ReviewEcoSal Plus2023
The EcoCyc Database (2023).
Abstract readReview
In one paragraph
Review in EcoSal Plus, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
0numbers the graph read from it
0cells of the map it votes in
68citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
68 citing papers in PubMed.
- Engineering Access to Stereoirregular Polymer Microstructures Enables Improved Processability of Microbial Poly(3-hydroxybutyrate).Biomacromolecules · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Pathogen species and capsule expression shape opportunistic transfer and the recipient response during plasmid RP4 conjugation.Communications biology · 2026Article
- Biofilm-driven LPS remodeling and colanic acid overproduction mediate biocide adaptation and antibiotic cross-resistance in E. coli.npj antimicrobials and resistance · 2026Article
- A Multi-Omics Approach Uncovers Divergent Mechanisms of Asthma in Normal Weight and Obese Children.Metabolites · 2026Article
- Abrogation of SOS mutagenesis by themSystems · 2026Article
- Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.Genome medicine · 2026Article
- Exploring the Diversity and Function of the SPFH-Domain Containing Proteins in Pseudomonas aeruginosa.Environmental microbiology reports · 2026Article
- Protein overabundance is driven by growth robustness.Science advances · 2026Article
- Identification of specific metabolic capacities associated with major extraintestinal pathogenicJournal of bacteriology · 2026Article
- Global analysis of protein degradation reveals instability of diverse regulators inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transcriptomic profiling of a commensal Escherichia coli lysogen in simulated intestinal fluid reveals broad changes in both core and accessory regions of the genome.BMC genomics · 2026Article
- METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions.GigaScience · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- QSProteome: a community-driven interactive platform for large-scale exploration and evaluation of predicted protein complex structures.Nucleic acids research · 2026Article
- Genetic Tools and Approaches to Study Bacterial Efflux Pumps.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle.Molecular cell · 2025Article
- Untargeted Metabolomics Identifies Faecal Filtrate-Derived Metabolites That DisruptInternational journal of molecular sciences · 2025Article
- Comparative transcriptomic analysis of perfluoroalkyl substances-induced responses of exponential and stationary phase Escherichia coli.BMC genomics · 2025Article
- Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors.
Peter D KarpBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Suzanne PaleyBioinformatics Research Group, SRI International, Menlo Park, California, USA.ORCID 0000-0001-5763-8935
Ron CaspiBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Anamika KothariBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Markus KrummenackerBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Peter E MidfordBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Lisa R MooreBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Pallavi SubhravetiBioinformatics Research Group, SRI International, Menlo Park, California, USA.
Socorro Gama-CastroPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Victor H TierrafriaPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Paloma LaraPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Luis Muñiz-RascadoPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
César Bonavides-MartinezPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Alberto Santos-ZavaletaPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Amanda MackieDepartment of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia.
Gwanggyu SunDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Travis A Ahn-HorstDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Heejo ChoiDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Markus W CovertDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Julio Collado-VidesPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Ian PaulsenSchool of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia.ORCID 0000-0001-9015-9418
Funding
The EcoCyc Model Organism Database for Escherichia coli [SRI Proposal ECU 14-631]U24GM077678 · NIGMS · SRI INTERNATIONAL · PI KARP, PETER D · 2006 to 2018
$12.3MDevelopment and Support of the Pathway Tools SoftwareR01AI160719 · NIAID · SRI INTERNATIONAL · PI PETER D KARP · 2021 to 2026
$5.9MThe EcoCyc Model Organism Database for Escherichia coliR01GM077678 · NIGMS · SRI INTERNATIONAL · PI KARP, PETER D · 2019 to 2022
$4.6MDeep Curation via an Integrated Whole-Cell Computational ModelR01LM013229 · NLM · STANFORD UNIVERSITY · PI COVERT, MARKUS W · 2020 to 2023
$1.5MNIAID NIH HHS R01 AI160719NIGMS NIH HHS R01 GM077678NIGMS NIH HHS U24 GM077678NIH HHS GM077678NIH HHS LM013229NIH HHS R01AI160719NLM NIH HHS R01 LM01322NLM NIH HHS R01 LM013229
Abstract
EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of
Indexed as
Escherichia coli K12Escherichia coli ProteinsComputational BiologyDatabases, GeneticEscherichia coliSoftwareEscherichia coli Proteinsbioinformaticsdatabase
Identifiers
What Socratic holds
Textmetadata
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.