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Article
Open AccessThe impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction of patients respond to the t...
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Article
Open AccesspTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation
The human transcriptome contains thousands of small open reading frames (sORFs) that encode microproteins whose functions remain largely unexplored. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary...
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Article
Open AccessRATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on map** reads to a reference genome, which preclud...
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Article
Non-muscle-invasive micropapillary bladder cancer has a distinct lncRNA profile associated with unfavorable prognosis
Molecular subty** of bladder cancer has revealed luminal tumors generally have a more favourable prognosis. However, some aggressive forms of variant histology, including micropapillary, are often classified...
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Article
Standardized annotation of translated open reading frames
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Article
LCOR mediates interferon-independent tumor immunogenicity and responsiveness to immune-checkpoint blockade in triple-negative breast cancer
Ligand-dependent corepressor (LCOR) mediates normal and malignant breast stem cell differentiation. Cancer stem cells (CSCs) generate phenotypic heterogeneity and drive therapy resistance, yet their role in im...
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Article
Open AccessImpact of uORFs in mediating regulation of translation in stress conditions
A large fraction of genes contains upstream ORFs (uORFs) in the 5′ untranslated region (5’UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing prematur...
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Article
Open AccessUncovering de novo gene birth in yeast using deep transcriptomics
De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material...
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Article
Open AccessRibosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome
The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeli...
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Article
Open AccessExtensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker’s yeast
Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is gen...
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Article
Open AccessTranscriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions
The objective of this experiment was to identify transcripts in baker’s yeast (Saccharomyces cerevisiae) that could have originated from previously non-coding genomic regions, or de novo. We generated this data t...
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Article
Translation of neutrally evolving peptides provides a basis for de novo gene evolution
Accumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In...
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Article
Open AccessZinc-finger domains in metazoans: evolution gone wild
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Article
Open AccessExtreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective con...
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Article
Open AccessHigh evolutionary turnover of satellite families in Caenorhabditis
The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the evolu...
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Article
Open AccessUncovering adaptive evolution in the human lineage
The recent increase in human polymorphism data, together with the availability of genome sequences from several primate species, provides an unprecedented opportunity to investigate how natural selection has s...
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Article
Open AccessEmergence of novel domains in proteins
Proteins are composed of a combination of discrete, well-defined, sequence domains, associated with specific functions that have arisen at different times during evolutionary history. The emergence of novel do...
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Accelerated Evolution of Genes of Recent Origin
The gene content of any genome is a rich mosaic of genes that have originated at different times during evolution. Among the most interesting properties related to gene age is the fact that younger genes tend ...
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Article
Open AccessPositional bias of general and tissue-specific regulatory motifs in mouse gene promoters
The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific t...
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Article
Open AccessHousekee** genes tend to show reduced upstream sequence conservation
Understanding the constraints that operate in mammalian gene promoter sequences is of key importance to understand the evolution of gene regulatory networks. The level of promoter conservation varies greatly a...
