Ribo-seq

Shoelaces: an interactive tool for ribosome profiling processing and visualization

Shoelaces automates ribosome profiling data processing and visualization, improving reproducibility by standardizing steps and reducing data loss in manual analysis.

Translation elongation and mRNA stability are coupled through the ribosomal A-site

The paper shows that faster translation elongation on optimal codons increases mRNA stability in yeast, with A-site tRNA decoding being the key factor driving mRNA decay.

Accurate design of translational output by a neural network model of ribosome distribution

The paper introduces a neural network model to predict translation elongation rates and validates it by designing synonymous variants that match predicted protein output in yeast.

Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace

The paper links Raman spectra and transcriptomes through a shared low-dimensional subspace, enabling reconstruction of gene expression profiles from Raman data.

Frequent translation of small open reading frames in evolutionary conserved lncRNA regions

The paper identifies translated open reading frames in conserved transcripts using ribosome profiling and finds they are enriched for functional micropeptides and non-ribosomal interactions.

Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain

The paper identifies the RagA-mTORC1 network as a key driver of neuropathic pain through cell-specific translational profiling in nociceptors.

Comprehensive profiling of translation initiation in influenza virus infected cells

This study identifies alternate translation initiation sites in influenza virus-infected cells, revealing a truncated neuraminidase protein and host transcript initiation patterns.

Cell type specific profiling of alternative translation identifies novel protein isoforms in the mouse brain

High-throughput inverse toeprinting reveals the complete sequence dependence of ribosome-targeting antibiotics

This study introduces inverse toeprinting to map ribosome arrest sites on mRNA and identifies sequence-specific arrest motifs for ribosome-targeting antibiotics.

Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum

The paper quantifies gene expression regulation at multiple layers in response to ER stress in cervical cancer cells over time, identifying shared and stress-specific regulatory events.

The transcriptional and translational landscape of equine torovirus

This study analyzes the transcription and translation of equine torovirus using RNA-seq and Ribo-seq, identifying novel open reading frames and subgenomic RNA synthesis mechanisms.

Organ-specific translation elongation rates measured by in vivo ribosome profiling

This study measures organ-specific translation elongation rates in mice using a labeling-free method involving translation inhibitors and ribosome profiling.

De Novo Annotation And Characterization Of The Translatome With Ribosome Profiling Data

This paper introduces RiboCode, a method for de novo translatome annotation using ribosome profiling data, showing improved efficiency, sensitivity, and accuracy in identifying novel ORFs across different yeast stress conditions.

Genome-wide translating mRNA analysis following ketamine reveals novel targets for antidepressant treatment

The paper uses RiboSeq to identify the translatome in mouse medial prefrontal cortex after ketamine treatment, revealing novel targets like VIPR2 for antidepressant action.

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

The paper quantifies factors affecting translation elongation rates using ribosome profiling data and shows exit tunnel interactions and nascent polypeptide hydropathy are key determinants.

Active ribosome profiling with RiboLace

The paper introduces RiboLace, a method to isolate active ribosomes for ribosome profiling, enabling high-resolution analysis of active translation.

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights

This study proposes transcript length as a key determinant of translation efficiency through a physical model of ribosome kinetics and mRNA circularisation.

Transcriptome-wide analysis of roles for tRNA modifications in translational regulation

The paper uses ribosome profiling and RNA-Seq in budding yeast to analyze the translational effects of tRNA modifications, identifying new roles in gene regulation and retroelement control.

RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs

The paper identifies RNA G-quadruplexes in 5-UTRs as repressive elements that hinder translation by promoting upstream open reading frames, and shows helicases interact with these structures to regulate translation.

Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors

This study uses ribosome profiling to show that eIF2 phosphorylation in erythroblasts selectively enhances translation of certain transcripts while reducing others, revealing a complex regulatory mechanism.

riboviz: analysis and visualization of ribosome profiling datasets

The paper introduces riboviz, a tool for analyzing and visualizing ribosome profiling datasets, providing both a backend pipeline and a web-based interface for comparison with public datasets.

Experience-dependent translational state defined by cell type-specific ribosome profiling

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

Translational contributions to tissue-specificity in rhythmic and constitutive gene expression.

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.

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial genomes.

REPARATION uses ribosome profiling data to improve bacterial genome annotation by identifying novel ORFs and refining existing ones.

Translation efficiency is maintained at elevated temperature in E. coli

The paper investigates how translation efficiency in E. coli remains stable under heat shock and finds that mRNA structure and cotranslational translocation influence this stability.

ROSE: a deep learning based framework for predicting ribosome stalling

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

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.

This study introduces RUST, a normalization method for Ribo-seq data, and shows it reveals variation in sequence determinants of ribosome footprint densities across datasets.

Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap

The paper introduces Ribomap, a method to improve ribosome occupancy estimation by assigning reads based on transcript abundance, leading to more accurate ribosome profiles.

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data

SPECtre improves detection of actively translated transcripts by using spectral coherence analysis of ribosome profiling data, achieving higher accuracy and sensitivity.

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

The paper identifies biases in ribosome profiling experiments in yeast, showing that CHX affects codon-specific elongation rates and alters the interpretation of translation dynamics.