ArticleCell reports2018
Bridging Genomics to Phenomics at Atomic Resolution through Variation Spatial Profiling.
Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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Who cites it
22 citing papers in PubMed.
- Alpha-1 antitrypsin deficiency: genetics, clinical manifestations, AI prognostics, and advanced imaging in liver disease.Annals of medicine and surgery (2012) · 2025Review
- Spatial covariance reveals isothiocyanate natural products adjust redox stress to restore function in alpha-1-antitrypsin deficiency.Cell reports. Medicine · 2025Article
- COPII cage assembly factor Sec13 integrates information flow regulating endomembrane function in response to human variation.Scientific reports · 2024Article
- Tracing genetic diversity captures the molecular basis of misfolding disease.Nature communications · 2024Article
- Understanding the host-pathogen evolutionary balance through Gaussian process modeling of SARS-CoV-2.Patterns (New York, N.Y.) · 2023Article
- Capturing the conversion of the pathogenic alpha-1-antitrypsin fold by ATF6 enhanced proteostasis.Cell chemical biology · 2023Article
- Triangulating variation in the population to define mechanisms for precision management of genetic disease.Structure (London, England : 1993) · 2022Article
- Towards generalizable predictions for G protein-coupled receptor variant expression.Biophysical journal · 2022Article
- Spatial covariance analysis reveals the residue-by-residue thermodynamic contribution of variation to the CFTR fold.Communications biology · 2022Article
- Common and rare myocilin variants: Predicting glaucoma pathogenicity based on genetics, clinical, and laboratory misfolding data.Human mutation · 2021Review
- Review
- Leveraging Population Genomics for Individualized Correction of the Hallmarks of Alpha-1 Antitrypsin Deficiency.Chronic obstructive pulmonary diseases (Miami, Fla.) · 2020Review
- Correction of Niemann-Pick type C1 trafficking and activity with the histone deacetylase inhibitor valproic acid.The Journal of biological chemistry · 2020Article
- Management of Hsp90-Dependent Protein Folding by Small Molecules Targeting the Aha1 Co-Chaperone.Cell chemical biology · 2020Article
- Phenotyping of RareCells · 2020Article
- Towards next generation therapies for cystic fibrosis: Folding, function and pharmacology of CFTR.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2020Review
- Article
- Individualized management of genetic diversity in Niemann-Pick C1 through modulation of the Hsp70 chaperone system.Human molecular genetics · 2020Article
- Quantitating the epigenetic transformation contributing to cholesterol homeostasis using Gaussian process.Nature communications · 2019Article
- HDAC inhibitors rescue multiple disease-causing CFTR variants.Human molecular genetics · 2019Article
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2 authors.
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Abstract
To understand the impact of genome sequence variation (the genotype) responsible for biological diversity and human health (the phenotype) including cystic fibrosis and Alzheimer's disease, we developed a Gaussian-process-based machine learning (ML) approach, variation spatial profiling (VSP). VSP uses a sparse collection of known variants found in the population that perturb the protein fold to define unknown variant function based on the emergent general principle of spatial covariance (SCV). SCV quantitatively captures the role of proximity in genotype-to-phenotype spatial-temporal relationships. Phenotype landscapes generated through SCV provide a platform that can be used to describe the functional properties that drive sequence-to-function-to-structure design of the polypeptide fold at atomic resolution. We provide proof of principle that SCV can enable the use of population-based genomic platforms to define the origins and mechanism of action of genotype-to-phenotype transformations contributing to the health and disease of an individual.
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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.