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.

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.

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.

Quantitative profiling of basal and stress-induced ribosome collisions

The paper quantifies disome levels across the transcriptome in yeast and human cells under basal and stress conditions, showing stress-induced increases and context-dependent redistribution.

Discovery of the TGCB microprotein translated from the lncRNA CHASERR

The paper identifies a microprotein, TGCB, encoded by the lncRNA CHASERR, and shows its deletion is linked to neurodevelopmental disorders.

Unveiling the small protein landscape of uropathogenic E. coli

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.

RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols

RiboBA improves ncORF identification by accounting for protocol-induced biases in ribosome profiling data.

RNA Structure Coordinates Translation Across the Meiotic Program

In yeast meiosis, flexibly folded mRNAs are preferentially translated while cytoplasmic RNA helicase levels dip; raising Ded1p or breaking CCW22 UTR pairing mistimes translation and disrupts meiotic progression.

Allele-specific expression is associated with lower translational efficiency in mouse embryos and stem cells

The paper investigates the relationship between allele-specific expression and translational efficiency in mouse embryos and stem cells, finding lower translational efficiency associated with allelic imbalance.

RSV competes with the host for translational machinery without a host shutoff strategy

This study shows RSV competes with host mRNAs for ribosomes without using host shutoff strategies, and avoids activating antiviral pathways that reduce cap-dependent translation.

Stress induces DCP2 translation via a stalling-dependent mechanism

The paper identifies DCP2 as an ISR-induced transcript whose translation is regulated by an overlapping ORF that acts as an inhibitory element, which is relieved during stress.

Alternative splicing expands and remodels the breast cancer proteoform landscape

The paper develops 3DisoGalaxy to study alternative splicing in breast cancer, finding that many transcripts produce translation-supported proteins and that functional divergence is concentrated in specific regions.

Sequence-intrinsic barriers define a class of translation-restricted uORFs in the human genome

The paper identifies translation-restricted uORFs in the human genome that act as sequence-intrinsic barriers to protein production, showing they are under purifying selection as cis-regulatory elements.

The extended Split-ORF pipeline: Prediction and evaluation of Split-ORFs using Ribo-seq data

The paper improves the Split-ORF pipeline to analyze Ribo-seq data, identifies over 14,000 candidate Split-ORF transcripts, and finds many show significant Ribo-seq coverage across cell types and diseases.

Subcellularly Resolved 3D Translatome in Mouse Oocytes and Early Embryos

The paper profiles the subcellularly resolved 3D translatome in mouse oocytes and early embryos, revealing spatially controlled translation patterns and embryo asymmetry.

Neuronal stop-codon readthrough is associated with ribosome pausing and appends lineage-restricted extensions that can alter protein localization in Drosophila

The paper identifies neuronal stop-codon readthrough in Drosophila, showing it produces C-terminal extensions that alter protein localization.

Mitochondrial translation termination, recycling, reinitiation, and rescue for in-frame and out-of-frame contexts

The paper investigates mitochondrial translation termination, recycling, and quality control mechanisms using Ribo-Seq and Disome-Seq, revealing roles of release factors and rescue mechanisms.

Overlapping upstream ORFs repress translation and expand proteome diversity in Arabidopsis

The paper identifies translated overlapping upstream ORFs (ouORFs) in Arabidopsis, showing they repress translation more than non-overlapping uORFs and generate protein diversity.

Novel 4D tensor decomposition-based approach integrating tri-omics profiling data can identify functionally relevant gene clusters

This paper introduces a 4D tensor decomposition method to integrate transcriptome, Ribo-seq, and proteome data, identifying gene clusters related to ribosome stacking and translational buffering.

Virus-driven tRNA competition universally represses host genes with similar codon usage

The paper shows viral infection represses host genes with codon usage similar to viruses, supporting multiple hypotheses about tRNA competition during infection.

Developmental and transcriptional programs that define the initiation of the forelimb

The paper identifies four stages of forelimb initiation in mouse embryos using scRNA-seq and other sequencing methods, revealing TBX5-target genes involved in limb development.

Decoding universal principles of codon-mediated regulation of gene expression

The paper develops a regression-based model to predict mRNA and protein abundance using codon weights derived from transcriptomic data, validated across multiple species.

Cytosolic and ER-associated ribosomes share rRNA 2'-O-methylation landscapes across human cell types

The paper compares 2'-O-methylation patterns of cytosolic and ER-associated ribosomes across human cell types and finds minimal compartment-specific differences.

Translatome and translation dynamics analysis of a RiboCancer cell line panel reveals that leukemia-associated Rps15 mutations rewire translation through codon-specific tRNA accommodation defects.

The paper analyzes translatome and translation dynamics in RiboCancer cell lines to show that Rps15 mutations disrupt tRNA accommodation, affecting translation efficiency and transcriptional regulation in CLL.

Identification of a large class of cancer-germline microproteins as a source of immunotherapeutic targets

The paper identifies a large class of non-canonical cancer-germline antigens (ncCGAs) from lncRNAs and mRNA untranslated regions, showing their potential as immunotherapeutic targets.

RiboPipe: efficient per-transcript codon-resolution ribo-seq coverage imputation for low-coverage transcripts

RiboPipe imputes codon-resolution Ribo-seq coverage for low-coverage transcripts using a unified framework that improves accuracy and efficiency.

Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1

The paper shows that Ded1 in yeast primarily stimulates translation by unwinding 5' UTR structures, not by suppressing upstream ORF translation.

5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions

This study shows 5-AzaC incorporation into mRNAs disrupts translation, causes ribosome collisions, and activates stress responses, contributing to its cytotoxicity beyond DNA hypomethylation.