ArticleNature genetics2011
Predicting phenotypic variation in yeast from individual genome sequences.
Article in Nature genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.Cell genomics · 2026Article
- Predicting natural variation in the yeast phenotypic landscape with machine learning.Molecular systems biology · 2025Article
- High-throughput deep learning variant effect prediction with Sequence UNET.Genome biology · 2023Article
- How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent.Molecular biology and evolution · 2021Article
- Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations.Biophysical journal · 2021Article
- Performance of Regression Models as a Function of Experiment Noise.Bioinformatics and biology insights · 2021Article
- Biophysical ambiguities prevent accurate genetic prediction.Nature communications · 2020Article
- Vitamin requirements and biosynthesis in Saccharomyces cerevisiae.Yeast (Chichester, England) · 2020Review
- Mitonuclear conflict and cooperation govern the integration of genotypes, phenotypes and environments.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype.Scientific reports · 2019Article
- The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae.Molecular systems biology · 2019Article
- A resource of variant effect predictions of single nucleotide variants in model organisms.Molecular systems biology · 2018Article
- Epigenetic control of variation and stochasticity in metabolic disease.Molecular metabolism · 2018Review
- Article
- Phenotype inference in aneLife · 2017Article
- A genetic signature of the evolution of loss of flight in the Galapagos cormorant.Science (New York, N.Y.) · 2017Article
- Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy.PLoS genetics · 2017Article
- Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling.Human mutation · 2017Article
- A global genetic interaction network maps a wiring diagram of cellular function.Science (New York, N.Y.) · 2016Article
- Predicting quantitative traits from genome and phenome with near perfect accuracy.Nature communications · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A central challenge in genetics is to predict phenotypic variation from individual genome sequences. Here we construct and evaluate phenotypic predictions for 19 strains of Saccharomyces cerevisiae. We use conservation-based methods to predict the impact of protein-coding variation within genes on protein function. We then rank strains using a prediction score that measures the total sum of function-altering changes in different sets of genes reported to influence over 100 phenotypes in genome-wide loss-of-function screens. We evaluate our predictions by comparing them with the observed growth rate and efficiency of 15 strains tested across 20 conditions in quantitative experiments. The median predictive performance, as measured by ROC AUC, was 0.76, and predictions were more accurate when the genes reported to influence a trait were highly connected in a functional gene network.
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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.