Conditioning of the immune system by the microbiome

DB Graham, RJ Xavier - Trends in Immunology, 2023 - cell.com
The human intestinal microbiome has coevolved with its host to establish a stable
homeostatic relationship with hallmark features of mutualistic symbioses, yet the mechanistic …

Deciphering the tumor immune microenvironment from a multidimensional omics perspective: insight into next-generation CAR-T cell immunotherapy and beyond

Z Zhou, J Wang, J Wang, S Yang, R Wang, G Zhang… - Molecular Cancer, 2024 - Springer
Tumor immune microenvironment (TIME) consists of intra-tumor immunological components
and plays a significant role in tumor initiation, progression, metastasis, and response to …

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system

PSL Schäfer, D Dimitrov, EJ Villablanca… - Nature …, 2024 - nature.com
The immune system comprises diverse specialized cell types that cooperate to defend the
host against a wide range of pathogenic threats. Recent advancements in single-cell and …

Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens

J Wohlwend, A Nathan, N Shalon, CR Crain… - Nature Machine …, 2025 - nature.com
Accurate in silico determination of CD8+ T cell epitopes would greatly enhance T cell-based
vaccine development, but current prediction models are not reliably successful. Here …

HLA-DM and HLA-DO interplay for the peptide editing of HLA class II in healthy tissues and leukemia

B Budeus, M Álvaro-Benito, P Crivello - Best Practice & Research Clinical …, 2024 - Elsevier
HLA class II antigen presentation is modulated by the activity of the peptide editor HLA-DM
and its antagonist HLA-DO, with their interplay controlling the peptide repertoires presented …

A journey to your self: The vague definition of immune self and its practical implications

B Koncz, GM Balogh… - Proceedings of the …, 2024 - National Acad Sciences
The identification of immunogenic peptides has become essential in an increasing number
of fields in immunology, ranging from tumor immunotherapy to vaccine development. The …

Emerging biochemical, microbial and immunological evidence in the search for why HLA-B∗ 27 confers risk for spondyloarthritis

EM Brown, PNU Nguyen, RJ Xavier - Cell Chemical Biology, 2025 - cell.com
The strong association of the human leukocyte antigen B∗ 27 alleles (HLA-B∗ 27) with
spondyloarthritis and related rheumatic conditions has long fascinated researchers, yet the …

How to predict binding specificity and ligands for new MHC-II alleles with MixMHC2pred

J Racle, D Gfeller - HLA Ty**: Methods and Protocols, 2024 - Springer
MHC-II molecules are key mediators of antigen presentation in vertebrate species and bind
to their ligands with high specificity. The very high polymorphism of MHC-II genes within …

HLA mismatches identified by a novel algorithm predict risk of antibody-mediated rejection from de novo donor-specific antibodies

X Zhang, NL Reinsmoen, JA Kobashigawa - Transplantation, 2024 - journals.lww.com
Background. The development of de novo donor-specific antibodies (dnDSA) and antibody-
mediated rejection (AMR) remains a barrier to long-term graft and patient survival. Most …

Cytotoxic Th1 cells mushroom after fungal exposures in Crohn's disease

M Stražar, RJ Xavier - Immunity, 2023 - cell.com
Cytotoxic Th1 cells mushroom after fungal exposures in Crohn’s disease: Immunity Skip to
Main Content Advertisement Immunity This journal offers authors two options (open access or …