Jordi Martorell‐Marugán

Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics

This paper introduces singleDeep, a deep learning pipeline for scRNA-Seq data analysis that improves phenotype prediction and provides insights into gene importance and cell types.

Polycomb repression during S/G2 phases restrain initiation of cell differentiation to the G1 phase of the cell cycle

The paper shows that Polycomb repression during S/G2 phases restricts differentiation gene activation, allowing it to occur primarily in G1 phase in mouse ESCs.

Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth

This study identifies placental DNA methylation changes linked to maternal smoking during pregnancy and their associations with birth outcomes using data from the PACE consortium.

A comprehensive and centralized database for exploring omics data in Autoimmune Diseases

ADEx is a database integrating omics data from autoimmune diseases, offering analysis tools for exploring transcriptomics and methylation studies.

Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases

The paper identifies four molecular clusters in systemic autoimmune diseases using transcriptome and methylome data, showing three stable aberrant patterns and one non-specific cluster.

DREIMT: a drug repositioning database and prioritization tool for immunomodulation.

DREIMT prioritizes immunomodulatory drugs by analyzing gene expression signatures and drug profiles.

Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells

The paper shows that PRC2 subunits are differentially recruited across the cell cycle in mESCs, enabling chromatin state changes that facilitate differentiation in G1.

mCSEA: Detecting subtle differentially methylated regions

mCSEA detects subtle differentially methylated regions in epigenetic data, outperforming existing tools and identifying methylation changes linked to metabolic disorders.

Identification and visualization of differential isoform expression in RNA-seq time series

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.