ArticleBioinformatics (Oxford, England)2019
Large-scale comparative analysis of microbial pan-genomes using PanOCT.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Escherichia coli Type III Secretion System 2 Is Associated With Patient Mortality in Bloodstream Infections.The Journal of infectious diseases · 2025Article
- Article
- Drug selection based on pan-genomics genetic features ofFrontiers in microbiology · 2025Article
- Serum susceptibility of Escherichia coli and its association with patient clinical outcomes.PloS one · 2024Article
- Complete Genome Sequence of Four Strains ofJournal of genomics · 2022Article
- PanACoTA: a modular tool for massive microbial comparative genomics.NAR genomics and bioinformatics · 2021Article
- Horizontal transfer and evolution of wall teichoic acid gene cassettes inF1000Research · 2021Article
- A pan-genome method to determine core regions of theF1000Research · 2021Article
- Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to OtherJournal of clinical microbiology · 2020Article
- Genetic Diversity AmongFrontiers in microbiology · 2020Article
- Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections.Microorganisms · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
summaryThe JCVI pan-genome pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (pan-genome ortholog clustering tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes and generate figures, tables and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used. AVAILABILITY AND IMPLEMENTATION: Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.
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.