Alessandro Bonetti

Detection of statistically robust interactions from diverse RNA-DNA ligation data

The paper introduces RADIAnT, a computational pipeline for detecting RNA-DNA interactions from ligation data, showing improved accuracy in identifying Malat1-DNA interactions and dynamic chromatin-associated RNAs.

Recombination of repeat elements generates somatic complexity in human genomes.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

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.

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

RADICL-seq maps genome-wide RNA-chromatin interactions in intact nuclei, revealing general and cell type-specific patterns of transcript occupancy and the role of transcription in chromatin structure.