ArticleNucleic acids research2015
The EMBL-EBI bioinformatics web and programmatic tools framework.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 570 papers, 1 of them a synthesis that pooled it.
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
570 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- A multifunctional PKS-NRPS megasynthetase in nematodes produces divergent signaling molecules that control different developmental arrests.Nature communications · 2026Article
- Hepatincolaceae (Alphaproteobacteria) Symbionts of Snapping ShrimpMicroorganisms · 2026Article
- A 2-pyrone-4,6-dicarboxylic acid biosensor for lignin valorization based on a newly identified transcriptional regulatory system.Biotechnology for biofuels and bioproducts · 2026Article
- Machine learning-guided discovery of spirocyclic inhibitors targeting Mycobacterium tuberculosis FtsZ.Folia microbiologica · 2026Article
- Genomic analysis of prophages from Burkholderia gladioli exposes extensive genetic diversity.BMC genomics · 2026Article
- A mutation-aware proteomics approach for designing a multi-epitope vaccine against multidrug-resistantMicrobiology spectrum · 2026Article
- Ancestral protein reconstruction reveals the mechanism of substrate specificity in FN3K-mediated deglycation.Communications biology · 2026Article
- Calcium Shock Enables Efficient and Programmable Particle Delivery for Genome Editing Applications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- circTGFBR2(3-6) acts as an assembly platform for RNA-binding protein IGF2BP3 and TGFBR1 mRNA to enhance breast cancer cell plasticity.Cell death and differentiation · 2026Article
- Deciphering the Biosynthetic Pathways and Regulatory Networks of the Active Components ofInternational journal of molecular sciences · 2026Article
- Identification of novel DNA gyrase B inhibitors inFrontiers in tuberculosis · 2026Article
- A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation.Mini reviews in medicinal chemistry · 2026Review
- Identification and prenatal diagnosis of a novel likely pathogenic ANOS1 variant in a large Chinese Kallmann syndrome family.Frontiers in genetics · 2026Article
- Full-length transcriptome ofPlant biotechnology (Tokyo, Japan) · 2025Article
- Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms.Nature communications · 2025Article
- Proposed mechanism for Rft1-mediated scrambling of a dolichol-linked oligosaccharide.bioRxiv : the preprint server for biology · 2025Article
- tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations.bioRxiv : the preprint server for biology · 2025Article
- Rapid key gene discovery for bacterial shape: a cross-species machine learning approach.BMC microbiology · 2025Article
- Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.Applied biochemistry and biotechnology · 2025Review
510 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
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
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.