-
1
-
-
80053186137
-
Evolution and applications of plant pathway resources and databases
-
10.1093/bib/bbq083, 21949268
-
Sucaet Y, Deva T. Evolution and applications of plant pathway resources and databases. Brief Bioinform 2011, 12:530-544. http://www.ncbi.nlm.nih.gov/pubmed/21949268, 10.1093/bib/bbq083, 21949268.
-
(2011)
Brief Bioinform
, vol.12
, pp. 530-544
-
-
Sucaet, Y.1
Deva, T.2
-
2
-
-
0038458655
-
Creating and modeling metabolic and regulatory networks using text mining and fuzzy expert systems
-
Singapore: World Scientific Publishing, Wang JTL, Wu CH, Wang P
-
Dickerson JA, Berleant D, Cox Z, et al. Creating and modeling metabolic and regulatory networks using text mining and fuzzy expert systems. Computational Biology and Genome Informatics 2003, 207-238. Singapore: World Scientific Publishing, Wang JTL, Wu CH, Wang P.
-
(2003)
Computational Biology and Genome Informatics
, pp. 207-238
-
-
Dickerson, J.A.1
Berleant, D.2
Cox, Z.3
-
3
-
-
0037690801
-
MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis
-
10.1002/cfg.285, 2447407, 18629120
-
Wurtele ES, Li J, Diao L, et al. MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis. Comp Funct Genomics 2003, 4:239-245. 10.1002/cfg.285, 2447407, 18629120.
-
(2003)
Comp Funct Genomics
, vol.4
, pp. 239-245
-
-
Wurtele, E.S.1
Li, J.2
Diao, L.3
-
4
-
-
84874636650
-
-
Prague: Physica-Verlag/Springer
-
Lee EK, Cook D, Wurtele ES, et al. 'GeneGobi: Visual data analysis aid tools for microarray data', COMPSTAT 2004, 16th Symposium of IASC 2004, Prague: Physica-Verlag/Springer.
-
(2004)
'GeneGobi: Visual data analysis aid tools for microarray data', COMPSTAT 2004, 16th Symposium of IASC
-
-
Lee, E.K.1
Cook, D.2
Wurtele, E.S.3
-
5
-
-
19544363437
-
Using the biological taxonomy to access biological literature with PathBinderH
-
10.1093/bioinformatics/bti381, 15769838
-
Ding J, Viswanathan K, Berleant D, et al. Using the biological taxonomy to access biological literature with PathBinderH. Bioinformatics 2005, 21:2560-2562. 10.1093/bioinformatics/bti381, 15769838.
-
(2005)
Bioinformatics
, vol.21
, pp. 2560-2562
-
-
Ding, J.1
Viswanathan, K.2
Berleant, D.3
-
6
-
-
24644479105
-
Integration of metabolic networks and gene expression in virtual reality
-
10.1093/bioinformatics/bti581, 16020466
-
Yang Y, Engin L, Wurtele ES, et al. Integration of metabolic networks and gene expression in virtual reality. Bioinformatics 2005, 21:3645-3650. 10.1093/bioinformatics/bti581, 16020466.
-
(2005)
Bioinformatics
, vol.21
, pp. 3645-3650
-
-
Yang, Y.1
Engin, L.2
Wurtele, E.S.3
-
7
-
-
35848954365
-
MetNet: Systems biology software for Arabidopsis
-
Dordrecht: Springer, Nikolau BJ, Wurtele ES
-
Wurtele ES, Li L, Berleant D, et al. MetNet: Systems biology software for Arabidopsis. Concepts in plant metabolomics 2007, 145-158. Dordrecht: Springer, Nikolau BJ, Wurtele ES, http://metnetonline.org/Book_Nikolau_Proof.pdf.
-
(2007)
Concepts in plant metabolomics
, pp. 145-158
-
-
Wurtele, E.S.1
Li, L.2
Berleant, D.3
-
9
-
-
53949091794
-
Regulon organization of Arabidopsis
-
10.1186/1471-2229-8-99, 2567982, 18826618
-
Mentzen WI, Wurtele ES. Regulon organization of Arabidopsis. BMC Plant Biol 2008, 8:99. 10.1186/1471-2229-8-99, 2567982, 18826618.
-
(2008)
BMC Plant Biol
, vol.8
, pp. 99
-
-
Mentzen, W.I.1
Wurtele, E.S.2
-
10
-
-
48249145778
-
Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism
-
10.1186/1471-2229-8-76, 2483283, 18616834
-
Mentzen WI, Peng J, Ransom N, et al. Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism. BMC Plant Biol 2008, 8:76. 10.1186/1471-2229-8-76, 2483283, 18616834.
-
(2008)
BMC Plant Biol
, vol.8
, pp. 76
-
-
Mentzen, W.I.1
Peng, J.2
Ransom, N.3
-
11
-
-
84861449462
-
Evolution of the Chalcone Isomerase Fold from Fatty Acid-Binding to Stereospecific Enzyme
-
In press
-
Ngaki MN, Louie GV, Manning G, et al. Evolution of the Chalcone Isomerase Fold from Fatty Acid-Binding to Stereospecific Enzyme. Nature 2012, In press.
-
(2012)
Nature
-
-
Ngaki, M.N.1
Louie, G.V.2
Manning, G.3
-
12
-
-
78349298336
-
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet
-
10.1186/1756-0500-3-312, 2998519, 21083943
-
Sucaet Y, Wurtele ES. MetNetAPI: A flexible method to access and manipulate biological network data from MetNet. BMC Res Notes 2010, 3:312. 10.1186/1756-0500-3-312, 2998519, 21083943.
-
(2010)
BMC Res Notes
, vol.3
, pp. 312
-
-
Sucaet, Y.1
Wurtele, E.S.2
-
13
-
-
38549117301
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
2238876, 17965431
-
Caspi R, Foerster H, Fulcher CA, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2008, 36:D623-D631. 2238876, 17965431.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
-
14
-
-
27244443126
-
MetaCyc and AraCyc, metabolic pathway databases for plant research
-
10.1104/pp.105.060376, 1104157, 15888675
-
Zhang P, Foerster H, Tissier CP, et al. MetaCyc and AraCyc, metabolic pathway databases for plant research. Plant Physiol 2005, 138:27-37. 10.1104/pp.105.060376, 1104157, 15888675.
-
(2005)
Plant Physiol
, vol.138
, pp. 27-37
-
-
Zhang, P.1
Foerster, H.2
Tissier, C.P.3
-
15
-
-
33646907417
-
AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks
-
10.1104/pp.105.072280, 1400579, 16524982
-
Palaniswamy SK, James S, Sun H, et al. AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol 2006, 140:818-829. 10.1104/pp.105.072280, 1400579, 16524982.
-
(2006)
Plant Physiol
, vol.140
, pp. 818-829
-
-
Palaniswamy, S.K.1
James, S.2
Sun, H.3
-
16
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
10.1093/nar/gkh036, 308770, 14681407
-
Harris MA, Clark J, Ireland A, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-D261. 10.1093/nar/gkh036, 308770, 14681407.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
-
17
-
-
75849158230
-
Extensions and refinements
-
2808930, 19920128, The Gene Ontology in 2010
-
The Gene Ontology in 2010 extensions and refinements. Nucleic Acids Res 2010, 38:D331-D335. 2808930, 19920128, The Gene Ontology in 2010.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
-
18
-
-
38549144806
-
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
-
2238962, 17986450
-
Swarbreck D, Wilks C, Lamesch P, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008, 36:D1009-D1014. 2238962, 17986450.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Swarbreck, D.1
Wilks, C.2
Lamesch, P.3
-
19
-
-
12144291195
-
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
-
10.1111/j.1365-313X.2004.02016.x, 14996223
-
Thimm O, Blasing O, Gibon Y, et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 2004, 37:914-939. 10.1111/j.1365-313X.2004.02016.x, 14996223.
-
(2004)
Plant J
, vol.37
, pp. 914-939
-
-
Thimm, O.1
Blasing, O.2
Gibon, Y.3
-
20
-
-
34248531753
-
Locating proteins in the cell using TargetP
-
Emanuelsson O, Brunak S, von Heijne G, et al. Locating proteins in the cell using TargetP. SignalP and related tools, Nat Protoc 2007, 2:953-971.
-
(2007)
SignalP and related tools, Nat Protoc
, vol.2
, pp. 953-971
-
-
Emanuelsson, O.1
Brunak, S.2
von Heijne, G.3
-
21
-
-
1042279117
-
In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database
-
10.1105/tpc.017814, 341918, 14729914
-
Friso G, Giacomelli L, Ytterberg AJ, et al. In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 2004, 16:478-499. 10.1105/tpc.017814, 341918, 14729914.
-
(2004)
Plant Cell
, vol.16
, pp. 478-499
-
-
Friso, G.1
Giacomelli, L.2
Ytterberg, A.J.3
-
22
-
-
58149193219
-
PPDB, the Plant Proteomics Database at Cornell
-
10.1093/nar/gkn654, 2686560, 18832363
-
Sun Q, Zybailov B, Majeran W, et al. PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res 2009, 37:D969-D974. 10.1093/nar/gkn654, 2686560, 18832363.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sun, Q.1
Zybailov, B.2
Majeran, W.3
-
23
-
-
33645703733
-
Plprot: a comprehensive proteome database for different plastid types
-
10.1093/pcp/pcj005, 16418230
-
Kleffmann T, Hirsch-Hoffmann M, Gruissem W, et al. plprot: a comprehensive proteome database for different plastid types. Plant Cell Physiol 2006, 47:432-436. 10.1093/pcp/pcj005, 16418230.
-
(2006)
Plant Cell Physiol
, vol.47
, pp. 432-436
-
-
Kleffmann, T.1
Hirsch-Hoffmann, M.2
Gruissem, W.3
-
24
-
-
13444266365
-
AMPDB: the Arabidopsis Mitochondrial Protein Database
-
540002, 15608271
-
Heazlewood JL, Millar AH. AMPDB: the Arabidopsis Mitochondrial Protein Database. Nucleic Acids Res 2005, 33:D605-D610. 540002, 15608271.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Heazlewood, J.L.1
Millar, A.H.2
-
25
-
-
16544384619
-
AraPerox, A database of putative Arabidopsis proteins from plant peroxisomes
-
10.1104/pp.104.043695, 523325, 15333753
-
Reumann S, Ma C, Lemke S, et al. AraPerox, A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol 2004, 136:2587-2608. 10.1104/pp.104.043695, 523325, 15333753.
-
(2004)
Plant Physiol
, vol.136
, pp. 2587-2608
-
-
Reumann, S.1
Ma, C.2
Lemke, S.3
-
26
-
-
13444282422
-
Arabidopsis nucleolar protein database (AtNoPDB)
-
10.1093/nar/gki391, 540006, 15608277
-
Brown JW, Shaw PJ, Shaw P, et al. Arabidopsis nucleolar protein database (AtNoPDB). Nucleic Acids Res 2005, 33:D633-D636. 10.1093/nar/gki391, 540006, 15608277.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Brown, J.W.1
Shaw, P.J.2
Shaw, P.3
-
28
-
-
77956501805
-
PathwayAccess: Cell Designer plugins for pathway databases
-
10.1093/bioinformatics/btq423, 2935416, 20647521
-
Van Hemert JL, Dickerson JA. PathwayAccess: Cell Designer plugins for pathway databases. Bioinformatics 2010, 26:2345-2346. 10.1093/bioinformatics/btq423, 2935416, 20647521.
-
(2010)
Bioinformatics
, vol.26
, pp. 2345-2346
-
-
Van Hemert, J.L.1
Dickerson, J.A.2
-
30
-
-
13444259844
-
Reactome: a knowledgebase of biological pathways
-
540026, 15608231
-
Joshi-Tope G, Gillespie M, Vastrik I, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33:D428-D432. 540026, 15608231.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Joshi-Tope, G.1
Gillespie, M.2
Vastrik, I.3
-
31
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
10.1093/nar/gkn863, 2686536, 18981052
-
Matthews L, Gopinath G, Gillespie M, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009, 37:D619-D622. 10.1093/nar/gkn863, 2686536, 18981052.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
-
32
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
10.1101/gr.1239303, 403769, 14597658
-
Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
-
33
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
10.1093/bioinformatics/btg015, 12611808
-
Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
-
34
-
-
33845440240
-
Representing, storing and accessing molecular interaction data: a review of models and tools
-
10.1093/bib/bbl039, 17132622
-
Stromback L, Jakoniene V, Tan H, et al. Representing, storing and accessing molecular interaction data: a review of models and tools. Brief Bioinform 2006, 7:331-338. 10.1093/bib/bbl039, 17132622.
-
(2006)
Brief Bioinform
, vol.7
, pp. 331-338
-
-
Stromback, L.1
Jakoniene, V.2
Tan, H.3
-
35
-
-
33947725809
-
A review of standards for data exchange within systems biology
-
10.1002/pmic.200600438, 17370264
-
Stromback L, Hall D, Lambrix P. A review of standards for data exchange within systems biology. Proteomics 2007, 7:857-867. 10.1002/pmic.200600438, 17370264.
-
(2007)
Proteomics
, vol.7
, pp. 857-867
-
-
Stromback, L.1
Hall, D.2
Lambrix, P.3
-
36
-
-
77249125881
-
Enhancement of fruit shelf life by suppressing N-glycan processing enzymes
-
10.1073/pnas.0909329107, 2823905, 20133661
-
Meli VS, Ghosh S, Prabha TN, et al. Enhancement of fruit shelf life by suppressing N-glycan processing enzymes. Proc Natl Acad Sci U S A 2010, 107:2413-2418. 10.1073/pnas.0909329107, 2823905, 20133661.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 2413-2418
-
-
Meli, V.S.1
Ghosh, S.2
Prabha, T.N.3
-
37
-
-
33644874819
-
From genomics to chemical genomics: new developments in KEGG
-
10.1093/nar/gkj102, 1347464, 16381885
-
Kanehisa M, Goto S, Hattori M, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357. 10.1093/nar/gkj102, 1347464, 16381885.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
-
38
-
-
84874584387
-
'ChEBI - Chemical Entities of Biological Interest'
-
P dM, M E, M Z
-
P dM, M E, M Z 'ChEBI - Chemical Entities of Biological Interest'. NAR Molecular Biology Database Collection 2008, 36(Database issue):D344-D350. http://www.ncbi.nlm.nih.gov/pubmed/17932057, P dM, M E, M Z.
-
(2008)
NAR Molecular Biology Database Collection
, vol.36
, Issue.DATABASE ISSUE
-
-
-
39
-
-
84857745267
-
Database resources of the National Center for Biotechnology Information
-
10.1093/nar/gkr1184, 3245031, 22140104
-
Sayers EW, Barrett T, Benson DA, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2012, 40:D13-D25. 10.1093/nar/gkr1184, 3245031, 22140104.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
-
40
-
-
40249098693
-
Internet resources integrating many small-molecule databases
-
10.1080/10629360701843540, 18311630
-
Sitzmann M, Filippov IV, Nicklaus MC. Internet resources integrating many small-molecule databases. SAR QSAR Environ Res 2008, 19:1-9. 10.1080/10629360701843540, 18311630.
-
(2008)
SAR QSAR Environ Res
, vol.19
, pp. 1-9
-
-
Sitzmann, M.1
Filippov, I.V.2
Nicklaus, M.C.3
-
41
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
10.1093/nar/gkh063, 308797, 14681412
-
Kanehisa M, Goto S, Kawashima S, et al. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280. 10.1093/nar/gkh063, 308797, 14681412.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
-
42
-
-
33846085927
-
SUBA: the Arabidopsis Subcellular Database
-
10.1093/nar/gkl863, 1635339, 17071959
-
Heazlewood JL, Verboom RE, Tonti-Filippini J, et al. SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res 2007, 35:D213-D218. 10.1093/nar/gkl863, 1635339, 17071959.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Heazlewood, J.L.1
Verboom, R.E.2
Tonti-Filippini, J.3
-
43
-
-
78651330012
-
BRENDA, the enzyme information system in 2011
-
10.1093/nar/gkq1089, 3013686, 21062828
-
Scheer M, Grote A, Chang A, et al. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2011, 39:D670-D676. 10.1093/nar/gkq1089, 3013686, 21062828.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Scheer, M.1
Grote, A.2
Chang, A.3
-
44
-
-
38549123986
-
AtPID: Arabidopsis thaliana protein interactome database-an integrative platform for plant systems biology
-
2238993, 17962307
-
Cui J, Li P, Li G, et al. AtPID: Arabidopsis thaliana protein interactome database-an integrative platform for plant systems biology. Nucleic Acids Res 2008, 36:D999-D1008. 2238993, 17962307.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Cui, J.1
Li, P.2
Li, G.3
-
45
-
-
78651281217
-
EcoCyc: a comprehensive database of Escherichia coli biology
-
10.1093/nar/gkq1143, 3013716, 21097882
-
Keseler IM, Collado-Vides J, Santos-Zavaleta A, et al. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 2011, 39:D583-D590. 10.1093/nar/gkq1143, 3013716, 21097882.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Keseler, I.M.1
Collado-Vides, J.2
Santos-Zavaleta, A.3
-
46
-
-
77949524119
-
VitisNet: "Omics" integration through grapevine molecular networks
-
10.1371/journal.pone.0008365, 2791446, 20027228
-
Grimplet J, Cramer GR, Dickerson JA, et al. VitisNet: "Omics" integration through grapevine molecular networks. PLoS One 2009, 4:e8365. 10.1371/journal.pone.0008365, 2791446, 20027228.
-
(2009)
PLoS One
, vol.4
-
-
Grimplet, J.1
Cramer, G.R.2
Dickerson, J.A.3
-
47
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
10.1093/nar/28.1.27, 102409, 10592173
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
48
-
-
77955695587
-
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants
-
10.1104/pp.110.157396, 2923894, 20522724
-
Zhang P, Dreher K, Karthikeyan A, et al. Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 2010, 153:1479-1491. 10.1104/pp.110.157396, 2923894, 20522724.
-
(2010)
Plant Physiol
, vol.153
, pp. 1479-1491
-
-
Zhang, P.1
Dreher, K.2
Karthikeyan, A.3
-
49
-
-
84862203775
-
WikiPathways: building research communities on biological pathways
-
10.1093/nar/gkr1074, 3245032, 22096230
-
Kelder T, van Iersel MP, Hanspers K, et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res 2012, 40:D1301-D1307. 10.1093/nar/gkr1074, 3245032, 22096230.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kelder, T.1
van Iersel, M.P.2
Hanspers, K.3
-
50
-
-
79952201997
-
Gramene database: a hub for comparative plant genomics
-
10.1007/978-1-60761-682-5_18, 20931385
-
Jaiswal P. Gramene database: a hub for comparative plant genomics. Methods Mol Biol 2011, 678:247-275. 10.1007/978-1-60761-682-5_18, 20931385.
-
(2011)
Methods Mol Biol
, vol.678
, pp. 247-275
-
-
Jaiswal, P.1
|