Rick Gelhausen

This study identifies 338 previously unannotated small open reading frames in UPEC strain CFT073, with functional evidence for nine intergenic sORFs and potential roles in stress response.

This paper revises the genome annotation of Synechocystis using ribosome profiling and proteogenomics, identifying new genes and correcting existing annotations.

The paper expands the known proteome of Sinorhizobium meliloti by identifying 48 novel small proteins using Ribo-seq and proteogenomics.

The paper uses complementary Ribo-seq methods to map the translatome of Campylobacter jejuni, identifying novel small open reading frames and refining gene annotations.

The paper benchmarks ORF prediction tools for bacterial Ribo-seq data, finding DeepRibo performs well but none detect all novel sORFs with high sensitivity.

HRIBO is a workflow for analyzing bacterial Ribo-seq data to discover novel ORFs, using annotation-independent methods and integrating additional features for prioritization.

The paper introduces a workflow for identifying functional upstream open reading frames (uORFs) using ribosome profiling data and provides a human uORF annotation file.