Javier Quilez

Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications

This study evaluates Oxford Nanopore sequencing's performance in clinical genomics using reference samples, showing high accuracy for SNVs and SVs but challenges with INDELs and CNVs.

Pathogenicity Reassessment and Novel Variant Discovery in Inherited Retinal Disease through Population-Scale Genomics in the United Arab Emirates

The paper reassesses pathogenicity of variants in inherited retinal diseases using population-scale genomics in the UAE, identifying clinically relevant variants and highlighting discrepancies between clinical and population-based classifications.

CRAM compression: practical across-technologies considerations for large-scale sequencing projects

The paper evaluates CRAM compression performance across different sequencing technologies for the Emirati Genome Program, finding 40-70% compression with no data loss.

Higher-order chromatin organization defines Progesterone Receptor and PAX2 binding to regulate estradiol-primed endometrial cancer gene expression

The paper identifies progestin control regions (PgCRs) where PR and PAX2 bind to regulate gene expression in endometrial cancer cells.

Signalling Network of Breast Cancer Cells in Response to Progesterone

This study maps the dynamic signalling network in breast cancer cells responding to progesterone using antibody microarrays and phosphoproteomics, revealing new proteins and pathway connections.

TFIIIC binding to Alu elements controls gene expression via chromatin looping and histone acetylation

The paper shows TFIIIC binding to Alu elements regulates gene expression through chromatin looping and histone acetylation during serum starvation.

Hormone Control Regions mediate opposing steroid receptor-dependent genome organizations

The paper identifies Hormone-Control Regions (HCRs) that organize genome structure and mediate opposing transcriptional responses to steroid hormones in breast cancer cells.

Unliganded progesterone receptor governs estrogen receptor gene expression by regulating DNA methylation in breast cancer cells

The paper shows that the unliganded progesterone receptor (PR) maintains ESR1 expression and DNA methylation in hormone-deprived breast cancer cells, and that PR depletion leads to increased promoter methylation and reduced ESR1 expression.

OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

OneD improves Hi-C reproducibility for samples with abnormal karyotypes by addressing copy number variations, outperforming existing methods while maintaining performance on normal karyotypes.

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming

The paper shows transcription factors drive genome topology changes before gene expression during cell reprogramming.

Parallel sequencing lives, or what makes large sequencing projects successful

The paper compares two Hi-C samples, showing how adherence to FAIR principles leads to successful sequencing projects.