Simone Tiberi

DESpace2: detection of differential spatial patterns in spatial omics data

DESpace2 identifies differential spatial patterns in spatial omics data by comparing gene expression across experimental conditions.

Orchestrating Spatial Transcriptomics Analysis with Bioconductor

The paper provides an open-source online book for analyzing spatial transcriptomics data using Bioconductor in R, with reproducible code and datasets.

Beyond the Gene in Genetics: How Isoform-Resolved Analysis Empowers the Study of Both Common and Rare Genetic Variation

This study shows that analyzing genetic variants at the isoform level reveals significant associations with human phenotypes and rare variants, highlighting the importance of isoform-resolved analysis in genetics.

IsoBayes: a Bayesian approach for single-isoform proteomics inference

IsoBayes infers protein isoform presence and abundance using Bayesian methods integrating proteomics and transcriptomics data, showing good sensitivity and specificity in simulations and real datasets.

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes

DifferentialRegulation identifies differentially regulated genes by analyzing unspliced mRNA abundance across experimental conditions using a Bayesian hierarchical model.

DESpace: spatially variable gene detection via differential expression testing of spatial clusters

DESpace detects spatially variable genes by testing differential expression between spatial clusters across biological replicates, showing good performance and computational efficiency.

distinct: a novel approach to differential distribution analyses

distinct identifies differential distribution patterns in single-cell data by comparing empirical cumulative distribution functions, outperforming existing methods in detecting subtle changes.

A guide to trajectory inference and RNA velocity

This paper explains trajectory inference and RNA velocity methods for analyzing single-cell RNA-seq data to study cellular dynamics.

3'-5' crosstalk contributes to transcriptional bursting

The paper measures transcriptional bursting using Bayesian methods and shows that polymerase shuttling affects burst size and frequency, with implications for transcriptional noise.

BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty

BANDITS is a Bayesian method for differential splicing analysis using RNA-seq data, showing strong performance in simulated and experimental datasets.