Silvia F. Zanini

High-throughput sequencing of unmethylated DNA (UMR-seq) reveals extensive epigenetic variation in the hypomethylome of diverse plant species

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

Integrating Orthology and Cross-Species Transcriptomics to Unravel Root Drought Responses in Faba Bean and Maize

This study integrates orthology and cross-species transcriptomics to compare drought responses in faba bean and maize roots, revealing conserved and species-specific gene regulation strategies.

A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation

This paper trains a deep learning model to predict gene expression from regulatory sequences in plants and shows it captures positional regulatory effects and functional context.

Machine learning and multi-omic analysis reveal contrasting recombination landscape of A and C subgenomes of winter oilseed rape

The paper uses machine learning and multi-omic data to analyze recombination patterns in the A and C subgenomes of Brassica napus, finding distinct landscape features between them.

Integrative epigenomic analysis uncovers asymmetry of enhancer activity in Brassica napus

The paper identifies and characterizes super-enhancers in Brassica napus, revealing their asymmetrical distribution and functional impact on gene expression and regulatory processes.

Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus

This study uses pangenome graphs to analyze structural variants in Brassica napus, showing they impact gene expression and eQTL analysis better than single references.

Benchmarking Oxford Nanopore Read Alignment-Based Structural Variant Detection Tools in Crop Plant Genomes

This study benchmarks SV detection tools using Oxford Nanopore reads in crop plants, evaluating performance across different coverages and species.