Alessandro Sette

COMBO-RATE identifies promiscuous HLA restrictions by analyzing immune response data, outperforming existing tools and revealing broader HLA allele coverage for T cell epitopes.

The paper characterizes the pathogenicity of a newly emerged Andes virus (ANDV2026) in hamsters, showing high virulence, airborne shedding, and immune responses not previously described.

This study longitudinally tracks antigen-specific T cells in human upper airway tissues and blood, finding sustained memory T cell populations over 18 months.

This study shows that sustained delivery of a SARS-CoV-2 subunit vaccine in an adjuvanted hydrogel depot improves antibody responses in nonhuman primates compared to bolus vaccination.

The paper revises the standardization and validation pipeline for immune receptor data in the IEDB to improve data consistency and usability.

This study identifies CD1a-restricted T cell responses to canonical microbial peptides in leprosy, expanding the known ligands of CD1a and suggesting potential applications for mycobacterial immunity research.

The paper designs HLA class I superbinders using a computational framework, identifying peptides that bind multiple HLA alleles and showing broad immunogenic potential.

NetMHCIIphosPan predicts HLA class II antigen presentation of phosphorylated peptides using immunopeptidomics data, outperforming existing tools.

EPITOME is a multimodal pipeline that combines OCR, text matching, and VLMs to automate and enhance epitope data curation from scientific papers.

The paper introduces a method to study cell-cell interactions at single-cell resolution, revealing unique transcriptomic signatures in T cell-monocyte complexes during TB and dengue infection.

This study identifies CD4+ T cell epitopes in chronic chikungunya virus disease, revealing conserved epitopes across alphaviruses and providing tools for T cell response analysis.

This study examines T cell and antibody responses in vaccinated individuals over three years, finding stable T cell responses and increased regulatory T cells after multiple boosters.

The paper examines T cell responses to PINK1 and α-synuclein in prodromal Parkinson's disease, finding elevated reactivity comparable to clinically diagnosed PD.

The paper identifies that CDR1 and CDR2 sequence identities are more predictive of epitope similarity than CDR3, and develops BCRMatch to predict epitope binding based on antibody sequences.

The paper investigates T cell subsets in Parkinson's disease patients reactive to α-synuclein, finding reduced Granulysin+ CD4 cytotoxic TEM cells and altered CELSR2 expression.

PDI-TCR identifies Mtb-specific TCRs and characterizes their phenotypes in TB patients and healthy individuals, revealing distinct dynamics of specific and unspecific T cell responses.

This study compares immune responses to whole-cell and acellular pertussis vaccines, finding that Th1 polarization is maintained through an early interferon response in whole-cell vaccine recipients.

The paper shows that most Mtb-specific CD4+ T cells from LTBI individuals recognize infected macrophages, but some require exogenous antigen, and identifies effector functions associated with TB protection.

The paper analyzes T cell epitopes from H5N1 and seasonal influenza viruses, finding conserved epitopes and cross-reactivity, suggesting pre-existing immunity may reduce H5N1 severity.

The paper identifies PINK1 as an autoantigen targeted by T cells in Parkinson's disease, with reactivity predominantly observed in male patients.

This paper develops a machine learning model that integrates peptide and antigen features to predict immunogenic CD4+ T cell epitopes in bacteria, achieving high accuracy across multiple bacterial species.

The paper evaluates computational models predicting immune responses to Pertussis Booster vaccinations using a new community resource, finding that existing models perform poorly and new models show variable performance based on features and strategies.

This study shows that immunizing HLA-DRB1*15:01 mice with the alpha-synuclein epitope -syn32-46 causes intestinal inflammation, neuron loss, and constipation, mimicking prodromal Parkinson's disease features.

The paper introduces the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets for comparative vaccine response analysis.

The paper compares immune responses to a Tdap booster in adults primed with acellular (aP) or whole-cell (wP) pertussis vaccines, identifying divergent gene expression and antibody subtype patterns in aP-primed individuals.

This paper improves T cell epitope predictions by combining MHC binding affinities with antigen expression levels, showing better performance than methods using only binding or expression data.

This study shows SARS-CoV-2 infection in rhesus macaques induces Tfh cells and germinal center responses, with Th1 skewing and early IgG but delayed IgA.

This study identifies novel MHC-I antigens specific to dengue virus infection using an immuno-proteomics approach, revealing ligands associated with distinct HLA haplotypes and T-cell recognition.

DAFi identifies cell populations from flow cytometry data by combining recursive filtering and clustering with user-defined constraints, improving resolution of overlapping and rare populations.