ArticleeLife2022
Structure-guided isoform identification for the human transcriptome.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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Who cites it
27 citing papers in PubMed, 47 citations in OpenAlex.
- A structure-aware generative AI framework for revealing functional relationships in protein families.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- 3DSeqCheck: A Web-based Tool for Verifying Sequence Consistency Between a 3D Structure File and the Corresponding UniProt Entry.Journal of molecular biology · 2026Article
- Testing the reliability of AI-generated protein structures.bioRxiv : the preprint server for biology · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- VUStruct: A compute pipeline for high throughput and personalized structural biology.PLoS computational biology · 2026Article
- The promise of AlphaFold for gene structure annotation.Nucleic acids research · 2026Article
- DeepISO: deep learning-powered prediction of protein-protein interaction rewiring generated by alternative splicing.Genome biology · 2026Article
- Isoforms in action: The impact of transcript diversity in phenotype.Genetics and molecular biology · 2026Article
- AlphaSync is an enhanced AlphaFold structure database synchronized with UniProt.Nature structural & molecular biology · 2025Article
- Predicting the structural impact of human alternative splicing.Genome biology · 2025Article
- Isoswitching drives the aging process in human brains.bioRxiv : the preprint server for biology · 2025Article
- Integrating Arabidopsis and crop species gene discovery for crop improvement.The Plant cell · 2025Review
- PSAURON: a tool for assessing protein annotation across a broad range of species.NAR genomics and bioinformatics · 2025Article
- Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions.Current opinion in structural biology · 2025Review
- Protein language models learn evolutionary statistics of interacting sequence motifs.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- FLT3 targeting in the modern era: from clonal selection to combination therapies.International journal of hematology · 2024Review
- Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.Journal of proteome research · 2024Article
- Article
- Predicting the Structural Impact of Human Alternative Splicing.bioRxiv : the preprint server for biology · 2023Article
- CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure.Genome biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 3 countries.
Funding
Abstract
Recently developed methods to predict three-dimensional protein structure with high accuracy have opened new avenues for genome and proteome research. We explore a new hypothesis in genome annotation, namely whether computationally predicted structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by protein structure predictions, we evaluated over 230,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues. From this set of assembled transcripts, we identified hundreds of isoforms with more confidently predicted structure and potentially superior function in comparison to canonical isoforms in the latest human gene database. We illustrate our new method with examples where structure provides a guide to function in combination with expression and evolutionary evidence. Additionally, we provide the complete set of structures as a resource to better understand the function of human genes and their isoforms. These results demonstrate the promise of protein structure prediction as a genome annotation tool, allowing us to refine even the most highly curated catalog of human proteins. More generally we demonstrate a practical, structure-guided approach that can be used to enhance the annotation of any genome.
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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.