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Updated: Aug 17, 2025

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

Structure-guided isoform identification for the human transcriptome.

Markus J Sommer^1,2, Sooyoung Cha^3,4, Ales Varabyou^2,5

¹Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, United States.

|December 15, 2022

Summary

This summary is machine-generated.

Computational protein structure prediction aids genome annotation by identifying functional gene isoforms. This approach refines human gene catalogs and enhances understanding of protein function across species.

Keywords:

genetics genome annotation genomics human machine learning molecular biophysics mouse protein structure prediction proteomics structural biology transcriptomics

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Published on: February 18, 2022

Area of Science:

Genomics
Proteomics
Structural Biology

Background:

High-accuracy three-dimensional protein structure prediction methods are emerging.
Genome annotation requires identifying functional protein products from gene isoforms.

Purpose of the Study:

To test if computationally predicted protein structures can identify functional gene isoforms.
To refine genome annotation using structure-based functional inference.

Main Methods:

Evaluated over 230,000 human protein-coding gene isoforms using predicted structures.
Integrated structural data with expression and evolutionary evidence.
Compared predicted functional isoforms against canonical isoforms in human gene databases.

Main Results:

Identified hundreds of human gene isoforms with confident structures and potentially superior function.
Demonstrated structure-guided functional identification for specific gene isoforms.
Provided a comprehensive resource of predicted protein structures for human genes.

Conclusions:

Protein structure prediction is a valuable tool for genome annotation.
A practical, structure-guided approach can enhance genome annotation across species.
This method refines the human protein catalog and aids functional genomics research.