Fátima Al‐Shahrour

Clonucopya links tumor clonal architecture to drug prioritization by integrating subclonal inference and drug ranking tools in an end-to-end workflow.

This study identifies NGFR as a regulator of immune evasion in HNSCC, showing that its inhibition enhances antigen presentation and CD8+ T cell response to checkpoint blockade.

The paper presents a pan-cancer single-cell atlas linking intratumoral states to therapeutic vulnerabilities by integrating transcriptomics, copy-number alterations, and drug-response predictions across 34 tumor types.

The paper identifies CD74+ microglia/macrophages driven by MIF as clinically relevant subpopulations in brain metastasis and other CNS disorders, showing their role in disease progression and therapeutic targeting potential.

This study uses spatial transcriptomics to analyze drug responses in breast cancer tumors and identifies therapeutic heterogeneity linked to tumor location and microenvironment.

Beyondcell identifies drug-responsive subpopulations in single-cell RNA-seq data and proposes cancer-specific treatments by analyzing therapeutic clusters and differential drug sensitivity.

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

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

The paper provides a user guide to five online tools for exploring and visualizing PCAWG data, demonstrating their integration with external resources to enhance cancer genomics research.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

The paper investigates how 3D chromatin structure and chromatin environment influence DNA replication origin activation efficiency in mouse embryonic stem cells under stress and control conditions.

The paper constructs a disease interaction network from patient molecular profiles to uncover molecular mechanisms of comorbidity and identify associated genes and drugs.