-
1
-
-
10044281116
-
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
-
10.1186/gb-2004-5-8-r52, 507877, 15287974
-
Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol 2004, 5:R52. 10.1186/gb-2004-5-8-r52, 507877, 15287974.
-
(2004)
Genome Biol
, vol.5
-
-
Bonneau, R.1
Baliga, N.S.2
Deutsch, E.W.3
Shannon, P.4
Hood, L.5
-
2
-
-
0346494928
-
The ORFanage: an ORFan database
-
10.1093/nar/gkh116, 308850, 14681413
-
Siew N, Azaria Y, Fischer D. The ORFanage: an ORFan database. Nucleic Acids Res 2004, 32:D281-283. 10.1093/nar/gkh116, 308850, 14681413.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Siew, N.1
Azaria, Y.2
Fischer, D.3
-
3
-
-
0033119399
-
Errors in genome annotation
-
10.1016/S0168-9525(99)01706-0, 10203816
-
Brenner SE. Errors in genome annotation. Trends Genet 1999, 15:132-133. 10.1016/S0168-9525(99)01706-0, 10203816.
-
(1999)
Trends Genet
, vol.15
, pp. 132-133
-
-
Brenner, S.E.1
-
4
-
-
0035424599
-
Intrinsic errors in genome annotation
-
10.1016/S0168-9525(01)02348-4, 11485799
-
Devos D, Valencia A. Intrinsic errors in genome annotation. Trends Genet 2001, 17:429-431. 10.1016/S0168-9525(01)02348-4, 11485799.
-
(2001)
Trends Genet
, vol.17
, pp. 429-431
-
-
Devos, D.1
Valencia, A.2
-
5
-
-
0030660581
-
A genomic perspective on protein families
-
10.1126/science.278.5338.631, 9381173
-
Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
6
-
-
33748641351
-
EGASP: the human ENCODE Genome Annotation Assessment Project
-
10.1186/gb-2006-7-s1-s2, 1810551, 16925836
-
Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 2006, 7(Suppl 1):S2. 10.1186/gb-2006-7-s1-s2, 1810551, 16925836.
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
-
-
Guigo, R.1
Flicek, P.2
Abril, J.F.3
Reymond, A.4
Lagarde, J.5
Denoeud, F.6
Antonarakis, S.7
Ashburner, M.8
Bajic, V.B.9
Birney, E.10
-
7
-
-
0002636459
-
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
-
151185, 12537572
-
Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 2002, 3:RESEARCH0083. 151185, 12537572.
-
(2002)
Genome Biol
, vol.3
-
-
Misra, S.1
Crosby, M.A.2
Mungall, C.J.3
Matthews, B.B.4
Campbell, K.S.5
Hradecky, P.6
Huang, Y.7
Kaminker, J.S.8
Millburn, G.H.9
Prochnik, S.E.10
-
8
-
-
72449145463
-
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it
-
10.1042/BJ20091328, 3022307, 20001958
-
Hanson AD, Pribat A, Waller JC, de Crécy-Lagard V. 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it. Biochem J 2009, 425:1-11. 10.1042/BJ20091328, 3022307, 20001958.
-
(2009)
Biochem J
, vol.425
, pp. 1-11
-
-
Hanson, A.D.1
Pribat, A.2
Waller, J.C.3
de Crécy-Lagard, V.4
-
9
-
-
74549221383
-
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
-
10.1371/journal.pcbi.1000605, 2781113, 20011109
-
Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009, 5:e1000605. 10.1371/journal.pcbi.1000605, 2781113, 20011109.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
10
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
10.1093/nar/gki866, 1251668, 16214803
-
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33:5691-5702. 10.1093/nar/gki866, 1251668, 16214803.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crécy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
-
11
-
-
44849094233
-
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
-
10.1186/1471-2164-9-245, 2413144, 18500999
-
Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 2008, 9:245. 10.1186/1471-2164-9-245, 2413144, 18500999.
-
(2008)
BMC Genomics
, vol.9
, pp. 245
-
-
Vongsangnak, W.1
Olsen, P.2
Hansen, K.3
Krogsgaard, S.4
Nielsen, J.5
-
12
-
-
73149122136
-
Applications of genome-scale metabolic reconstructions
-
2795471, 19888215
-
Oberhardt MA, Palsson BO, Papin JA. Applications of genome-scale metabolic reconstructions. Mol Syst Biol 2009, 5:320. 2795471, 19888215.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 320
-
-
Oberhardt, M.A.1
Palsson, B.O.2
Papin, J.A.3
-
13
-
-
77952294431
-
An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching
-
Saqi M, Dobson RJ, Kraben P, Hodgson DA, Wild DL. An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching. J Integr Bioinform 2009, 6:107.
-
(2009)
J Integr Bioinform
, vol.6
, pp. 107
-
-
Saqi, M.1
Dobson, R.J.2
Kraben, P.3
Hodgson, D.A.4
Wild, D.L.5
-
14
-
-
36249028746
-
Finding novel metabolic genes through plant-prokaryote phylogenomics
-
10.1016/j.tim.2007.10.008, 17997099
-
de Crécy-Lagard V, Hanson AD. Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol 2007, 15:563-570. 10.1016/j.tim.2007.10.008, 17997099.
-
(2007)
Trends Microbiol
, vol.15
, pp. 563-570
-
-
de Crécy-Lagard, V.1
Hanson, A.D.2
-
15
-
-
27544456832
-
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
-
10.1186/1741-7007-3-7, 1082884, 15784138
-
Haas B, Wortman J, Ronning C, Hannick L, Smith R, Maiti R, Chan A, Yu C, Farzad M, Wu D, et al. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biology 2005, 3:7. 10.1186/1741-7007-3-7, 1082884, 15784138.
-
(2005)
BMC Biology
, vol.3
, pp. 7
-
-
Haas, B.1
Wortman, J.2
Ronning, C.3
Hannick, L.4
Smith, R.5
Maiti, R.6
Chan, A.7
Yu, C.8
Farzad, M.9
Wu, D.10
-
16
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
10.1093/nar/30.7.1575, 101833, 11917018
-
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
17
-
-
0037249633
-
The TIGRFAMs database of protein families
-
10.1093/nar/gkg128, 165575, 12520025
-
Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003, 31:371-373. 10.1093/nar/gkg128, 165575, 12520025.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 371-373
-
-
Haft, D.H.1
Selengut, J.D.2
White, O.3
-
18
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
19
-
-
0003584921
-
SEQUENCE-EVOLUTION-FUNCTION. Computational approaches in comparative genomics
-
Kluwer Academic Publishers
-
Koonin EV, Galperin MY. SEQUENCE-EVOLUTION-FUNCTION. Computational approaches in comparative genomics. 2003, Kluwer Academic Publishers.
-
(2003)
-
-
Koonin, E.V.1
Galperin, M.Y.2
-
20
-
-
0037126071
-
From the Cover: Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
-
10.1073/pnas.182432999, 129430, 12218172
-
Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D. From the Cover: Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A 2002, 99:12246-12251. 10.1073/pnas.182432999, 129430, 12218172.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 12246-12251
-
-
Martin, W.1
Rujan, T.2
Richly, E.3
Hansen, A.4
Cornelsen, S.5
Lins, T.6
Leister, D.7
Stoebe, B.8
Hasegawa, M.9
Penny, D.10
-
21
-
-
0037249498
-
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
-
10.1093/nar/gkg076, 165523, 12519987
-
Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucl Acids Res 2003, 31:224-228. 10.1093/nar/gkg076, 165523, 12519987.
-
(2003)
Nucl Acids Res
, vol.31
, pp. 224-228
-
-
Rhee, S.Y.1
Beavis, W.2
Berardini, T.Z.3
Chen, G.4
Dixon, D.5
Doyle, A.6
Garcia-Hernandez, M.7
Huala, E.8
Lander, G.9
Montoya, M.10
-
22
-
-
50649114261
-
Annotating genes of known and unknown function by large-scale coexpression analysis
-
10.1104/pp.108.117366, 2330292, 18354039
-
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu J-K, Cushman JC, Gollery M, Girke T. Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol 2008, 147:41-57. 10.1104/pp.108.117366, 2330292, 18354039.
-
(2008)
Plant Physiol
, vol.147
, pp. 41-57
-
-
Horan, K.1
Jang, C.2
Bailey-Serres, J.3
Mittler, R.4
Shelton, C.5
Harper, J.F.6
Zhu, J.-K.7
Cushman, J.C.8
Gollery, M.9
Girke, T.10
-
23
-
-
79958861315
-
The use of subsystems to encode biosynthesis of vitamins and cofactors
-
Elsevier, Mander L, Lui H-W
-
Osterman A, Overbeek R, Rodionov D. The use of subsystems to encode biosynthesis of vitamins and cofactors. Comprehensive Natural Products II Chemistry and Biology 2010, 7:141-115. Elsevier, Mander L, Lui H-W.
-
(2010)
Comprehensive Natural Products II Chemistry and Biology
, vol.7
, pp. 141-1115
-
-
Osterman, A.1
Overbeek, R.2
Rodionov, D.3
-
24
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
10.1073/pnas.96.6.2896, 15866, 10077608
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 1999, 96:2896-2901. 10.1073/pnas.96.6.2896, 15866, 10077608.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
25
-
-
0033832615
-
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
-
10.1101/gr.10.8.1204, 310926, 10958638
-
Huynen M, Snel B, Lathe W, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 2000, 10:1204-1210. 10.1101/gr.10.8.1204, 310926, 10958638.
-
(2000)
Genome Res
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe, W.3
Bork, P.4
-
26
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
10.1101/gr.GR-1619R, 11230160
-
Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 2001, 11:356-372. 10.1101/gr.GR-1619R, 11230160.
-
(2001)
Genome Res
, vol.11
, pp. 356-372
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Kondrashov, A.S.3
Koonin, E.V.4
-
27
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
10.1016/S0968-0004(98)01274-2, 9787636
-
Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem Sci 1998, 23:324-328. 10.1016/S0968-0004(98)01274-2, 9787636.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
28
-
-
0038104857
-
Genomic gene clustering analysis of pathways in Eukaryotes
-
10.1101/gr.737703, 430880, 12695325
-
Lee JM, Sonnhammer ELL. Genomic gene clustering analysis of pathways in Eukaryotes. Genome Res 2003, 13:875-882. 10.1101/gr.737703, 430880, 12695325.
-
(2003)
Genome Res
, vol.13
, pp. 875-882
-
-
Lee, J.M.1
Sonnhammer, E.L.L.2
-
29
-
-
0029847554
-
Selfish operons: horizontal transfer may drive the evolution of gene clusters
-
1207444, 8844169
-
Lawrence JG, Roth JR. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 1996, 143:1843-1860. 1207444, 8844169.
-
(1996)
Genetics
, vol.143
, pp. 1843-1860
-
-
Lawrence, J.G.1
Roth, J.R.2
-
30
-
-
0036533931
-
Identifying functional links between genes using conserved chromosomal proximity
-
10.1016/S0168-9525(01)02621-X, 11932011
-
Yanai I, Mellor JC, DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends Genet 2002, 18:176. 10.1016/S0168-9525(01)02621-X, 11932011.
-
(2002)
Trends Genet
, vol.18
, pp. 176
-
-
Yanai, I.1
Mellor, J.C.2
DeLisi, C.3
-
31
-
-
13444264729
-
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox
-
10.1104/pp.104.046367, 523327, 15375207
-
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 2004, 136:2621-2632. 10.1104/pp.104.046367, 523327, 15375207.
-
(2004)
Plant Physiol
, vol.136
, pp. 2621-2632
-
-
Zimmermann, P.1
Hirsch-Hoffmann, M.2
Hennig, L.3
Gruissem, W.4
-
32
-
-
20244380782
-
GMD@CSB.DB: the Golm Metabolome Database
-
10.1093/bioinformatics/bti236, 15613389
-
Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P, Weckwerth W, Gibon Y, Stitt M, et al. GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 2005, 21:1635-1638. 10.1093/bioinformatics/bti236, 15613389.
-
(2005)
Bioinformatics
, vol.21
, pp. 1635-1638
-
-
Kopka, J.1
Schauer, N.2
Krueger, S.3
Birkemeyer, C.4
Usadel, B.5
Bergmuller, E.6
Dormann, P.7
Weckwerth, W.8
Gibon, Y.9
Stitt, M.10
-
33
-
-
22044437388
-
The Botany Array Resource: e-Northerns, expression angling, and promoter analyses
-
10.1111/j.1365-313X.2005.02437.x, 15960624
-
Toufighi K, Brady SM, Austin R, Ly E, Provart NJ. The Botany Array Resource: e-Northerns, expression angling, and promoter analyses. Plant J 2005, 43:153-163. 10.1111/j.1365-313X.2005.02437.x, 15960624.
-
(2005)
Plant J
, vol.43
, pp. 153-163
-
-
Toufighi, K.1
Brady, S.M.2
Austin, R.3
Ly, E.4
Provart, N.J.5
-
34
-
-
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, Peltier J-B, Rudella A, Sun Q, van Wijk KJ. 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
Peltier, J.-B.4
Rudella, A.5
Sun, Q.6
van Wijk, K.J.7
-
35
-
-
13444266365
-
AMPDB: the Arabidopsis Mitochondrial Protein Database
-
540002, 15608271
-
Heazlewood JL, Millar AH. AMPDB: the Arabidopsis Mitochondrial Protein Database. Nucleic Acids Res 2005, 33:D605-610. 540002, 15608271.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Heazlewood, J.L.1
Millar, A.H.2
-
36
-
-
0037398732
-
Missing genes in metabolic pathways: a comparative genomics approach
-
10.1016/S1367-5931(03)00027-9, 12714058
-
Osterman A, Overbeek R. Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 2003, 7:238-251. 10.1016/S1367-5931(03)00027-9, 12714058.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 238-251
-
-
Osterman, A.1
Overbeek, R.2
-
37
-
-
33646171940
-
Identifying metabolic enzymes with multiple types of association evidence
-
10.1186/1471-2105-7-177, 1450304, 16571130
-
Kharchenko P, Chen L, Freund Y, Vitkup D, Church G. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 2006, 7:177. 10.1186/1471-2105-7-177, 1450304, 16571130.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 177
-
-
Kharchenko, P.1
Chen, L.2
Freund, Y.3
Vitkup, D.4
Church, G.5
-
38
-
-
13244268322
-
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
-
10.1186/1471-2105-5-76, 446185, 15189570
-
Green ML, Karp PD. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 2004, 5:76. 10.1186/1471-2105-5-76, 446185, 15189570.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 76
-
-
Green, M.L.1
Karp, P.D.2
-
39
-
-
54349094713
-
Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms?
-
10.1016/j.pt.2008.08.004, 2720532, 18805734
-
Hyde JE, Dittrich S, Wang P, Sims PF, de Crécy-Lagard V, Hanson AD. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms?. Trends Parasitol 2008, 24:502-8. 10.1016/j.pt.2008.08.004, 2720532, 18805734.
-
(2008)
Trends Parasitol
, vol.24
, pp. 502-508
-
-
Hyde, J.E.1
Dittrich, S.2
Wang, P.3
Sims, P.F.4
de Crécy-Lagard, V.5
Hanson, A.D.6
-
40
-
-
67649403399
-
6-pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria
-
10.1128/JB.00416-09, 2698474, 19395485
-
Pribat A, Jeanguenin L, Lara-Nunez A, Ziemak MJ, Hyde JE, de Crécy-Lagard V, Hanson AD. 6-pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria. J Bacteriol 2009, 191:4158-4165. 10.1128/JB.00416-09, 2698474, 19395485.
-
(2009)
J Bacteriol
, vol.191
, pp. 4158-4165
-
-
Pribat, A.1
Jeanguenin, L.2
Lara-Nunez, A.3
Ziemak, M.J.4
Hyde, J.E.5
de Crécy-Lagard, V.6
Hanson, A.D.7
-
41
-
-
56549119570
-
Turning a hobby into a job: how duplicated genes find new functions
-
10.1038/nrg2482, 19015656
-
Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 2008, 9:938-950. 10.1038/nrg2482, 19015656.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 938-950
-
-
Conant, G.C.1
Wolfe, K.H.2
-
42
-
-
70449732603
-
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
-
10.1186/1471-2164-10-470, 2770081, 19822009
-
Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crécy-Lagard V. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics 2009, 10:470. 10.1186/1471-2164-10-470, 2770081, 19822009.
-
(2009)
BMC Genomics
, vol.10
, pp. 470
-
-
Haas, C.E.1
Rodionov, D.A.2
Kropat, J.3
Malasarn, D.4
Merchant, S.S.5
de Crécy-Lagard, V.6
-
43
-
-
70349125919
-
Contributions of Zur-controlled ribosomal proteins to growth under zinc starvation conditions
-
10.1128/JB.00802-09, 2747910, 19648245
-
Gabriel S, Helmann J. Contributions of Zur-controlled ribosomal proteins to growth under zinc starvation conditions. J Bacteriol 2009, 191:6116-6122. 10.1128/JB.00802-09, 2747910, 19648245.
-
(2009)
J Bacteriol
, vol.191
, pp. 6116-6122
-
-
Gabriel, S.1
Helmann, J.2
-
44
-
-
77953735433
-
A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life
-
10.1073/pnas.0911586107, 2890791, 20489182
-
Waller JC, Alvarez S, Naponelli V, Lara-Nunez A, Blaby IK, Da Silva V, Ziemak MJ, Vickers TJ, Beverley SM, Edison AS, et al. A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life. Proc Natl Acad Sci U S A 2010, 107:10412-10417. 10.1073/pnas.0911586107, 2890791, 20489182.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 10412-10417
-
-
Waller, J.C.1
Alvarez, S.2
Naponelli, V.3
Lara-Nunez, A.4
Blaby, I.K.5
Da Silva, V.6
Ziemak, M.J.7
Vickers, T.J.8
Beverley, S.M.9
Edison, A.S.10
-
45
-
-
78650655390
-
Moonlighting glutamate formiminotransferases can functionally replace 5-formyltetrahydrofolate cycloligase
-
10.1074/jbc.M110.190504, 20952389
-
Jeanguenin L, Lara-Nùñez A, Pribat A, Hamner M, Gregory JF, Rice KC, de Crécy-Lagard V, Hanson AD. Moonlighting glutamate formiminotransferases can functionally replace 5-formyltetrahydrofolate cycloligase. J Biol Chem 2010, 285:41557-66. 10.1074/jbc.M110.190504, 20952389.
-
(2010)
J Biol Chem
, vol.285
, pp. 41557-41566
-
-
Jeanguenin, L.1
Lara-Nùñez, A.2
Pribat, A.3
Hamner, M.4
Gregory, J.F.5
Rice, K.C.6
de Crécy-Lagard, V.7
Hanson, A.D.8
-
46
-
-
66049143558
-
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins
-
10.1371/journal.pbio.1000096, 2672614, 19402753
-
Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, et al. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 2009, 7:e96. 10.1371/journal.pbio.1000096, 2672614, 19402753.
-
(2009)
PLoS Biol
, vol.7
-
-
Hu, P.1
Janga, S.C.2
Babu, M.3
Diaz-Mejia, J.J.4
Butland, G.5
Yang, W.6
Pogoutse, O.7
Guo, X.8
Phanse, S.9
Wong, P.10
-
47
-
-
30744438630
-
Expression analysis of up-regulated genes responding to plumbagin in Escherichia coli
-
10.1128/JB.188.2.456-463.2006, 1347270, 16385035
-
Chen J-W, Sun C-M, Sheng W-L, Wang Y-C, Syu W. Expression analysis of up-regulated genes responding to plumbagin in Escherichia coli. J Bacteriol 2006, 188:456-463. 10.1128/JB.188.2.456-463.2006, 1347270, 16385035.
-
(2006)
J Bacteriol
, vol.188
, pp. 456-463
-
-
Chen, J.-W.1
Sun, C.-M.2
Sheng, W.-L.3
Wang, Y.-C.4
Syu, W.5
-
48
-
-
33644844014
-
Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation
-
10.1111/j.1365-2958.2005.04932.x, 16359333
-
Tomotake O, Masayuki H, Yoshiho I, Masayuki S, Tsutomu S, Tsutomu K, Jun-ichi K. Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation. Mol Microbiol 2006, 59:265-275. 10.1111/j.1365-2958.2005.04932.x, 16359333.
-
(2006)
Mol Microbiol
, vol.59
, pp. 265-275
-
-
Tomotake, O.1
Masayuki, H.2
Yoshiho, I.3
Masayuki, S.4
Tsutomu, S.5
Tsutomu, K.6
Jun-ichi, K.7
-
49
-
-
40749086415
-
Mitochondrial Iba57p is required for Fe/S cluster formation on aconitase and activation of radical SAM enzymes
-
10.1128/MCB.01963-07, 2258791, 18086897
-
Gelling C, Dawes IW, Richhardt N, Lill R, Muhlenhoff U. Mitochondrial Iba57p is required for Fe/S cluster formation on aconitase and activation of radical SAM enzymes. Mol Cell Biol 2008, 28:1851-1861. 10.1128/MCB.01963-07, 2258791, 18086897.
-
(2008)
Mol Cell Biol
, vol.28
, pp. 1851-1861
-
-
Gelling, C.1
Dawes, I.W.2
Richhardt, N.3
Lill, R.4
Muhlenhoff, U.5
-
50
-
-
0007489131
-
Citrovorum factor and the synthesis of formylglutamic acid
-
Silverman M, Keresztesy JC, Koval GJ, Gardiner RC. Citrovorum factor and the synthesis of formylglutamic acid. J Biol Chem 1957, 226:83-94.
-
(1957)
J Biol Chem
, vol.226
, pp. 83-94
-
-
Silverman, M.1
Keresztesy, J.C.2
Koval, G.J.3
Gardiner, R.C.4
-
51
-
-
0020629259
-
Glutamate formyl- and formimino-transferase activities from pig liver
-
10.1139/o83-035, 6883161
-
Bortoluzzi LC, MacKenzie RE. Glutamate formyl- and formimino-transferase activities from pig liver. Can J Biochem Cell Biol 1983, 61:248-253. 10.1139/o83-035, 6883161.
-
(1983)
Can J Biochem Cell Biol
, vol.61
, pp. 248-253
-
-
Bortoluzzi, L.C.1
MacKenzie, R.E.2
-
52
-
-
22544470317
-
5-Formyltetrahydrofolate is an inhibitory but well tolerated metabolite in Arabidopsis leaves
-
10.1074/jbc.M503106200, 15888445
-
Goyer A, Collakova E, de la Garza RD, Quinlivan EP, Williamson J, Gregory JF, Shachar-Hill Y, Hanson AD. 5-Formyltetrahydrofolate is an inhibitory but well tolerated metabolite in Arabidopsis leaves. J Biol Chem 2005, 280:26137-26142. 10.1074/jbc.M503106200, 15888445.
-
(2005)
J Biol Chem
, vol.280
, pp. 26137-26142
-
-
Goyer, A.1
Collakova, E.2
de la Garza, R.D.3
Quinlivan, E.P.4
Williamson, J.5
Gregory, J.F.6
Shachar-Hill, Y.7
Hanson, A.D.8
-
53
-
-
0016174519
-
The enzymatic synthesis of N-(purin-6-ylcarbamoyl)threonine, an anticodon-adjacent base in transfer ribonucleic acid
-
10.1021/bi00719a024, 4609459
-
Elkins BN, Keller EB. The enzymatic synthesis of N-(purin-6-ylcarbamoyl)threonine, an anticodon-adjacent base in transfer ribonucleic acid. Biochemistry 1974, 13:4622-4628. 10.1021/bi00719a024, 4609459.
-
(1974)
Biochemistry
, vol.13
, pp. 4622-4628
-
-
Elkins, B.N.1
Keller, E.B.2
-
54
-
-
0015329948
-
Biosynthesis of N-(purin-6-ylcarbamoyl)-L-threonine riboside. Incorporation of L-threonine in vivo into modified nucleoside of transfer ribonucleic acid
-
1178692, 4561775
-
Chheda GB, Hong CI, Piskorz CF, Harmon GA. Biosynthesis of N-(purin-6-ylcarbamoyl)-L-threonine riboside. Incorporation of L-threonine in vivo into modified nucleoside of transfer ribonucleic acid. Biochem J 1972, 127:515-519. 1178692, 4561775.
-
(1972)
Biochem J
, vol.127
, pp. 515-519
-
-
Chheda, G.B.1
Hong, C.I.2
Piskorz, C.F.3
Harmon, G.A.4
-
55
-
-
0015530484
-
Biosynthesis and specific labeling of N-(purin-6-ylcarbamoyl)threonine of Escherichia coli transfer RNA
-
10.1016/S0006-291X(72)80216-X, 4550699
-
Powers DM, Peterkofsky A. Biosynthesis and specific labeling of N-(purin-6-ylcarbamoyl)threonine of Escherichia coli transfer RNA. Biochem Biophys Res Commun 1972, 46:831. 10.1016/S0006-291X(72)80216-X, 4550699.
-
(1972)
Biochem Biophys Res Commun
, vol.46
, pp. 831
-
-
Powers, D.M.1
Peterkofsky, A.2
-
56
-
-
0034491066
-
The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding
-
10.1110/ps.9.12.2557, 2144518, 11206077
-
Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci 2000, 9:2557-2566. 10.1110/ps.9.12.2557, 2144518, 11206077.
-
(2000)
Protein Sci
, vol.9
, pp. 2557-2566
-
-
Teplova, M.1
Tereshko, V.2
Sanishvili, R.3
Joachimiak, A.4
Bushueva, T.5
Anderson, W.F.6
Egli, M.7
-
57
-
-
13444259766
-
The YrdC protein--a putative ribosome maturation factor
-
Kaczanowska M, Rydén-Aulin M. The YrdC protein--a putative ribosome maturation factor. Biochim Biophys Acta 2005, 1727:87.
-
(2005)
Biochim Biophys Acta
, vol.1727
, pp. 87
-
-
Kaczanowska, M.1
Rydén-Aulin, M.2
-
58
-
-
0026694534
-
Isolation and characterization of SUA5, a novel gene required for normal growth in Saccharomyces cerevisiae
-
1205092, 1325384
-
Na JG, Pinto I, Hampsey M. Isolation and characterization of SUA5, a novel gene required for normal growth in Saccharomyces cerevisiae. Genetics 1992, 131:791-801. 1205092, 1325384.
-
(1992)
Genetics
, vol.131
, pp. 791-801
-
-
Na, J.G.1
Pinto, I.2
Hampsey, M.3
-
59
-
-
0001184472
-
Mechanisms of RNA-Modifying and Editing Enzymes
-
Washington, D.C.: ASM Press, Grosjean H, Benne R
-
Garcia GA, Goodenough-Lashua M. Mechanisms of RNA-Modifying and Editing Enzymes. Modification and Editing of RNA 1998, 135-168. Washington, D.C.: ASM Press, Grosjean H, Benne R.
-
(1998)
Modification and Editing of RNA
, pp. 135-168
-
-
Garcia, G.A.1
Goodenough-Lashua, M.2
-
60
-
-
66249095330
-
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
-
10.1093/nar/gkp152, 2685093, 19287007
-
El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crécy-Lagard V. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 2009, 37:2894-2909. 10.1093/nar/gkp152, 2685093, 19287007.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 2894-2909
-
-
El Yacoubi, B.1
Lyons, B.2
Cruz, Y.3
Reddy, R.4
Nordin, B.5
Agnelli, F.6
Williamson, J.R.7
Schimmel, P.8
Swairjo, M.A.9
de Crécy-Lagard, V.10
-
61
-
-
40549120596
-
The RAST server: rapid annotations using subsystems technology
-
10.1186/1471-2164-9-75, 2265698, 18261238
-
Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. 10.1186/1471-2164-9-75, 2265698, 18261238.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.1
Bartels, D.2
Best, A.3
DeJongh, M.4
Disz, T.5
Edwards, R.6
Formsma, K.7
Gerdes, S.8
Glass, E.9
Kubal, M.10
-
62
-
-
76349125292
-
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
-
10.1038/nbt.1603, 2857375, 20118918
-
Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 2010, 28:149-156. 10.1038/nbt.1603, 2857375, 20118918.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 149-156
-
-
Lee, I.1
Ambaru, B.2
Thakkar, P.3
Marcotte, E.M.4
Rhee, S.Y.5
-
63
-
-
36448988254
-
Predicting protein function from sequence and structure
-
10.1038/nrm2281, 18037900
-
Lee D, Redfern O, Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007, 8:995-1005. 10.1038/nrm2281, 18037900.
-
(2007)
Nat Rev Mol Cell Biol
, vol.8
, pp. 995-1005
-
-
Lee, D.1
Redfern, O.2
Orengo, C.3
-
64
-
-
53749099905
-
Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy
-
10.1371/journal.pone.0003337, 2556097, 18836531
-
Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, et al. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One 2008, 3:e3337. 10.1371/journal.pone.0003337, 2556097, 18836531.
-
(2008)
PLoS One
, vol.3
-
-
Jung, K.H.1
Dardick, C.2
Bartley, L.E.3
Cao, P.4
Phetsom, J.5
Canlas, P.6
Seo, Y.S.7
Shultz, M.8
Ouyang, S.9
Yuan, Q.10
-
65
-
-
72449176838
-
A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses
-
Ogata Y, Suzuki H, Shibata D. A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses. J Wood Sci 2009, 55:395-400.
-
(2009)
J Wood Sci
, vol.55
, pp. 395-400
-
-
Ogata, Y.1
Suzuki, H.2
Shibata, D.3
-
66
-
-
38549146472
-
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library
-
2238859, 17947330
-
Larmande P, Gay C, Lorieux M, Perin C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, et al. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res 2008, 36:D1022-1027. 2238859, 17947330.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Larmande, P.1
Gay, C.2
Lorieux, M.3
Perin, C.4
Bouniol, M.5
Droc, G.6
Sallaud, C.7
Perez, P.8
Barnola, I.9
Biderre-Petit, C.10
-
67
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
10.1093/bioinformatics/btm404, 17846036
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948. 10.1093/bioinformatics/btm404, 17846036.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
69
-
-
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
-
70
-
-
0036081012
-
BRENDA, enzyme data and metabolic information
-
10.1093/nar/30.1.47, 99121, 11752250
-
Schomburg I, Chang A, Schomburg D. BRENDA, enzyme data and metabolic information. Nucleic Acids Res 2002, 30:47-49. 10.1093/nar/30.1.47, 99121, 11752250.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 47-49
-
-
Schomburg, I.1
Chang, A.2
Schomburg, D.3
-
71
-
-
63849246525
-
Protein structure prediction on the Web: a case study using the Phyre server
-
Kelley LA, Sternberg MJE. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009, 4:363-371.
-
(2009)
Nat Protoc
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.E.2
-
72
-
-
75549090603
-
The Pfam protein families database
-
10.1093/nar/gkp985, 2808889, 19920124
-
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-222. 10.1093/nar/gkp985, 2808889, 19920124.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
-
73
-
-
22244489084
-
The MicrobesOnline Web site for comparative genomics
-
10.1101/gr.3844805, 1172046, 15998914
-
Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP. The MicrobesOnline Web site for comparative genomics. Genome Res 2005, 15:1015-1022. 10.1101/gr.3844805, 1172046, 15998914.
-
(2005)
Genome Res
, vol.15
, pp. 1015-1022
-
-
Alm, E.J.1
Huang, K.H.2
Price, M.N.3
Koche, R.P.4
Keller, K.5
Dubchak, I.L.6
Arkin, A.P.7
-
74
-
-
0033971754
-
EcoGene: a genome sequence database for Escherichia coli K-12
-
10.1093/nar/28.1.60, 102481, 10592181
-
Rudd KE. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 2000, 28:60-64. 10.1093/nar/28.1.60, 102481, 10592181.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 60-64
-
-
Rudd, K.E.1
-
75
-
-
58149179979
-
EcoCyc: a comprehensive view of Escherichia coli biology
-
10.1093/nar/gkn751, 2686493, 18974181
-
Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, et al. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 2009, 37:D464-470. 10.1093/nar/gkn751, 2686493, 18974181.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Keseler, I.M.1
Bonavides-Martinez, C.2
Collado-Vides, J.3
Gama-Castro, S.4
Gunsalus, R.P.5
Johnson, D.A.6
Krummenacker, M.7
Nolan, L.M.8
Paley, S.9
Paulsen, I.T.10
-
76
-
-
75549086645
-
CyanoBase: the cyanobacteria genome database update 2010
-
10.1093/nar/gkp915, 2808859, 19880388
-
Nakao M, Okamoto S, Kohara M, Fujishiro T, Fujisawa T, Sato S, Tabata S, Kaneko T, Nakamura Y. CyanoBase: the cyanobacteria genome database update 2010. Nucleic Acids Res 2010, 38:D379-D381. 10.1093/nar/gkp915, 2808859, 19880388.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Nakao, M.1
Okamoto, S.2
Kohara, M.3
Fujishiro, T.4
Fujisawa, T.5
Sato, S.6
Tabata, S.7
Kaneko, T.8
Nakamura, Y.9
-
77
-
-
58149197594
-
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
-
10.1093/nar/gkn861, 2686508, 18978025
-
Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS. Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res 2009, 37:D483-488. 10.1093/nar/gkn861, 2686508, 18978025.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Winsor, G.L.1
Van Rossum, T.2
Lo, R.3
Khaira, B.4
Whiteside, M.D.5
Hancock, R.E.6
Brinkman, F.S.7
-
78
-
-
58149197587
-
ATTED-II provides coexpressed gene networks for Arabidopsis
-
10.1093/nar/gkn807, 2686564, 18953027
-
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K. ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 2009, 37:D987-991. 10.1093/nar/gkn807, 2686564, 18953027.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Obayashi, T.1
Hayashi, S.2
Saeki, M.3
Ohta, H.4
Kinoshita, K.5
-
79
-
-
58149193219
-
PPDB, the Plant Proteomics Database at Cornell
-
10.1093/nar/gkn654, 2686560, 18832363
-
Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ. PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res 2009, 37:D969-974. 10.1093/nar/gkn654, 2686560, 18832363.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sun, Q.1
Zybailov, B.2
Majeran, W.3
Friso, G.4
Olinares, P.D.5
van Wijk, K.J.6
-
80
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
-
10.1093/nar/gkl971, 1669775, 17142228
-
Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007, 35:D301-303. 10.1093/nar/gkl971, 1669775, 17142228.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
81
-
-
48549105771
-
Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms
-
10.1104/pp.107.114090, 2287330, 18245455
-
Naponelli V, Noiriel A, Ziemak MJ, Beverley SM, Lye LF, Plume AM, Botella JR, Loizeau K, Ravanel S, Rebeille F, et al. Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms. Plant Physiol 2008, 146:1515-1527. 10.1104/pp.107.114090, 2287330, 18245455.
-
(2008)
Plant Physiol
, vol.146
, pp. 1515-1527
-
-
Naponelli, V.1
Noiriel, A.2
Ziemak, M.J.3
Beverley, S.M.4
Lye, L.F.5
Plume, A.M.6
Botella, J.R.7
Loizeau, K.8
Ravanel, S.9
Rebeille, F.10
-
82
-
-
79952281325
-
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification
-
10.1038/emboj.2010.363, 21285948
-
El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset J-P, Iwata-Reuyl D, G Murzin A, de Crécy V. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 2011, 30:882-893. 10.1038/emboj.2010.363, 21285948.
-
(2011)
EMBO J
, vol.30
, pp. 882-893
-
-
El Yacoubi, B.1
Hatin, I.2
Deutsch, C.3
Kahveci, T.4
Rousset, J.-P.5
Iwata-Reuyl, D.6
G Murzin, A.7
de Crécy, V.8
-
83
-
-
69949120428
-
Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
-
10.1074/jbc.M109.021253, 2757207, 19586914
-
Engqvist M, Drincovich MF, Flugge UI, Maurino VG. Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways. J Biol Chem 2009, 284:25026-25037. 10.1074/jbc.M109.021253, 2757207, 19586914.
-
(2009)
J Biol Chem
, vol.284
, pp. 25026-25037
-
-
Engqvist, M.1
Drincovich, M.F.2
Flugge, U.I.3
Maurino, V.G.4
-
84
-
-
77950361036
-
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA
-
10.1093/nar/gkp1073, 2831307, 19965768
-
Kimura S, Suzuki T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res 2010, 38:1341-1352. 10.1093/nar/gkp1073, 2831307, 19965768.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1341-1352
-
-
Kimura, S.1
Suzuki, T.2
-
85
-
-
71249093497
-
Arabidopsis OBG-like GTPase (AtOBGL) is localized in chloroplasts and has an essential function in embryo development
-
10.1093/mp/ssp073, 19995735
-
Chigri F, Sippel C, Kolb M, Vothknecht UC. Arabidopsis OBG-like GTPase (AtOBGL) is localized in chloroplasts and has an essential function in embryo development. Mol Plant 2009, 2:1373-1383. 10.1093/mp/ssp073, 19995735.
-
(2009)
Mol Plant
, vol.2
, pp. 1373-1383
-
-
Chigri, F.1
Sippel, C.2
Kolb, M.3
Vothknecht, U.C.4
-
86
-
-
54449085447
-
Molecular identification of pseudouridine-metabolizing enzymes
-
10.1074/jbc.M804122200, 18591240
-
Preumont A, Snoussi K, Stroobant V, Collet JF, Van Schaftingen E. Molecular identification of pseudouridine-metabolizing enzymes. J Biol Chem 2008, 283:25238-25246. 10.1074/jbc.M804122200, 18591240.
-
(2008)
J Biol Chem
, vol.283
, pp. 25238-25246
-
-
Preumont, A.1
Snoussi, K.2
Stroobant, V.3
Collet, J.F.4
Van Schaftingen, E.5
-
87
-
-
75749104141
-
The chloroplast protein BPG2 functions in brassinosteroid-mediated post-transcriptional accumulation of chloroplast rRNA
-
10.1111/j.1365-313X.2009.04077.x, 19919572
-
Komatsu T, Kawaide H, Saito C, Yamagami A, Shimada S, Nakazawa M, Matsui M, Nakano A, Tsujimoto M, Natsume M, et al. The chloroplast protein BPG2 functions in brassinosteroid-mediated post-transcriptional accumulation of chloroplast rRNA. Plant J 2010, 61:409-422. 10.1111/j.1365-313X.2009.04077.x, 19919572.
-
(2010)
Plant J
, vol.61
, pp. 409-422
-
-
Komatsu, T.1
Kawaide, H.2
Saito, C.3
Yamagami, A.4
Shimada, S.5
Nakazawa, M.6
Matsui, M.7
Nakano, A.8
Tsujimoto, M.9
Natsume, M.10
-
88
-
-
57749113172
-
The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition
-
10.1074/jbc.M804837200, 2583316, 18801747
-
Sudhamsu J, Lee GI, Klessig DF, Crane BR. The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition. J Biol Chem 2008, 283:32968-32976. 10.1074/jbc.M804837200, 2583316, 18801747.
-
(2008)
J Biol Chem
, vol.283
, pp. 32968-32976
-
-
Sudhamsu, J.1
Lee, G.I.2
Klessig, D.F.3
Crane, B.R.4
-
89
-
-
72449163174
-
Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly
-
2805927, 19817716
-
Schwenkert S, Netz DJ, Frazzon J, Pierik AJ, Bill E, Gross J, Lill R, Meurer J. Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly. Biochem J 2009, 425:207-214. 2805927, 19817716.
-
(2009)
Biochem J
, vol.425
, pp. 207-214
-
-
Schwenkert, S.1
Netz, D.J.2
Frazzon, J.3
Pierik, A.J.4
Bill, E.5
Gross, J.6
Lill, R.7
Meurer, J.8
-
90
-
-
14744279245
-
The eukaryotic P loop NTPase Nbp35: an essential component of the cytosolic and nuclear iron-sulfur protein assembly machinery
-
10.1073/pnas.0406447102, 552912, 15728363
-
Hausmann A, Aguilar DJ, Balk J, Pierik AJ, Muhlenhoff U, Lill R. The eukaryotic P loop NTPase Nbp35: an essential component of the cytosolic and nuclear iron-sulfur protein assembly machinery. Proc Natl Acad Sci U S A 2005, 102:3266-3271. 10.1073/pnas.0406447102, 552912, 15728363.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 3266-3271
-
-
Hausmann, A.1
Aguilar, D.J.2
Balk, J.3
Pierik, A.J.4
Muhlenhoff, U.5
Lill, R.6
-
91
-
-
77952314717
-
The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase
-
10.1093/nar/gkp1189, 2853112, 20047967
-
Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kotter P, Engels JW, Heckel A, Karas M, Entian KD, et al. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res 2010, 38:2387-2398. 10.1093/nar/gkp1189, 2853112, 20047967.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 2387-2398
-
-
Wurm, J.P.1
Meyer, B.2
Bahr, U.3
Held, M.4
Frolow, O.5
Kotter, P.6
Engels, J.W.7
Heckel, A.8
Karas, M.9
Entian, K.D.10
-
92
-
-
67651213552
-
Molecular identification of omega-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2
-
10.1016/j.biochi.2009.07.002, 19596042
-
Jaisson S, Veiga-da-Cunha M, Van Schaftingen E. Molecular identification of omega-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2. Biochimie 2009, 91:1066-1071. 10.1016/j.biochi.2009.07.002, 19596042.
-
(2009)
Biochimie
, vol.91
, pp. 1066-1071
-
-
Jaisson, S.1
Veiga-da-Cunha, M.2
Van Schaftingen, E.3
-
93
-
-
67651202156
-
Identification of the putative tumor suppressor Nit2 as omega-amidase, an enzyme metabolically linked to glutamine and asparagine transamination
-
10.1016/j.biochi.2009.07.003, 2745200, 19595734
-
Krasnikov BF, Chien CH, Nostramo R, Pinto JT, Nieves E, Callaway M, Sun J, Huebner K, Cooper AJ. Identification of the putative tumor suppressor Nit2 as omega-amidase, an enzyme metabolically linked to glutamine and asparagine transamination. Biochimie 2009, 91:1072-1080. 10.1016/j.biochi.2009.07.003, 2745200, 19595734.
-
(2009)
Biochimie
, vol.91
, pp. 1072-1080
-
-
Krasnikov, B.F.1
Chien, C.H.2
Nostramo, R.3
Pinto, J.T.4
Nieves, E.5
Callaway, M.6
Sun, J.7
Huebner, K.8
Cooper, A.J.9
-
94
-
-
6044267984
-
Crystal Structure of the YgfZ Protein from Escherichia coli Suggests a folate-dependent regulatory role in one-carbon metabolism
-
10.1128/JB.186.21.7134-7140.2004, 523196, 15489424
-
Teplyakov A, Obmolova G, Sarikaya E, Pullalarevu S, Krajewski W, Galkin A, Howard AJ, Herzberg O, Gilliland GL. Crystal Structure of the YgfZ Protein from Escherichia coli Suggests a folate-dependent regulatory role in one-carbon metabolism. J Bacteriol 2004, 186:7134-7140. 10.1128/JB.186.21.7134-7140.2004, 523196, 15489424.
-
(2004)
J Bacteriol
, vol.186
, pp. 7134-7140
-
-
Teplyakov, A.1
Obmolova, G.2
Sarikaya, E.3
Pullalarevu, S.4
Krajewski, W.5
Galkin, A.6
Howard, A.J.7
Herzberg, O.8
Gilliland, G.L.9
-
95
-
-
0029018327
-
Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
-
177145, 7608087
-
Guzman LM, Belin D, Carson MJ, Beckwith J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 1995, 177:4121-4130. 177145, 7608087.
-
(1995)
J Bacteriol
, vol.177
, pp. 4121-4130
-
-
Guzman, L.M.1
Belin, D.2
Carson, M.J.3
Beckwith, J.4
-
96
-
-
34249683768
-
Tight modulation of Escherichia coli bacterial biofilm formation through controlled expression of adhesion factors
-
10.1128/AEM.02625-06, 1907114, 17384304
-
Da Re S, Le Quere B, Ghigo J-M, Beloin C. Tight modulation of Escherichia coli bacterial biofilm formation through controlled expression of adhesion factors. Appl Environ Microbiol 2007, 73:3391-3403. 10.1128/AEM.02625-06, 1907114, 17384304.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 3391-3403
-
-
Da Re, S.1
Le Quere, B.2
Ghigo, J.-M.3
Beloin, C.4
|