ArticleNucleic acids research2020
LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Meta-analysis of theMicrobial genomics · 2022Pooled it
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- First comprehensive whole genome sequencing report of a multidrug-resistantNew microbes and new infections · 2026Article
- Decentralized nanopore genomics reveals diverseMicrobial genomics · 2026Article
- Comparative genomics ofMicrobial genomics · 2026Article
- Comprehensive genomic characterization and public health implications of multidrug-resistant Escherichia coli from poultry in Noakhali, Bangladesh.BMC microbiology · 2026Article
- Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh.Scientific reports · 2025Article
- Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh.Scientific reports · 2025Article
- First report on comprehensive genomic analysis of a multidrug-resistant Enterobacter asburiae isolated from diabetic foot infection from Bangladesh.Scientific reports · 2025Article
- Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in Gauteng South Africa.Scientific reports · 2024Article
- 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy inMicrobial genomics · 2024Article
- Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas.Genome biology and evolution · 2024Article
- Draft genomes of meropenem-resistantMicrobiology resource announcements · 2024Article
- Whole Genome Sequencing: Applications in Clinical Bacteriology.Medical principles and practice : international journal of the Kuwait University, Health Science Centre · 2024Review
- A recently collectedMicrobial genomics · 2024Article
- Identification of closely related species inFrontiers in microbiology · 2024Article
- Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex.Molecular plant pathology · 2023Article
- Genomic delineation and description of species and within-species lineages in the genusFrontiers in microbiology · 2023Article
- Characterization ofFrontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.
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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.