Sonia Tarazona

The paper evaluates normalization methods and quantification pipelines for long-read RNA sequencing across PacBio and ONT platforms, showing platform-specific impacts on accuracy.

Coxmos provides an interpretable survival analysis tool for high-dimensional and multi-omic data, outperforming existing methods while enhancing model interpretability.

The paper investigates the YMC phase transitions by integrating metabolic, chromatin, and transcriptional data, finding that metabolite accumulation mediates the shift between HOC and LOC phases.

MOSim generates synthetic bulk and single-cell multi-omics datasets for benchmarking methods that analyze regulatory networks across various omics layers.

MORE constructs phenotype-specific multi-omic regulatory networks using regression-based modeling and variable selection, showing improved accuracy and efficiency over existing tools.

MAMBA integrates semi-quantitative metabolomic data with gene-centric omics to improve metabolic network characterization and metabolite prediction in yeast under heat stress.

The paper introduces immuneREF, a method to quantify immune repertoire similarity across health and disease, finding that healthy and diseased repertoires are more similar than previously thought.

Acorde identifies co-expression networks of alternative isoforms from single-cell data and detects co-differential isoform usage in neural cell types.

The paper introduces a conceptual framework and bioinformatics pipeline for multi-omics data integration, validated on TCGA datasets to enhance feature identification compared to single-omics analysis.

The paper introduces tappAS, a framework for analyzing the functional impact of differential splicing, showing AltTP plays a major role in neural development by altering protein function and regulation.

The paper presents STATegra, a multi-omics dataset of mouse B-cell differentiation combining 10 omics technologies to study dynamic cellular processes.

PaintOmics 3 provides a web tool for integrated visualization and pathway analysis of multi-omics data, supporting various omic types and offering interactive features for biological interpretation.

The paper introduces Iso-maSigPro, a tool for identifying differential isoform expression in RNA-seq time series and provides clustering and visualization functions for analyzing isoform-level gene expression patterns.