Xabier Agirre

Stromal and Endothelial Transcriptional Changes during progression from MGUS to Myeloma and after Treatment Response

This study identifies transcriptional changes in stromal and endothelial cells during MGUS to myeloma progression and treatment response, revealing a tumor-permissive BME signature that is modulated by therapy.

Beyond synthetic lethality in large-scale metabolic and regulatory network models via genetic minimal intervention sets

The paper introduces genetic Minimal Intervention Sets (gMISs) to identify lethal genetic interactions beyond synthetic lethality in human cells and demonstrates their application in cancer research.

Mapping Disease Transitions from Premalignant, Asymptomatic to Advanced Myeloma through Integrative Epigenomic and Transcriptional Analyses

This study maps epigenetic and transcriptional changes in myeloma progression from precursor to advanced stages, identifying key transcription factors involved in disease development.

gMCStool: automated network-based tool to search for metabolic vulnerabilities in cancer

gMCStool identifies metabolic vulnerabilities in cancer by predicting synthetic lethal interactions using genome-scale metabolic networks and RNA-seq data.

BOSO: a novel feature selection algorithm for linear regression with high-dimensional data

BOSO is a novel feature selection algorithm for linear regression that outperforms existing methods in high-dimensional datasets, demonstrated through drug sensitivity prediction in cancer.

Identifying Lethal Dependencies with HUGE Predictive Power from Large-Scale Functional Genomic Screens

The paper improves prediction of lethal gene dependencies using the HUGE method, achieving 75x higher statistical power than existing methods in cancer genomics.

A network-based approach to integrate nutrient environment in the prediction of synthetic lethality in cancer metabolism

This paper introduces a network-based method to predict synthetic lethality in cancer metabolism by integrating genetic interactions and nutrient environments, identifying potential vulnerabilities in tumor cells.

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

This study examines 3D genome architecture changes during B cell differentiation and in B cell neoplasias using Hi-C and multi-omic data, revealing dynamic compartment shifts and tumor-specific chromatin reorganization.