Matteo Chiara

The paper identifies distinctive H5N1 viral genome signatures linked to repeated spillovers into U.S. dairy cattle, highlighting genetic diversity and geographic origins.

FluWarning detects emerging influenza A virus spillovers using codon bias and dinucleotide composition anomalies, identifying pdm09 and B3.13 genotypes before their spread.

This study investigates how mutations in the HEADING DATE 1 gene affect rice transcription and cell wall composition under different day length conditions.

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

This paper introduces RecombinHunt, a data-driven method for detecting recombinant viral genomes, which accurately identifies recombinant SARS-CoV-2 lineages and applies to other viral epidemics.

This study uses pan-genomic data to analyze D4Z4 repeats and CpG methylation in FSHD, finding low methylation correlates with SMCHD1 variants but not clinical phenotypes.

This study uses unsupervised clustering of SARS-CoV-2 genomic sequences to reveal hidden genetic diversity and proposes an automated framework for improved genomic surveillance.

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

This study identifies Fos as a key regulator of neural stem cell self-renewal, showing it rescues proliferation and interacts with Sox2 through a gene regulatory network involving Socs3.

VINYL prioritizes genetic variants using survival analysis, showing higher accuracy and sensitivity than existing methods in clinical studies.

This study introduces a classification system for SARS-CoV-2 genomes, identifies 12 clusters and 4 super-clusters, and estimates the virus's emergence as early as 2019.

Laniakea provides a cloud-based platform to deploy Galaxy instances on-demand across heterogeneous infrastructures, enabling customizable and scalable bioinformatics workflows.

The paper analyzes SARS-CoV-2 genome sequences to determine if geographic clades show distinct evolutionary patterns, finding no evidence of adaptive evolution in protein-coding genes.

The paper presents a high-quality genome assembly for the European barn swallow using SMRT long reads and Bionano DLS optical maps, achieving a scaffold N50 of over 25.95 Mbp.