Fidel Ramírez

AXL-GAS6/PROS1 Interaction: A Critical Switch Between Aberrant- and Healthy Repair Following Alveolar Lung Injury

This study investigates ligand-specific AXL signaling in IPF, showing GAS6 promotes basal cell proliferation while PROS1 inhibits it, with implications for therapeutic targets.

JUNB O-GlcNAcylation-mediated promoter accessibility of metabolic genes modulates distinct epithelial lineage in pulmonary fibrosis

The paper identifies O-GlcNAcylation of JUNB as a regulator of promoter accessibility in metabolic genes, driving aberrant epithelial lineage in IPF.

Spatial Transcriptomic Characterization of Novel Pathologic Niches in IPF

The paper uses spatial transcriptomics to identify novel pathologic niches in IPF lung tissue and their cellular composition and communication.

A Single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

The paper introduces a Galaxy-based suite for scRNA-seq analysis, offering workflows, training resources, and tools for preprocessing, normalization, and clustering across 10x and alternative platforms.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

The paper develops a scaffolding algorithm using Hi-C data to assemble chromosome-length genomes in Drosophila species, revealing conserved 3D regulatory topologies despite extensive genome shuffling.

Partially methylated domains are hallmarks of a cell specific epigenome topology

The paper identifies partially methylated domains (PMDs) as widespread epigenomic features across human and mouse cells, showing cell-type specificity and links to gene expression, replication timing, and proliferation.

Community-driven data analysis training for biology

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

Ultra-parallel ChIP-seq by barcoding of intact nuclei

This paper introduces a method for ultra-parallelized ChIP-seq using barcoded intact nuclei, enabling high-throughput analysis of chromatin-associated proteins.

High-resolution TADs reveal DNA sequences underlying genome organization in flies

The paper identifies DNA motifs at TAD boundaries in flies and shows they encode 3D genome architecture, with an online database for exploration.