-
1
-
-
77954935933
-
A model of redox kinetics implicates the thiol proteome in cellular hydrogen peroxide responses
-
Adimora NJ, Jones DP, and Kemp ML. A model of redox kinetics implicates the thiol proteome in cellular hydrogen peroxide responses. Antioxid Redox Signal 13: 731-743, 2010.
-
(2010)
Antioxid Redox Signal
, vol.13
, pp. 731-743
-
-
Adimora, N.J.1
Jones, D.P.2
Kemp, M.L.3
-
2
-
-
45449117673
-
An introduction to systems biology
-
Chapman & Hall/CRC, London
-
Alon U. An Introduction to Systems Biology. Design Principles of Biological Circuits. Chapman & Hall/CRC, London, 2007.
-
(2007)
Design Principles of Biological Circuits
-
-
Alon, U.1
-
3
-
-
75549087047
-
The IntAct molecular interaction database in 2010
-
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, and Hermjakob H. The IntAct molecular interaction database in 2010. Nucleic Acids Res 38: D525-D531, 2010.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Aranda, B.1
Achuthan, P.2
Alam-Faruque, Y.3
Armean, I.4
Bridge, A.5
Derow, C.6
Feuermann, M.7
Ghanbarian, A.T.8
Kerrien, S.9
Khadake, J.10
Kerssemakers, J.11
Leroy, C.12
Menden, M.13
Michaut, M.14
Montecchi-Palazzi, L.15
Neuhauser, S.N.16
Orchard, S.17
Perreau, V.18
Roechert, B.19
Van Eijk, K.20
Hermjakob, H.21
more..
-
4
-
-
67749140118
-
Scale-free networks: A decade and beyond
-
Barabasi AL. Scale-free networks: a decade and beyond. Science 325: 412-413, 2009.
-
(2009)
Science
, vol.325
, pp. 412-413
-
-
Barabasi, A.L.1
-
5
-
-
78650373804
-
Network medicine: A network-based approach to human disease
-
Barabasi AL, Gulbahce N, and Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 12: 56-68, 2011.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 56-68
-
-
Barabasi, A.L.1
Gulbahce, N.2
Loscalzo, J.3
-
6
-
-
77954699474
-
Systems metabolic engineering: Genome-scale models and beyond
-
Blazeck J and Alper H. Systems metabolic engineering: genome-scale models and beyond. BiotechnolJ5:647-659, 2010.
-
(2010)
BiotechnolJ
, vol.5
, pp. 647-659
-
-
Blazeck, J.1
Alper, H.2
-
8
-
-
0022873550
-
Determination of thiol proteins using monobromobimane labeling and highperformance liquid chromatographic analysis: Application to Escherichia coli thioredoxin
-
Chinn PC, Pigiet V, and Fahey RC. Determination of thiol proteins using monobromobimane labeling and highperformance liquid chromatographic analysis: application to Escherichia coli thioredoxin. Anal Biochem 159: 143-149, 1986.
-
(1986)
Anal Biochem
, vol.159
, pp. 143-149
-
-
Chinn, P.C.1
Pigiet, V.2
Fahey, R.C.3
-
9
-
-
0037053371
-
The yeast glutaredoxins are active as glutathione peroxidases
-
Collinson EJ, Wheeler GL, Garrido EO, Avery AM, Avery SV, and Grant CM. The yeast glutaredoxins are active as glutathione peroxidases. J Biol Chem 277: 16712-16717, 2002.
-
(2002)
J Biol Chem
, vol.277
, pp. 16712-16717
-
-
Collinson, E.J.1
Wheeler, G.L.2
Garrido, E.O.3
Avery, A.M.4
Avery, S.V.5
Grant, C.M.6
-
10
-
-
0036803249
-
Nanotransducers in cellular redox signaling: Modification of thiols by reactive oxygen and nitrogen species
-
Cooper CE, Patel RP, Brookes PS, and Darley-Usmar VM. Nanotransducers in cellular redox signaling: modification of thiols by reactive oxygen and nitrogen species. Trends Bio-chem Sci 27: 489-492, 2002.
-
(2002)
Trends Bio-chem Sci
, vol.27
, pp. 489-492
-
-
Cooper, C.E.1
Patel, R.P.2
Brookes, P.S.3
Darley-Usmar, V.M.4
-
11
-
-
0035281870
-
Metabolic modeling of mi-crobial strains in silico
-
Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin, II, Selkov E, and Palsson BO. Metabolic modeling of mi-crobial strains in silico. Trends Biochem Sci 26: 179-186, 2001.
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 179-186
-
-
Covert, M.W.1
Schilling, C.H.2
Famili, I.3
Edwards, J.S.4
Goryanin, I.I.5
Selkov, E.6
Palsson, B.O.7
-
12
-
-
59849129012
-
Protein S-glutathionylation: A regulatory device from bacteria to humans
-
Dalle-Donne I, Rossi R, Colombo G, Giustarini D, and Mil-zani A. Protein S-glutathionylation: a regulatory device from bacteria to humans. Trends Biochem Sci 34: 85-96, 2009.
-
(2009)
Trends Biochem Sci
, vol.34
, pp. 85-96
-
-
Dalle-Donne, I.1
Rossi, R.2
Colombo, G.3
Giustarini, D.4
Mil-Zani, A.5
-
13
-
-
33749506763
-
From in vivo to in silico biology and back
-
Di Ventura B, Lemerle C, Michalodimitrakis K, and Serrano L. From in vivo to in silico biology and back. Nature 443: 527-533, 2006.
-
(2006)
Nature
, vol.443
, pp. 527-533
-
-
Di Ventura, B.1
Lemerle, C.2
Michalodimitrakis, K.3
Serrano, L.4
-
14
-
-
78149403333
-
Hubs and bottlenecks in plant molecular signalling networks
-
Dietz KJ, Jacquot JP, and Harris G. Hubs and bottlenecks in plant molecular signalling networks. New Phytol 188: 919-938, 2010.
-
(2010)
New Phytol
, vol.188
, pp. 919-938
-
-
Dietz, K.J.1
Jacquot, J.P.2
Harris, G.3
-
15
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist AM, Herrgard MJ, Thiele I, Reed JL, and Palsson BO. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7: 129-143, 2009.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
17
-
-
79960286223
-
Signal transduction by reactive oxygen species
-
Finkel T. Signal transduction by reactive oxygen species. J Cell Biol 194: 7-15, 2011.
-
(2011)
J Cell Biol
, vol.194
, pp. 7-15
-
-
Finkel, T.1
-
18
-
-
77956207316
-
Changing paradigms in thiology from antioxidant defense toward redox regulation
-
Flohe L. Changing paradigms in thiology from antioxidant defense toward redox regulation. Methods Enzymol 473: 1-39, 2010.
-
(2010)
Methods Enzymol
, vol.473
, pp. 1-39
-
-
Flohe, L.1
-
19
-
-
79952582563
-
Thiol peroxidases mediate specific genome-wide regulation of gene expression in response to hydrogen peroxide
-
Fomenko DE, Koc A, Agisheva N, Jacobsen M, Kaya A, Malinouski M, Rutherford JC, Siu KL, Jin DY, Winge DR, and Gladyshev VN. Thiol peroxidases mediate specific genome-wide regulation of gene expression in response to hydrogen peroxide. Proc Natl Acad Sci U S A 108: 2729-2734, 2011.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 2729-2734
-
-
Fomenko, D.E.1
Koc, A.2
Agisheva, N.3
Jacobsen, M.4
Kaya, A.5
Malinouski, M.6
Rutherford, J.C.7
Siu, K.L.8
Jin, D.Y.9
Winge, D.R.10
Gladyshev, V.N.11
-
20
-
-
33751279892
-
Thioredoxin and protein kinases in redox signaling
-
Fujino G, Noguchi T, Takeda K, and Ichijo H. Thioredoxin and protein kinases in redox signaling. Semin Cancer Biol 16: 427-435, 2006.
-
(2006)
Semin Cancer Biol
, vol.16
, pp. 427-435
-
-
Fujino, G.1
Noguchi, T.2
Takeda, K.3
Ichijo, H.4
-
21
-
-
64549106959
-
Mechanistic and kinetic details of catalysis of thiol-disulfide exchange by glutaredoxins and potential mechanisms of regulation
-
Gallogly MM, Starke DW, and Mieyal JJ. Mechanistic and kinetic details of catalysis of thiol-disulfide exchange by glutaredoxins and potential mechanisms of regulation. Antioxid Redox Signal 11: 1059-1081, 2009.
-
(2009)
Antioxid Redox Signal
, vol.11
, pp. 1059-1081
-
-
Gallogly, M.M.1
Starke, D.W.2
Mieyal, J.J.3
-
22
-
-
84861199916
-
A mathematical modelling approach to assessing the reliability of biomark-ers of glutathione metabolism
-
Geenen S, du Preez FB, Reed M, Nijhout HF, Kenna JG, Wilson ID, Westerhoff HV, and Snoep JL. A mathematical modelling approach to assessing the reliability of biomark-ers of glutathione metabolism. Eur J Pharm Sci 46: 233-243, 2012.
-
(2012)
Eur J Pharm Sci
, vol.46
, pp. 233-243
-
-
Geenen, S.1
Du Preez, F.B.2
Reed, M.3
Nijhout, H.F.4
Kenna, J.G.5
Wilson, I.D.6
Westerhoff, H.V.7
Snoep, J.L.8
-
23
-
-
84866034431
-
Systems biology tools for toxicology
-
Geenen S, Taylor PN, Snoep JL, Wilson ID, Kenna JG, and Westerhoff HV. Systems biology tools for toxicology. Arch Toxicol 86: 1251-1271, 2012.
-
(2012)
Arch Toxicol
, vol.86
, pp. 1251-1271
-
-
Geenen, S.1
Taylor, P.N.2
Snoep, J.L.3
Wilson, I.D.4
Kenna, J.G.5
Westerhoff, H.V.6
-
24
-
-
0021284165
-
Redox control of enzyme activities by thiol/disulfide exchange
-
Gilbert HF. Redox control of enzyme activities by thiol/disulfide exchange. Methods Enzymol 107: 330-351, 1984.
-
(1984)
Methods Enzymol
, vol.107
, pp. 330-351
-
-
Gilbert, H.F.1
-
25
-
-
72649107557
-
A key role for mitochondria in endo-thelial signaling by plasma cysteine/cystine redox potential
-
Go YM, Park H, Koval M, Orr M, Reed M, Liang Y, Smith D, Pohl J, and Jones DP. A key role for mitochondria in endo-thelial signaling by plasma cysteine/cystine redox potential. Free Radic Biol Med 48: 275-283, 2010.
-
(2010)
Free Radic Biol Med
, vol.48
, pp. 275-283
-
-
Go, Y.M.1
Park, H.2
Koval, M.3
Orr, M.4
Reed, M.5
Liang, Y.6
Smith, D.7
Pohl, J.8
Jones, D.P.9
-
26
-
-
34547140875
-
The human disease network
-
Goh KI, Cusick ME, Valle D, Childs B, Vidal M, and Bar-abasi AL. The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690, 2007.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 8685-8690
-
-
Goh, K.I.1
Cusick, M.E.2
Valle, D.3
Childs, B.4
Vidal, M.5
Bar-Abasi, A.L.6
-
27
-
-
0021715523
-
Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects
-
Goldbeter A and Koshland DE, Jr. Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects. J Biol Chem 259: 14441-14447, 1984.
-
(1984)
J Biol Chem
, vol.259
, pp. 14441-14447
-
-
Goldbeter, A.1
Koshland, Jr.D.E.2
-
28
-
-
77649334110
-
Thioredoxins function as deglutathio-nylase enzymes in the yeast Saccharomyces cerevisiae
-
Greetham D, Vickerstaff J, Shenton D, Perrone GG, Dawes IW, and Grant CM. Thioredoxins function as deglutathio-nylase enzymes in the yeast Saccharomyces cerevisiae. BMC Biochem 11: 3, 2010.
-
(2010)
BMC Biochem
, vol.11
, Issue.3
-
-
Greetham, D.1
Vickerstaff, J.2
Shenton, D.3
Perrone, G.G.4
Dawes, I.W.5
Grant, C.M.6
-
29
-
-
0345276418
-
New equations for redox and nano-signal transduction
-
Hancock JT, Desikan R, Neill SJ, and Cross AR. New equations for redox and nano-signal transduction. J Theor Biol 226: 65-68, 2004.
-
(2004)
J Theor Biol
, vol.226
, pp. 65-68
-
-
Hancock, J.T.1
Desikan, R.2
Neill, S.J.3
Cross, A.R.4
-
30
-
-
28844480498
-
Thiol redox control via thioredoxin and glutaredoxin systems
-
Holmgren A, Johansson C, Berndt C, Lonn ME, Hudemann C, and Lillig CH. Thiol redox control via thioredoxin and glutaredoxin systems. Biochem Soc Trans 33: 1375-1377, 2005.
-
(2005)
Biochem Soc Trans
, vol.33
, pp. 1375-1377
-
-
Holmgren, A.1
Johansson, C.2
Berndt, C.3
Lonn, M.E.4
Hudemann, C.5
Lillig, C.H.6
-
31
-
-
77952311188
-
Thioredoxin and thioredoxin reduc-tase: Current research with special reference to human disease
-
Holmgren A and Lu J. Thioredoxin and thioredoxin reduc-tase: current research with special reference to human disease. Biochem Biophys Res Commun 396: 120-124, 2010.
-
(2010)
Biochem Biophys Res Commun
, vol.396
, pp. 120-124
-
-
Holmgren, A.1
Lu, J.2
-
32
-
-
0029790351
-
Ultrasensitivity in the mitogen-activated protein kinase cascade
-
Huang CY and Ferrell JE, Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci U S A 93: 10078-10083, 1996.
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 10078-10083
-
-
Huang, C.Y.1
Ferrell, Jr.J.E.2
-
33
-
-
79961027577
-
Applications and trends in systems biology in biochemistry
-
Hubner K, Sahle S, and Kummer U. Applications and trends in systems biology in biochemistry. FEBS J 278: 2767-2857, 2011.
-
(2011)
FEBS J
, vol.278
, pp. 2767-2857
-
-
Hubner, K.1
Sahle, S.2
Kummer, U.3
-
34
-
-
33749005947
-
The thiol-based redox networks of pathogens: Unexploited targets in the search for new drugs
-
Jaeger T and Flohe L. The thiol-based redox networks of pathogens: unexploited targets in the search for new drugs. Biofactors 27: 109-120, 2006.
-
(2006)
Biofactors
, vol.27
, pp. 109-120
-
-
Jaeger, T.1
Flohe, L.2
-
35
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong H, Mason SP, Barabasi AL, and Oltvai ZN. Lethality and centrality in protein networks. Nature 411: 41-42, 2001.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
36
-
-
33744962865
-
Redefining oxidative stress
-
Jones DP. Redefining oxidative stress. Antioxid Redox Signal 8: 1865-1879, 2006.
-
(2006)
Antioxid Redox Signal
, vol.8
, pp. 1865-1879
-
-
Jones, D.P.1
-
37
-
-
55149107716
-
Radical-free biology of oxidative stress
-
Jones DP. Radical-free biology of oxidative stress. Am J Physiol Cell Physiol 295: C849-C868, 2008.
-
(2008)
Am J Physiol Cell Physiol
, vol.295
-
-
Jones, D.P.1
-
38
-
-
77958608330
-
Redox sensing: Orthogonal control in cell cycle and apoptosis signalling
-
Jones DP. Redox sensing: orthogonal control in cell cycle and apoptosis signalling. J Intern Med 268: 432-448, 2010.
-
(2010)
J Intern Med
, vol.268
, pp. 432-448
-
-
Jones, D.P.1
-
39
-
-
79851512636
-
Mapping the cysteine proteome: Analysis of redox-sensing thiols
-
Jones DP and Go YM. Mapping the cysteine proteome: analysis of redox-sensing thiols. Curr Opin Chem Biol 15: 103-112, 2011.
-
(2011)
Curr Opin Chem Biol
, vol.15
, pp. 103-112
-
-
Jones, D.P.1
Go, Y.M.2
-
40
-
-
84864258618
-
A whole-cell computational model predicts phenotype from genotype
-
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Jr., Assad-Garcia N, Glass JI, and Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell 150: 389-401, 2012.
-
(2012)
Cell
, vol.150
, pp. 389-401
-
-
Karr, J.R.1
Sanghvi, J.C.2
MacKlin, D.N.3
Gutschow, M.V.4
Jacobs, J.M.5
Bolival, Jr.B.6
Assad-Garcia, N.7
Glass, J.I.8
Covert, M.W.9
-
41
-
-
39949085437
-
Nonequilibrium thermodynamics of thiol/disulfide redox systems: A perspective on redox systems biology
-
Kemp M, Go YM, and Jones DP. Nonequilibrium thermodynamics of thiol/disulfide redox systems: a perspective on redox systems biology. Free Radic Biol Med 44: 921-937, 2008.
-
(2008)
Free Radic Biol Med
, vol.44
, pp. 921-937
-
-
Kemp, M.1
Go, Y.M.2
Jones, D.P.3
-
42
-
-
34147189103
-
Systems biology standards-the community speaks
-
Klipp E, Liebermeister W, Helbig A, Kowald A, and Schaber J. Systems biology standards-the community speaks. Nat Biotechnol 25: 390-391, 2007.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 390-391
-
-
Klipp, E.1
Liebermeister, W.2
Helbig, A.3
Kowald, A.4
Schaber, J.5
-
43
-
-
84861706924
-
Mechanisms and dynamics in the thiol/disulfide redox regulatory network: Transmitters, sensors and targets
-
Konig J, Muthuramalingam M, and Dietz KJ. Mechanisms and dynamics in the thiol/disulfide redox regulatory network: transmitters, sensors and targets. Curr Opin Plant Biol 15: 261-268, 2012.
-
(2012)
Curr Opin Plant Biol
, vol.15
, pp. 261-268
-
-
Konig, J.1
Muthuramalingam, M.2
Dietz, K.J.3
-
44
-
-
33745322651
-
Glu-tathione half-cell reduction potential: A universal stress marker and modulator of programmed cell death?
-
Kranner I, Birtic S, Anderson KM, and Pritchard HW. Glu-tathione half-cell reduction potential: a universal stress marker and modulator of programmed cell death? Free Radic Biol Med 40: 2155-2165, 2006.
-
(2006)
Free Radic Biol Med
, vol.40
, pp. 2155-2165
-
-
Kranner, I.1
Birtic, S.2
Anderson, K.M.3
Pritchard, H.W.4
-
45
-
-
79953906141
-
The pentose phosphate pathway is a metabolic redox sensor and regulates transcription during the antioxidant response
-
Kruger A, Gruning NM, Wamelink MM, Kerick M, Kirpy A, Parkhomchuk D, Bluemlein K, Schweiger MR, Soldatov A, Lehrach H, Jakobs C, and Ralser M. The pentose phosphate pathway is a metabolic redox sensor and regulates transcription during the antioxidant response. Antioxid Redox Signal 15: 311-324, 2011.
-
(2011)
Antioxid Redox Signal
, vol.15
, pp. 311-324
-
-
Kruger, A.1
Gruning, N.M.2
Wamelink, M.M.3
Kerick, M.4
Kirpy, A.5
Parkhomchuk, D.6
Bluemlein, K.7
Schweiger, M.R.8
Soldatov, A.9
Lehrach, H.10
Jakobs, C.11
Ralser, M.12
-
46
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, and Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23: 1509-1515, 2005.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1509-1515
-
-
Le Novere, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
Collado-Vides, J.6
Crampin, E.J.7
Halstead, M.8
Klipp, E.9
Mendes, P.10
Nielsen, P.11
Sauro, H.12
Shapiro, B.13
Snoep, J.L.14
Spence, H.D.15
Wanner, B.L.16
-
47
-
-
77953934646
-
BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, and Laibe C. BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4: 92, 2010.
-
(2010)
BMC Syst Biol
, vol.4
, Issue.92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.I.10
Snoep, J.L.11
Hucka, M.12
Le Novere, N.13
Laibe, C.14
-
48
-
-
84860918589
-
MINT, the molecular interaction database: 2012 update
-
Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, and Cesareni G. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40: D857-D861, 2012.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Licata, L.1
Briganti, L.2
Peluso, D.3
Perfetto, L.4
Iannuccelli, M.5
Galeota, E.6
Sacco, F.7
Palma, A.8
Nardozza, A.P.9
Santonico, E.10
Castagnoli, L.11
Cesareni, G.12
-
49
-
-
79957441981
-
The disulfide proteome and other reactive cysteine proteomes: Analysis and functional significance
-
Lindahl M, Mata-Cabana A, and Kieselbach T. The disulfide proteome and other reactive cysteine proteomes: analysis and functional significance. Antioxid Redox Signal 14: 2581-2642, 2011.
-
(2011)
Antioxid Redox Signal
, vol.14
, pp. 2581-2642
-
-
Lindahl, M.1
Mata-Cabana, A.2
Kieselbach, T.3
-
50
-
-
79955879494
-
Controllability of complex networks
-
Liu YY, Slotine JJ, and Barabasi AL. Controllability of complex networks. Nature 473: 167-173, 2011.
-
(2011)
Nature
, vol.473
, pp. 167-173
-
-
Liu, Y.Y.1
Slotine, J.J.2
Barabasi, A.L.3
-
51
-
-
26444433869
-
In-tracellular redox state: Towards quantitative description
-
Martinovich GG, Cherenkevich SN, and Sauer H. In-tracellular redox state: towards quantitative description. Eur Biophys J 34: 937-942, 2005.
-
(2005)
Eur Biophys J
, vol.34
, pp. 937-942
-
-
Martinovich, G.G.1
Cherenkevich, S.N.2
Sauer, H.3
-
52
-
-
33947619951
-
Graph theory and networks in Biology
-
Mason O and Verwoerd M. Graph theory and networks in Biology. IET Syst Biol 1: 89-119, 2007.
-
(2007)
IET Syst Biol
, vol.1
, pp. 89-119
-
-
Mason, O.1
Verwoerd, M.2
-
53
-
-
31744435331
-
Control of glu-tathione and phytochelatin synthesis under cadmium stress. Pathway modelling for plants
-
Mendoza-Cotzatl DG and Moreno-Sanchez R. Control of glu-tathione and phytochelatin synthesis under cadmium stress. Pathway modelling for plants. J Theor Biol 238: 919-936, 2006.
-
(2006)
J Theor Biol
, vol.238
, pp. 919-936
-
-
Mendoza-Cotzatl, D.G.1
Moreno-Sanchez, R.2
-
54
-
-
51349088530
-
Molecular mechanisms and clinical implications of reversible protein S-glutathionylation
-
Mieyal JJ, Gallogly MM, Qanungo S, Sabens EA, and Shelton MD. Molecular mechanisms and clinical implications of reversible protein S-glutathionylation. Antioxid Redox Signal 10: 1941-1988, 2008.
-
(2008)
Antioxid Redox Signal
, vol.10
, pp. 1941-1988
-
-
Mieyal, J.J.1
Gallogly, M.M.2
Qanungo, S.3
Sabens, E.A.4
Shelton, M.D.5
-
55
-
-
36048938363
-
The rate of cellular hydrogen peroxide removal shows dependency on GSH: Mathematical insight into in vivo H2O2 and GPx concentrations
-
Ng CF, Schafer FQ, Buettner GR, and Rodgers VG. The rate of cellular hydrogen peroxide removal shows dependency on GSH: mathematical insight into in vivo H2O2 and GPx concentrations. Free Radic Res 41: 1201-1211, 2007.
-
(2007)
Free Radic Res
, vol.41
, pp. 1201-1211
-
-
Ng, C.F.1
Schafer, F.Q.2
Buettner, G.R.3
Rodgers, V.G.4
-
56
-
-
33845917628
-
Reactions of yeast thioredoxin peroxidases i and II with hydrogen peroxide and peroxynitrite: Rate constants by competitive kinetics
-
Ogusucu R, Rettori D, Munhoz DC, Netto LE, and Augusto O. Reactions of yeast thioredoxin peroxidases I and II with hydrogen peroxide and peroxynitrite: rate constants by competitive kinetics. Free Radic Biol Med 42: 326-334, 2007.
-
(2007)
Free Radic Biol Med
, vol.42
, pp. 326-334
-
-
Ogusucu, R.1
Rettori, D.2
Munhoz, D.C.3
Netto, L.E.4
Augusto, O.5
-
57
-
-
4544344218
-
Web-based kinetic modelling using JWS Online
-
Olivier BG and Snoep JL. Web-based kinetic modelling using JWS Online. Bioinformatics 20: 2143-2144, 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 2143-2144
-
-
Olivier, B.G.1
Snoep, J.L.2
-
58
-
-
0041761698
-
Functions of thiol-disulfide oxidoreductases in E. coli: Redox myths, realities, and practicalities
-
Ortenberg R and Beckwith J. Functions of thiol-disulfide oxidoreductases in E. coli: redox myths, realities, and practicalities. Antioxid Redox Signal 5: 403-411, 2003.
-
(2003)
Antioxid Redox Signal
, vol.5
, pp. 403-411
-
-
Ortenberg, R.1
Beckwith, J.2
-
60
-
-
58249083279
-
Enzymes or redox couples? the kinetics of thioredoxin and glutaredoxin reactions in a systems biology context
-
Pillay CS, Hofmeyr JH, Olivier BG, Snoep JL, and Rohwer JM. Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context. Biochem J 417: 269-275, 2009.
-
(2009)
Biochem J
, vol.417
, pp. 269-275
-
-
Pillay, C.S.1
Hofmeyr, J.H.2
Olivier, B.G.3
Snoep, J.L.4
Rohwer, J.M.5
-
61
-
-
78951478981
-
The logic of kinetic regulation in the thioredoxin system
-
Pillay CS, Hofmeyr JH, and Rohwer JM. The logic of kinetic regulation in the thioredoxin system. BMC Syst Biol 5: 15, 2011.
-
(2011)
BMC Syst Biol
, vol.5
, Issue.15
-
-
Pillay, C.S.1
Hofmeyr, J.H.2
Rohwer, J.M.3
-
62
-
-
37549072681
-
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress
-
Ralser M, Wamelink MM, Kowald A, Gerisch B, Heeren G, Struys EA, Klipp E, Jakobs C, Breitenbach M, Lehrach H, and Krobitsch S. Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. J Biol 6: 10, 2007.
-
(2007)
J Biol
, vol.6
, pp. 10
-
-
Ralser, M.1
Wamelink, M.M.2
Kowald, A.3
Gerisch, B.4
Heeren, G.5
Struys, E.A.6
Klipp, E.7
Jakobs, C.8
Breitenbach, M.9
Lehrach, H.10
Krobitsch, S.11
-
63
-
-
0034770083
-
Roles of thiol-redox pathways in bacteria
-
Ritz D and Beckwith J. Roles of thiol-redox pathways in bacteria. Annu Rev Microbiol 55: 21-48, 2001.
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 21-48
-
-
Ritz, D.1
Beckwith, J.2
-
64
-
-
0035371184
-
Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple
-
Schafer FQ and Buettner GR. Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple. Free Radic Biol Med 30: 1191-1212, 2001.
-
(2001)
Free Radic Biol Med
, vol.30
, pp. 1191-1212
-
-
Schafer, F.Q.1
Buettner, G.R.2
-
65
-
-
77951612556
-
BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, and Palsson BO. BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinform 11: 213, 2010.
-
(2010)
BMC Bioinform
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
66
-
-
32044435851
-
Towards building the silicon cell: A modular approach
-
Snoep JL, Bruggeman F, Olivier BG, and Westerhoff HV. Towards building the silicon cell: a modular approach. Biosystems 83: 207-216, 2006.
-
(2006)
Biosystems
, vol.83
, pp. 207-216
-
-
Snoep, J.L.1
Bruggeman, F.2
Olivier, B.G.3
Westerhoff, H.V.4
-
67
-
-
84856991721
-
Mathematics. Critical truths about power laws
-
Stumpf MP and Porter MA. Mathematics. Critical truths about power laws. Science 335: 665-666, 2012.
-
(2012)
Science
, vol.335
, pp. 665-666
-
-
Stumpf, M.P.1
Porter, M.A.2
-
68
-
-
15444372528
-
Subnets of scale-free networks are not scale-free: Sampling properties of networks
-
Stumpf MP, Wiuf C, and May RM. Subnets of scale-free networks are not scale-free: sampling properties of networks. Proc Natl Acad Sci U S A 102: 4221-4224, 2005.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 4221-4224
-
-
Stumpf, M.P.1
Wiuf, C.2
May, R.M.3
-
69
-
-
84867313408
-
RedoxDB-a curated database for experimentally verified protein oxidative modification
-
Sun MA, Wang Y, Cheng H, Zhang Q, Ge W, and Guo D. RedoxDB-a curated database for experimentally verified protein oxidative modification. Bioinformatics 28: 2551-2552, 2012.
-
(2012)
Bioinformatics
, vol.28
, pp. 2551-2552
-
-
Sun, M.A.1
Wang, Y.2
Cheng, H.3
Zhang, Q.4
Ge, W.5
Guo, D.6
-
70
-
-
77956048572
-
Genome-scale metabolic networks
-
Terzer M, Maynard ND, Covert MW, and Stelling J. Genome-scale metabolic networks. Wiley Interdiscip Rev Syst Biol Med 1: 285-297, 2009.
-
(2009)
Wiley Interdiscip Rev Syst Biol Med
, vol.1
, pp. 285-297
-
-
Terzer, M.1
Maynard, N.D.2
Covert, M.W.3
Stelling, J.4
-
71
-
-
79851510399
-
The redoxome: Proteomic analysis of cellular redox networks
-
Thamsen M and Jakob U. The redoxome: proteomic analysis of cellular redox networks. Curr Opin Chem Biol 15: 113-119, 2011.
-
(2011)
Curr Opin Chem Biol
, vol.15
, pp. 113-119
-
-
Thamsen, M.1
Jakob, U.2
-
72
-
-
34447518686
-
The system biology of thiol redox system in Escherichia coli and yeast: Differential functions in oxidative stress, iron metabolism and DNA synthesis
-
Toledano MB, Kumar C, Le Moan N, Spector D, and Tacnet F. The system biology of thiol redox system in Escherichia coli and yeast: differential functions in oxidative stress, iron metabolism and DNA synthesis. FEBS Lett 581: 3598-3607, 2007.
-
(2007)
FEBS Lett
, vol.581
, pp. 3598-3607
-
-
Toledano, M.B.1
Kumar, C.2
Le Moan, N.3
Spector, D.4
Tacnet, F.5
-
73
-
-
0037297417
-
Non-reciprocal regulation of the redox state of the glutathione- glutaredoxin and thioredoxin systems
-
Trotter EW and Grant CM. Non-reciprocal regulation of the redox state of the glutathione-glutaredoxin and thioredoxin systems. EMBO Rep 4: 184-188, 2003.
-
(2003)
EMBO Rep
, vol.4
, pp. 184-188
-
-
Trotter, E.W.1
Grant, C.M.2
-
74
-
-
58149305794
-
An empirical framework for binary interactome mapping
-
Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabasi AL, and Vidal M. An empirical framework for binary interactome mapping. Nat Methods 6: 83-90, 2009.
-
(2009)
Nat Methods
, vol.6
, pp. 83-90
-
-
Venkatesan, K.1
Rual, J.F.2
Vazquez, A.3
Stelzl, U.4
Lemmens, I.5
Hirozane-Kishikawa, T.6
Hao, T.7
Zenkner, M.8
Xin, X.9
Goh, K.I.10
Yildirim, M.A.11
Simonis, N.12
Heinzmann, K.13
Gebreab, F.14
Sahalie, J.M.15
Cevik, S.16
Simon, C.17
De Smet, A.S.18
Dann, E.19
Smolyar, A.20
Vinayagam, A.21
Yu, H.22
Szeto, D.23
Borick, H.24
Dricot, A.25
Klitgord, N.26
Murray, R.R.27
Lin, C.28
Lalowski, M.29
Timm, J.30
Rau, K.31
Boone, C.32
Braun, P.33
Cusick, M.E.34
Roth, F.P.35
Hill, D.E.36
Tavernier, J.37
Wanker, E.E.38
Barabasi, A.L.39
Vidal, M.40
more..
-
75
-
-
79952674000
-
Interactome networks and human disease
-
Vidal M, Cusick ME, and Barabasi AL. Interactome networks and human disease. Cell 144: 986-998, 2011.
-
(2011)
Cell
, vol.144
, pp. 986-998
-
-
Vidal, M.1
Cusick, M.E.2
Barabasi, A.L.3
-
76
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, and Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403, 2002.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
Von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
77
-
-
5044227742
-
The evolution of molecular biology into systems biology
-
Westerhoff HV and Palsson BO. The evolution of molecular biology into systems biology. Nat Biotechnol 22: 1249-1252, 2004.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1249-1252
-
-
Westerhoff, H.V.1
Palsson, B.O.2
-
78
-
-
34250658998
-
Bayesian methods in bioinformatics and computational systems biology
-
Wilkinson DJ. Bayesian methods in bioinformatics and computational systems biology. Brief Bioinform 8: 109-116, 2007.
-
(2007)
Brief Bioinform
, vol.8
, pp. 109-116
-
-
Wilkinson, D.J.1
-
79
-
-
48449107159
-
Thiol chemistry and specificity in redox signaling
-
Winterbourn CC and Hampton MB. Thiol chemistry and specificity in redox signaling. Free Radic Biol Med 45: 549-561, 2008.
-
(2008)
Free Radic Biol Med
, vol.45
, pp. 549-561
-
-
Winterbourn, C.C.1
Hampton, M.B.2
-
80
-
-
33845997473
-
Modeling the reactions of superoxide and myeloperoxidase in the neutrophil phagosome: Implications for microbial killing
-
Winterbourn CC, Hampton MB, Livesey JH, and Kettle AJ. Modeling the reactions of superoxide and myeloperoxidase in the neutrophil phagosome: implications for microbial killing. J Biol Chem 281: 39860-39869, 2006.
-
(2006)
J Biol Chem
, vol.281
, pp. 39860-39869
-
-
Winterbourn, C.C.1
Hampton, M.B.2
Livesey, J.H.3
Kettle, A.J.4
-
81
-
-
34247622363
-
The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
-
Yu H, Kim PM, Sprecher E, Trifonov V, and Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Com-put Biol 3: e59, 2007.
-
(2007)
PLoS Com-put Biol
, vol.3
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
Trifonov, V.4
Gerstein, M.5
|