ライフサイエンスコーパス: metabolic network

1 he gene products' catalyzed reactions in the metabolic network.

2 erstood from the topological features of the metabolic network.

3 the set of reactions used to fill gaps in a metabolic network.

4 predicted enzymatic reactions in the tomato metabolic network.

5 xity and the plasticity of the plant primary metabolic network.

6 the carbon and nitrogen flows in the fungal metabolic network.

7 nesis in the context of a perturbed systemic metabolic network.

8 in scale from atomistic details to an entire metabolic network.

9 rs, in the context of the human genome-scale metabolic network.

10 uate progress in reconstruction of the yeast metabolic network.

11 ng such enzyme promiscuity in the space of a metabolic network.

12 PK is indeed a member of the plant terpenoid metabolic network.

13 presence of a reaction in a given organism's metabolic network.

14 evaluated using Parkinson's disease-related metabolic network.

15 disorder is itself associated with a unique metabolic network.

16 nd overlay the transcriptional response on a metabolic network.

17 e ito977 model of Saccharomyces cerevisiae's metabolic network.

18 ealed nonuniform assimilation throughout the metabolic network.

19 ivity of enamines and imines may perturb the metabolic network.

20 rts inhibition of all other reactions in the metabolic network.

21 e number of overall reactions or size of the metabolic network.

22 ation is pivotal to understanding the larger metabolic network.

23 and their products, regulatory circuits and metabolic networks.

24 s is thermodynamically constrained in modern metabolic networks.

25 nformation on the function and regulation of metabolic networks.

26 annotation of enzymes and the description of metabolic networks.

27 ting structural and functional properties of metabolic networks.

28 nctional predictions made with the resulting metabolic networks.

29 rate estimation of metabolic fluxes in large metabolic networks.

30 Illustrator (SAMMI) for the visualization of metabolic networks.

31 graph search to work in the context of these metabolic networks.

32 nsion over available reconstructed bacterial metabolic networks.

33 ) by employing state-of-the-art genome-scale metabolic networks.

34 ore different time-dependent ecosystem-level metabolic networks.

35 t on the host regulation of cecum-associated metabolic networks.

36 tative method for determining fluxes through metabolic networks.

37 bolites that anchored interconnected central metabolic networks.

38 f the Gene ontology and the KEGG database of metabolic networks.

39 athways to these compounds in large putative metabolic networks.

40 scover enzymes of previously uncharacterized metabolic networks.

41 ns that link chloroplastic and mitochondrial metabolic networks.

42 studies have also yielded novel insight into metabolic networks.

43 biochemical reactions that constitute plant metabolic networks.

44 al associations to generate richly connected metabolic networks.

45 the composition, structure and regulation of metabolic networks.

46 tracing data into annotated or custom-built metabolic networks.

47 ve been used successfully to simulate cancer metabolic networks.

48 able to analyze large-scale and genome-scale metabolic networks.

49 data representing flows of materials within metabolic networks.

50 sed by measuring the carbon flow through the metabolic network ((13)C-metabolic flux analysis) in dev

51 cells can concurrently decrease the elevated metabolic network activity in parkinsonian brains on an

52 nts are important in providing the necessary metabolic network activity.

53 bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions,

54 gulation, as well as how the actions of this metabolic network affect other cells in the tumor microe

55 ese strain optimization algorithms utilize a metabolic network alone, with few approaches providing s

56 Both correlation studies and metabolic network analyses allowed the description of a

57 generated from an unbiased correlation-based metabolic network analysis (approach 2), and the results

58 We conclude that metabolic network analysis confirmed the validity of the

59 armacogenomic and clinical data with a human metabolic network and find that non-pharmacokinetic meta

60 ome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles.

61 randomly delete a number of reactions from a metabolic network and rate the different algorithms on t

62 ue to their analysis within the context of a metabolic network and reinforces the relevance of the ap

63 etatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches

64 ve enabled the estimation of a multi-species metabolic network and the associated short-term response

65 fine-tune the balance between the endogenous metabolic network and the introduced enzymes.

66 acting pairs of organisms within a community metabolic network and whether that interaction has a pos

67 gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these

68 ctories, (iii) metabolic entropies, and (iv) metabolic networks and correlations in space and time.

69 than the antagonized strain: that is, larger metabolic networks and growth on more carbon sources.

70 to differential regulation of adipose tissue metabolic networks and inflammatory pathways, increased

71 l fingerprints to efficiently navigate large metabolic networks and propose enzymatic connections bet

72 our understanding of cellular signalling and metabolic networks and resulted in variety of applicatio

73 The reconstruction of metabolic networks and the three-dimensional coverage of

74 NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as

75 onding biosynthetic pathway, and the role of metabolic network architecture in optimizing its functio

76 bolites are preserved in fossils and because metabolic networks are difficult to experimentally chara

77 Metabolic networks are extensively regulated to facilita

78 g the transition in order to determine which metabolic networks are operational.

79 Metabolic networks are webs of integrated reactions orga

80 ) was proposed to determine the hot spots in metabolic networks, around which transcriptional regulat

81 e way for the reconstruction of genome-scale metabolic networks as a powerful tool for understanding

82 for fast, context-specific visualization of metabolic networks as well as the development of standar

83 L-fucose major changes in the central carbon metabolic network, as well as an increased activity of t

84 pping the global structure of the organism's metabolic network at a given instant.

85 proach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity sc

86 dependence of the human red blood cell (RBC) metabolic network between 4 and 37 degrees C through abs

87 Essential metabolic networking between these compartments and thei

88 This synergistic remodeling of hepatic metabolic networks blunted inflammatory onset, prevented

89 line of communication between signaling and metabolic networks, but also highlight the unusual abili

90 his work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzyme

91 learners, because they require knowledge of metabolic networks, carbon transitions, and computer pro

92 ye movement sleep behaviour disorder-related metabolic network characterized by increased activity in

93 y reported more complex methods that rely on metabolic network comparisons.

94 ndrial functional alterations and changes in metabolic networks connected to mitochondria following H

95 riacylglycerol (TAG) biosynthesis involves a metabolic network containing multiple different diacylgl

96 ions may have altered the microbiota-host co-metabolic network, contributing to the growing list of W

97 We compiled metabolic networks corresponding to four healthy and can

98 Metabolic network databases are of increasing importance

99 Unable to generate new enzyme paradigms and metabolic networks de novo, organisms have evolved strat

100 and for exploring the way in which the plant metabolic network delivers specific outcomes in differen

101 Cells need to rewire their metabolic network depending on the available carbon sour

102 particular genes on or off, and that complex metabolic networks determine the levels of transcription

103 Here we show that metabolic networks differ significantly in their intrins

104 wn that the induction of the galactose (GAL) metabolic network does not solely depend on the exhausti

105 rs of evolution have yielded today's complex metabolic networks driven by efficient and highly specia

106 enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ec

107 he functions of TPP in the regulation of the metabolic networks during photoperiod transition using p

108 nalyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted).

109 tabolic liabilities in ccRCC, whose emergent metabolic network enforces outstanding anabolic requirem

110 bolic network, we observe that these ruminal metabolic networks exhibit properties consistent with di

111 ections and challenges faced by the field of metabolic network flux phenotyping.

112 e main computational approach for predicting metabolic network fluxes, flux balance analysis, often u

113 s work aimed at reconstructing a carbon core metabolic network for D. salina CCAP 19/18 based on the

114 bon pathway (SGOCP) is a crucially important metabolic network for tumorigenesis, of unanticipated co

115 tion has been a great success in redesigning metabolic networks for biochemical overproduction.

116 indicating that Arabidopsis lacks efficient metabolic networks for biosynthesis and catabolism of hy

117 In the web-service, we have pre-assembled metabolic networks for humans, mice, Arabidopsis and yea

118 To explore the metabolic networks for nitrogen assimilation in this bac

119 sults define core properties of the nitrogen metabolic network from M. tuberculosis, such as: (i) the

120 driver reactions facilitating control of 23 metabolic networks from all kingdoms of life.

121 fying the necessary condition are present in metabolic networks from diverse species, suggesting prev

122 ns converges to an organo-sulfur-based proto-metabolic network fuelled by a thioester- and redox-driv

123 ites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding ce

124 -sensitive gene groups (Gene Ontology terms, metabolic networks, gene families, and predicted interac

125 ms biology framework, such as a Genome-Scale Metabolic Network (GSMN) that allows the dynamic interac

126 de novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome,

127 fficient calculation of EFMs in genome-scale metabolic networks (GSMNs) is still a challenge.

128 onstraints on the predictive capabilities of metabolic networks has not been investigated in detail.

129 The genome-scale models of metabolic networks have been broadly applied in phenotyp

130 Genome scale metabolic networks have been used to study prokaryotes a

131 HepatoDyn includes a large metabolic network, highly detailed kinetic laws, and is

132 nderstanding and manipulation of genetic and metabolic networks; however, their implementation in the

133 entify biologically tolerable diversity of a metabolic network in an optimized culture.

134 c tracing of glycerol flux through the lipid metabolic network in developing seeds.

135 a side-by-side comparison in a medium scale metabolic network in Escherichia Coli, we show that aCFP

136 mporal and dynamic changes of the eicosanoid metabolic network in mouse bone marrow-derived macrophag

137 Our results suggest a flexible metabolic network in P. tricornutum that tunes intercomp

138 ng of the complex regulatory mechanisms of a metabolic network in response to chilling injury in toma

139 is of the Arabidopsis (Arabidopsis thaliana) metabolic network in the chloroplast and related cellula

140 However, the role of astroglial metabolic networks in behavior is unclear.

141 systems by exploiting the crosstalk between metabolic networks in cells, leading to a protein enviro

142 The complexity of metabolic networks in microbial communities poses an unr

143 Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to en

144 vious conceptual models describing microbial metabolic networks in OMZs.

145 scuss how recent efforts delineating rewired metabolic networks in pancreatic cancer have revealed ne

146 rative resource to study transcriptional and metabolic networks in skeletal muscle in the context of

147 r knowledge, regulation of the proteomic and metabolic networks in the ShB-resistant transgenic rice

148 To better explore the reconfiguration of metabolic networks in these transformants, we generated

149 Here we show that metabolic networks include a hierarchy of reactions base

150 synaptic plasticity in stress by astrocytic metabolic networks indicates a broader role of astrocyte

151 ade possible by allosteric regulation of the metabolic network, interplay between the signaling pathw

152 ems monitoring, new biomarkers discovery and metabolic network investigations.

153 Anchorage-independent growth reprogrammes a metabolic network involving serine, alanine and pyruvate

154 Our results indicate resilience of the metabolic network irrespective of inflammation.

155 onclude that the reconstruction of the yeast metabolic network is indeed gradually improving through

156 on of the serine, glycine, one-carbon (SGOC) metabolic network is required for neuroendocrine prostat

157 viability, suggesting that the mitochondrial metabolic network is unable to compensate when exposed t

158 Understanding the control of large-scale metabolic networks is central to biology and medicine.

159 Uncovering the underlying metabolic networks is essential for elucidating the phys

160 Our understanding of individual metabolic networks is increasing as we learn more about

161 Gap filling for the reconstruction of metabolic networks is to restore the connectivity of met

162 Taken together, our experimentally validated metabolic network leads to a deeper understanding of the

163 olic rates) but has not been examined at the metabolic network level.

164 nomy can be considerably more similar at the metabolic network level.

165 the metabolomics data revealed that the same metabolic network-level trends previously reported for R

166 Metabolic network mapping is a widely used approach for

167 ourse metabolomic data within the context of metabolic network maps.

168 UF1 bacterium, through which the commensal metabolic network may improve gut bacterial cross-feedin

169 These results suggest how metabolic networks may balance costs and benefits, with

170 ms, which are prohibitively slow as putative metabolic networks may exceed 1 million compounds.

171 Abnormal metabolic networks may provide markers of idiopathic rap

172 es, found from the solution of a constrained metabolic network model of the cellular metabolism, to t

173 onding metabolic states using a genome-scale metabolic network model.

174 Stoichiometric metabolic network modeling integrated with "omics" data

175 terogeneity, we performed spatially-resolved metabolic network modeling of the prostate cancer microe

176 s inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies uti

177 microbial community function using microbial metabolic network modeling.

178 bacteria using metabolomics and genome-based metabolic network modeling.

179 pply MONGOOSE to the analysis of 98 existing metabolic network models and find that the biomass react

180 sets for the construction of tissue-specific metabolic network models and to constrain the range of p

181 Gene regulatory and metabolic network models have been used successfully in

182 Genome-scale metabolic network models have been used successfully to

183 gh nonengineered reactions of the endogenous metabolic network must also adapt, which is not evident

184 The metabolic network of a cell represents the catabolic and

185 The curated model of the metabolic network of Anabaena sp. PCC 7120 enhances our

186 The reconstructed metabolic network of D. salina presented in this work is

187 Folate-mediated one-carbon metabolism is a metabolic network of interconnected pathways that is req

188 ach containing the full genome and predicted metabolic network of one organism, including metabolites

189 daptations of microbial community structure, metabolic network of SOC decomposition, and trophic inte

190 The metabolic network of sphingolipids plays important roles

191 Here, we reconstructed a genome-scale metabolic network of the rat liver that will allow for e

192 describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic pro

193 of structures and functions of genome-scale metabolic networks of 17 microorganisms.

194 ens that target multiple pathways within the metabolic networks of activated human T cells.

195 ome compositions could be used to deduce the metabolic networks of Earth's earliest ecosystems and, p

196 We apply it to metabolic networks of increasing dimensionality.

197 o have played a key role in the evolution of metabolic networks of photosynthetic organisms by connec

198 ral carbon sources and the other by creating metabolic networks of predicted genomes.

199 end to function at the interface between the metabolic networks of the host and pathogen.

200 ons are reflected in the organization of the metabolic networks of the interacting species, and intro

201 Kinetic models of metabolic networks offer the promise of quantitative phe

202 iver models described either by genome scale metabolic networks or an object-oriented approach.

203 ce towards a unique solution either in large metabolic networks or when small sets of measurements ar

204 On directed metabolic networks, our framework yields insights into p

205 Electric and metabolic network parameters were measured using several

206 principle, poor scalability with the size of metabolic networks, potential numeric issues or low quan

207 ximum a posteriori estimation in a synthetic metabolic network problem with a larger number of parame

208 nally quantify how robustly a genome-derived metabolic network produces a given set of metabolites un

209 ntegrating gene regulation data with a human metabolic network prompted the establishment of an open-

210 enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balance

211 scale models of the Saccharomyces cerevisiae metabolic network published since 2003 to evaluate progr

212 Metabolic network reconstruction and assessment of metab

213 Metabolic network reconstruction and associated fecal me

214 Utilizing a metabolic network reconstruction for the model organism

215 rulence-linked pathways using a genome-scale metabolic network reconstruction of Pseudomonas aerugino

216 Using both linear models and a genome-scale metabolic network reconstruction of the parasite to inte

217 Current methods for automated metabolic network reconstruction rely on gene and reacti

218 process of deriving a metabolic model from a metabolic network reconstruction to facilitate mechanist

219 We combine metabolic network reconstruction with metatranscriptomic

220 Genome-scale metabolic network reconstructions (GENREs) are repositor

221 Genome-scale metabolic network reconstructions also enable a high-thr

222 ontextualize essentiality using genome-scale metabolic network reconstructions and demonstrate the ut

223 Metabolic network reconstructions are often incomplete.

224 Over the last decade, genome-scale metabolic network reconstructions have assisted in our a

225 Bottom-up metabolic network reconstructions have been developed fo

226 formalized methods to quantitatively assess metabolic network reconstructions independently of any p

227 constraints reduce the feasible space, draft metabolic network reconstructions may need more extensiv

228 Genome-scale metabolic network reconstructions reveal metabolic diffe

229 For most metabolic network reconstructions tested, BoostGAPFILL s

230 nd integrate this modeling with genome-scale metabolic network reconstructions to identify metabolic

231 roof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the var

232 Medusa to guide the curation of genome-scale metabolic network reconstructions.

233 on and analysis of ensembles of genome-scale metabolic network reconstructions.

234 Since changes in the metabolic network reflect interactions between genetic,

235 we are challenged with understanding global metabolic network regulation and the resulting metabolic

236 However, the contribution of the broader metabolic network, relevant to species-specific strategi

237 Redundancy in this complex metabolic network renders the rational engineering of cy

238 often been limited to targeted or simplified metabolic network representations due to computational d

239 building and analyzing models use different metabolic network representations.

240 we use manifold learning to map the space of metabolic networks representing thousands of bacterial g

241 Given this paradox, the metabolic network required to sustain the Fe-scavenging

242 is insufficient, whereas viewing the entire metabolic network results in information overload.

243 Metabolic network rewiring is the rerouting of metabolis

244 example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vit

245 Thus, Cx43-mediated astrocyte metabolic networks serve as an endogenous mechanism used

246 Finally, analysis of gene and metabolic networks showed that OT triggers cell apoptosi

247 enting complex cellular processes, including metabolic networks, signal transduction and gene regulat

248 Computational approaches, such as metabolic network simulations and machine learning, coul

249 crobes that had evolved enzyme machinery and metabolic network stability in the anoxic world.

250 Deciphering the mechanisms of regulation of metabolic networks subjected to perturbations, including

251 How primordial metabolic networks such as the reverse tricarboxylic aci

252 yotic species, the software provides several metabolic network templates, including those for chemohe

253 is less sensitive to the completeness of the metabolic network than pFBA.

254 utida KT2440 to investigate the constitutive metabolic network that achieves co-utilization of glucos

255 ws how coupled catalytic cycles can create a metabolic network that allows the creation and persevera

256 tabolic model (GEM) of the Toxoplasma gondii metabolic network that incorporates genetic, transcripto

257 dary metabolites as integrated components of metabolic networks that are dynamically shaped by enviro

258 rotrophic microorganisms, creating intricate metabolic networks that determine the extent of carbon r

259 ely that there can exist different community metabolic networks that have the same metabolic inputs a

260 gnificant impact on our ability to use large metabolic networks that lack annotation of promiscuous r

261 rial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield.

262 ition, pancreatic cancer cells have adaptive metabolic networks that sustain proliferation in vitro a

263 As one of the key nodes in the metabolic network, the forkhead transcription factor FOX

264 For example, for metabolic networks, these decisions include (1) how to i

265 straint-based reconstruction and analysis of metabolic networks, this uncertainty is present both dur

266 eliably defines the qualitative state of the metabolic network throughout this metabolic decay proces

267 produce biomass, influence the state of the metabolic network thus directly affecting predictions.

268 rated transcriptional regulatory network and metabolic network to guide metabolic engineering applica

269 es gene expression measurements into a human metabolic network to infer new cancer-mediated pathway c

270 etabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism.

271 transcriptional, epigenetic, signalling and metabolic networks to constitute multi-lineage competenc

272 vates kinases including AKT/mTOR that engage metabolic networks to support the energetic demands of a

273 te determines these interaction indices from metabolic network topology, and can be used for small- o

274 Metabolic networks undergo gene expression regulation in

275 Maternal metabolites and metabolic networks underlying associations between mater

276 reconstruction of the cardiac mitochondrial metabolic network using constraint-based methods, under

277 rapid parameterization of kinetic models of metabolic networks using a curated metabolic model and a

278 es a framework for comprehensive analysis of metabolic networks using mass balances and elementary me

279 n the development of other organism-specific metabolic network visualizations.

280 The metabolic network was constructed using the P. tricornut

281 tion of the (13)C/(15)N label throughout the metabolic network was evaluated with gas chromatography-

282 introduces a second catalytic cycle into the metabolic network, was used to close the first cycle.

283 or linking the microbial network to a bovine metabolic network, we observe that these ruminal metabol

284 translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that

285 alyze these data in the context of fruit fly metabolic networks, we developed Flyscape, an open-acces

286 Core metabolic networks were computed from taxa and genes ide

287 All are members of a metabolic network where substantial cross-feeding takes

288 e the spectral properties of real social and metabolic networks, where we observe that a lack of info

289 named OptRAM (Optimization of Regulatory And Metabolic Networks), which can identify combinatorial op

290 e effect of this biochemical activity on the metabolic network, which impacts organism fitness.

291 quences enables construction of genome-scale metabolic networks, which are useful tools for studying

292 essitate consideration of the interconnected metabolic network while studying the metabolism of cance

293 early life is hidden in the architecture of metabolic networks, whose reactions could have been cata

294 mycoides capri, we assembled a near-complete metabolic network with 98% of enzymatic reactions suppor

295 Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replicati

296 active (i.e., reactions of the genome-scale metabolic network with a non-zero expression level after

297 on by M. tuberculosis and reveals a flexible metabolic network with characteristics that are likely a

298 resent a model for this surprisingly complex metabolic network with multiple IAN sources and channeli

299 These adaptations reveal a metabolic network with the regulatory capacity to mount

300 hallenging because cells have evolved robust metabolic networks with hard-wired, tightly regulated li