
-
Nishioka, T.1
Kasama, T.2
Kinumi, T.3
Makabe, H.4
Matsuda, F.5
Miura, D.6
Miyashita, M.7
Nakamura, T.8
Tanaka, K.9
Yamamoto, A.10
-
47
-
-
84858790233
-
Metabolomics: The apogee of the omics trilogy
-
Patti GJ, Yanes O, Siuzdak G. 2012. Metabolomics: The apogee of the omics trilogy. Nat Rev Mol Cell Biol 13(4):263–269.
-
(2012)
Nat Rev Mol Cell Biol
, vol.13
, Issue.4
, pp. 263-269
-
-
Patti, G.J.1
Yanes, O.2
Siuzdak, G.3
-
48
-
-
84875787706
-
Automated pipeline for de novo metabolite identification using mass- spectrometry-based metabolomics
-
Peironcely JE, Rojas-Chertó M, Tas A, Vreeken R, Reijmers T, Coulier L, Hankemeier T. 2013. Automated pipeline for de novo metabolite identification using mass- spectrometry-based metabolomics. Anal Chem 85(7):3576–3583.
-
(2013)
Anal Chem
, vol.85
, Issue.7
, pp. 3576-3583
-
-
Peironcely, J.E.1
Rojas-Chertó, M.2
Tas, A.3
Vreeken, R.4
Reijmers, T.5
Coulier, L.6
Hankemeier, T.7
-
49
-
-
79951640091
-
Computing fragmentation trees from tandem mass spectrometry data
-
Rasche F, Svatoš A, Maddula RK, Böttcher C, Böcker S. 2011. Computing fragmentation trees from tandem mass spectrometry data. Anal Chem 83(4):1243–1251.
-
(2011)
Anal Chem
, vol.83
, Issue.4
, pp. 1243-1251
-
-
Rasche, F.1
Svatoš, A.2
Maddula, R.K.3
Böttcher, C.4
Böcker, S.5
-
50
-
-
84876246881
-
Finding maximum colorful subtrees in practice
-
Rauf I, Rasche F, Nicolas F, Böcker S. 2013. Finding maximum colorful subtrees in practice. J Comput Biol 20(4):1–11.
-
(2013)
J Comput Biol
, vol.20
, Issue.4
, pp. 1-11
-
-
Rauf, I.1
Rasche, F.2
Nicolas, F.3
Böcker, S.4
-
51
-
-
84866362686
-
Substructure-based annotation of high-resolution multistage MSn spectral trees
-
Ridder L, van der Hooft JJJ, Verhoeven S, de Vos RCH, van Schaik R, Vervoort J. 2012. Substructure-based annotation of high-resolution multistage MSn spectral trees. Rapid Commun Mass Spectrom 26(20):2461–2471.
-
(2012)
Rapid Commun Mass Spectrom
, vol.26
, Issue.20
, pp. 2461-2471
-
-
Ridder, L.1
van der Hooft, J.J.J.2
Verhoeven, S.3
de Vos, R.C.H.4
van Schaik, R.5
Vervoort, J.6
-
52
-
-
84879199446
-
Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea
-
Ridder L, van der Hooft JJJ, Verhoeven S, de Vos RCH, Bino RJ, Vervoort J. 2013. Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea. Anal Chem 85(12):6033–6040.
-
(2013)
Anal Chem
, vol.85
, Issue.12
, pp. 6033-6040
-
-
Ridder, L.1
van der Hooft, J.J.J.2
Verhoeven, S.3
de Vos, R.C.H.4
Bino, R.J.5
Vervoort, J.6
-
53
-
-
84956908632
-
Automatic compound annotation from mass spectrometry data using MAGMa
-
Ridder L, van der Hooft JJJ, Verhoeven S. 2014. Automatic compound annotation from mass spectrometry data using MAGMa. Mass Spectrom 3(2):S0033.
-
(2014)
Mass Spectrom
, vol.3
, Issue.2
, pp. S0033
-
-
Ridder, L.1
van der Hooft, J.J.J.2
Verhoeven, S.3
-
54
-
-
84901267802
-
In silico prediction and automatic LC-MS(n) annotation of green tea metabolites in urine
-
Ridder L, van der Hooft JJJ, Verhoeven S, de Vos RCH, Vervoort J, Bino RJ. 2014. In silico prediction and automatic LC-MS(n) annotation of green tea metabolites in urine. Anal Chem 86(10):4767–4774.
-
(2014)
Anal Chem
, vol.86
, Issue.10
, pp. 4767-4774
-
-
Ridder, L.1
van der Hooft, J.J.J.2
Verhoeven, S.3
de Vos, R.C.H.4
Vervoort, J.5
Bino, R.J.6
-
55
-
-
84863479215
-
Metabolite identification using automated comparison of high-resolution multistage mass spectral trees
-
Rojas-Chertó M, Peironcely JE, Kasper PT, van der Hooft JJJ, de Vos RCH, Vreeken RJ, Hankemeier T, Reijmers TH. 2012. Metabolite identification using automated comparison of high-resolution multistage mass spectral trees. Anal Chem 84(13):5524–5534.
-
(2012)
Anal Chem
, vol.84
, Issue.13
, pp. 5524-5534
-
-
Rojas-Chertó, M.1
Peironcely, J.E.2
Kasper, P.T.3
van der Hooft, J.J.J.4
de Vos, R.C.H.5
Vreeken, R.J.6
Hankemeier, T.7
Reijmers, T.H.8
-
56
-
-
84877343392
-
Computational mass spectrometry for small molecules
-
Scheubert K, Hufsky F, Böcker S. 2013. Computational mass spectrometry for small molecules. J Cheminform 5(12).
-
(2013)
J Cheminform
, vol.5
, Issue.12
-
-
Scheubert, K.1
Hufsky, F.2
Böcker, S.3
-
57
-
-
84958544112
-
-
Berlin, Springer
-
Scheubert K, Hufsky F, Böcker S. 2014. Multiple mass spectrometry fragmentation trees revisited: Boosting performance and quality. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2014), volume 8701 of Lect Notes Comput Sci, pages 217–231. Berlin: Springer.
-
(2014)
Multiple mass spectrometry fragmentation trees revisited: Boosting performance and quality. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2014), volume 8701 of Lect Notes Comput Sci, pages 217–231
-
-
Scheubert, K.1
Hufsky, F.2
Böcker, S.3
-
58
-
-
85016485767
-
CASMI: And the winner is
-
Schymanski EL, Neumann S. 2013. CASMI: And the winner is. Metabolites 3(2):412–439.
-
(2013)
Metabolites
, vol.3
, Issue.2
, pp. 412-439
-
-
Schymanski, E.L.1
Neumann, S.2
-
59
-
-
84912017975
-
The critical assessment of small molecule identification (CASMI): Challenges and solutions
-
Schymanski EL, Neumann S. 2013. The critical assessment of small molecule identification (CASMI): Challenges and solutions. Metabolites 3(3):517–538.
-
(2013)
Metabolites
, vol.3
, Issue.3
, pp. 517-538
-
-
Schymanski, E.L.1
Neumann, S.2
-
60
-
-
84859376463
-
Consensus structure elucidation combining GC/EI-MS, structure generation and calculated properties
-
Schymanski EL, Gallampois CMJ, Krauss M, Meringer M, Neumann S, Schulze T, Wolf S, Brack W. 2012. Consensus structure elucidation combining GC/EI-MS, structure generation and calculated properties. Anal Chem 84(7):3287–3295.
-
(2012)
Anal Chem
, vol.84
, Issue.7
, pp. 3287-3295
-
-
Schymanski, E.L.1
Gallampois, C.M.J.2
Krauss, M.3
Meringer, M.4
Neumann, S.5
Schulze, T.6
Wolf, S.7
Brack, W.8
-
61
-
-
60649112635
-
Determination of ion structures in structurally related compounds using precursor ion fingerprinting
-
Sheldon MT, Mistrik R, Croley TR. 2009. Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J Am Soc Mass Spectrom 20(3):370–376.
-
(2009)
J Am Soc Mass Spectrom
, vol.20
, Issue.3
, pp. 370-376
-
-
Sheldon, M.T.1
Mistrik, R.2
Croley, T.R.3
-
62
-
-
84900839280
-
Metabolite identification through multiple kernel learning on fragmentation trees
-
Shen H, Dührkop K, Böcker S, Rousu J. 2014. Metabolite identification through multiple kernel learning on fragmentation trees. Bioinformatics 30(12):i157–i164.
-
(2014)
Bioinformatics
, vol.30
, Issue.12
, pp. i157-i164
-
-
Shen, H.1
Dührkop, K.2
Böcker, S.3
Rousu, J.4
-
63
-
-
84865769818
-
Mass spectral reference libraries: An ever-expanding resource for chemical identification
-
Stein SE. 2012. Mass spectral reference libraries: An ever-expanding resource for chemical identification. Anal Chem 84(17):7274–7282.
-
(2012)
Anal Chem
, vol.84
, Issue.17
, pp. 7274-7282
-
-
Stein, S.E.1
-
64
-
-
34748888866
-
Proposed minimum reporting standards for chemical analysis
-
Sumner LW, Amberg A, Barrett D, Beale M, Beger R, Daykin C, Fan T, Fiehn O, Goodacre R, Griffin JL, Hankemeier T, Hardy N, Harnly J, Higashi R, Kopka J, Lane A, Lindon JC, Marriott P, Nicholls A, Reily M, Thaden J, Viant MR. 2007. Proposed minimum reporting standards for chemical analysis. Metabolomics 3(3):211–221.
-
(2007)
Metabolomics
, vol.3
, Issue.3
, pp. 211-221
-
-
Sumner, L.W.1
Amberg, A.2
Barrett, D.3
Beale, M.4
Beger, R.5
Daykin, C.6
Fan, T.7
Fiehn, O.8
Goodacre, R.9
Griffin, J.L.10
Hankemeier, T.11
Hardy, N.12
Harnly, J.13
Higashi, R.14
Kopka, J.15
Lane, A.16
Lindon, J.C.17
Marriott, P.18
Nicholls, A.19
Reily, M.20
Thaden, J.21
Viant, M.R.22
more..
-
65
-
-
0142104153
-
Small molecules as mathematical partitions
-
Sweeney DL. 2003. Small molecules as mathematical partitions. Anal Chem 75(20):5362–5373.
-
(2003)
Anal Chem
, vol.75
, Issue.20
, pp. 5362-5373
-
-
Sweeney, D.L.1
-
66
-
-
84866390901
-
Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts
-
van der Hooft JJJ, Akermi M, Ünlü FY, Mihaleva V, Roldan VG, Bino RJ, de Vos RCH, Vervoort J. 2012. Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts. J Agric Food Chem 60(36):8841–8850.
-
(2012)
J Agric Food Chem
, vol.60
, Issue.36
, pp. 8841-8850
-
-
van der Hooft, J.J.J.1
Akermi, M.2
Ünlü, F.Y.3
Mihaleva, V.4
Roldan, V.G.5
Bino, R.J.6
de Vos, R.C.H.7
Vervoort, J.8
-
67
-
-
84865476110
-
Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake
-
van der Hooft JJJ, de Vos RCH, Mihaleva V, Bino RJ, Ridder L, de Roo N, Jacobs DM, van Duynhoven JPM, Vervoort J. 2012. Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake. Anal Chem 84(16):7263–7271.
-
(2012)
Anal Chem
, vol.84
, Issue.16
, pp. 7263-7271
-
-
van der Hooft, J.J.J.1
de Vos, R.C.H.2
Mihaleva, V.3
Bino, R.J.4
Ridder, L.5
de Roo, N.6
Jacobs, D.M.7
van Duynhoven, J.P.M.8
Vervoort, J.9
-
68
-
-
84930182757
-
Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics
-
Vaniya A, Fiehn O. 2015. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics. Trends Anal Chem 69:52–61.
-
(2015)
Trends Anal Chem
, vol.69
, pp. 52-61
-
-
Vaniya, A.1
Fiehn, O.2
-
69
-
-
84907885060
-
MIDAS: A database-searching algorithm for metabolite identification in metabolomics
-
Wang Y, Kora G, Bowen BP, Pan C. 2014. MIDAS: A database-searching algorithm for metabolite identification in metabolomics. Anal Chem 86(19):9496–9503.
-
(2014)
Anal Chem
, vol.86
, Issue.19
, pp. 9496-9503
-
-
Wang, Y.1
Kora, G.2
Bowen, B.P.3
Pan, C.4
-
70
-
-
84862999012
-
Mass spectral molecular networking of living microbial colonies
-
Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. 2012. Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci USA 109(26):E1743–E1752.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.26
, pp. E1743-E1752
-
-
Watrous, J.1
Roach, P.2
Alexandrov, T.3
Heath, B.S.4
Yang, J.Y.5
Kersten, R.D.6
van der Voort, M.7
Pogliano, K.8
Gross, H.9
Raaijmakers, J.M.10
Moore, B.S.11
Laskin, J.12
Bandeira, N.13
Dorrestein, P.C.14
-
71
-
-
84951207956
-
-
Berlin, Springer
-
White WTJ, Beyer S, Dührkop K, Chimani M, Böcker S. 2015. Speedy colorful subtrees. In Proc. of Computing and Combinatorics Conference (COCOON 2015), volume 9198 of Lect Notes Comput Sci, pages 310–322. Berlin: Springer.
-
(2015)
Speedy colorful subtrees. In Proc. of Computing and Combinatorics Conference (COCOON 2015), volume 9198 of Lect Notes Comput Sci, pages 310–322
-
-
White, W.T.J.1
Beyer, S.2
Dührkop, K.3
Chimani, M.4
Böcker, S.5
-
72
-
-
84876148784
-
HMDB 3. 0: The Human Metabolome Database in 2013
-
Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y, Djoumbou Y, Mandal R, Aziat F, Dong E, Bouatra S, Sinelnikov I, Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T, Perez-Pineiro R, Eisner R, Allen F, Neveu V, Greiner R, Scalbert A. 2013. HMDB 3. 0: The Human Metabolome Database in 2013. Nucleic Acids Res 41:D801–D807.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D801-D807
-
-
Wishart, D.S.1
Jewison, T.2
Guo, A.C.3
Wilson, M.4
Knox, C.5
Liu, Y.6
Djoumbou, Y.7
Mandal, R.8
Aziat, F.9
Dong, E.10
Bouatra, S.11
Sinelnikov, I.12
Arndt, D.13
Xia, J.14
Liu, P.15
Yallou, F.16
Bjorndahl, T.17
Perez-Pineiro, R.18
Eisner, R.19
Allen, F.20
Neveu, V.21
Greiner, R.22
Scalbert, A.23
more..
-
73
-
-
77952302069
-
In silico fragmentation for computer assisted identification of metabolite mass spectra
-
Wolf S, Schmidt S, Müller-Hannemann M, Neumann S. 2010. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11(148).
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.148
-
-
Wolf, S.1
Schmidt, S.2
Müller-Hannemann, M.3
Neumann, S.4
-
74
-
-
84906328199
-
Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS
-
Zhang Q, Ortega M, Shi Y, Wang H, Melby J O, Tang W, Mitchell DA, van der Donk WA. 2014. Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS. Proc Natl Acad Sci USA 111(33):12031–12036.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.33
, pp. 12031-12036
-
-
Zhang, Q.1
Ortega, M.2
Shi, Y.3
Wang, H.4
Melby, J.O.5
Tang, W.6
Mitchell, D.A.7
van der Donk, W.A.8
|