Ribo-seq

RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references, achieving high accuracy in genomic placement and transcript-level abundance estimation.

RAPPL-Seq enables rapid, high-sensitivity ribosome profiling of scarce samples by improving RPF recovery efficiency and reducing processing time.

The paper shows that SNORA81-guided pseudouridylation at a specific 28S rRNA site influences selective translation and ovarian cancer cell proliferation.

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.

RiboFlow v2 improves ribosome profiling analysis by incorporating genome alignment and configurable handling of multimapping reads, revealing gene-specific differences in coverage and translation efficiency.

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.

sORF-Trans2MS is a two-module deep learning framework that predicts Ribo-supported sORFs and MS-supported microproteins, improving prediction and extending discovery to underrepresented candidates.

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.

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

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.

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.

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 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 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.

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.

The paper profiles terminating ribosomes to show sequence-dependent pausing at stop codons and its impact on translation fidelity and protein diversity.

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

This paper uses Raman spectroscopy and machine learning to classify brain tumor cell types at single-cell resolution, achieving high accuracy in distinguishing IDH1 mutation status and histological subtypes.

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

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

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.

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.

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

The paper analyzes translational buffering across human and mouse datasets, finding conserved patterns and highlighting the role of cellular context in gene expression regulation.

This study uses ribosome profiling to show that steatohepatitis-associated HCC has extensive translational alterations affecting hundreds of genes and revealing novel translated regions.

The paper identifies translational repression of 5' TOP mRNAs in exhausted human CD8+ T cells despite elevated mTOR activity.

The paper identifies eIF3d and eIF3e as mediators of hypoxia-induced translational control and shows that small molecules can inhibit this process.

The paper identifies eQTLs, rQTLs, and pQTLs in the human brain and shows that many eQTL effects are attenuated post-transcriptionally, yet still correlate with schizophrenia GWAS signals.

The paper identifies rRNA methylation dynamics as a mechanism regulating translation efficiency and HSC fitness during hematopoietic differentiation.

The paper identifies and characterizes non-canonical ORFs in mammals, showing their evolutionary conservation and functional integration into the proteome.