ArticleNucleic acids research2013
EcoGene 3.0.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
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
119 citing papers in PubMed.
- Overexpression of Escherichia coli yaiX Confers Multidrug Resistance and Enhances Virulence in the Silkworm Infection Model.Microbiology and immunology · 2026Article
- Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.Briefings in bioinformatics · 2025Article
- About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature.Biology direct · 2023Article
- Plasticity and Stereotypic Rewiring of the Transcriptome Upon Bacterial Evolution of Antibiotic Resistance.Molecular biology and evolution · 2023Article
- The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12.Metallomics : integrated biometal science · 2022Article
- Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli.Nucleic acids research · 2022Article
- Escherichia coli cell factories with altered chromosomal replication scenarios exhibit accelerated growth and rapid biomass production.Microbial cell factories · 2022Article
- T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason.Frontiers in microbiology · 2022Article
- A Shift to Human Body Temperature (37°C) Rapidly Reprograms Multiple Adaptive Responses in Escherichia coli That Would Facilitate Niche Survival and Colonization.Journal of bacteriology · 2021Article
- digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes.BMC bioinformatics · 2021Article
- Network pharmacology-based study to explore the mechanism of the Yiqi Gubiao pill in lung cancer treatment.Oncology letters · 2021Article
- Dynamics of chromosomal target search by a membrane-integrated one-component receptor.PLoS computational biology · 2021Article
- Engineering of the Recombinant Expression and PEGylation Efficiency of the Therapeutic Enzyme Human Thymidine Phosphorylase.Frontiers in bioengineering and biotechnology · 2021Article
- StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.Frontiers in bioinformatics · 2021Review
- Three Ribosomal Operons ofFrontiers in microbiology · 2021Article
- Differential Packaging Into Outer Membrane Vesicles Upon Oxidative Stress Reveals a General Mechanism for Cargo Selectivity.Frontiers in microbiology · 2021Article
- Experimental determination of evolutionary barriers to horizontal gene transfer.BMC microbiology · 2020Article
- Properties of protein unfolded states suggest broad selection for expanded conformational ensembles.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions.Bioinformatics (Oxford, England) · 2020Article
- Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action.Nature communications · 2019Article
59 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
2 authors.
Funding
Abstract
EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.