ArticleNucleic acids research2014
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 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
72 citing papers in PubMed, 179 citations in OpenAlex.
- gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota.Journal of molecular biology · 2026Article
- EvoSNR-Prom: Predicting promoters at single-nucleotide resolution with label-aware transfer learning of the pretrained EVO model.PLoS computational biology · 2026Article
- Actinobacteria TFDB: An integrated view of transcription factors in Actinobacteria.Engineering microbiology · 2026Article
- Article
- Mobile-CRISPRi as a tool for genetic manipulation in the intracellular pathogenApplied and environmental microbiology · 2026Article
- Plasticity in a bacterial global regulatory switch that drives a shift in antibiotic resistance and virulence.FEMS microbes · 2026Article
- Bacterial warfare is associated with virulence and antimicrobial resistance.Nature communications · 2025Article
- Engineered Marine Biofilms for Ocean Environment Monitoring.ACS synthetic biology · 2025Article
- antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.Nucleic acids research · 2025Article
- Rewiring of cell morphology by Small protein B enhances stress tolerance and colonization in Aeromonas veronii under adverse conditions.Nucleic acids research · 2025Article
- Article
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.Briefings in bioinformatics · 2024Article
- Coding genomes with gapped pattern graph convolutional network.Bioinformatics (Oxford, England) · 2024Article
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- Comparative Genomics ofPHAGE (New Rochelle, N.Y.) · 2023Article
- From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry.FEMS microbiology reviews · 2023Review
- Transcription factor-based biosensors for screening and dynamic regulation.Frontiers in bioengineering and biotechnology · 2023Review
- Draft Genome Sequence of the Tomato Stem Endophyte Bacillus safensis TS3.Microbiology resource announcements · 2022Article
12 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
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The influx of high-throughput data and the need for complex models to describe the interaction of prokaryotic transcription factors (TF) with their target sites pose new challenges for TF-binding site databases. CollecTF (http://collectf.umbc.edu) compiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored data and fully customizable access to its records. CollecTF integrates multiple sources of data automatically and openly, allowing users to dynamically redefine binding motifs and their experimental support base. Data quality and currency are fostered in CollecTF by adopting a sustainable model that encourages direct author submissions in combination with in-house validation and curation of published literature. CollecTF entries are periodically submitted to NCBI for integration into RefSeq complete genome records as link-out features, maximizing the visibility of the data and enriching the annotation of RefSeq files with regulatory information. Seeking to facilitate comparative genomics and machine-learning analyses of regulatory interactions, in its initial release CollecTF provides domain-wide coverage of two TF families (LexA and Fur), as well as extensive representation for a clinically important bacterial family, the Vibrionaceae.
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.