ArticleG3 (Bethesda, Md.)2018
Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants.
Article in G3 (Bethesda, Md.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed.
- Large DNA and protein language models enhance discovery of deleterious mutations in maize.Genome biology · 2025Article
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- Decoding nature's grammar with DNA language models.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sodium azide mutagenesis induces a unique pattern of mutations.PLoS genetics · 2025Article
- Plant conservation in the age of genome editing: opportunities and challenges.Genome biology · 2024Review
- Genetic structure and first genome-wide insights into the adaptation of a wild relative of grapevine,Evolutionary applications · 2023Article
- VariBench, new variation benchmark categories and data sets.Frontiers in bioinformatics · 2023Article
- If it ain't broke, don't fix it: evaluating the effect of increased recombination on response to selection for wheat breeding.G3 (Bethesda, Md.) · 2022Article
- Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds.Breeding science · 2022Article
- Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression.Molecular biology and evolution · 2022Article
- Genetic load: genomic estimates and applications in non-model animals.Nature reviews. Genetics · 2022Review
- PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants.Plant biotechnology journal · 2022Article
- Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach.PLoS computational biology · 2022Article
- Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes.Molecular biology and evolution · 2022Article
- Fitness Effects of Mutations: An Assessment of PROVEAN Predictions Using Mutation Accumulation Data.Genome biology and evolution · 2022Article
- PON-All: Amino Acid Substitution Tolerance Predictor for All Organisms.Frontiers in molecular biosciences · 2022Article
- Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia.Molecular biology and evolution · 2021Article
- Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics.Plant biotechnology journal · 2021Article
- The patterns of deleterious mutations during the domestication of soybean.Nature communications · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910
Indexed as
Identifiers
What OpenQuestion holds
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.