Alexander Martinez‐Fundichely

cfOncoXpress predicts tumor gene expression from cell-free DNA whole-genome sequences using fragmentation patterns and copy number aberrations, outperforming existing methods in prostate and breast cancers.

The paper identifies genomic alterations in the YAP/TAZ pathway associated with stem cell-like castration-resistant prostate cancer using transcriptomic and whole-genome sequencing data.

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

This study identifies 3D regulatory hubs in glioblastoma stem cells and shows their role in oncogenic programs through computational and experimental analysis.

The paper uses systems biology analysis of whole-genome sequences from 298 SB case-control pairs to identify key pathways and genes associated with spina bifida risk.

This paper introduces DeepMILO, a deep learning model to predict how non-coding variants affect 3D chromatin loops, finding that mutations at loop boundaries are linked to upregulation of BCL2 in lymphoma.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

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

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

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

The paper analyzes 2500 cancer genomes to assess the molecular functional impact of mutations, finding that some putative passenger variants may influence gene activity and contribute to cancer phenotypes.