Fabio Luciani

Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease

This study identifies clonal IEL expansion and epithelial remodelling in RCD1 using single-cell multi-omics, showing distinct immune and epithelial states compared to ACD.

Identifying the Minimal Number of Protein Markers for Cell Type Annotation Using MiniMarS

MiniMarS identifies the minimal number of protein markers for cell type annotation across multiple datasets and improves rare population identification.

Temporal dynamics of viral fitness and the adaptive immune response in HCV infection

This study examines how viral fitness and immune responses interact in HCV infection, showing fitness decreases early but rebounds with mutations, and strong CD8+ T-cell responses drive chronic infection.

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

This study evaluates the analytical validity of nanopore sequencing for SARS-CoV-2 genome analysis, finding high accuracy for SNVs but limitations in detecting short indels and low-frequency variants.

Exploring and analysing immune single cell multi-omics data with VDJView

VDJView is a tool for analysing immune single-cell multi-omics data, integrating gene expression, immune receptors, and clinical metadata to identify antigen-specific gene signatures and clonal expansions.

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

This paper introduces RAGE-seq, a method combining long-read and short-read sequencing to analyze lymphocyte clonal and transcriptional features in breast cancer tissues.

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

VDJPuzzle 2.0 reconstructs full-length B-cell receptor sequences from scRNA-seq with high accuracy, validated against Sanger sequencing.

Impact Of Sequencing Depth And Read Length On Single Cell RNA Sequencing Data: Lessons From T Cells

This study examines how sequencing depth and read length affect scRNA-seq data quality, finding that sufficient depth and length improve TCRβ reconstruction and gene expression accuracy in T cells.