Rubén Molina-Fernández

ModCRElib: A standalone package to model cis-regulatory elements.

ModCRElib is a package for modeling cis-regulatory elements, offering tools for TF-DNA interaction analysis, binding motif prediction, and regulatory complex modeling.

Network-Based Analysis of Human Astrocytes Links Aging to Neurodegenerative and Cardiovascular Diseases

The paper identifies a 127-gene core network in human astrocytes linking aging to neurodegenerative and cardiovascular diseases through proteostasis and stress signaling.

Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements

The paper introduces a structure-based learning approach to predict TF binding preferences and model TF regulatory complexes, demonstrating its effectiveness over existing methods in cases of remote homology.

Comparative analysis of mammal genomes unveils key genomic variability for human lifespan.

This paper identifies amino acid changes and genes associated with longevity across mammals, showing their potential to improve human lifespan heritability interpretation.

RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis

RADI improves the computational efficiency of direct-coupling analysis by reducing the alphabet size, achieving faster execution with comparable or better accuracy than traditional methods.

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.

The paper develops a computational method to predict DNA-binding preferences of C2H2-ZF domains using structural models and applies it to predict CTCF's binding sites.

A collection of designed peptides to target SARS-Cov-2 - ACE2 interaction: PepI-Covid19 database.

The paper introduces PepI-Covid19, a database of peptides targeting SARS-CoV-2 RBD-ACE2 interaction, designed using PiPreD method to preserve key interactions.