Beatrice Borsari

Epigenetic characterization of pseudogenes across human tissues

The paper characterizes the epigenetic features of pseudogenes across human tissues and identifies differences compared to protein-coding transcripts and lncRNAs.

chronODE: A framework to integrate time-series multi-omics data based on ordinary differential equations combined with machine learning

chronODE integrates time-series multi-omics data using ordinary differential equations and machine learning to model gene and chromatin dynamics during brain development.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations

This paper uses wearable data and AI to identify genetic associations with psychiatric disorders by creating intermediate phenotypes from continuous physiological features.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

Intronic enhancers regulate the expression of genes involved in tissue-specific functions and homeostasis

The paper shows that tissue-specific enhancers are mostly intronic and regulate genes involved in tissue-specific functions, while housekeeping genes are controlled by intergenic enhancers.

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

The paper identifies and analyzes splicing quantitative trait loci (sQTLs) across multiple tissues using the GTEx dataset, revealing their role in splicing regulation and disease.

Dynamics of gene expression and chromatin marking during cell state transition

The paper tracks transcriptomic and epigenomic changes during human pre-B cell to macrophage transdifferentiation, finding coordinated chromatin state transitions and gene activation patterns.

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.

Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay

The paper identifies novel autoregulatory feedback loops where RNA-binding proteins regulate their own expression via alternative splicing and nonsense-mediated mRNA decay.