ArticleGigaScience2020
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 97 citations in OpenAlex.
- Fine mapping of QPm.caas-4BL.2 for adult-plant resistance to powdery mildew in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A natural allele of TaSCE1-A1 confers drought resistance in wheat.Nature plants · 2026Article
- Genome-wide characterization and adaptive evolution of favorable gibberellin 2-oxidase alleles contributing to wheat agronomic traits.Journal of advanced research · 2026Article
- Gene editing and association analysis of circadian clock gene TaPRR59 highlights its importance in yield-related traits in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pangenome identification and functional characterization of AHL genes in wheat (Triticum aestivum L.) reveal the role of TaAHL67 in grain weight regulation.BMC plant biology · 2025Article
- Unveiling the wheat NTP gene family: insights from genome-wide identification and TaNTP6 haplotype analysis.BMC plant biology · 2025Article
- Translational regulation plasticity shapes wheat grain adaptation to heat stress.Genome biology · 2025Article
- Identification and validation of functional markers for the superoxide dismutase gene TaSOD-B2 in common wheat.BMC plant biology · 2025Article
- The TaMYB44-TaMYB1 module regulates grain amylose biosynthesis and flour viscosity in wheat.Plant communications · 2025Article
- The TaCEP15 peptide signaling cascade modulates primary root length and drought tolerance in wheat.Science advances · 2025Article
- Nitrogen enhances post-drought recovery in wheat by modulating TaSnRK2.10-mediated regulation of TaNLP7.Nature plants · 2025Article
- TaIRE1-mediated unconventional splicing of the TabZIP60 mRNA and the miR172 precursor regulates heat stress tolerance in wheat.Journal of integrative plant biology · 2025Article
- Identification of quantitative trait loci and candidate genes underlying kernel traits of wheat (Triticum aestivum L.) in response to drought stress.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- TaPP2C-a6 interacts with TaDOG1Ls and regulates seed dormancy and germination in wheat.Plant biotechnology journal · 2025Article
- Identification of a novel dwarfing gene,Molecular breeding : new strategies in plant improvement · 2025Article
- Large-scale integration of meta-QTL and genome-wide association study identifies genomic regions and candidate genes for photosynthetic efficiency traits in bread wheat.BMC genomics · 2025Article
- TaDL interacts with TaB3 and TaNF-YB1 to synergistically regulate the starch synthesis and grain quality in bread wheat.Journal of integrative plant biology · 2025Article
- Linkage and association analysis to identify wheat pre-harvest sprouting resistance genetic regions and develop KASP markers.Molecular breeding : new strategies in plant improvement · 2025Article
- Identification of a von Willebrand factor type A protein affecting both grain and flag leaf morphologies in wheat.Science China. Life sciences · 2024Article
- Pleiotropic phenotypic effects of the TaCYP78A family on multiple yield-related traits in wheat.Plant biotechnology journal · 2024Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate genomic variations across hundreds or even thousands of samples in the post-genomic era. The management and exploration of these large-scale genomic variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new genomic variation data in diverse species.
resultsHere, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale genomic variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize genomic variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence variations.
conclusionsSnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.
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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.