Ioannis Xénarios

Comparative evaluation of genotyping and low-pass sequencing for pharmacogenetic variant and phenotype inference

This study compares genotyping arrays and low-pass whole-genome sequencing for pharmacogenetic variant and phenotype inference, finding high concordance but improved variant coverage with LP-WGS.

Evaluation of the Ultima Genomics UG 100™ sequencing platform for clinical services

This paper evaluates the Ultima Genomics UG 100 sequencing platform's ability to identify short variants, particularly in long homopolymer regions, compared to Illumina NovaSeq 6000 for clinical use.

A combined computational and experimental approach to successfully predict the behavior of metastatic tumor-associated macrophages in humanbreast cancer

The paper identifies pro-metastatic TAMs in breast cancer and develops a computational-experimental framework to predict and inhibit their activity through pathway analysis and drug screening.

Integrating knowledge, omics and AI to develop patient-specific virtual avatars

The paper develops a method to create personalized regulatory networks for cancer patients using PDX models, integrating gene expression data and genetic algorithms with GCNs to predict treatment outcomes.

Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms

Seq2scFv annotates and characterizes scFv sequences from long-read sequencing data to improve antibody discovery.

Improving population scale statistical phasing with whole-genome sequencing data

This paper introduces SAPPHIRE, a method that improves haplotype phasing accuracy using whole-genome sequencing data by refining phase calls with read-level information.

Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models

The paper presents genome assemblies for NOD/SCID and BALB/c Nude mouse strains to improve understanding and usage of these immunocompromised models.

PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data

PAPET identifies 5-methylcytosine from PacBio SequelII data using a probabilistic framework, achieving high specificity and precision comparable to PacBio's own method.

Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing

Repeat Detector accurately measures expanded tandem repeats and identifies interrupted alleles in targeted DNA sequencing data from Huntington's disease patients.

Towards mouse genetic-specific RNA-sequencing read mapping

The paper evaluates the impact of reference bias on transcriptome and eQTL analysis in mouse genetic studies and proposes improved reference strategies.

A novel anti-influenza combined therapy assessed by single cell RNA-sequencing

This study evaluates a combined anti-influenza therapy using single cell RNA sequencing to show its effectiveness in inhibiting viral replication across different epithelial cell types.

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

This study investigates whether CAG/CTG repeat expansion alters chromatin folding using 4C sequencing and finds that chromatin contacts remain stable despite repeat expansion.

HAMAP rules as SPARQL - A portable annotation pipeline for genomes and proteomes

The paper translates HAMAP proteome annotation rules into SPARQL queries for reusable genome and proteome annotation across different datasets.

PamgeneAnalyzeR open and reproducible pipeline for kinase profiling

The paper introduces an R package for automated and reproducible analysis of kinase activity data from PamChip(R) arrays.

Simple and complex interactions between sleep-wake driven and circadian processes shape daily genome regulatory dynamics in the mouse

This study examines how sleep deprivation affects gene expression and chromatin accessibility in mice, revealing long-term genomic regulatory changes.

A multi-omics digital research object for the genetics of sleep regulation.

The paper presents a multi-omics digital research object for studying sleep regulation in mice, integrating diverse datasets and analytics to enhance data reusability and reproducibility.

Enzyme annotation in UniProtKB using Rhea

The paper updates UniProtKB enzyme annotations using Rhea, replacing textual descriptions with structured biochemical reaction data and improving search capabilities.

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

The paper reanalyzes the contribution of proteasomal spliced peptides to the HLA-I ligandome and finds that only 2-4% of the ligandome may be explained by such peptides.

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

The paper shows taxon sampling unevenly impacts gene tree nodes and introduces a two-step method to construct more reliable model gene trees using SwissTree.