-
1
-
-
0036717194
-
The druggable genome
-
10.1038/nrd892 12209152
-
Hopkins AL Groom CR The druggable genome Nature reviews 2002, 1(9):727-730 10.1038/nrd892 12209152
-
(2002)
Nature Reviews
, vol.1
, Issue.9
, pp. 727-730
-
-
Hopkins, A.L.1
Groom, C.R.2
-
2
-
-
33747890136
-
Observing local and global properties of metabolic pathways: 'Load points' and 'choke points' in the metabolic networks
-
10.1093/bioinformatics/btl181 16682421
-
Rahman SA Schomburg D Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks Bioinformatics 2006, 22(14):1767-1774 10.1093/bioinformatics/btl181 16682421
-
(2006)
Bioinformatics
, vol.22
, Issue.14
, pp. 1767-1774
-
-
Rahman, S.A.1
Schomburg, D.2
-
3
-
-
2442636351
-
Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
-
479120 15078855 10.1101/gr.2050304
-
Yeh I Hanekamp T Tsoka S Karp PD Altman RB Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery Genome Res 2004, 14(5):917-924 479120 15078855 10.1101/gr.2050304
-
(2004)
Genome Res
, vol.14
, Issue.5
, pp. 917-924
-
-
Yeh, I.1
Hanekamp, T.2
Tsoka, S.3
Karp, P.D.4
Altman, R.B.5
-
4
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
10.1038/73786 10700151
-
Schuster S Fell DA Dandekar T A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks Nat Biotechnol 2000, 18(3):326-332 10.1038/73786 10700151
-
(2000)
Nat Biotechnol
, vol.18
, Issue.3
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
6
-
-
0033834719
-
Import of host delta-aminolevulinate dehydratase into the malarial parasite: Identification of a new drug target
-
10.1038/78659 10932227
-
Bonday ZQ Dhanasekaran S Rangarajan PN Padmanaban G Import of host delta-aminolevulinate dehydratase into the malarial parasite: identification of a new drug target Nat Med 2000, 6(8):898-903 10.1038/ 78659 10932227
-
(2000)
Nat Med
, vol.6
, Issue.8
, pp. 898-903
-
-
Bonday, Z.Q.1
Dhanasekaran, S.2
Rangarajan, P.N.3
Padmanaban, G.4
-
7
-
-
2942579562
-
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions
-
29061 11001586 10.1186/1471-2105-1-1
-
Edwards JS Palsson BO Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions BMC Bioinformatics 2000, 1:1 29061 11001586 10.1186/1471-2105-1-1
-
(2000)
BMC Bioinformatics
, vol.1
, pp. 1
-
-
Edwards, J.S.1
Palsson, B.O.2
-
8
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
1911197 17593909 10.1038/msb4100155
-
Feist AM Henry CS Reed JL Krummenacker M Joyce AR Karp PD Broadbelt LJ Hatzimanikatis V Palsson BO A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information Molecular systems biology 2007, 3:121 1911197 17593909 10.1038/msb4100155
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
9
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
1949037 17625511 10.1038/msb4100162
-
Schuetz R Kuepfer L Sauer U Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Molecular systems biology 2007, 3:119 1949037 17625511 10.1038/msb4100162
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
10
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
-
1681482 16738554 10.1038/msb4100050 0008
-
Baba T Ara T Hasegawa M Takai Y Okumura Y Baba M Datsenko KA Tomita M Wanner BL Mori H Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection Molecular systems biology 2006, 2:2006 0008 1681482 16738554 10.1038/msb4100050
-
(2006)
Molecular Systems Biology
, vol.2
, pp. 2006
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
Baba, M.6
Datsenko, K.A.7
Tomita, M.8
Wanner, B.L.9
Mori, H.10
-
11
-
-
35348934254
-
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data
-
10.1074/jbc.M703759200 17573341
-
Oh YK Palsson BO Park SM Schilling CH Mahadevan R Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data J Biol Chem 2007, 282(39):28791-28799 10.1074/jbc.M703759200 17573341
-
(2007)
J Biol Chem
, vol.282
, Issue.39
, pp. 28791-28799
-
-
Oh, Y.K.1
Palsson, B.O.2
Park, S.M.3
Schilling, C.H.4
Mahadevan, R.5
-
12
-
-
33751567092
-
Experimental and computational assessment of conditionally essential genes in Escherichia coli
-
1698209 17012394 10.1128/JB.00740-06
-
Joyce AR Reed JL White A Edwards R Osterman A Baba T Mori H Lesely SA Palsson BO Agarwalla S Experimental and computational assessment of conditionally essential genes in Escherichia coli J Bacteriol 2006, 188(23):8259-8271 1698209 17012394 10.1128/JB.00740-06
-
(2006)
J Bacteriol
, vol.188
, Issue.23
, pp. 8259-8271
-
-
Joyce, A.R.1
Reed, J.L.2
White, A.3
Edwards, R.4
Osterman, A.5
Baba, T.6
Mori, H.7
Lesely, S.A.8
Palsson, B.O.9
Agarwalla, S.10
-
13
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox
-
10.1038/nprot.2007.99 17406635
-
Becker SA Feist AM Mo ML Hannum G Palsson BO Herrgard MJ Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox Nature protocols 2007, 2(3):727-738 10.1038/nprot.2007.99 17406635
-
(2007)
Nature Protocols
, vol.2
, Issue.3
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
15
-
-
0141843591
-
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
-
10.1021/ja036030u 14505407
-
Hattori M Okuno Y Goto S Kanehisa M Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways J Am Chem Soc 2003/09/25 2003, 125(39):11853-11865 10.1021/ja036030u 14505407
-
(2003)
J Am Chem Soc 2003/09/25
, vol.125
, Issue.39
, pp. 11853-11865
-
-
Hattori, M.1
Okuno, Y.2
Goto, S.3
Kanehisa, M.4
-
16
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
10.1038/nrg1272 14735121
-
Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5(2):101-113 10.1038/nrg1272 14735121
-
(2004)
Nat Rev Genet
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
17
-
-
0035823264
-
The small world inside large metabolic networks
-
1088812 11522199
-
Wagner A Fell DA The small world inside large metabolic networks Proceedings 2001, 268(1478):1803-1810 1088812 11522199
-
(2001)
Proceedings
, vol.268
, Issue.1478
, pp. 1803-1810
-
-
Wagner, A.1
Fell, D.A.2
-
18
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
10.1038/nature02456 15129285
-
Covert MW Knight EM Reed JL Herrgard MJ Palsson BO Integrating high-throughput and computational data elucidates bacterial networks Nature 2004, 429(6987):92-96 10.1038/nature02456 15129285
-
(2004)
Nature
, vol.429
, Issue.6987
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
19
-
-
33645792897
-
Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms
-
1434775 16524469 10.1186/1471-2105-7-119
-
König R Schramm G Oswald M Seitz H Sager S Zapatka M Reinelt G Eils R Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms BMC Bioinformatics 2006, 7:119 1434775 16524469 10.1186/1471-2105-7-119
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 119
-
-
König, R.1
Schramm, G.2
Oswald, M.3
Seitz, H.4
Sager, S.5
Zapatka, M.6
Reinelt, G.7
Eils, R.8
-
20
-
-
33645757123
-
Low degree metabolites explain essential reactions and enhance modularity in biological networks
-
1434774 16524470 10.1186/1471-2105-7-118 2006/03/10
-
Samal A Singh S Giri V Krishna S Raghuram N Jain S Low degree metabolites explain essential reactions and enhance modularity in biological networks BMC Bioinformatics 2006/03/10 2006, 7:118 1434774 16524470 10.1186/1471-2105-7-118
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 118
-
-
Samal, A.1
Singh, S.2
Giri, V.3
Krishna, S.4
Raghuram, N.5
Jain, S.6
-
21
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
146917 9254694 10.1093/nar/25.17.3389
-
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(17):3389-3402 146917 9254694 10.1093/ nar/25.17.3389
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, 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
-
23
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
34 Database issue 1347430 16381955 10.1093/nar/gkj067
-
Wishart DS Knox C Guo AC Shrivastava S Hassanali M Stothard P Chang Z Woolsey J DrugBank: A comprehensive resource for in silico drug discovery and exploration Nucleic Acids Res 2005/12/31 2006, 34 Database issue D668-72 1347430 16381955 10.1093/nar/gkj067
-
(2006)
Nucleic Acids Res 2005/12/31
, vol.34
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Shrivastava, S.4
Hassanali, M.5
Stothard, P.6
Chang, Z.7
Woolsey, J.8
-
24
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
36 Database issue 2238879 18077471 2007/12/14
-
Kanehisa M Araki M Goto S Hattori M Hirakawa M Itoh M Katayama T Kawashima S Okuda S Tokimatsu T Yamanishi Y KEGG for linking genomes to life and the environment Nucleic Acids Res 2007/12/14 2008, 36 Database issue D480-4 2238879 18077471
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
Hattori, M.4
Hirakawa, M.5
Itoh, M.6
Katayama, T.7
Kawashima, S.8
Okuda, S.9
Tokimatsu, T.10
Yamanishi, Y.11
-
25
-
-
34249802323
-
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
-
1884177 17488495 10.1186/1471-2105-8-149
-
Schramm G Zapatka M Eils R König R Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli BMC Bioinformatics 2007, 8(1):149 1884177 17488495 10.1186/1471-2105-8-149
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.1
, pp. 149
-
-
Schramm, G.1
Zapatka, M.2
Eils, R.3
König, R.4
-
26
-
-
23644452487
-
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/ GPR): An in silico genome-scale characterization of single- and double-deletion mutants
-
1196094 16077130 10.1128/JB.187.16.5818-5830.2005
-
Thiele I Vo TD Price ND Palsson BO Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single- and double-deletion mutants J Bacteriol 2005, 187(16):5818-5830 1196094 16077130 10.1128/JB.187.16.5818-5830.2005
-
(2005)
J Bacteriol
, vol.187
, Issue.16
, pp. 5818-5830
-
-
Thiele, I.1
Vo, T.D.2
Price, N.D.3
Palsson, B.O.4
-
27
-
-
33645462347
-
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
-
1681478 16738551 10.1038/msb4100046
-
Feist AM Scholten JC Palsson BO Brockman FJ Ideker T Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri Molecular systems biology 2006, 2:2006 0004 1681478 16738551 10.1038/msb4100046
-
(2006)
Molecular Systems Biology
, vol.2
-
-
Feist, A.M.1
Scholten, J.C.2
Palsson, B.O.3
Brockman, F.J.4
Ideker, T.5
-
28
-
-
34447317247
-
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
-
1925256 17555602 10.1186/1752-0509-1-26
-
Jamshidi N Palsson BO Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets BMC systems biology 2007, 1:26 1925256 17555602 10.1186/1752-0509-1-26
-
(2007)
BMC Systems Biology
, vol.1
, pp. 26
-
-
Jamshidi, N.1
Palsson, B.O.2
-
29
-
-
3843128481
-
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
-
442145 15197165 10.1101/gr.2250904
-
Duarte NC Herrgard MJ Palsson BO Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model Genome Res 2004, 14(7):1298-1309 442145 15197165 10.1101/ gr.2250904
-
(2004)
Genome Res
, vol.14
, Issue.7
, pp. 1298-1309
-
-
Duarte, N.C.1
Herrgard, M.J.2
Palsson, B.O.3
-
30
-
-
38549117301
-
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
36 Database issue 2238876 17965431
-
Caspi R Foerster H Fulcher CA Kaipa P Krummenacker M Latendresse M Paley S Rhee SY Shearer AG Tissier C Walk TC Zhang P Karp PD The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases Nucleic acids research 2008, 36 Database issue D623-31 2238876 17965431
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
Kaipa, P.4
Krummenacker, M.5
Latendresse, M.6
Paley, S.7
Rhee, S.Y.8
Shearer, A.G.9
Tissier, C.10
Walk, T.C.11
Zhang, P.12
Karp, P.D.13
|