Ribo-seq

Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

The paper investigates mRNA localization and translation in midbrain dopaminergic neurons, finding no axonal localization but dendritic ribosomes and mRNAs related to dopamine synthesis and release.

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

The paper benchmarks ORF prediction tools for bacterial Ribo-seq data, finding DeepRibo performs well but none detect all novel sORFs with high sensitivity.

Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy

Raman2RNA predicts single-cell RNA expression profiles from live-cell Raman microscopy images using machine learning, achieving high accuracy in tracking cell state transitions during reprogramming.

Phosphorylation of Ribosomal Protein S6 differentially affects mRNA translation based on ORF length

The paper shows that RPS6 phosphorylation decreases during mRNA translation, affecting translation efficiency more for short CDS mRNAs than long ones.

miRbiom: Machine-Learning on Bayesian Causal Nets of RBP-miRNA interactions successfully predicts miRNA profiles

miRbiom uses Bayesian causal networks of RBP-miRNA interactions to predict miRNA profiles with high accuracy without requiring separate miRNA profiling experiments.

An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus

The paper identifies HNRNPC and PABPC4 as regulators of alternative polyadenylation that suppress breast cancer metastasis by controlling mRNA translation.

Arabidopsis uORF-containing mRNAs behave differently from NMD targets

The paper identifies actively translated uORFs in Arabidopsis and shows they reduce mRNA stability and translation differently from NMD targets.

Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns

The paper shows splicing modulators cause translational repression by inducing condensate-prone intron-derived proteins that inhibit mTORC1 and trigger proteotoxic stress.

The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner

This study shows that cycloheximide affects ribosome profiling data differently in yeast and human cells, suggesting that CHX may not be necessary for accurate human ribosome profiling.

SmProt: a reliable repository with comprehensive annotation of small proteins identified from ribosome profiling

SmProt provides a comprehensive and reliable repository of small proteins identified from ribosome profiling, including curated data from multiple species and sources.

Ribocutter: Cas9-mediated rRNA depletion from multiplexed riboseq libraries

The paper introduces a Cas9-based method and software tool to efficiently deplete rRNA/ncRNA contaminants from Ribo-seq libraries, significantly increasing useful reads while minimizing off-target effects.

ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data

ribofootPrinter provides a Python toolkit for analyzing ribosome profiling data, offering simplicity and adaptability for specialized needs.

Identification of novel translated small ORFs in Escherichia coli using complementary ribosome profiling approaches

The paper identifies 365 novel small ORFs in E. coli using ribosome profiling with antibiotics to stall ribosomes at start and stop codons, showing many encode unstable proteins not under purifying selection.

Trans control of cardiac mRNA translation in a protein length-dependent fashion

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.

ORFik: a comprehensive R toolkit for the analysis of translation

ORFik is an R/Bioconductor toolkit for analyzing translation data, supporting multiple high-throughput assays and providing over 30 translation-related metrics.

Accurate Virus Identification with Interpretable Raman Signatures by Machine Learning

This paper develops a machine learning model using Raman spectroscopy to accurately identify viruses, achieving high accuracy in classifying virus types and subtypes.

Translational control of fungal gene expression during the wheat-Fusarium graminearum interaction

This study uses ribosome profiling to analyze translational regulation in Fusarium graminearum during wheat infection, revealing discordance between transcription and translation, novel ORFs, and roles for uORFs and miRNAs.

smORFer: a modular algorithm to detect small ORFs in prokaryotes

smORFer detects small ORFs in prokaryotes using a modular algorithm that integrates structural features and Fourier transform for accurate identification.

Deep conservation of ribosome stall sites across RNA processing genes

The paper identifies conserved ribosome stall sites across multiple species using ribosome profiling data, finding that specific amino acids facilitate stalling in RNA processing genes.

DDX3 depletion represses translation of mRNAs with complex 5' UTRs

This study identifies mRNAs regulated by DDX3 depletion using ribosome profiling and RNA-seq, showing DDX3 preferentially affects a subset of transcripts with complex 5' UTRs.

High-throughput 5'P sequencing enables the study of degradation-associated ribosome stalls.

The paper introduces HT-5Pseq, a method to study degradation-associated ribosome stalls, finding that Arginine before stop codons is enriched in these stalls, while TAA stop codons are more common in stable mRNAs.

RNA-Ribo Explorer: interactive mining and visualisation of Ribosome profiling data

RNA-Ribo Explorer provides an interactive tool for analyzing and visualizing Ribo-seq data to explore translation dynamics and detect changes in RNA translation across conditions.

Ribo-ODDR: Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

Ribo-ODDR improves rRNA depletion in Ribo-seq by designing experiment-specific oligos, increasing sequencing depth and information yield.

Inferring translational heterogeneity from ribosome profiling data

The paper identifies sequences differentially translated across mRNAs using Ribo-seq data from yeast, linking them to translation regulation mechanisms.

Ribosome Profiling Reveals a Dichotomy Between Ribosome Occupancy of Nuclear-Encoded and Mitochondrial-Encoded OXPHOS mRNA Transcripts in a Striatal Cell Model of Huntington Disease

The paper uses ribosome profiling to show that mitochondrial-encoded OXPHOS mRNA translation is increased while nuclear-encoded OXPHOS mRNA translation is decreased in Huntington disease striatal cells.

Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters

The paper evaluates the k-Seq method for measuring ribozyme kinetics, identifying factors affecting accuracy and proposing guidelines to improve data quality.

Natural variation of the cardiac transcriptome in humans

The paper examines gene-expression variation in human hearts, identifying highly variable genes linked to immune response and disease phenotypes.

Improved computational analysis of ribosome dynamics from 5'P degradome data using fivepeseq

The paper introduces fivepseq, a tool for analyzing 5P degradome data, revealing insights into ribosome dynamics and gene-specific features in yeast and Arabidopsis.

Ribosome profiling reveals ribosome stalling on tryptophan codons upon oxidative stress in fission yeast

This study uses ribosome profiling to show that oxidative stress in fission yeast causes ribosome stalling on tryptophan codons due to reduced charged tRNA-Tryptophan, revealing a novel role for tRNA availability in stress response.

FMRP Links Optimal Codons to mRNA stability in Neurons

This study shows FMRP stabilizes mRNAs with optimal codons in neurons, linking codon usage to mRNA stability and contributing to FXS pathogenesis.