ReviewEcoSal Plus2025
The EcoCyc database (2025).
Abstract readReview
In one paragraph
Review in EcoSal Plus, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
0numbers the graph read from it
0cells of the map it votes in
19citing 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
19 citing papers in PubMed.
- Identification of proteins interacting with the N-terminal half of endoribonuclease RNase E inRNA biology · 2026Article
- Combinatorial action of regulatory systems generates colistin heteroresistance.Science advances · 2026Article
- Comparative Characterization of σInternational journal of molecular sciences · 2026Article
- An end-to-end computational framework for "Record-seq" transcriptional recording data.Bioinformatics (Oxford, England) · 2026Article
- Article
- The allostery principle supports the symbolic character of signaling circuits: gene regulation provides a form of intelligence to living systems.Theory in biosciences = Theorie in den Biowissenschaften · 2026Article
- Fine modulation of carbon flow in central carbon metabolism via ribosome-binding site modification inMetabolic engineering communications · 2026Article
- Comparative analysis of gene importance inmSystems · 2026Article
- Review
- Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research.Nature communications · 2026Review
- Uncovering resistance pathways to first- and last-line antibiotics inMicrobial genomics · 2026Article
- From genes to collective modes: biological constraints shape metabolic evolution.bioRxiv : the preprint server for biology · 2026Article
- Bayesian analysis of longitudinal RB-TnSeq resolves the fitness seascape in fluctuating environments.bioRxiv : the preprint server for biology · 2026Article
- Proteome-wide analysis of protein stability in Escherichia coli under acid stress.Journal of industrial microbiology & biotechnology · 2026Article
- Chaperone dependency during biogenesis does not correlate with chaperone dependency during refolding.Molecular systems biology · 2026Article
- Article
- Using CRISPRi inJournal of microbiology & biology education · 2025Article
- Impeding pathways of intrinsic resistance in Escherichia coli confers antibiotic sensitization and resistance proofing.PLoS biology · 2025Article
- Chaperone Dependency during Primary Protein Biogenesis Does Not Correlate with Chaperone Dependency duringbioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
23 authors.
Peter D KarpBioinformatics Research Group, SRI International, Menlo Park, California, USA.ORCID 0000-0002-5876-6418
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, Mexico.
Víctor H TierrafriaPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
Paloma LaraPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
Luis Muñiz-RascadoPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
César Bonavides-MartinezPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
Alberto Santos-ZavaletaPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
Amanda MackieSchool of Natural 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.
Riley JuenemannDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Cyrus N M KnudsenDepartment 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, Mexico.
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
$4.6MThe BioCyc, MetaCyc, and EcoCyc Knowledge BasesR24GM150703 · NIGMS · SRI INTERNATIONAL · PI PETER D KARP · 2023 to 2026
$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 R24 GM150703NIGMS NIH HHS U24 GM077678NIH HHS 1R24GM150703NLM NIH HHS R01 LM013229
Abstract
EcoCyc is a bioinformatics database (DB) available at EcoCyc.org that describes the genome and the biochemical machinery of
Indexed as
Databases, GeneticEscherichia coli K12Genome, BacterialComputational BiologyEscherichia coliGene Expression Regulation, BacterialMetabolic Networks and PathwaysOperonSoftwarebioinformaticsdatabaseEscherichia coli
Identifiers
What OpenQuestion 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 OpenQuestion graph.