ArticleMethods in molecular biology (Clifton, N.J.)2022
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Divergent roles of ent-kaurene oxidase paralogs in rice momilactone biosynthesis.Journal of integrative plant biology · 2026Article
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
- Transcriptomic characterization of Coccidioides morphological states using RiboMarker-enhanced RNA sequencing.G3 (Bethesda, Md.) · 2026Article
- A sorghum-anchored pan-grass syntenic gene set in grasses.NAR genomics and bioinformatics · 2026Article
- Genomic dissection of iron toxicity tolerance in rice identifies key loci, candidate genes, and associated haplotypes.Scientific reports · 2026Article
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- Structural Variants Contribute to Phenotypic Variation in Maize.Molecular ecology · 2025Article
- Uncrossing the 'X': Characterization of alternative alleles for KSLX in Oryza.Phytochemistry · 2025Article
- Decoding nitrogen uptake efficiency in maize and sorghum: insights from comparative gene regulatory networks.The Plant journal : for cell and molecular biology · 2025Article
- Towards an official gene nomenclature for Populus trichocarpa.Tree physiology · 2025Review
- Genome-wide characterization of ZmCRY genes: unveiling stress response mechanisms and the role of ZmCRYPHR2 in salinity tolerance.BMC plant biology · 2025Article
- High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye.Genome biology · 2025Article
- Foxtail millet research in supporting climate change resilience efforts: Bibliometric analysis and focused literature review.Heliyon · 2025Review
- Structural variants contribute to phenotypic variation in maize.bioRxiv : the preprint server for biology · 2024Article
- Double-barreled defense: dualaBIOTECH · 2024Article
- Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes.Plant physiology · 2024Article
- Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular Evolution of RAMOSA1 (RA1) in Land Plants.Biomolecules · 2024Article
- Four enzymes control natural variation in the steroid core ofbioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
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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.