R34K99 last accessed: 2022-11-04

ecocyc
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

Other names: EcoCyc, EcoCyc Database, Encyclopedia of E. coli Genes and Metabolism, ecocyc

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc has been curated from 37,000 publications as of 2019. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.

Webpage:

https://ecocyc.org/

Licence:

Name: BioCyc Database License
URL: https://biocyc.org/download-flatfiles.shtml

Publications:

Publications
More detailed information about this field from each metasource.

EcoCyc: fusing model organism databases with systems biology
PMID: 23143106
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12
PMID: 27899573
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

EcoCyc: a comprehensive database of Escherichia coli biology
PMID: 21097882
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

The EcoCyc Database
PMID: 26442933
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

EcoCyc: fusing model organism databases with systems biology PubMed citations: 288.

288 articles citing: EcoCyc: fusing model organism databases with systems biology

Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors. PMID:35610252
Genome-wide promoter assembly in E. coli measured at single-base resolution. PMID:35483960
The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes. PMID:35479634
Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. PMID:35449049
Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity. PMID:35285724
Overexpression of Oxidoreductase YghA Confers Tolerance of Furfural in Ethanologenic Escherichia coli Strain SSK42. PMID:34586907
Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli. PMID:34150501
Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. PMID:33947801
Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli. PMID:33856016
Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. PMID:33013782
Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments. PMID:32994326
Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation. PMID:32983020
A Decrease in Transcription Capacity Limits Growth Rate upon Translation Inhibition. PMID:32900870
Identification of protein complexes and functional modules in E. coli PPI networks. PMID:32762711
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation. PMID:32703847
Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis. PMID:32665268
Impact of C-terminal amino acid composition on protein expression in bacteria. PMID:32449593
Effects of nest type and sex on blood saccharide profiles in Humboldt penguins (Spheniscus humboldti): Implications for habitat conservation. PMID:32437361
Reduced Genome of the Gut Symbiotic Bacterium "Candidatus Benitsuchiphilus tojoi" Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect. PMID:32435239
Comprehensive Functional Analysis of Escherichia coli Ribosomal RNA Methyltransferases. PMID:32174967
Bioprocess Optimization for the Production of Aromatic Compounds With Metabolically Engineered Hosts: Recent Developments and Future Challenges. PMID:32154231
An analytical theory of balanced cellular growth. PMID:32144263
A Deep Learning Approach to Antibiotic Discovery. PMID:32084340
Genetic Variability of the AcrAB-TolC Multidrug Efflux Pump Underlies SkQ1 Resistance in Gram-Negative Bacteria. PMID:31993240
Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot. PMID:31795935
RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles. PMID:31761494
Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli. PMID:31464375
A whole-cell, high-throughput hydrogenase assay to identify factors that modulate [NiFe]-hydrogenase activity. PMID:31455635
Transcriptome analysis to understand the effects of the toxoflavin and tropolone produced by phytopathogenic Burkholderia on Escherichia coli. PMID:31452043
A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli. PMID:31050661
Enzyme promiscuity shapes adaptation to novel growth substrates. PMID:30962359
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. PMID:30698741
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. PMID:30612223
Reframing gene essentiality in terms of adaptive flexibility. PMID:30558585
BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes. PMID:30519231
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis. PMID:30286091
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PMID:30240424
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. PMID:30210483
SMRT-Cappable-seq reveals complex operon variants in bacteria. PMID:30201986
Plant data visualisation using network graphs. PMID:30186704
Bio-production of gaseous alkenes: ethylene, isoprene, isobutene. PMID:30181774
In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. PMID:30113670
In Silico Prediction of Large-Scale Microbial Production Performance: Constraints for Getting Proper Data-Driven Models. PMID:30105090
Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. PMID:30054360
Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database. PMID:30040192
Engineering of Escherichia coli for Krebs cycle-dependent production of malic acid. PMID:30012131
Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. PMID:29990378
Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling. PMID:29988585
Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli. PMID:29941428
Partnering With a Pest: Genomes of Hemlock Woolly Adelgid Symbionts Reveal Atypical Nutritional Provisioning Patterns in Dual-Obligate Bacteria. PMID:29860412
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. PMID:29728462
High mutation rates limit evolutionary adaptation in Escherichia coli. PMID:29702649
YtfB, an OapA Domain-Containing Protein, Is a New Cell Division Protein in Escherichia coli. PMID:29686141
Random sequences rapidly evolve into de novo promoters. PMID:29670097
Extensive reshaping of bacterial operons by programmed mRNA decay. PMID:29668692
Identifying New Small Proteins in Escherichia coli. PMID:29645342
Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. PMID:29551268
Evolutionary loss and replacement of Buchnera, the obligate endosymbiont of aphids. PMID:29362506
Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure. PMID:29338696
Phenotype inference in an Escherichia coli strain panel. PMID:29280730
Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium. PMID:29240841
Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli. PMID:29222445
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes. PMID:29220462
Mapping the small RNA interactome in bacteria using RIL-seq. PMID:29215635
Molecular Basis of Bacterial Longevity. PMID:29184015
Translation efficiency is maintained at elevated temperature in Escherichia coli. PMID:29183994
Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont. PMID:29181447
The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli. PMID:29088115
Genome-Wide Discovery of Genes Required for Capsule Production by Uropathogenic Escherichia coli. PMID:29066548
A genome-wide screen in Escherichia coli reveals that ubiquinone is a key antioxidant for metabolism of long-chain fatty acids. PMID:29042439
Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. PMID:29036494
Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations. PMID:28961727
MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PMID:28948108
Affected energy metabolism under manganese stress governs cellular toxicity. PMID:28928443
Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. PMID:28914880
The interdependent network of gene regulation and metabolism is robust where it needs to be. PMID:28912490
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. PMID:28911113
EsrE-A yigP Locus-Encoded Transcript-Is a 3' UTR sRNA Involved in the Respiratory Chain of E. coli. PMID:28900423
Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli. PMID:28824593
Development of a new fluorescent reporter:operator system: location of AraC regulated genes in Escherichia coli K-12. PMID:28774286
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. PMID:28727789
Construction of a fur null mutant and RNA-sequencing provide deeper global understanding of the Aliivibrio salmonicida Fur regulon. PMID:28717590
Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor. PMID:28709932
Transposable Elements Mediate Adaptive Debilitation of Flagella in Experimental Escherichia coli Populations. PMID:28646326
CRISPR Interference (CRISPRi) Inhibition of luxS Gene Expression in E. coli: An Approach to Inhibit Biofilm. PMID:28603699
Universal attenuators and their interactions with feedback loops in gene regulatory networks. PMID:28575450
A shortened, two-enzyme pathway for 2,3-butanediol production in Escherichia coli. PMID:28547323
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. PMID:28499419
The Long Hunt for pssR-Looking for a Phospholipid Synthesis Transcriptional Regulator, Finding the Ribosome. PMID:28484043
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. PMID:28472402
DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli. PMID:28438119
Outlining Core Pathways of Amyloid Toxicity in Bacteria with the RepA-WH1 Prionoid. PMID:28421043
SSER: Species specific essential reactions database. PMID:28420402
Genomic and transcriptomic landscape of Escherichia coli BL21(DE3). PMID:28379538
Strategies towards digital and semi-automated curation in RegulonDB. PMID:28365731
Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis Revealed by Metabolic Modeling. PMID:28348026
rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining. PMID:28335718
Adaptation of Escherichia coli to Long-Term Serial Passage in Complex Medium: Evidence of Parallel Evolution. PMID:28289732
Pirated Siderophores Promote Sporulation in Bacillus subtilis. PMID:28283524
Bacteria Getting into Shape: Genetic Determinants of E. coli Morphology. PMID:28270582
Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. PMID:28264512
Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance. PMID:28263303
A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades. PMID:28248218
Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points. PMID:28169831
Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes. PMID:28158295
Discovering missing reactions of metabolic networks by using gene co-expression data. PMID:28150713
Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. PMID:28115545
The Differential Effects of Anesthetics on Bacterial Behaviors. PMID:28099463
CRISPRi-mediated metabolic engineering of E. coli for O-methylated anthocyanin production. PMID:28095853
Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon. PMID:28073397
Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. PMID:28067866
Coordinated regulation of acid resistance in Escherichia coli. PMID:28061857
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications. PMID:28040748
Self-regulated 1-butanol production in Escherichia coli based on the endogenous fermentative control. PMID:28031744
Can we replace curation with information extraction software? PMID:28025341
Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints. PMID:27999902
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains. PMID:27996047
Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase. PMID:27981240
Colonic luminal microbiota and bacterial metabolite composition in pregnant Huanjiang mini-pigs: effects of food composition at different times of pregnancy. PMID:27917879
A Novel Protective Vaccine Antigen from the Core Escherichia coli Genome. PMID:27904885
Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli. PMID:27899632
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. PMID:27899573
Tailor-made transcriptional biosensors for optimizing microbial cell factories. PMID:27837353
Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. PMID:27822522
Defining synonymous codon compression schemes by genome recoding. PMID:27776354
A Comparison of the Costs and Benefits of Bacterial Gene Expression. PMID:27711251
The Tip of the Iceberg: On the Roles of Regulatory Small RNAs in the Virulence of Enterohemorrhagic and Enteropathogenic Escherichia coli. PMID:27709103
All Three Endogenous Quinone Species of Escherichia coli Are Involved in Controlling the Activity of the Aerobic/Anaerobic Response Regulator ArcA. PMID:27656164
Spatiotemporal microbial evolution on antibiotic landscapes. PMID:27609891
Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. PMID:27599549
Global Mapping of Small RNA-Target Interactions in Bacteria. PMID:27588604
Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model. PMID:27567672
How much does curation cost? PMID:27504008
Expanding the genetic code of Escherichia coli with phosphotyrosine. PMID:27477338
Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts. PMID:27462311
Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PMID:27428627
The target spectrum of SdsR small RNA in Salmonella. PMID:27407104
Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. PMID:27364158
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PMID:27351952
The fitness effects of a point mutation in Escherichia coli change with founding population density. PMID:27344657
NrdR Transcription Regulation: Global Proteome Analysis and Its Role in Escherichia coli Viability and Virulence. PMID:27275780
CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA. PMID:27220470
A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model. PMID:27195968
Reinventing the Wheel and Making It Round Again: Evolutionary Convergence in Buchnera-Serratia Symbiotic Consortia between the Distantly Related Lachninae Aphids Tuberolachnus salignus and Cinara cedri. PMID:27190007
sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. PMID:27137887
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. PMID:27135538
The healthy human microbiome. PMID:27122046
Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. PMID:27109914
Genome scale patterns of supercoiling in a bacterial chromosome. PMID:27025941
An integrated text mining framework for metabolic interaction network reconstruction. PMID:27019783
Cellular Growth Arrest and Persistence from Enzyme Saturation. PMID:27010473
How Archiving by Freezing Affects the Genome-Scale Diversity of Escherichia coli Populations. PMID:26988250
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies. PMID:26958858
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. PMID:26951675
A Comparison of the ATP Generating Pathways Used by S. Typhimurium to Fuel Replication within Human and Murine Macrophage and Epithelial Cell Lines. PMID:26930214
Markovian language model of the DNA and its information content. PMID:26909179
ydfD encodes a novel lytic protein in Escherichia coli. PMID:26887840
Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles. PMID:26884158
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. PMID:26873250
Plasmidic Expression of nemA and yafC* Increased Resistance of Ethanologenic Escherichia coli LY180 to Nonvolatile Side Products from Dilute Acid Treatment of Sugarcane Bagasse and Artificial Hydrolysate. PMID:26826228
Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters. PMID:26811318
A robust platform for chemical genomics in bacterial systems. PMID:26792836
Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes. PMID:26766575
Codon influence on protein expression in E. coli correlates with mRNA levels. PMID:26760206
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris. PMID:26712940
Predicting the impact of promoter variability on regulatory outputs. PMID:26675057
Overflow metabolism in Escherichia coli results from efficient proteome allocation. PMID:26632588
Representation and inference of cellular architecture for metabolic reconstruction and modeling. PMID:26628588
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. PMID:26614125
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. PMID:26586805
An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. PMID:26578563
Semi-supervised prediction of gene regulatory networks using machine learning algorithms. PMID:26564975
Undergraduate Biocuration: Developing Tomorrow's Researchers While Mining Today's Data. PMID:26557796
Identification of bacterial sRNA regulatory targets using ribosome profiling. PMID:26546513
BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference. PMID:26537179
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Transcription factor-based biosensors in biotechnology: current state and future prospects. PMID:26521244
First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes. PMID:26500250
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli. PMID:26463009
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. PMID:26454094
Solving a Bloody Mess: B-Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood-Feeding Arthropods and the Leech Haementeria officinalis. PMID:26454017
Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production. PMID:26442259
Metabolic engineering of Escherichia coli into a versatile glycosylation platform: production of bio-active quercetin glycosides. PMID:26377568
Stationary-Phase Persisters to Ofloxacin Sustain DNA Damage and Require Repair Systems Only during Recovery. PMID:26330511
Genomic and Phenomic Study of Mammary Pathogenic Escherichia coli. PMID:26327312
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. PMID:26322134
Protein acetylation dynamics in response to carbon overflow in Escherichia coli. PMID:26264774
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. PMID:26261351
Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure. PMID:26194219
A bacterial homolog YciH of eukaryotic translation initiation factor eIF1 regulates stress-related gene expression and is unlikely to be involved in translation initiation fidelity. PMID:26177339
A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior. PMID:26172209
Influence of the yjiL-mdtM Gene Cluster on the Antibacterial Activity of Proline-Rich Antimicrobial Peptides Overcoming Escherichia coli Resistance Induced by the Missing SbmA Transporter System. PMID:26169420
Real sequence effects on the search dynamics of transcription factors on DNA. PMID:26154484
Arsenophonus and Sodalis Symbionts in Louse Flies: an Analogy to the Wigglesworthia and Sodalis System in Tsetse Flies. PMID:26150448
A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons. PMID:26117546
YjjQ Represses Transcription of flhDC and Additional Loci in Escherichia coli. PMID:26078445
Databases for Microbiologists. PMID:26013493
Computational Metabolomics Operations at BioCyc.org. PMID:26011592
Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12. PMID:26010885
Using Genome-scale Models to Predict Biological Capabilities. PMID:26000478
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. PMID:25982966
Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon. PMID:25982672
Endogenous generation of hydrogen sulfide and its regulation in Shewanella oneidensis. PMID:25972854
An ace up their sleeve: a transcriptomic approach exposes the AceI eﬄux protein of Acinetobacter baumannii and reveals the drug eﬄux potential hidden in many microbial pathogens. PMID:25954261
Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes. PMID:25927816
Genetic basis of persister tolerance to aminoglycosides in Escherichia coli. PMID:25852159
Complete Genome Sequences of Escherichia coli Strains 1303 and ECC-1470 Isolated from Bovine Mastitis. PMID:25814601
Relation between chemotaxis and consumption of amino acids in bacteria. PMID:25807888
DNA template dependent accuracy variation of nucleotide selection in transcription. PMID:25799551
Toxicity mechanisms identification via gene set enrichment analysis of time-series toxicogenomics data: impact of time and concentration. PMID:25785649
Computational protein design enables a novel one-carbon assimilation pathway. PMID:25775555
Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PMID:25774498
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli. PMID:25735747
Protein complexes in bacteria. PMID:25723151
An event-driven approach for studying gene block evolution in bacteria. PMID:25717195
Lean-proteome strains - next step in metabolic engineering. PMID:25705616
EcoliNet: a database of cofunctional gene network for Escherichia coli. PMID:25650278
Genome rearrangements can make and break small RNA genes. PMID:25601101
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. PMID:25583150
Hierarchy of non-glucose sugars in Escherichia coli. PMID:25539838
NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. PMID:25533955
Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. PMID:25518064
Activation of RidA chaperone function by N-chlorination. PMID:25517874
Adaptation of anaerobic cultures of Escherichia coli K-12 in response to environmental trimethylamine-N-oxide. PMID:25471524
A bacterial mutant library as a tool to study the attack of a defensin peptide. PMID:25430675
GenoBase: comprehensive resource database of Escherichia coli K-12. PMID:25399415
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. PMID:25378328
RNAcentral: an international database of ncRNA sequences. PMID:25352543
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. PMID:25304508
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Chromosome position effects on gene expression in Escherichia coli K-12. PMID:25209233
Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds. PMID:25200799
Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification. PMID:25177315
Emergence of robust growth laws from optimal regulation of ribosome synthesis. PMID:25149558
Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli. PMID:25108218
Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. PMID:25085490
A quantitative toxicogenomics assay reveals the evolution and nature of toxicity during the transformation of environmental pollutants. PMID:25010344
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. PMID:24974895
Colony-live--a high-throughput method for measuring microbial colony growth kinetics--reveals diverse growth effects of gene knockouts in Escherichia coli. PMID:24964927
Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. PMID:24962091
PubServer: literature searches by homology. PMID:24957597
Nitrogen stress response and stringent response are coupled in Escherichia coli. PMID:24947454
MIRA: mutual information-based reporter algorithm for metabolic networks. PMID:24931981
Curation accuracy of model organism databases. PMID:24923819
Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli. PMID:24910100
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. PMID:24903516
Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli. PMID:24837290
A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa. PMID:24782516
Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. PMID:24727267
A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. PMID:24723921
EF4 knockout E. coli cells exhibit lower levels of cellular biosynthesis under acidic stress. PMID:24706296
A small heat shock protein enables Escherichia coli to grow at a lethal temperature of 50°C conceivably by maintaining cell envelope integrity. PMID:24659772
Coordination of microbial metabolism. PMID:24658329
The metabolic potential of Escherichia coli BL21 in defined and rich medium. PMID:24656150
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. PMID:24643865
Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage. PMID:24586888
Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium. PMID:24559297
Widespread suppression of intragenic transcription initiation by H-NS. PMID:24449106
Genome degeneration and adaptation in a nascent stage of symbiosis. PMID:24407854
Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. PMID:24398322
POMO--Plotting Omics analysis results for Multiple Organisms. PMID:24365393
Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database. PMID:24363340
Dynamic transcriptional response of Escherichia coli to inclusion body formation. PMID:24338599
Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli. PMID:24335284
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. PMID:24314206
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). PMID:24293654
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. PMID:24203708
Coupling between noise and plasticity in E. coli. PMID:24122054
Dead end metabolites--defining the known unknowns of the E. coli metabolic network. PMID:24086468
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. PMID:24084808
Experimental approaches for defining functional roles of microbes in the human gut. PMID:24024637
Comparative genomics boosts target prediction for bacterial small RNAs. PMID:23980183
Lability and liability of endogenous copper pools. PMID:23913325
Flavoproteins are potential targets for the antibiotic roseoflavin in Escherichia coli. PMID:23836860
Metabolic engineering for high yielding L(-)-carnitine production in Escherichia coli. PMID:23718679
Emerging tools for synthetic genome design. PMID:23708771
Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance. PMID:23651997
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 PubMed citations: 246.

246 articles citing: The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

Global transcriptomic response of Escherichia coli to p-coumaric acid. PMID:35858942
Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli. PMID:35857216
Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability. PMID:35798838
Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters. PMID:35776118
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. PMID:35685359
A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance. PMID:35577863
Elucidation of host and symbiont contributions to peptidoglycan metabolism based on comparative genomics of eight aphid subfamilies and their Buchnera. PMID:35522718
Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. PMID:35487919
Genome-wide promoter assembly in E. coli measured at single-base resolution. PMID:35483960
RNase III Participates in the Adaptation to Temperature Shock and Oxidative Stress in Escherichia coli. PMID:35456749
On the influence of several factors on pathway enrichment analysis. PMID:35453140
Proteome-wide landscape of solubility limits in a bacterial cell. PMID:35449391
The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress. PMID:35416044
Identification of Bacterial Drug-Resistant Cells by the Convolutional Neural Network in Transmission Electron Microscope Images. PMID:35369486
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions: The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control. PMID:35269716
Dual-function Spot 42 RNA encodes a 15-amino acid protein that regulates the CRP transcription factor. PMID:35239441
Sensory Systems and Transcriptional Regulation in Escherichia coli. PMID:35237580
Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. PMID:35216300
A tRNA modifying enzyme as a tunable regulatory nexus for bacterial stress responses and virulence. PMID:35212379
High-Throughput Screening of a Promoter Library Reveals New Persister Mechanisms in Escherichia Coli. PMID:35196813
Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. PMID:35174104
Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology. PMID:35167766
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PMID:35130271
Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses. PMID:35089687
Disentangling direct from indirect relationships in association networks. PMID:34992138
Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. PMID:34966369
Escherichia coli SymE is a DNA-binding protein that can condense the nucleoid. PMID:34964191
RNase III, Ribosome Biogenesis and Beyond. PMID:34946208
Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth. PMID:34941903
The economy of chromosomal distances in bacterial gene regulation. PMID:34911953
Gain of Spontaneous clpX Mutations Boosting Motility via Adaption to Environments in Escherichia coli. PMID:34900963
Chemical biology-whole genome engineering datasets predict new antibacterial combinations. PMID:34874820
Multiple Novel Traits without Immediate Benefits Originate in Bacteria Evolving on Single Antibiotics. PMID:34865131
Cellular Self-Digestion and Persistence in Bacteria. PMID:34835393
ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen. PMID:34809459
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440
Selection for Phage Resistance Reduces Virulence of Shigella flexneri. PMID:34788068
Building Structural Models of a Whole Mycoplasma Cell. PMID:34774566
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. PMID:34762392
Quantifying the regulatory role of individual transcription factors in Escherichia coli. PMID:34758318
Potentiating antibiotic efficacy via perturbation of non-essential gene expression. PMID:34741116
On the optimality of the enzyme-substrate relationship in bacteria. PMID:34699521
The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome. PMID:34684271
Parallelism of intestinal secretory IgA shapes functional microbial fitness. PMID:34646015
DNA Replication-Transcription Conflicts Do Not Significantly Contribute to Spontaneous Mutations Due to Replication Errors in Escherichia coli. PMID:34634932
Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. PMID:34630943
First-principles model of optimal translation factors stoichiometry. PMID:34590582
Mining RNA-seq data reveals the massive regulon of GcvB small RNA and its physiological significance in maintaining amino acid homeostasis in Escherichia coli. PMID:34543491
Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. PMID:34499567
Transcriptional and Post-Transcriptional Polar Effects in Bacterial Gene Deletion Libraries. PMID:34491080
Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism. PMID:34486768
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods. PMID:34469744
Bacterial resistance to CRISPR-Cas antimicrobials. PMID:34446818
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. PMID:34428301
Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters. PMID:34427530
Identification and Characterization of Pleiotropic High-Persistence Mutations in the Beta Subunit of the Bacterial RNA Polymerase. PMID:34424038
Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. PMID:34413462
The EcoCyc Database in 2021. PMID:34394059
Hawaiian Nysius Insects Rely on an Obligate Symbiont with a Reduced Genome That Retains a Discrete Nutritional Profile to Match Their Plant Seed Diet. PMID:34383896
Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. PMID:34382933
A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing. PMID:34365505
Nonrefoldability is Pervasive Across the E. coli Proteome. PMID:34308638
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. PMID:34214468
Natural Selection Shapes Maintenance of Orthologous sRNAs in Divergent Host-Restricted Bacterial Genomes. PMID:34213555
Reliable identification of protein-protein interactions by crosslinking mass spectrometry. PMID:34117231
R2DT is a framework for predicting and visualising RNA secondary structure using templates. PMID:34108470
Designing an irreversible metabolic switch for scalable induction of microbial chemical production. PMID:34103495
Effects of FUdR on gene expression in the C. elegans bacterial diet OP50. PMID:34103088
Acid-Sensing Histidine Kinase With a Redox Switch. PMID:34093469
Prediction of Novel Bacterial Small RNAs From RIL-Seq RNA-RNA Interaction Data. PMID:34093460
Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. PMID:34072091
Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals. PMID:34069865
Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses. PMID:33975962
Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry. PMID:33958766
A Dynamic, Ring-Forming Bactofilin Critical for Maintaining Cell Size in the Obligate Intracellular Bacterium Chlamydia trachomatis. PMID:33941579
Biosynthesis of Commodity Chemicals From Oil Palm Empty Fruit Bunch Lignin. PMID:33897677
Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals. PMID:33863914
Riboflavin instability is a key factor underlying the requirement of a gut microbiota for mosquito development. PMID:33827929
Genomic diversity and molecular epidemiology of Pasteurella multocida. PMID:33822782
Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli. PMID:33785570
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation. PMID:33763039
Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification. PMID:33748186
Single-molecule insight into stalled replication fork rescue in Escherichia coli. PMID:33744948
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. PMID:33726670
Facile accelerated specific therapeutic (FAST) platform develops antisense therapies to counter multidrug-resistant bacteria. PMID:33712689
Metabolic fitness landscapes predict the evolution of antibiotic resistance. PMID:33664488
Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations. PMID:33650807
Proteome-minimized outer membrane vesicles from Escherichia coli as a generalized vaccine platform. PMID:33643549
Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis. PMID:33608555
Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase. PMID:33573428
A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them. PMID:33562654
Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12. PMID:33561236
The Regulator OmpR in Yersinia enterocolitica Participates in Iron Homeostasis by Modulating Fur Level and Affecting the Expression of Genes Involved in Iron Uptake. PMID:33540627
Independent component analysis recovers consistent regulatory signals from disparate datasets. PMID:33529205
NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks. PMID:33489751
Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. PMID:33441451
Respiratory chain components are required for peptidoglycan recognition protein-induced thiol depletion and killing in Bacillus subtilis and Escherichia coli. PMID:33420211
Engineering Sensors for Gene Expression Burden. PMID:33405229
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. PMID:33371386
Atlas: Automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages. PMID:33367504
A High-Throughput Method for Screening for Genes Controlling Bacterial Conjugation of Antibiotic Resistance. PMID:33361328
Metabolites Potentiate Nitrofurans in Nongrowing Escherichia coli. PMID:33361301
Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. PMID:33336183
The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli. PMID:33318048
Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties. PMID:33306798
The functional proteome landscape of Escherichia coli. PMID:33299184
A Multi-Scale Approach to Modeling E. coli Chemotaxis. PMID:33286869
Genetic Architecture and Fitness of Bacterial Interspecies Hybrids. PMID:33247724
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. PMID:33174603
Systems evaluation reveals novel transporter YohJK renders 3-hydroxypropionate tolerance in Escherichia coli. PMID:33149261
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. PMID:33073387
The protein translation machinery is expressed for maximal efficiency in Escherichia coli. PMID:33067428
High-throughput mapping of the phage resistance landscape in E. coli. PMID:33048924
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. PMID:33045728
Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage. PMID:33020480
Modulation of Escherichia coli Translation by the Specific Inactivation of tRNAGly Under Oxidative Stress. PMID:33014012
Expression Profile of Multidrug Resistance Efflux Pumps During Intracellular Life of Adherent-Invasive Escherichia coli Strain LF82. PMID:33013734
Correlated chromosomal periodicities according to the growth rate and gene expression. PMID:32968121
Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. PMID:32955440
DrpB (YedR) Is a Nonessential Cell Division Protein in Escherichia coli. PMID:32900831
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli. PMID:32790204
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
The gain-of-function allele bamA E470K bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly. PMID:32675245
High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria. PMID:32675236
Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli. PMID:32670425
A Comprehensive Coexpression Network Analysis in Vibrio cholerae. PMID:32636337
Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering. PMID:32626694
The Adaptive Response to Long-Term Nitrogen Starvation in Escherichia coli Requires the Breakdown of Allantoin. PMID:32571968
Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis. PMID:32543366
A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility. PMID:32514543
Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. PMID:32487739
Engineered triply orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. PMID:32472101
Adaptor protein RapZ activates endoribonuclease RNase E by protein-protein interaction to cleave a small regulatory RNA. PMID:32424019
Investigating the dynamics of microbial consortia in spatially structured environments. PMID:32415107
Escherichia coli YcaQ is a DNA glycosylase that unhooks DNA interstrand crosslinks. PMID:32409837
Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis. PMID:32385082
Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. PMID:32341074
Evolution of new enzymes by gene duplication and divergence. PMID:32250558
Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements. PMID:32238808
Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing. PMID:32211022
Tailoring a Global Iron Regulon to a Uropathogen. PMID:32209682
Bacterially produced metabolites protect C. elegans neurons from degeneration. PMID:32208418
Metabolite Sequestration Enables Rapid Recovery from Fatty Acid Depletion in Escherichia coli. PMID:32184249
Global profile changes in transcripts induced with a phosphate analogue: implications for gene regulation. PMID:32172469
Genetic and Chemical-Genetic Interactions Map Biogenesis and Permeability Determinants of the Outer Membrane of Escherichia coli. PMID:32156814
Low mutational load and high mutation rate variation in gut commensal bacteria. PMID:32155146
Systematic Localization of Escherichia coli Membrane Proteins. PMID:32127419
A High-Throughput Interbacterial Competition Screen Identifies ClpAP in Enhancing Recipient Susceptibility to Type VI Secretion System-Mediated Attack by Agrobacterium tumefaciens. PMID:32117077
A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition. PMID:32059782
Quantitative Connection between Cell Size and Growth Rate by Phospholipid Metabolism. PMID:32046235
Critical Role for the Extended N Terminus of Chlamydial MreB in Directing Its Membrane Association and Potential Interaction with Divisome Proteins. PMID:32041796
Formate dehydrogenase, ubiquinone, and cytochrome bd-I are required for peptidoglycan recognition protein-induced oxidative stress and killing in Escherichia coli. PMID:32029761
Dynamic insights on transcription initiation and RNA processing during bacterial adaptation. PMID:31992590
Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin. PMID:31986134
Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli. PMID:31819215
Biogenesis and functions of aminocarboxypropyluridine in tRNA. PMID:31804502
The Escherichia coli transcriptome mostly consists of independently regulated modules. PMID:31797920
An sRNA Screen for Reversal of Quinolone Resistance in Escherichia coli. PMID:31744901
Pleione: A tool for statistical and multi-objective calibration of Rule-based models. PMID:31641245
Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems. PMID:31624345
Systematic identification of metabolites controlling gene expression in E. coli. PMID:31578326
Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae. PMID:31555234
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline. PMID:31504032
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. PMID:31503285
Knockout of acetoacetate degradation pathway gene atoDA enhances the toxicity tolerance of Escherichia coli to isopropanol and acetone. PMID:31497461
Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli. PMID:31464375
Genome-wide mapping of regions preferentially targeted by the human DNA-cytosine deaminase APOBEC3A using uracil-DNA pulldown and sequencing. PMID:31431505
Toward a Synthetic Yeast Endosymbiont with a Minimal Genome. PMID:31419116
Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments. PMID:31329973
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database. PMID:31319812
Forecasting cell fate during antibiotic exposure using stochastic gene expression. PMID:31312728
Mutations in the Global Transcription Factor CRP/CAP: Insights from Experimental Evolution and Deep Sequencing. PMID:31303977
Estimation of Transcription Factor Activity in Knockdown Studies. PMID:31270369
Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. PMID:31239393
Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization. PMID:31208335
Trouble is coming: Signaling pathways that regulate general stress responses in bacteria. PMID:31197038
Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes. PMID:31194874
Characterization of the pleiotropic LysR-type transcription regulator LeuO of Escherichia coli. PMID:31184713
Inefficient Secretion of Anti-sigma Factor FlgM Inhibits Bacterial Motility at High Temperature. PMID:31170626
Nanocalorimetry Reveals the Growth Dynamics of Escherichia coli Cells Undergoing Adaptive Evolution during Long-Term Stationary Phase. PMID:31152016
Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth of Escherichia coli. PMID:31126940
The Synthetic Phenotype of ΔbamB ΔbamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF. PMID:31113901
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. PMID:31080069
Transcriptional Regulation Contributes to Prioritized Detoxification of Hydrogen Peroxide over Nitric Oxide. PMID:31061166
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2. PMID:31060509
Simultaneously inhibiting undecaprenyl phosphate production and peptidoglycan synthases promotes rapid lysis in Escherichia coli. PMID:31022322
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PMID:31009451
Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes. PMID:30991941
Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase. PMID:30971496
Differential proteostatic regulation of insoluble and abundant proteins. PMID:30903148
Photocatalytic antibacterial application of zinc oxide nanoparticles and self-assembled networks under dual UV irradiation for enhanced disinfection. PMID:30880977
Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli. PMID:30843055
In silico simulations of occurrence of transcription factor binding sites in bacterial genomes. PMID:30823869
Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications. PMID:30790000
Temporal order and precision of complex stress responses in individual bacteria. PMID:30765425
sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs. PMID:30700509
A crash course in sequencing for a microbiologist. PMID:30684135
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. PMID:30659179
Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. PMID:30638812
Bioprospecting of Native Efflux Pumps To Enhance Furfural Tolerance in Ethanologenic Escherichia coli. PMID:30635383
Using a Chemical Genetic Screen to Enhance Our Understanding of the Antimicrobial Properties of Gallium against Escherichia coli. PMID:30634525
Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. PMID:30633903
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. PMID:30626386
Combining multiple functional annotation tools increases coverage of metabolic annotation. PMID:30567498
Transcriptional Landscape of a bla KPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10. PMID:30559731
Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation. PMID:30536863
The EcoCyc Database. PMID:30406744
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PMID:30403660
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. PMID:30395280
Improving network inference algorithms using resampling methods. PMID:30314469
Genome-wide analysis of fitness data and its application to improve metabolic models. PMID:30305012
Knowledge-based biomedical Data Science. PMID:30294517
Analysis of differentially upregulated proteins in ptsHIcrr- and rppH- mutants in Escherichia coli during an adaptive laboratory evolution experiment. PMID:30284012
Development of a Metabolite Sensor for High-Throughput Detection of Aldehydes in Escherichia Coli. PMID:30191150
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
Optimal Allocation of Bacterial Protein Resources under Nonlethal Protein Maturation Stress. PMID:30122293
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. PMID:30115066
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. PMID:30107613
Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops. PMID:30096859
On the Origin of Compositional Features of Ribosomes. PMID:30059996
Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data. PMID:30050664
Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. PMID:30042196
Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli. PMID:30040820
Using a Chemical Genetic Screen to Enhance Our Understanding of the Antibacterial Properties of Silver. PMID:29986482
Thermal proteome profiling in bacteria: probing protein state in vivo. PMID:29980614
Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli. PMID:29973927
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis. PMID:29875739
Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network. PMID:29856734
CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD<sup/> PMID:29681497
Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry. PMID:29606352
Burden-driven feedback control of gene expression. PMID:29578536
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
Transcriptome Profiling Reveals Interplay of Multifaceted Stress Response in Escherichia coli on Exposure to Glutathione and Ciprofloxacin. PMID:29468195
Evaluation of reaction gap-filling accuracy by randomization. PMID:29444634
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Roles of elusive translational GTPases come to light and inform on the process of ribosome biogenesis in bacteria. PMID:29235176
Update notifications for the BioCyc collection of databases. PMID:29220477
Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. PMID:29199098
Selective labeling and unlabeling strategies in protein solid-state NMR spectroscopy. PMID:29197975
The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity. PMID:29133912
The MetaCyc database of metabolic pathways and enzymes. PMID:29059334
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. PMID:28981567
EcoCyc: a comprehensive database of Escherichia coli biology PubMed citations: 210.

210 articles citing: EcoCyc: a comprehensive database of Escherichia coli biology

Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments. PMID:35749361
The Escherichia coli serS gene promoter region overlaps with the rarA gene. PMID:35427362
Biosynthetic Pathway and Metabolic Engineering of Succinic Acid. PMID:35350186
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PMID:35130271
Curating COBRA Models of Microbial Metabolism. PMID:34719001
Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. PMID:34327153
Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. PMID:34254822
Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12. PMID:34220787
ActS activates peptidoglycan amidases during outer membrane stress in Escherichia coli. PMID:33660879
A Modelling Framework Linking Resource-Based Stochastic Translation to the Optimal Design of Synthetic Constructs. PMID:33430483
Transcriptome-based design of antisense inhibitors potentiates carbapenem efficacy in CRE Escherichia coli. PMID:33199638
Efficient production of myo-inositol in Escherichia coli through metabolic engineering. PMID:32448266
Global responses to oxytetracycline treatment in tetracycline-resistant Escherichia coli. PMID:32439837
Escherichia coli Small Proteome. PMID:32385980
Dissection of the mutation accumulation process during bacterial range expansions. PMID:32293258
A Strategic Target Rescues Trimethoprim Sensitivity in Escherichia coli. PMID:32240953
Symbiont replacements reset the co-evolutionary relationship between insects and their heritable bacteria. PMID:32076126
Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci. PMID:31440434
Protein interaction networks revealed by proteome coevolution. PMID:31296772
Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. PMID:31084583
Measuring cis-regulatory energetics in living cells using allelic manifolds. PMID:30570483
A New Role of OmpR in Acid and Osmotic Stress in Salmonella and E. coli. PMID:30524381
Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks. PMID:30459629
The EcoCyc Database. PMID:30406744
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. PMID:29529243
Structure of outer membrane protein G in lipid bilayers. PMID:29233991
O2 availability impacts iron homeostasis in Escherichia coli. PMID:29087312
Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis. PMID:28854637
The rph-1-Encoded Truncated RNase PH Protein Inhibits RNase P Maturation of Pre-tRNAs with Short Leader Sequences in the Absence of RppH. PMID:28808133
A Bacterial Stress Response Regulates Respiratory Protein Complexes To Control Envelope Stress Adaptation. PMID:28760851
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PMID:28727725
Genome-Wide Transcriptional Dynamics in the Companion Bacterial Symbionts of the Glassy-Winged Sharpshooter (Cicadellidae: Homalodisca vitripennis) Reveal Differential Gene Expression in Bacteria Occupying Multiple Host Organs. PMID:28705905
Universal attenuators and their interactions with feedback loops in gene regulatory networks. PMID:28575450
Optimizing complex phenotypes through model-guided multiplex genome engineering. PMID:28545477
LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks. PMID:28265516
Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution. PMID:28217741
A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida. PMID:27933319
The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli. PMID:27879333
Experimental Evolution of Metabolic Dependency in Bacteria. PMID:27814362
A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut. PMID:27812114
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks. PMID:27695050
Hypothesis: type I toxin-antitoxin genes enter the persistence field-a feedback mechanism explaining membrane homoeostasis. PMID:27672159
Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. PMID:27618147
Constrained Allocation Flux Balance Analysis. PMID:27355325
The fitness effects of a point mutation in Escherichia coli change with founding population density. PMID:27344657
Endonucleolytic cleavages by RNase E generate the mature 3' termini of the three proline tRNAs in Escherichia coli. PMID:27288443
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
A protein constructed de novo enables cell growth by altering gene regulation. PMID:26884172
Functional state modelling approach validation for yeast and bacteria cultivations. PMID:26740778
Biocuration with insufficient resources and fixed timelines. PMID:26708987
The propagation of perturbations in rewired bacterial gene networks. PMID:26670742
Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons. PMID:26670385
A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli. PMID:26545295
Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli. PMID:26501058
Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism. PMID:26469081
The EcoCyc Database. PMID:26442933
Overcoming Challenges in Engineering the Genetic Code. PMID:26348789
The Escherichia coli NarL receiver domain regulates transcription through promoter specific functions. PMID:26307095
Cautions about the reliability of pairwise gene correlations based on expression data. PMID:26167162
Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. PMID:26148351
Defining bacterial regulons using ChIP-seq. PMID:26032817
Predicting internal cell fluxes at sub-optimal growth. PMID:25890056
Inference of quantitative models of bacterial promoters from time-series reporter gene data. PMID:25590141
The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli. PMID:25549361
Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites. PMID:25542851
The loose evolutionary relationships between transcription factors and other gene products across prokaryotes. PMID:25515977
Microarray analysis of the Escherichia coli response to CdTe-GSH Quantum Dots: understanding the bacterial toxicity of semiconductor nanoparticles. PMID:25496196
Mycofumigation by the volatile organic compound-producing Fungus Muscodor albus induces bacterial cell death through DNA damage. PMID:25452287
CONSTRICTOR: constraint modification provides insight into design of biochemical networks. PMID:25422896
Finished Genome Sequence of Escherichia coli K-12 Strain HMS174 (ATCC 47011). PMID:25414489
Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608). PMID:25414488
Revealing the amino acid composition of proteins within an expanded genetic code. PMID:25378305
An assembly funnel makes biomolecular complex assembly efficient. PMID:25360818
An online system for metabolic network analysis. PMID:25267793
Essential is not irreplaceable: fitness dynamics of experimental E. coli RNase P RNA heterologous replacement. PMID:25266807
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. PMID:25222563
Molecular and functional profiling of the polyamine content in enteroinvasive E. coli : looking into the gap between commensal E. coli and harmful Shigella. PMID:25192335
Processing of the seven valine tRNAs in Escherichia coli involves novel features of RNase P. PMID:25183518
Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks. PMID:25182846
The influence of repressor DNA binding site architecture on transcriptional control. PMID:25161193
Towards an informative mutant phenotype for every bacterial gene. PMID:25112473
A quantitative toxicogenomics assay reveals the evolution and nature of toxicity during the transformation of environmental pollutants. PMID:25010344
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
The Metabolic Interplay between Plants and Phytopathogens. PMID:24957887
Genomics of rapid adaptation to antibiotics: convergent evolution and scalable sequence amplification. PMID:24850796
Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PMID:24809820
Novel MntR-independent mechanism of manganese homeostasis in Escherichia coli by the ribosome-associated protein HflX. PMID:24794564
Antibiotic-free segregational plasmid stabilization in Escherichia coli owing to the knockout of triosephosphate isomerase (tpiA). PMID:24745552
Determining the control circuitry of redox metabolism at the genome-scale. PMID:24699140
Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals. PMID:24688679
The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PMID:24603758
Single cell kinetics of phenotypic switching in the arabinose utilization system of E. coli. PMID:24586851
Nutrient salvaging and metabolism by the intracellular pathogen Legionella pneumophila. PMID:24575391
Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia. PMID:24467879
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. PMID:24314206
Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. PMID:24296575
Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in 'Chlorochromatium aggregatum'. PMID:24285361
Growth rate-coordinated transcriptome reorganization in bacteria. PMID:24252326
Analysis of fluorescent reporters indicates heterogeneity in glucose uptake and utilization in clonal bacterial populations. PMID:24238347
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. PMID:24234441
Integrating in silico resources to map a signaling network. PMID:24233784
Gene product 0.4 increases bacteriophage T7 competitiveness by inhibiting host cell division. PMID:24218612
How does Tremblaya princeps get essential proteins from its nested partner Moranella endobia in the Mealybug Planoccocus citri? PMID:24204799
Automated design of bacterial genome sequences. PMID:24160255
The sensory histidine kinases TorS and EvgS tend to form clusters in Escherichia coli cells. PMID:24147062
The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. PMID:24146625
CRISPR interference (CRISPRi) for sequence-specific control of gene expression. PMID:24136345
Improving acetate tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PMID:24124618
Quantitative influence of macromolecular crowding on gene regulation kinetics. PMID:24121687
Antibacterial mechanisms identified through structural systems pharmacology. PMID:24112686
The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone. PMID:24098145
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. PMID:24059635
Overexpression of fetA (ybbL) and fetB (ybbM), Encoding an Iron Exporter, Enhances Resistance to Oxidative Stress in Escherichia coli. PMID:24038693
Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect. PMID:23918810
Pyrimidine homeostasis is accomplished by directed overflow metabolism. PMID:23903661
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. PMID:23899370
A genome-wide screen for identifying all regulators of a target gene. PMID:23892289
Anaerobic expression of the gadE-mdtEF multidrug efflux operon is primarily regulated by the two-component system ArcBA through antagonizing the H-NS mediated repression. PMID:23874328
H-NS is a novel transcriptional modulator of the ribonucleotide reductase genes in Escherichia coli. PMID:23873909
Engaging students in a bioinformatics activity to introduce gene structure and function. PMID:23858361
Protein level identification of the Listeria monocytogenes sigma H, sigma L, and sigma C regulons. PMID:23841528
Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PMID:23818864
GoSynthetic database tool to analyse natural and engineered molecular processes. PMID:23813641
Efficient translation initiation dictates codon usage at gene start. PMID:23774758
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. PMID:23744946
Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants. PMID:23729647
A semi-automated genome annotation comparison and integration scheme. PMID:23725374
Compensation of the metabolic costs of antibiotic resistance by physiological adaptation in Escherichia coli. PMID:23716056
Genetic characterization of moaB mutants of Escherichia coli. PMID:23680484
Dual function of the McaS small RNA in controlling biofilm formation. PMID:23666921
The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. PMID:23658223
The genome organization of Thermotoga maritima reflects its lifestyle. PMID:23637642
Parallel exploitation of diverse host nutrients enhances Salmonella virulence. PMID:23633950
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). PMID:23630983
A flood-based information flow analysis and network minimization method for gene regulatory networks. PMID:23617932
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Computing minimal nutrient sets from metabolic networks via linear constraint solving. PMID:23537498
The complete genome and phenome of a community-acquired Acinetobacter baumannii. PMID:23527001
Improving ethanol tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PMID:23469036
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis. PMID:23390353
Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli. PMID:23385483
Analysis of Soluble protein complexes in Shigella flexneri reveals the influence of temperature on the amount of lipopolysaccharide. PMID:23378524
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. PMID:23352146
Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics. PMID:23341768
Genome-scale engineering for systems and synthetic biology. PMID:23340847
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. PMID:23340840
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. PMID:23327937
Analysis of omics data with genome-scale models of metabolism. PMID:23247105
The Escherichia coli peripheral inner membrane proteome. PMID:23230279
Rho and NusG suppress pervasive antisense transcription in Escherichia coli. PMID:23207917
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. PMID:23203884
BSRD: a repository for bacterial small regulatory RNA. PMID:23203879
Modelling translation initiation under the influence of sRNA. PMID:23203192
EcoGene 3.0. PMID:23197660
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. PMID:23194155
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. PMID:23193253
WholeCellKB: model organism databases for comprehensive whole-cell models. PMID:23175606
Global identification of prokaryotic glycoproteins based on an Escherichia coli proteome microarray. PMID:23145077
Protein aggregation caused by aminoglycoside action is prevented by a hydrogen peroxide scavenger. PMID:23122414
ECMDB: the E. coli Metabolome Database. PMID:23109553
Comparison of the functions of glutathionylspermidine synthetase/amidase from E. coli and its predicted homologues YgiC and YjfC. PMID:23097746
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Antivirulence genes: insights into pathogen evolution through gene loss. PMID:23045475
Regulatory network operations in the Pathway Tools software. PMID:22998532
Evaluation of research in biomedical ontologies. PMID:22962340
Regulation of the histidine utilization (hut) system in bacteria. PMID:22933560
Computational design of genomic transcriptional networks with adaptation to varying environments. PMID:22927389
A selective force favoring increased G+C content in bacterial genes. PMID:22908296
Antisense transcription is pervasive but rarely conserved in enteric bacteria. PMID:22872780
Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations. PMID:22870390
The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA. PMID:22847818
VirB-mediated positive feedback control of the virulence gene regulatory cascade of Shigella flexneri. PMID:22821978
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. PMID:22821013
Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli. PMID:22783906
Regulatory role of cAMP receptor protein over Escherichia coli fumarase genes. PMID:22752906
Burkholderia pseudomallei known siderophores and hemin uptake are dispensable for lethal murine melioidosis. PMID:22745846
Isobutyraldehyde production from Escherichia coli by removing aldehyde reductase activity. PMID:22731523
Borrelia burgdorferi harbors a transport system essential for purine salvage and mammalian infection. PMID:22710875
Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. PMID:22694848
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PMID:22693442
Altered tRNA characteristics and 3' maturation in bacterial symbionts with reduced genomes. PMID:22689638
Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. PMID:22638572
The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. PMID:22618875
Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization. PMID:22393408
Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. PMID:22389370
Exploring and linking biomedical resources through multidimensional semantic spaces. PMID:22373409
Suppression of a dnaKJ deletion by multicopy dksA results from non-feedback-regulated transcripts that originate upstream of the major dksA promoter. PMID:22267514
Construction and completion of flux balance models from pathway databases. PMID:22262672
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. PMID:22232676
Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes. PMID:22223756
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Three-stage assembly of the cysteine synthase complex from Escherichia coli. PMID:22179612
More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli. PMID:22168595
Identification of tumor-specific Salmonella Typhimurium promoters and their regulatory logic. PMID:22140114
CharProtDB: a database of experimentally characterized protein annotations. PMID:22140108
Rhea--a manually curated resource of biochemical reactions. PMID:22135291
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PMID:22125499
The UniProt-GO Annotation database in 2011. PMID:22123736
The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim. PMID:22122981
Semantic annotation of biological concepts interplaying microbial cellular responses. PMID:22122862
High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system. PMID:22114197
Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes. PMID:22075923
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli. PMID:21992408
Engineering strategy of yeast metabolism for higher alcohol production. PMID:21902829
Enzymes are enriched in bacterial essential genes. PMID:21738765
Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting. PMID:21726468
The EcoCyc Database PubMed citations: 30.

30 articles citing: The EcoCyc Database

Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Escherichia coli cell factories with altered chromosomal replication scenarios exhibit accelerated growth and rapid biomass production. PMID:35729580
Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PMID:34170902
Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B. PMID:33997676
Best practices on the differential expression analysis of multi-species RNA-seq. PMID:33926528
Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli. PMID:33731833
Behind the shield of Czc: ZntR controls expression of the gene for the zinc-exporting P-type ATPase ZntA in Cupriavidus metallidurans. PMID:33685972
Mutant Strains of Escherichia coli and Methicillin-Resistant Staphylococcus aureus Obtained by Laboratory Selection To Survive on Metallic Copper Surfaces. PMID:33067196
Attractor Concepts to Evaluate the Transcriptome-wide Dynamics Guiding Anaerobic to Aerobic State Transition in Escherichia coli. PMID:32246034
Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing. PMID:32211022
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth. PMID:32196485
Genome-Based Metabolic Reconstruction Unravels the Key Role of B12 in Methionine Auxotrophy of an Ortho-Phenylphenol-Degrading Sphingomonas haloaromaticamans. PMID:31998277
Manganese Is Required for the Rapid Recovery of DNA Synthesis following Oxidative Challenge in Escherichia coli. PMID:31570529
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. PMID:31032842
Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria. PMID:30232266
The Pseudomonas aeruginosa Complement of Lactate Dehydrogenases Enables Use of d- and l-Lactate and Metabolic Cross-Feeding. PMID:30206167
Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis. PMID:29875739
Mathematical modelling of microbes: metabolism, gene expression and growth. PMID:29187637
Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. PMID:29046437
Mechanisms for Differential Protein Production in Toxin-Antitoxin Systems. PMID:28677629
Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. PMID:28648779
Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. PMID:28526842
Comparative genomics and evolution of transcriptional regulons in Proteobacteria. PMID:28348857
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. PMID:27933038
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. PMID:27899573
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
Analysis tools for the interplay between genome layout and regulation. PMID:27294345
Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. PMID:26843427
Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli. PMID:26406465
Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. PMID:26030905

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enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

publication
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

regulation of post-translational protein modification
metasource: Fairsharing.org
version: FAIRsharing.org: EcoCyc; EcoCyc E. coli Database; DOI: https://doi.org/10.25504/FAIRsharing.65dmtr; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

bioinformatics
metasource: re3data.org
version: re3data.org: EcoCyc Database; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34K99 last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: EcoCyc Database; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34K99 last accessed: 2022-11-04

life sciences
metasource: re3data.org
version: re3data.org: EcoCyc Database; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34K99 last accessed: 2022-11-04

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

gene regulation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:21.214205

enzyme genome molecular interaction pathway model protein publication regulation of gene expression regulation of post-translational protein modification bioinformatics genomics life sciences molecular interactions, pathways and networks gene expression transcription factors and regulatory sites model organisms gene regulation

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BioCyc

EchoBase

RegulonDB

PEC - Profiling of E. coli Chromosome

The Coli Genetic Stock Center

PortEco

Essential genes in E. coli

CoryneRegNet 6.0 - Corynebacterial Regulation Network

PROkariotIC Database Of Gene-Regulation

ECMDB

EhecRegNet

EcoliWiki: A Wiki-based community resource for Escherichia coli

MetaCyc

Bacterial Protein Interaction Database

HumanCyc

GenoBase

Regulation of Gene Expression Ontolology

PAZAR

Biological General Repository for Interaction Datasets

Reactome - a curated knowledgebase of biological pathways