Silvia Bottini

Identification, evolutionary history and characteristics of orphan genes in root-knot nematodes

The paper identifies and characterizes orphan genes in eight root-knot nematode species, finding they contribute to parasitism and are expressed during the infective juvenile stage.

Accelerate the discovery of genetic variants in mitochondrial diseases with VIOLA: Variant PrIOritization using Latent space

VIOLA prioritizes pathogenic variants in mitochondrial diseases using a variational autoencoder and outlier detection, outperforming existing methods in a patient cohort.

A knowledge graph and topological data analysis framework to disentangle the tomato-multi pathogens complex gene regulatory network

The paper constructs a knowledge graph and uses topological data analysis to uncover the gene regulatory network of tomato's response to multiple pathogens, identifying key transcription factors and regulatory hubs.

Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER.

The paper introduces MOnSTER, a tool for clustering and scoring protein sequence motifs, and applies it to identify specific motifs in plant-parasitic nematode effectors.

Definition of the effector landscape across 13 Phytoplasma proteomes with LEAPH and EffectorComb

The paper introduces LEAPH, a machine learning tool for predicting phytoplasma effector proteins, and EffectorComb, an app for analyzing these predictions, identifying 2089 putative effectors across 13 proteomes.

Benchmarking feature selection and feature extraction methods to improve the performances of machine-learning algorithms for patient classification using metabolomics biomedical data.

This paper benchmarks feature selection and extraction methods to enhance machine-learning performance in patient classification using metabolomics data.