ArticleNucleic acids research2018
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 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
79 citing papers in PubMed.
- De novo genome assembly of Texas wintergrass [Nassella leucotricha {Trin. & Rupr.} Pohl] supports diagnostic marker development and phylogenetic analysis of species within the family Poaceae.G3 (Bethesda, Md.) · 2026Article
- AgroLD: a knowledge graph for the plant sciences.BMC genomic data · 2025Article
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- Foxtail millet research in supporting climate change resilience efforts: Bibliometric analysis and focused literature review.Heliyon · 2025Review
- Identification and preliminary characterization of conserved uncharacterized proteins fromPlant direct · 2023Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- SyntenyViewer: a comparative genomics-driven translational research tool.Database : the journal of biological databases and curation · 2023Article
- WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.Genomics, proteomics & bioinformatics · 2023Article
- Toward a data infrastructure for the Plant Cell Atlas.Plant physiology · 2023Review
- Using knowledge graphs to infer gene expression in plants.Frontiers in artificial intelligence · 2023Article
- Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants.GigaScience · 2022Article
- A cascade of bHLH-regulated pathways programs maize anther development.The Plant cell · 2022Article
- PlantGF: an analysis and annotation platform for plant gene families.Database : the journal of biological databases and curation · 2022Article
- Evaluation of gene flow and genetic diversity in rice accessions across Kurdistan region-iraq using SSR markers.Molecular biology reports · 2022Article
- Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy.Journal of experimental botany · 2022Review
- LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.Nucleic acids research · 2022Article
- CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach.Frontiers in artificial intelligence · 2022Article
- Scripting Analyses of Genomes in Ensembl Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Structural and Functional Characterization at the Molecular Level of the MATE Gene Family in Wheat in Silico.Contrast media & molecular imaging · 2022Article
19 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
39 authors.
Funding
Abstract
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.
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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.