-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
84868334617
-
Engineering a cyanobacterial cell factory for production of lactic acid
-
Angermayr SA, Paszota M, Hellingwerf KJ (2012) Engineering a cyanobacterial cell factory for production of lactic acid. Appl Environ Microbiol 78: 7098-7106
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 7098-7106
-
-
Angermayr, S.A.1
Paszota, M.2
Hellingwerf, K.J.3
-
3
-
-
84861659423
-
Photorespiration has a dual origin and manifold links to central metabolism
-
Bauwe H, Hagemann M, Kern R, Timm S (2012) Photorespiration has a dual origin and manifold links to central metabolism. Curr Opin Plant Biol 15: 269-275
-
(2012)
Curr Opin Plant Biol
, vol.15
, pp. 269-275
-
-
Bauwe, H.1
Hagemann, M.2
Kern, R.3
Timm, S.4
-
4
-
-
84876576325
-
Computational solutions for omics data
-
Berger B, Peng J, Singh M (2013) Computational solutions for omics data. Nat Rev Genet 14: 333-346
-
(2013)
Nat Rev Genet
, vol.14
, pp. 333-346
-
-
Berger, B.1
Peng, J.2
Singh, M.3
-
5
-
-
84892989181
-
Reconciliation of metabolites and biochemical reactions for metabolic networks
-
Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M (2014) Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform 15: 123-135
-
(2014)
Brief Bioinform
, vol.15
, pp. 123-135
-
-
Bernard, T.1
Bridge, A.2
Morgat, A.3
Moretti, S.4
Xenarios, I.5
Pagni, M.6
-
7
-
-
0242487787
-
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84: 647-657
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
8
-
-
33947617349
-
Biodiesel from microalgae
-
Chisti Y (2007) Biodiesel from microalgae. Biotechnol Adv 25: 294-306
-
(2007)
Biotechnol Adv
, vol.25
, pp. 294-306
-
-
Chisti, Y.1
-
9
-
-
78751638661
-
Engineering cyanobacteria to generate high-value products
-
Ducat DC, Way JC, Silver PA (2011) Engineering cyanobacteria to generate high-value products. Trends Biotechnol 29: 95-103
-
(2011)
Trends Biotechnol
, vol.29
, pp. 95-103
-
-
Ducat, D.C.1
Way, J.C.2
Silver, P.A.3
-
11
-
-
55949125406
-
The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
-
Eisenhut M, Ruth W, Haimovich M, Bauwe H, Kaplan A, Hagemann M (2008) The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants. Proc Natl Acad Sci USA 105: 17199-17204
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 17199-17204
-
-
Eisenhut, M.1
Ruth, W.2
Haimovich, M.3
Bauwe, H.4
Kaplan, A.5
Hagemann, M.6
-
12
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
Funahashi A, Tanimura N, Morohashi M, Kitano H (2003) CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1: 159-162
-
(2003)
BIOSILICO
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
14
-
-
79960264362
-
Full-length transcriptome assembly from RNA-seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29: 644-652
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
-
15
-
-
68949206409
-
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
-
Gstaiger M, Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10: 617-627
-
(2009)
Nat Rev Genet
, vol.10
, pp. 617-627
-
-
Gstaiger, M.1
Aebersold, R.2
-
16
-
-
84873272026
-
CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803
-
Hernandez-Prieto MA, Futschik ME (2012) CyanoEXpress: a web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803. Bioinformation 8: 634-638
-
(2012)
Bioinformation
, vol.8
, pp. 634-638
-
-
Hernandez-Prieto, M.A.1
Futschik, M.E.2
-
17
-
-
79951493627
-
On the future of genomic data
-
Kahn SD (2011) On the future of genomic data. Science 331: 728-729
-
(2011)
Science
, vol.331
, pp. 728-729
-
-
Kahn, S.D.1
-
18
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
19
-
-
77956710803
-
The metabolic network of Synechocystis sp. PCC 6803: Systemic properties of autotrophic growth
-
Knoop H, Zilliges Y, Lockau W, Steuer R (2010) The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. Plant Physiol 154: 410-422
-
(2010)
Plant Physiol
, vol.154
, pp. 410-422
-
-
Knoop, H.1
Zilliges, Y.2
Lockau, W.3
Steuer, R.4
-
20
-
-
78650985721
-
The importance of energy balance in improving photosynthetic productivity
-
Kramer DM, Evans JR (2011) The importance of energy balance in improving photosynthetic productivity. Plant Physiol 155: 70-78
-
(2011)
Plant Physiol
, vol.155
, pp. 70-78
-
-
Kramer, D.M.1
Evans, J.R.2
-
21
-
-
84855499408
-
MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases
-
Kumar A, Suthers PF, Maranas CD (2012) MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics 13: 6
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 6
-
-
Kumar, A.1
Suthers, P.F.2
Maranas, C.D.3
-
22
-
-
79961121106
-
BKM-react, an integrated biochemical reaction database
-
Lang M, Stelzer M, Schomburg D (2011) BKM-react, an integrated biochemical reaction database. BMC Biochem 12: 42
-
(2011)
BMC Biochem
, vol.12
, pp. 42
-
-
Lang, M.1
Stelzer, M.2
Schomburg, D.3
-
23
-
-
68449103579
-
The systems biology graphical notation
-
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, et al (2009) The systems biology graphical notation. Nat Biotechnol 27: 735-741
-
(2009)
Nat Biotechnol
, vol.27
, pp. 735-741
-
-
Le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Schreiber, F.5
Sorokin, A.6
Demir, E.7
Wegner, K.8
Aladjem, M.I.9
Wimalaratne, S.M.10
-
24
-
-
84883809652
-
Basic concepts and principles of stoichiometric modeling of metabolic networks
-
Maarleveld TR, Khandelwal RA, Olivier BG, Teusink B, Bruggeman FJ (2013) Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J 8: 997-1008
-
(2013)
Biotechnol J
, vol.8
, pp. 997-1008
-
-
Maarleveld, T.R.1
Khandelwal, R.A.2
Olivier, B.G.3
Teusink, B.4
Bruggeman, F.J.5
-
25
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5: 264-276
-
(2003)
Metab Eng
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
26
-
-
84879002382
-
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
-
McCloskey D, Palsson BO, Feist AM (2013) Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 9: 661
-
(2013)
Mol Syst Biol
, vol.9
, pp. 661
-
-
McCloskey, D.1
Palsson, B.O.2
Feist, A.M.3
-
27
-
-
84857137366
-
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
-
Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I (2012) Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proc Natl Acad Sci USA 109: 2678-2683
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 2678-2683
-
-
Nogales, J.1
Gudmundsson, S.2
Knight, E.M.3
Palsson, B.O.4
Thiele, I.5
-
29
-
-
84872862096
-
Cyanobacterial conversion of carbon dioxide to 2, 3-butanediol
-
Oliver JW, Machado IM, Yoneda H, Atsumi S (2013) Cyanobacterial conversion of carbon dioxide to 2, 3-butanediol. Proc Natl Acad Sci USA 110: 1249-1254
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 1249-1254
-
-
Oliver, J.W.1
McHado, I.M.2
Yoneda, H.3
Atsumi, S.4
-
34
-
-
84868275739
-
Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803
-
Saha R, Verseput AT, Berla BM, Mueller TJ, Pakrasi HB, Maranas CD (2012) Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS ONE 7: e48285
-
(2012)
PLoS ONE
, vol.7
-
-
Saha, R.1
Verseput, A.T.2
Berla, B.M.3
Mueller, T.J.4
Pakrasi, H.B.5
Maranas, C.D.6
-
35
-
-
80053085147
-
A practical guide to genome-scale metabolic models and their analysis
-
Santos F, Boele J, Teusink B (2011) A practical guide to genome-scale metabolic models and their analysis. Methods Enzymol 500: 509-532
-
(2011)
Methods Enzymol
, vol.500
, pp. 509-532
-
-
Santos, F.1
Boele, J.2
Teusink, B.3
-
36
-
-
77951612556
-
BiGG: A Biochemical Genetic and Genomic knowledgebase of large-scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, Palsson BO (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large-scale metabolic reconstructions. BMC Bioinformatics 11: 213
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
37
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2. 0
-
Schellenberger J, Que RM, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, et al (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0. Nat Protoc 6: 1290-1307
-
(2011)
Nat Protoc
, vol.6
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.M.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
Zielinski, D.C.7
Bordbar, A.8
Lewis, N.E.9
Rahmanian, S.10
-
38
-
-
45249121010
-
Transcript profiling indicates that the absence of PsbO affects the coordination of C and N metabolism in Synechocystis sp. PCC 6803
-
Schriek S, Aguirre-von-Wobeser E, Nodop A, Becker A, Ibelings BW, Bok J, Staiger D, Matthijs HC, Pistorius EK, Michel KP (2008) Transcript profiling indicates that the absence of PsbO affects the coordination of C and N metabolism in Synechocystis sp. PCC 6803. Physiol Plant 133: 525-543
-
(2008)
Physiol Plant
, vol.133
, pp. 525-543
-
-
Schriek, S.1
Aguirre-von-Wobeser, E.2
Nodop, A.3
Becker, A.4
Ibelings, B.W.5
Bok, J.6
Staiger, D.7
Matthijs, H.C.8
Pistorius, E.K.9
Michel, K.P.10
-
39
-
-
62349093923
-
Detection of an L-amino acid dehydrogenase activity in Synechocystis sp. PCC 6803
-
Schriek S, Kahmann U, Staiger D, Pistorius EK, Michel KP (2009) Detection of an L-amino acid dehydrogenase activity in Synechocystis sp. PCC 6803. J Exp Bot 60: 1035-1046
-
(2009)
J Exp Bot
, vol.60
, pp. 1035-1046
-
-
Schriek, S.1
Kahmann, U.2
Staiger, D.3
Pistorius, E.K.4
Michel, K.P.5
-
40
-
-
39149106178
-
Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
-
Schriek S, Rückert C, Staiger D, Pistorius EK, Michel KP (2007) Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803. BMC Genomics 8: 437
-
(2007)
BMC Genomics
, vol.8
, pp. 437
-
-
Schriek, S.1
Rückert, C.2
Staiger, D.3
Pistorius, E.K.4
Michel, K.P.5
-
41
-
-
28844474830
-
Flux balance analysis of photoautotrophic metabolism
-
Shastri AA, Morgan JA (2005) Flux balance analysis of photoautotrophic metabolism. Biotechnol Prog 21: 1617-1626
-
(2005)
Biotechnol Prog
, vol.21
, pp. 1617-1626
-
-
Shastri, A.A.1
Morgan, J.A.2
-
42
-
-
79551587720
-
Cytoscape 2. 8: New features for data integration and network visualization
-
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2. 8: new features for data integration and network visualization. Bioinformatics 27: 431-432
-
(2011)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.L.4
Ideker, T.5
-
43
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121
-
(2010)
Nat Protoc
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
44
-
-
57749195712
-
RNA-seq: A revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
45
-
-
83755181765
-
The tricarboxylic acid cycle in cyanobacteria
-
Zhang S, Bryant DA (2011) The tricarboxylic acid cycle in cyanobacteria. Science 334: 1551-1553
-
(2011)
Science
, vol.334
, pp. 1551-1553
-
-
Zhang, S.1
Bryant, D.A.2
|