Juan Miguel Mosquera

EXaCT-2 is a whole exome sequencing platform that detects various cancer-related genomic features with high accuracy and sensitivity, outperforming standard assays in detecting sub-clonal mutations and molecular metrics.

This paper introduces ppmSeq, a sequencing technology that improves accuracy and efficiency in detecting SNVs by sequencing both DNA strands, showing superior performance in clinical applications like ctDNA detection.

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.

This study develops a pan-cancer PDO platform to preserve tumor heterogeneity and identify therapeutic vulnerabilities, finding that 58% of PDOs respond to Talazoparib and combination screens reveal resistance-overcoming drugs.

The paper uses CRISPR-Cas9 screens in breast cancer organoids from African ancestry patients to identify essential kinases and show synergy between EGFR and FGFR1 inhibitors.

The paper analyzes whole-genome sequencing data from a pan-cancer cohort to define HRD, showing it extends beyond BRCA1/2 mutations and highlights the benefits of WGS over commercial assays for HRD detection.

This study examines how mutagenesis and extrachromosomal DNA contribute to urothelial cancer evolution, revealing clonal APOBEC3 mutations and chemotherapy-induced mutational bursts within ecDNA.

This paper introduces UTAG, a method to automatically identify tissue structures in multiplexed imaging data, showing it can detect higher-order tissue organization and relate it to disease states.

This paper introduces a weakly-supervised method to predict tumor purity from H&E stained slides, achieving high accuracy and enabling clinical applications.

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Pore-C reads multi-way chromatin contacts directly off unamplified Nanopore long reads, recovering Hi-C-scale features while also resolving rearranged cancer alleles and supporting de novo assembly.

This study identifies molecular subgroups of BPH and suggests mTOR inhibitors as a potential therapy for specific subtypes.

This study reports that 17% of advanced cancer patients have clinically relevant germline variants, with higher rates of cancer-associated variants compared to control cohorts.