By capturing and sequencing the RNA fragments protected by translating ribosomes,
ribosome profiling provides snapshots of translation at subcodon resolution. The growing …

Ongoing efforts to generate a complete and accurate annotation of the genome have
revealed a significant blind spot for small proteins (< 100 amino acids) originating from short …

A large body of evidence indicates that genome annotation pipelines have biased our view
of coding sequences because they generally undersample small proteins and peptides. The …

RNA endowed with both protein-coding and noncoding functions is referred to as 'dual-
function RNA','binary functional RNA (bifunctional RNA)'or 'cncRNA (coding and noncoding …

Abstract1 Short open reading frame (sORF)–encoded polypeptides (SEPs) have recently
emerged as key regulators of major cellular processes. Computational methods for the …

Orphan genes, lacking detectable homologs in outgroup species, typically represent 10–
30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de …

Small proteins specifically refer to proteins consisting of less than 100 amino acids
translated from small open reading frames (sORFs), which were usually missed in previous …

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a
machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by …

As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode
short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides …

Building a reference set of protein-coding open reading frames (ORFs) has revolutionized
biological process discovery and understanding. Traditionally, gene models have been …