Michael L. Tress

The paper identifies 105 dual coding regions under purifying selection in both reading frames, with many linked to brain development and neural functions.

The paper analyzes discrepancies in coding gene annotations across three human gene sets and finds that over 2,000 genes likely have unsettled coding status.

The paper shows that upstream translations are often degraded, suggesting inefficient initiation and implications for protein annotation.

The paper analyzes the PeptideAtlas database to identify unannotated coding genes and aberrant translation, finding 34 novel ORFs with peptide evidence.

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

The paper identifies LOC124908094 as the functional WASH1 gene and reclassifies other WASH1 genes as pseudogenes using the T2T-CHM13 genome assembly.

The paper shows that APPRIS principal isoforms and MANE Select transcripts align well with main protein isoforms and are critical for clinical variant interpretation.

The paper reports results from the CAFA3 challenge, showing improved computational protein function prediction and new annotations for over 1000 genes through experimental screens in C. albicans, P. aureginosa, and Drosophila.

The paper reanalyzes the CHESS database's new protein-coding predictions and finds most are false positives due to homology errors and lack of experimental evidence.

SQANTI characterizes long-read transcript sequences to assess quality and improve quantification of full-length transcriptomes.