Gisela Gabernet

The paper integrates gene expression and B cell receptor data to capture complementary B cell information, revealing substructure supported by both transcriptional and receptor features.

This paper identifies 23 candidate causal genes for critical COVID-19 by integrating severity-stratified, longitudinal cis-eQTL mapping with GWAS signals from 1,031 patients.

AMULETY generates language model embeddings for adaptive immune receptor sequences using pre-trained models, enabling users to leverage different models for downstream applications.

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

The paper identifies a multi-omics recovery factor predictive of long COVID using data from the IMPACC study, showing it can predict LC risk early after infection.

The paper introduces nf-core/airrflow, a Nextflow-based workflow for processing AIRR-seq data, validated on simulated and real datasets to analyze immune receptor repertoires.

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

The paper compares RNA-seq pipeline versions and tool combinations to assess their impact on differential expression and gene classification consistency across species.

nf-root automates apoplastic pH analysis in plant root images using deep learning, achieving near-human performance and reducing analysis time.

The paper introduces a pipeline for metagenome assembly and binning using Nextflow, enabling the reconstruction of MAGs from shotgun metagenomic data.

This paper introduces Swarm Learning, a decentralized machine learning approach for disease classification using transcriptomic data, demonstrating its effectiveness in developing classifiers for COVID-19, tuberculosis, and leukemias while preserving privacy.

The paper proposes a FAIR-compliant data management system integrating imaging and omics data using Service Oriented Architecture principles, demonstrating its use in plant biology and hepatocellular carcinoma studies.