Fédérico Marini

This study compares the transcriptional responses of human blood to neutron and photon irradiation, identifying gene signatures and RBE values to distinguish neutron exposure.

Nanopore long-read RNA-seq of leukocytes from 4 Gy X-irradiated blood (three donors, 6 h) recovers p53 signaling and reveals isoform-level regulation plus candidate unannotated FBXO22/PHPT1 isoforms.

The paper introduces MIRNAPEX, a framework that accounts for alternative polyadenylation to better understand miRNA differential expression by integrating target-gene expression and 3'UTR isoform usage.

This study identifies kinome activity and transcriptomic changes in human neutrophils after TREM-1 activation, revealing potential kinase targets for inflammatory and cancer therapies.

This paper shows menin inhibitors increase CLEC12A expression in AML, making it more responsive to CLEC12A-targeted CAR T cells, improving treatment outcomes.

This paper benchmarks second-generation single-cell-informed deconvolution tools for bulk RNA-seq, revealing performance differences based on data characteristics and providing an ecosystem called omnideconv.

DoReMiTra provides a unified radiation transcriptomics dataset collection with standardized metadata and pre-processed data for benchmarking and integrative analysis.

CIA provides a reference-free method for cell type annotation in scRNA-seq data, outperforming existing approaches with lower computational cost.

GeDi streamlines functional enrichment results by clustering gene sets and integrating PPI data, improving interpretation and hypothesis generation.

The paper develops a computational framework to predict GD2 expression across cancer types using pathway topology and transcriptome data, validated by flow cytometry and literature.

This paper shows that inhibiting KDM6B reduces monocyte activation and skin inflammation in a psoriasis model by restoring H3K27me3 and suppressing inflammatory gene expression.

This study shows that cholangiocytes generate new hepatocytes during zebrafish liver regeneration after partial injury during growth.

This study uses RNA-seq to analyze gene expression changes in human blood after X-ray exposure, identifying novel radiosensitive genes and pathways.

The paper compares CCR8+ Treg cells in tumor and tumor-free tissues using chromatin accessibility and DNA methylation, finding high similarity suggesting tumor microenvironment activation of tissue Treg cells.

Dedifferentiated fibroblasts sequentially induce and resolve neutrophil-driven inflammation through cytokine release to facilitate axon regeneration after spinal cord injury in zebrafish.

HuBMAPR provides an R client for accessing HuBMAP data, enabling efficient programmatic discovery and retrieval of spatial-resolution biological data.

This paper introduces a workflow for allele-specific immune gene quantification in scRNA-seq data, validated across datasets and platforms.

The paper benchmarks eight tools for identifying and quantifying alternative polyadenylation sites from RNA-seq data using real, synthetic, and 3'-end sequencing data.

Magnetique provides an interactive web tool to explore transcriptome signatures of heart failure using RNA-seq data from cardiomyopathy patients and donors.

SimBu simulates bulk RNA-seq data with variable cell type composition to create in silico gold standards for evaluating deconvolution methods.

GeneTonic provides an R/Bioconductor package to streamline RNA-seq data interpretation by integrating differential expression and functional enrichment analyses into interactive visualizations and reports.

The paper introduces easier, an R/Bioconductor package that predicts antitumor immune response from bulk RNA-seq data, outperforming existing methods in four cancers.

annoFuse filters and prioritizes oncogenic gene fusions from RNA-Seq data, improving identification of clinically relevant fusions in cancer datasets.

The paper introduces the ideal R/Bioconductor package for interactive and reproducible differential expression analysis of RNA-seq data, providing visualization tools and HTML report generation.

TREND-DB catalogs the dynamic landscape of alternative polyadenylation by analyzing transcriptome changes after depleting >170 proteins involved in gene regulation and epigenetics.

This paper provides an overview of single-cell RNA sequencing analysis using Bioconductor, highlighting its tools and methods for handling high-dimensional data.

TAF-ChIP enables high-quality ChIP-Seq results from low cell numbers, matching conventional ChIP-Seq datasets in epigenetic profiles.

pcaExplorer provides an interactive R/Bioconductor tool for RNA-seq PCA analysis, enabling reproducible exploration and visualization of principal components.

The paper identifies PCF11 as a critical regulator of alternative polyadenylation in neuroblastoma, linking it to cell fate reprogramming and spontaneous tumor regression.

The paper shows that the pre-EJC regulates RNA polymerase II pausing and prevents premature elongation, with consequences for exon skipping and differentiation.