M. Mar Albà

PHYRE, a Translated uORF, is Required for Phytochrome B Translation and Photomorphogenesis in Arabidopsis

The paper identifies a uORF, PHYRE, essential for phytochrome B translation and photomorphogenesis in Arabidopsis, showing its role in translational regulation.

Identification of a large class of cancer-germline microproteins as a source of immunotherapeutic targets

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.

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

Oncogenes and tumor suppressor genes are enriched in stop-loss mutations generating protein extensions

The paper identifies stop-loss mutations in cancer genomes, showing enrichment in cancer-related genes and potential immunological consequences.

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

The paper identifies conserved microproteins from upstream ORFs in yeast using Ribo-Seq and Nanopore data, showing they are subject to purifying selection.

An expanded reference catalog of translated open reading frames for biomedical research

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

Predicting immunotherapy response in advanced bladder cancer: a meta-analysis of six independent cohorts

This study identifies factors predicting immunotherapy response in advanced bladder cancer using data from six cohorts.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Non-canonical ORFs are an important source of tumor-specific antigens in a liver cancer meta-cohort

The paper identifies non-canonical ORFs as a significant source of tumor-specific antigens in liver cancer, showing they can trigger immune responses and are shared among a substantial proportion of patients.

RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

RATTLE reconstructs and quantifies transcripts from Nanopore sequencing without a reference genome, showing accuracy and scalability across simulated and experimental data.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome

The paper introduces ORQAS, a pipeline for quantifying translation of transcript isoforms using ribosome profiling, and finds that differential splicing impacts translation across species.

Extensive post-transcriptional buffering of gene expression in the response to oxidative stress in baker yeast

The paper compares RNA-Seq and Ribo-Seq for gene expression analysis under oxidative stress in baker's yeast, finding Ribo-Seq better correlates with protein abundance.