Ribo-seq

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

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.

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.

This paper introduces CaCoFold-R3D, a method that jointly predicts RNA 3D motifs and secondary structure using evolutionary information, demonstrating its effectiveness for RNA structure prediction.

The paper analyzes ribosome profiling data to show translation efficiency covariation (TEC) is conserved across human and mouse cells, revealing gene functions not evident from RNA or protein co-expression.

This study uses Massively Parallel Ribosome Profiling to identify thousands of viral ORFs, including non-canonical ones, and shows their impact on HLA-I peptides and protein synthesis regulation.

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

This paper introduces RP3, a pipeline combining proteogenomics and ribosome profiling to identify microprotein-encoding smORFs missed by Ribo-Seq alone, improving detection and confidence.

This study introduces RiboGL, a model combining graph and recurrent neural networks to predict ribosome density from mRNA secondary structure, outperforming existing methods.

GRASPS identifies more differentially expressed transcripts with higher fold changes and significance in TDP-43 ALS models, revealing previously missed disease pathways.

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

The paper uses ribosome profiling to show how iron deficiency affects protein translation in yeast by altering gene expression and RNA-binding protein activity.

This study introduces riboPLATE-seq, a method for generating paired libraries of ribosome-associated and total mRNA, and demonstrates its use in detecting translational changes caused by kinase inhibitors.

The paper identifies a trans locus in rats that causes a protein length-dependent shift in translational efficiency, affecting cardiac hypertrophy and sarcomere protein stoichiometry.

This paper introduces selective 40S footprinting to study translation initiation in human cells, revealing that scanning ribosomes remain cap-tethered and only one ribosome scans a 5UTR at a time.

The paper uses disome-seq to detect ribosome collisions during translation, revealing their role in recruiting co-translational chaperones for protein folding.

The paper presents a comprehensive analysis of AATF's RNA interactions, revealing its role in ribosome biogenesis through binding to pre-rRNA and mRNAs of ribosome factors.

This study shows mutant huntingtin (mHtt) stalls ribosomes and suppresses protein synthesis independently of FMRP, using ribosome profiling in HD cells and mouse models.

The paper uses retapamulin-assisted ribosome profiling to identify alternative translation start sites in E. coli, revealing new proteins and regulatory roles.

The paper introduces TRiP, a method for cell type-specific ribosome profiling, and shows experience-induced changes in translation in mouse CA1 pyramidal cells.

The paper investigates how translation efficiency contributes to tissue-specific rhythmic and constitutive gene expression in kidney and liver, revealing translational control mechanisms and compensation effects.

ROSE predicts ribosome stalling from ribosome profiling data, showing better performance than conventional models and revealing regulatory factors and functional interactions.