Yari Ciani

T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variants

The paper evaluates the T2T-CHM13 reference genome's impact on mapping bias and alignment accuracy at disease-associated variants, finding reduced bias and improved precision.

The RNA cargo of plasma-derived extracellular vesicles in mCRPC patients captures cancer cells and tumor microenvironment signals

The paper profiles EV-RNA and cfDNA from mCRPC patients to identify prognostic biomarkers and tumor microenvironment signals.

The human RNA-DNA interactome is cell type-specific and dynamic

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

Extracellular Vesicles heterogeneity through the lens of multiomics

This study provides a multiomics resource of cancer extracellular vesicles, showing correlations between LO proteins and prostate cancer progression, and demonstrating the feasibility of single-cell RNA-Seq on EVs.

ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent Transcription Replication Conflicts in Triple Negative Breast Cancer

The paper identifies ANP32E as a driver of vulnerability to ATR inhibitors in triple-negative breast cancer by promoting R-loop-dependent transcription replication conflicts and genomic instability.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.