Aldo Hernández-Corchado

The paper introduces ecCLIP for high-resolution RBP binding maps and Pythia for structure-aware RNA-protein interaction modeling, improving RNA half-life prediction and variant effect assessment.

This study identifies TACC3 as a coordinator of translation and epitranscriptomic reprogramming that determines cancer cell sensitivity or tolerance to mitotic stress induced by microtubule targeting agents.

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

The paper investigates ribosome clusters in neuronal RNA granules, finding they contain stalled ribosomes and unique 3D structures that avoid quality-control mechanisms.

This study identifies 59 gene expression programs in RCC that reveal subtype identity and metastatic trajectories, including a metastatic signature linked to poor clinical outcomes.

The paper identifies intra-genic mutational robustness through alternative splicing in cancer, showing it can complement inter-genic robustness and is associated with worse disease outcomes.

This study identifies cancer-driven suppression of muscle stem cell differentiation in cachectic mice through GDF15 and MMP9, revealing a new mechanism of muscle wasting.

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

The paper identifies genomic binding sites of 166 poorly characterized human transcription factors, revealing that some bind to dark matter DNA and others to regulatory regions.

The paper introduces Mach-1, an RNA foundation model that predicts transcriptome architecture from DNA sequence, validated through experimental perturbations and CRISPR editing.

This study shows that the niche environment significantly influences skeletal muscle stem cell transcriptional activity, with some age-related changes being reversible through exposure to a young niche.

The paper introduces JAMS models to analyze how cytosine methylation affects TF binding in vivo, finding that 45% of TFs are inhibited by methylation while only 6% prefer it.