Ribo-seq

RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references

RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references, achieving high accuracy in genomic placement and transcript-level abundance estimation.

RAPPL-Seq Enables Rapid, High-Sensitivity Ribosome Profiling of Scarce Samples

RAPPL-Seq enables rapid, high-sensitivity ribosome profiling of scarce samples by improving RPF recovery efficiency and reducing processing time.

A ribosomal pseudouridine drives an oncogenic translation program

The paper shows that SNORA81-guided pseudouridylation at a specific 28S rRNA site influences selective translation and ovarian cancer cell proliferation.

Anisomycin-induced ribosome collisions follow a dose-dependent positional rule, distinct from the UV-induced collision landscape

Low- and high-dose anisomycin confine ribosome collisions to a dose-shifted zone just past the start codon, whereas 30 min after UV, collisions appear more dispersed and favor highly translated mRNAs.

Robust ORF Deconvolution from Multiple Ribo-seq Datasets with Group LASSO Penalty

PRICE 2 improves detection of short and overlapping ORFs using group LASSO regularization, outperforming existing tools and enabling discovery of more cryptic MHC-I peptides.

RiboFlow v2: a configurable ribosome profiling pipeline reveals measurements sensitive to read-mapping methodology

RiboFlow v2 improves ribosome profiling analysis by incorporating genome alignment and configurable handling of multimapping reads, revealing gene-specific differences in coverage and translation efficiency.

RiboWin: A computational framework to identify non-canonical open reading frames

RiboWin identifies non-canonical open reading frames by expanding search space to pseudogenes and enforcing replicate concordance, revealing novel sORFs previously missed by existing tools.