Alexandra–Chloé Villani

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

The paper introduces scAtlasTb, a framework for building and optimizing single-cell reference atlases, demonstrating its application on three Human Cell Atlas projects.

The paper constructs a multi-omics single-cell atlas of human RPE and choroid, identifying cell types, aging patterns, and genetic risk factors for AMD.

This study identifies CD8+TOX+ T-cells as a specific marker for autoimmune hepatitis using single-nucleus RNA sequencing.

The paper identifies a cDC2-Treg feedback circuit in barrier tissues that limits Th2 cell expansion during allergic inflammation.

This paper constructs a single-cell atlas of circulating immune cells to understand inflammation across diseases and develops a classifier for inflammatory diseases.

This study compares T cell phenotypes and clonotypes from bronchoalveolar lavage and endobronchial brushings in healthy controls and allergic asthmatics, finding distinct transcriptional and TCR repertoire features.

This study identifies a novel CD8+ TIL subset that uses lymphotoxin and IFN pathways to kill cancer cells, linking LTB expression to clinical response in melanoma.

The paper identifies a sensory neuron-intrinsic mTORC1 signaling mechanism that establishes neuroimmune memory, enhancing allergic immunity upon allergen re-exposure.

This study uses spatial transcriptomics to identify CD8+ T cell-driven mechanisms of kidney damage in ICI-AIN, showing increased IFN-γ signaling and proinflammatory myeloid cell activation.

This study identifies IL-1 and IL-6 as key drivers of neuroinflammation in HSV encephalitis, showing they are not reduced by corticosteroids and are associated with poor outcomes.

This study identifies AP-1 transcription factors as key regulators of TRM development across tissues using scRNA-seq and ATAC-seq, revealing a novel mechanism for TRM reactivation.

This study shows that airway basal stem cells maintain intraepithelial airway macrophages via Notch signaling, enabling localized allergic inflammation in the trachea but not distal lung tissues.

The paper analyzes 6 million T cells from 91 studies to identify TCR sequence convergence patterns and their association with functional and cellular T cell phenotypes.

The paper generates a multi-modal atlas of thyroid and blood cells from HT, GD, and controls, revealing shared immune niches despite distinct disease mechanisms.

This study creates a single-nucleus and spatial transcriptomic atlas of the COVID-19 liver, revealing cellular and functional disruptions associated with organ damage.

This study identifies immune cell types and biomarkers in irMyocarditis using single-cell RNA sequencing and TCR analysis across heart, blood, and tumor tissues.

The paper presents AIDA, a diverse single-cell RNA-seq atlas of immune cells, revealing sub-continental diversity impacts on immune cell properties and identifying functional genetic variants.

This paper introduces scTab, a deep learning model for cross-tissue cell type annotation in single-cell RNA-seq, showing improved performance over linear models and demonstrating scalability with larger datasets.

This study identifies three germline variants associated with immune-related adverse events in patients treated with immune checkpoint inhibitors.

The paper identifies obesity-related TREM2high macrophages in diabetic mouse and human kidney through single-cell transcriptomics and cross-species comparison.

The paper uses plasma proteomics to identify tissue-specific cell death and cell-cell interaction mediators in severe COVID-19 patients, linking them to survival outcomes and viral infection effects.

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

The paper uses CAMAP to predict SARS-CoV-2 MHC-I peptides, identifies 48 vaccine candidates covering most HLA haplotypes and strains, and provides an interactive portal for exploration.

Cumulus is a cloud-based framework for analyzing large-scale sc/snRNA-seq data, improving efficiency and scalability while maintaining result quality.

The paper identifies genoinformative markers (GIMs) in mammalian spermatogenesis showing allelic expression bias, suggesting selective sweeps and evolutionary conflict between germline and somatic functions.

The paper uses single-cell transcriptomics to map hematopoiesis in human fetal liver, identifying cell differentiation trajectories and shifts in hematopoietic composition during development.

The paper was withdrawn due to the inclusion of confidential information about a third party.

Seven single-cell and single-nucleus protocols run side by side on the same cell lines, PBMCs and mouse cortex, analysed through one pipeline: 10x Chromium led the high-throughput methods.

The paper identifies genetic variants influencing isoform usage in the anti-viral response, revealing ERAP2's role in balancing selection and influenza-specific regulation.