ArticleBriefings in bioinformatics2018
Plant genome and transcriptome annotations: from misconceptions to simple solutions.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
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- Progressive salinity drives flavonoid branch reprogramming in Anoectochilus roxburghii.BMC plant biology · 2026Article
- Integrative approach to identify robust pattern recognition receptors in Eucalyptus grandis: novel candidates for disease resistance.Plant molecular biology · 2026Article
- Large-scale mining of plant genomes unlocks the diversity of oxidosqualene cyclases.Nature chemical biology · 2026Article
- First draft genome of the decaploid species,GigaByte (Hong Kong, China) · 2026Article
- The cryo-EM structure of Photosystem I from Chromera velia with a bound superoxide dismutase heterodimer.Nature communications · 2025Article
- Predicting precursors of plant specialized metabolites using DeepMol automated machine learning.Journal of integrative bioinformatics · 2025Article
- AtSubP-2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning.The plant genome · 2025Article
- MicroRNAs in Plant Genetic Regulation of Drought Tolerance and Their Function in Enhancing Stress Adaptation.Plants (Basel, Switzerland) · 2025Review
- Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery.International journal of molecular sciences · 2024Review
- Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata.BMC genomics · 2024Article
- Evidence-based unification of potato gene models with the UniTato collaborative genome browser.Frontiers in plant science · 2024Article
- Automatic annotation of the bHLH gene family in plants.BMC genomics · 2023Article
- Identification and preliminary characterization of conserved uncharacterized proteins fromPlant direct · 2023Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology.International journal of molecular sciences · 2023Review
- The potential of integrative phenomics to harness underutilized crops for improving stress resilience.Frontiers in plant science · 2023Article
- Transcriptome analysis of mulberry (Morus alba L.) leaves to identify differentially expressed genes associated with post-harvest shelf-life elongation.Scientific reports · 2022Article
- NewAntioxidants (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources.
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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.