EcoCyc: a comprehensive database resource for Escherichia coli

scientific article

EcoCyc: a comprehensive database resource for Escherichia coli is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/nar/KeselerCGIPPPK05
P356DOI10.1093/NAR/GKI108
P8608Fatcat IDrelease_pryrhmotizgw5ndaofvwqw7coq
P3181OpenCitations bibliographic resource ID4175296
P932PMC publication ID540062
P698PubMed publication ID15608210
P5875ResearchGate publication ID8122274

P50authorPeter D. KarpQ23823647
Ian T. PaulsenQ30347968
Julio Collado-VidesQ56518622
Martin Peralta-GilQ58232814
Socorro Gama-CastroQ107268584
P2093author name stringIngrid M Keseler
Suzanne Paley
John Ingraham
P2860cites workThe EcoCyc DatabaseQ24548415
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databasesQ24800167
The complete genome sequence of Escherichia coli K-12Q27860542
MetaCyc: a multiorganism database of metabolic pathways and enzymes.Q34934265
An evidence ontology for use in pathway/genome databases.Q38522119
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12Q40403678
Evaluation of computational metabolic-pathway predictions for Helicobacter pyloriQ48300082
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databasesQ48561495
P433issueDatabase issue
P407language of work or nameEnglishQ1860
P921main subjectEscherichia coliQ25419
databaseQ8513
P304page(s)D334-7
P577publication date2005-01-01
P1433published inNucleic Acids ResearchQ135122
P1476titleEcoCyc: a comprehensive database resource for Escherichia coli
P478volume33

Reverse relations

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Q33519509Model of transcriptional activation by MarA in Escherichia coli
Q33937490Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger
Q28249970Multicopy suppression underpins metabolic evolvability
Q36360689Multidimensional annotation of the Escherichia coli K-12 genome
Q25257688NPInter: the noncoding RNAs and protein related biomacromolecules interaction database
Q51868865Network Analysis Tools: from biological networks to clusters and pathways
Q33516038Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase
Q44357465New insights on transcriptional responses of genes involved in carbon central metabolism, respiration and fermentation to low ATP levels in Escherichia coli
Q54450690On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli.
Q38253830Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.
Q42431633Optimization based automated curation of metabolic reconstructions
Q53975052Optimizing information flow in small genetic networks. III. A self-interacting gene
Q33481679PANTHER pathway: an ontology-based pathway database coupled with data analysis tools
Q36182282PAX of mind for pathway researchers
Q24538614PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways
Q38371609PaperBLAST: Text Mining Papers for Information about Homologs
Q42122006Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
Q34719855Parallel genomic evolution and metabolic interdependence in an ancient symbiosis
Q36069213Pathway information for systems biology
Q37512835Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli
Q33319517Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor
Q33345033Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps
Q28492567Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa
Q42021181Principles of transcriptional regulation and evolution of the metabolic system in E. coli
Q46882757Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis
Q33968979PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes
Q38034483Promoter engineering: Recent advances in controlling transcription at the most fundamental level
Q38294358Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70.
Q33321436Protein abundance profiling of the Escherichia coli cytosol
Q33221063Protein complexes of the Escherichia coli cell envelope.
Q33464828QUBIC: a qualitative biclustering algorithm for analyses of gene expression data
Q28551034Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance
Q100737105Quantifying the distribution of protein oligomerization degree reflects cellular information capacity
Q28471595Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks
Q33871402Rational design and construction of an efficient E. coli for production of diapolycopendioic acid
Q34253865Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
Q33417923Reconstruction of metabolic pathways for the cattle genome
Q31126762Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data
Q41963464Reengineering Escherichia coli for Succinate Production in Mineral Salts Medium
Q33277970Regulation of metabolic networks by small molecule metabolites
Q25257226RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
Q34586477RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
Q34502598Robust Salmonella metabolism limits possibilities for new antimicrobials.
Q51147220Role of energetic coenzyme pools in the production of L-carnitine by Escherichia coli.
Q24656073STRING 8--a global view on proteins and their functional interactions in 630 organisms
Q34017079Selection of organisms for the co-evolution-based study of protein interactions
Q35130227Selective promoter recognition by chlamydial sigma28 holoenzyme
Q30476280Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis
Q33674408Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1.
Q33281445SigmaE regulates and is regulated by a small RNA in Escherichia coli
Q33941080Simplivariate models: uncovering the underlying biology in functional genomics data
Q54208178Single-target regulators form a minor group of transcription factors in Escherichia coli K-12.
Q79956680Solid-state NMR spectroscopy of 10% 13C labeled ubiquitin: spectral simplification and stereospecific assignment of isopropyl groups
Q36740092Spatial effects on the speed and reliability of protein-DNA search
Q28476307Stability of metabolic correlations under changing environmental conditions in Escherichia coli--a systems approach
Q51638739Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids
Q34561324Stochastic oscillations induced by intrinsic fluctuations in a self-repressing gene
Q33459140Stochasticity in protein levels drives colinearity of gene order in metabolic operons of Escherichia coli
Q33315469Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression
Q27647725Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance
Q34598769Structure and function of negative feedback loops at the interface of genetic and metabolic networks
Q42055252Studying Gene Expression: Database Searches and Promoter Fusions to Investigate Transcriptional Regulation in Bacteria
Q24625342Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis
Q41965066Sxy induces a CRP-S regulon in Escherichia coli.
Q40366182Systematic discovery of drug interaction mechanisms
Q24672160Systems biology of the structural proteome
Q37691412Systems metabolic engineering: genome-scale models and beyond
Q51084165Temporal gene-expression in Escherichia coli K-12 biofilms
Q28249847Text mining for metabolic pathways, signaling cascades, and protein networks
Q43032876The 3D rRNA modification maps database: with interactive tools for ribosome analysis
Q36748792The 8 annual bio-ontologies meeting
Q92642799The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Q58550212The EcoCyc Database
Q34568046The EcoCyc Database.
Q29615370The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
Q28476170The Modular Organization of Protein Interactions in Escherichia coli
Q41874281The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli
Q36672604The R1 conjugative plasmid increases Escherichia coli biofilm formation through an envelope stress response.
Q36088411The Role of CzcRS Two-Component Systems in the Heavy Metal Resistance of Pseudomonas putida X4
Q25256865The UCSC Archaeal Genome Browser
Q25257513The comprehensive updated regulatory network of Escherichia coli K-12.
Q50855804The effect of global transcriptional regulators on the anaerobic fermentative metabolism of Escherichia coli
Q24644242The incoherent feed-forward loop can generate non-monotonic input functions for genes
Q41050075The interdependent network of gene regulation and metabolism is robust where it needs to be.
Q37341147The model repository of the models of infectious disease agent study.
Q22066364The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons
Q33483002The transcriptional response of Pasteurella multocida to three classes of antibiotics
Q40987640The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase
Q43188623Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis
Q35130080Time-dependent proteome alterations under osmotic stress during aerobic and anaerobic growth in Escherichia coli
Q36537441Time-dependent translational response of E. coli to excess Zn(II).
Q64911823Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data.
Q36371202Towards multidimensional genome annotation
Q35179220Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes
Q36962799Transcription coupled nucleotide excision repair in Escherichia coli can be affected by changing the arginine at position 529 of the beta subunit of RNA polymerase.
Q38306585Transcription factor distribution in Escherichia coli: studies with FNR protein.
Q36701127Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors
Q34088373Transcription-coupled nucleotide excision repair of a gene transcribed by bacteriophage T7 RNA polymerase in Escherichia coli
Q36953406Transcriptional activation by MarA, SoxS and Rob of two tolC promoters using one binding site: a complex promoter configuration for tolC in Escherichia coli
Q33265217Transcriptional regulation by competing transcription factor modules
Q33834461Transcriptional response of E. coli upon FimH-mediated fimbrial adhesion
Q35075626Transcriptional response of Escherichia coli to TPEN.
Q35537097TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
Q37213785Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
Q34607120Using Consensus Bayesian Network to Model the Reactive Oxygen Species Regulatory Pathway
Q37776507Using Genomics to Develop Novel Antibacterial Therapeutics
Q31111982Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
Q38440753VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
Q33302866Visualizing regulatory interactions in metabolic networks
Q51945468What process is glycolytic stoichiometry optimal for?
Q57194708Whole genome microarray analysis of the expression profile of Escherichia coli in response to exposure to para-nitrophenol
Q35759645YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity.
Q42122269YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling
Q27921426kpath: integration of metabolic pathway linked data
Q37202654sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes
Q24532860sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes

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