Luı́s A. Nunes Amaral

This study analyzes trends in internationalization and interdisciplinarity in scientific journals using OpenAlex metadata, finding increasing internationalization but disparities across disciplines.

The paper develops a model to distinguish biologically relevant from spurious transcription factor binding events using distance thresholds and validates it with RNA Polymerase II recruitment and mRNA expression data.

The paper analyzes how research attention on disease-target relationships predicts clinical trial success using Open Targets data.

The paper examines alveolar T cell responses in SARS-CoV-2 pneumonia patients, finding that early interferon signaling and targeting of structural proteins correlate with better clinical outcomes.

The paper identifies a bias in gene selection between -omics experiments and publication, introduces a tool to find understudied genes, and demonstrates its application in vertebrate aging research.

The paper investigates how energy metabolism affects the regulatory impact of activators on gene expression using a mathematical model and experimental validation in Drosophila.

The paper shows that a two-fold change in the Pnt/Yan transcription factor ratio drives photoreceptor fate transitions in Drosophila eye progenitor cells, revealing a mechanism for ultrasensitivity.

The paper identifies a systemic age-dependent transcriptome imbalance driven by transcript length across multiple species and shows its correlation with splicing factors and environmental stressors.

The paper develops an information-theory-based method to improve cell type annotation and reproducibility in scRNA-seq analysis by benchmarking feature selection and clustering approaches.

Fly-QMA automates the analysis of mosaic imaginal discs in Drosophila by segmenting cells, annotating clones, and quantifying gene expression changes.

The paper shows that layered weak repression synchronizes developmental gene regulation with cellular metabolism, and that reducing metabolism can compensate for loss of repressors.

Single-cell RNA-seq of lung tissue from transplant donors, fibrosis patients, and a living patient identifies cell type-specific disease-associated molecular pathways in pulmonary fibrosis.

The paper shows that bacterial species with faster growth rates have more SD-led genes, linking translation initiation mechanisms to growth strategies and environmental conditions.