Francesco Lescai

nanorepertoire: an end-to-end Nextflow pipeline for nanobody repertoire analysis

nanorepertoire is an end-to-end Nextflow pipeline for analyzing camelid nanobody repertoires, providing standardized and reproducible analysis of AIRR-seq data.

SIEVE: Sparse Interpretable Exome Variant Explainer

SIEVE is a deep-learning framework for variant and gene prioritization in exome studies, achieving strong discrimination and recovering known associations across diseases.

Bioinf-Farma: supervised integration of epitope prediction and recombinant protein developability for automated vaccine candidate prioritization

BIOINF-farma integrates epitope prediction and developability assessment to prioritize vaccine candidates by combining antigenicity and expression feasibility scores.

Adaptive disorder as the hallmark of nanobodies antigen-binding loops

This study identifies nanobody CDRs using deep learning and structural analysis, finding that their disorder and conformational diversity are adaptive features.

Eduomics: a Nextflow pipeline to simulate -omics data for education

Eduomics is a Nextflow pipeline that simulates genomic and transcriptomic data for educational purposes, providing realistic clinical scenarios to enhance bioinformatics learning.

Spiroplasma impairs testes gene expression in Glossina fuscipes fuscipes

This study examines the impact of Spiroplasma infection on testes gene expression in G. f. fuscipes, finding significant downregulation of genes related to sperm motility and energy metabolism.

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery

The paper presents an optimized variant calling pipeline that reduces storage and runtime costs for DNA sequencing analysis.

hgtseq: a standard pipeline to study horizontal gene transfer

hgtseq is a pipeline for analyzing horizontal gene transfer from sequencing data, showcasing its performance on mammalian exome datasets.

Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia

Exomes of 24,248 schizophrenia cases and 97,322 controls implicate ultra-rare damaging variants in 10 genes, including GRIN2A and GRIA3, with odds ratios of 3 to 50.

Meta-analysis of Scandinavian Schizophrenia Exomes

This study performs a meta-analysis of Scandinavian schizophrenia exomes, identifying three genes associated with the disorder and highlighting shared genetic architecture with high-functioning autism.

Quantifying the impact of rare and ultra-rare coding variation across the phenotypic spectrum

The paper investigates the impact of rare protein truncating variants on 13 quantitative traits and 10 diseases using whole-exome sequencing data from 100,296 individuals, finding increased risk for several disorders and associations with other phenotypes.

ASD and ADHD have a similar burden of rare protein-truncating variants

The paper investigates the genetic burden of rare protein-truncating variants in ASD and ADHD, finding similar patterns of enrichment.

Estimating the functional impact of INDELs in transcription factor binding sites: a genome-wide landscape

The paper introduces a bioinformatic method to predict the functional impact of INDELs in transcription factor binding sites, showing that deletions have the most severe effects while insertions are mostly neutral.