A systems biology approach sheds new light on Escherichia coli acid resistance

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A systems biology approach sheds new light on Escherichia coli acid resistance is …
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scholarly articleQ13442814

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P356DOI10.1093/NAR/GKR338
P932PMC publication ID3177180
P698PubMed publication ID21690099
P5875ResearchGate publication ID51235436

P50authorIan R HendersonQ61805760
Philipp AntczakQ63352461
Peter A LundQ38591014
P2093author name stringFrancesco Falciani
Matthew D Johnson
Anna Stincone
Ayesha S Rahman
Jeffrey Cole
Nazish Daudi
P2860cites workARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular ContextQ21284234
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Two types of mechanosensitive channels in the Escherichia coli cell envelope: solubilization and functional reconstitutionQ24531485
pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coliQ24539204
GadY, a small-RNA regulator of acid response genes in Escherichia coliQ24563573
Significance analysis of microarrays applied to the ionizing radiation responseQ24606608
Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110Q24672423
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A comparison of normalization methods for high density oligonucleotide array data based on variance and biasQ27860710
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesQ27860739
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR productsQ27860842
Growth and survival of Escherichia coli O157:H7 under acidic conditions.Q39796886
Specific cesium transport via the Escherichia coli Kup (TrkD) K+ uptake systemQ39948694
Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coliQ41063822
Metabolomic and transcriptomic stress response of Escherichia coliQ41330142
Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivityQ41863185
Autoinduction of the ompR response regulator by acid shock and control of the Salmonella enterica acid tolerance responseQ42522471
Modulation of Shigella virulence in response to available oxygen in vivoQ42563797
DNA sequence and analysis of the bet genes encoding the osmoregulatory choline-glycine betaine pathway of Escherichia coliQ42625454
Products of the Escherichia coli acid fitness island attenuate metabolite stress at extremely low pH and mediate a cell density-dependent acid resistanceQ42845453
Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori.Q47261526
A versatile low-copy-number cloning vector derived from plasmid FQ48069818
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.Q48124990
The promoter of the operon encoding the F0F1 ATPase of Streptococcus pneumoniae is inducible by pH.Q48340691
The Escherichia coli AraC-family regulators GadX and GadW activate gadE, the central activator of glutamate-dependent acid resistanceQ50069893
Effect of oxygen concentration and redox potential on recovery of sublethally heat-damaged cells of Escherichia coli O157:H7, Salmonella enteritidis and Listeria monocytogenesQ50130237
An overlap between osmotic and anaerobic stress responses: a potential role for DNA supercoiling in the coordinate regulation of gene expressionQ50194798
Computation with the KEGG pathway database.Q51647348
Fast optimal leaf ordering for hierarchical clustering.Q52058310
Functional reconstitution and characterization of AqpZ, the E. coli water channel protein.Q54076183
The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system.Q54090787
Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics.Q54383140
Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.Q54537142
K+-transport protein TrkA of Escherichia coli is a peripheral membrane protein that requires other trk gene products for attachment to the cytoplasmic membrane.Q54723987
GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coliQ57176924
Roles of the trkB and trkC gene products of Escherichia coli in K+ transportQ69891796
The use of multi-parameter flow cytometry to compare the physiological response of Escherichia coli W3110 to glucose limitation during batch, fed-batch and continuous culture cultivationsQ73162185
Multiparameter flow cytometry of bacteriaQ76376926
Exploration, normalization, and summaries of high density oligonucleotide array probe level dataQ27861098
Principal components analysis to summarize microarray experiments: application to sporulation time seriesQ28141235
TM4: a free, open-source system for microarray data management and analysisQ29547339
TM4 microarray software suiteQ29618829
Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12.Q33259655
Rapid acid treatment of Escherichia coli: transcriptomic response and recoveryQ33321349
Acid tolerance of enterohemorrhagic Escherichia coliQ33489673
Osmolytes contribute to pH homeostasis of Escherichia coliQ33553294
pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12.Q33554062
Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE.Q33922436
Survival of uropathogenic Escherichia coli in the murine urinary tract is dependent on OmpRQ33923814
A hierarchical unsupervised growing neural network for clustering gene expression patternsQ33936864
Isolation and sequencing of Escherichia coli gene proP reveals unusual structural features of the osmoregulatory proline/betaine transporter, ProP.Q34359329
Gastric acid barrier to ingested microorganisms in man: studies in vivo and in vitroQ34474809
Acid resistance in enteric bacteriaQ34522511
Functional heterogeneity of RpoS in stress tolerance of enterohemorrhagic Escherichia coli strainsQ34718799
Escherichia coli gene expression responsive to levels of the response regulator EvgA.Q34838928
Sensing and adapting to acid stressQ35007627
Mechanisms of acid resistance in enterohemorrhagic Escherichia coliQ35192892
Acid resistance in Escherichia coli.Q35215224
Escherichia coli acid resistance: tales of an amateur acidophileQ35923268
Acid and base resistance in Escherichia coli and Shigella flexneri: role of rpoS and growth pH.Q36106069
Adaptive acidification tolerance response of Salmonella typhimurium.Q36158004
B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coliQ36276976
The "dashpot" mechanism of stretch-dependent gating in MscS.Q36412611
Linkage map of Escherichia coli K-12, edition 8Q37056213
Escherichia coli glutamate- and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potentialQ37494481
Reverse engineering cellular networks.Q38303089
Control of acid resistance in Escherichia coliQ39496012
OmpR regulates the stationary-phase acid tolerance response of Salmonella enterica serovar typhimuriumQ39587145
Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase systemQ39679110
Gene expression profiling of the pH response in Escherichia coliQ39680649
P275copyright licenseCreative Commons Attribution-NonCommercial 3.0 UnportedQ18810331
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesCytoscapeQ3699942
P433issue17
P407language of work or nameEnglishQ1860
P921main subjectEscherichia coliQ25419
systems biologyQ815297
P304page(s)7512-7528
P577publication date2011-06-19
P1433published inNucleic Acids ResearchQ135122
P1476titleA systems biology approach sheds new light on Escherichia coli acid resistance
P478volume39

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cites work (P2860)
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