Ribo-seq

The Translational Landscape of Reactive Astrocytes Reveals the Impact of eIF2B-mediated Dysregulation in VWM Disease

This study investigates eIF2B5 mutations in astrocytes, revealing disrupted mRNA translation and metabolic defects in Vanishing White Matter Disease.

RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling

RIBOSS integrates long- and short-read sequencing to detect novel translational events in prokaryotic and eukaryotic transcriptomes.

Unveiling novel conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.

This study uses ribosome profiling to identify conserved HIV-1 alternative open reading frames (ARFs) that encode T cell antigens, revealing new targets for vaccination.

Extensive location bias of the GPCR-dependent translatome via site-selective activation of mTOR

This study identifies translational regulation by GPCRs, showing that beta2-AR activation selectively induces translation of TOP motif-containing genes via endosomal mTOR.

A Novel Regulation on the Developmental Checkpoint Protein Sda that Controls Sporulation and Biofilm Formation in Bacillus subtilis

The paper identifies a serine codon hierarchy that affects translation efficiency in Bacillus subtilis, showing that TCN codons cause ribosome pausing and regulate gene expression, including the sda gene involved in sporulation and biofilm formation.

Deep learning to decode sites of RNA translation in normal and cancerous tissues

This paper introduces RiboTIE, a transformer model for mapping RNA translation, showing high precision and sensitivity in normal and cancerous tissues.

A ggplot-based single-gene viewer reveals insights into the translatome and other nucleotide-resolution omics data

ggRibo is an R package that visualizes single-gene omics data, including Ribo-seq and RNA-seq, with nucleotide resolution to study gene expression and regulation.

A pan-cancer atlas of therapeutic T cell targets

ImmunoVerse integrates RNA-Seq and immunopeptidomes to catalog 28,446 tumor-specific HLA-presented antigens across 21 cancers, including a splicing-derived PMEL peptide with T cell expansion support.

The rapid degradation of translated upstream regions points to an inefficient translation initiation process

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

Cell-type specific prediction of RNA stability from RNA-protein interactions

The paper predicts RNA degradation and translation levels from RBP binding data using machine learning, finding in vivo binding sites are more important than predicted ones.

Upstream open reading frames buffer translational variability during Drosophila evolution and development

This study shows uORFs reduce translational variability in Drosophila across development and evolution, with buffering effects observed in gene expression and phenotypes.

Perturbations in eIF3 subunit stoichiometry alter expression of ribosomal proteins and key components of the MAPK signaling pathways.

The paper shows that altering eIF3 subunit levels affects the translatome, particularly impacting MAPK signaling and ribosomal protein expression in HeLa cells.

Genome-Wide Identification of Stable RNA Secondary Structures Across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics

The paper identifies stable RNA secondary structures across organisms using chemical probing data and introduces a database for these structures.

Striatal cell-type-specific molecular signatures reveal therapeutic targets in a model of dystonia

The paper identifies cell-type-specific molecular changes in dystonia by analyzing translatomes of dSPNs and iSPNs in DRD mice, revealing glutamatergic signaling disruptions and identifying LRRK2 inhibition as a therapeutic target.

PneumoBrowse 2: An integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae

PneumoBrowse 2 provides an updated integrated platform for genome annotation and multi-omics data analysis of Streptococcus pneumoniae, enhancing research into its biology and potential treatments.

Elongation factor P controls ribosomal frameshift of a Salmonella antimicrobial resistance gene

This study shows elongation factor P controls ribosome pause to suppress frameshift in Salmonella's ugtL gene, affecting antimicrobial resistance and virulence.

Sense codon-misassociated eRF1 elicits ribosome stalling and induction of quality control

This study shows that eRF1 transiently binds to UUA sense codons, causing ribosome stalling and triggering quality control mechanisms in human cells.

The Integration of Proteogenomics and Ribosome Profiling Circumvents Key Limitations to Increase the Coverage and Confidence of Novel Microproteins

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.

Translational profiling reveals novel gene expression changes in the direct and indirect pathways in a mouse model of LDOPA-induced dyskinesia

The paper uses TRAP-Bac to study translational gene expression changes in direct and indirect pathways of LDOPA-induced dyskinesia in mice, identifying pathway-specific gene expression patterns.

RiboGraph: An interactive visualization system for ribosome profiling data at read length resolution

RiboGraph provides an interactive visualization tool for ribosome profiling data, enabling real-time analysis at read length resolution without preprocessing.

Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq

The paper compares Ribo-seq analysis tools for detecting translated small open reading frames, finding low agreement and tool-specific biases.

Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly

The paper investigates the coordination of chloroplast and cytoplasmic protein synthesis during light/dark transitions in plants, revealing translational control in chloroplasts and mRNA abundance control in the cytoplasm.

Ribosome Profiling Reveals Translational Reprogramming via mTOR Activation in Omacetaxine Resistant Multiple Myeloma

This study identifies translational reprogramming via mTOR activation as a mechanism of omacetaxine resistance in multiple myeloma and suggests combination therapy with mTOR inhibitors.

Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations

This study identifies UTR mutations that disrupt translation by altering polysome profiles and RNA structures, with a focus on uORF initiation sites and SRSF2 binding motifs.

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

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

Truncated protein isoforms generate diversity of protein localization and function in yeast

The paper identifies 388 N-terminally truncated protein isoforms in yeast, showing they have distinct localization and functions compared to annotated proteins.

CircRNA-Pro: A Novel Toolkit for High-Precision Detection of Differentially Expressed Circular RNAs and Translatable Circular RNAs

CircRNA-Pro detects differentially expressed and translatable circRNAs using integrated algorithms and validation against databases, validated on breast cancer and SARS-CoV-2 datasets.

GRASPS: a simple-to-operate translatome technology reveals omics-hidden disease-associated pathways in TDP-43-related amyotrophic lateral sclerosis

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

A transient brain endothelial translatome response to endotoxin is associated with mild cognitive changes post-shock in young mice

KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction

KaMRaT reduces the dimensionality of k-mer count matrices from high-throughput sequencing data to identify condition-specific sequences.