Impact That Matters
From concept to rigorous experimental design — through feasibility, implementation, data generation, and knowledge extraction — we transform complex immunological questions into actionable insights. Our work drives new hypotheses, medical translation, and lasting impact.
ImmSilico builds on decades of pioneering research that has advanced immunology and transformed data‑driven discovery. This proven track record is the backbone of our mission today: delivering rigorous, high‑impact consultancy for the future of immune health.
Proven Impact
Our experts have contributed to landmark studies featured in leading journals:
Checkpoint Inhibitor Tracking in T Cells
As a major step forward in understanding immune-related adverse events in cancer patients receiving checkpoint blockade therapy, we used advanced imaging and molecular profiling to track T cells bound by checkpoint inhibitors in the intestinal tissue of patients with checkpoint-induced colitis.
Cancer Cell 2024
Single Cell Atlas of Colonic CD8+ T Cells in Ulcerative Colitis
Through pioneering single-cell RNA sequencing in a collaborative effort, ImmSilico helped construct a comprehensive atlas of colonic CD8+ T cells in both healthy individuals and those with ulcerative colitis. This work revealed the heterogeneity and functional states of these cells, offering deeper insight into UC mechanisms and paving the way for targeted therapies.
Nature Medicine 2020
Spatiotemporal Analysis of Human Intestinal Development
In collaboration with world-leading researchers, the ImmSilico team leveraged single-cell and spatial transcriptomics to map intestinal development. This study delivered an unprecedented view of the crypt–villus axis and revealed new insights into neural, vascular, and immune maturation in the gut
Cell 2020
Use Case
Advancing T Cell Tracking with Integrated scRNA and TCR-seq
Challenge: “we are thinking about capabilities of scRNA-seq/TCRseq experiment to complement our tracking of antigen-specific CD4 and CD8 T cells in vivo. We would likely use MX-XX-GP tumours and then try to get sequence-tagged tetramers for GP tetramers targeting CD8 and CD4 T cells. I was advised by bioinformatically-minded collaborators that the TCR-seq would work better with a model antigen expressed in the system. We have had good success with scRNA-seq in our models, but never tried TCR-seq and local advice would be hugely useful.
Many thanks for any help you can provide.”
Solution: Strategic experimental design combining both technologies — depending on if repertoire architecture and clonal expansion is the key aim and/or if molecular and cellular phenotype of T cells are essential— for comprehensive immune profiling.
Impact: Enabled tracking of GP-specific CD4/CD8 T cells in tumour model with sequence tagged tetramers. The collaboration had led to new hypothesis and further experiments, made the foundations for a new grant application.
Connecting tRNA Biology to Antigen Presentation and T Cell Response in Cancer
Challenge: “We've discovered that tRNA modifications directly shape the MHC-II immunopeptidome in cancer—a novel mechanism with major implications for immunotherapy. We have compelling data from immunopeptidomics and TCR sequencing, but we need expertise to identify the most immunogenic peptides and map them to their cognate TCRs. We need to bridge this gap to fully understand the functional significance of our discoveries.."
Solution: Strategic in silico strategy was suggested to identify, for further functional validation, a handful of peptides and map them to their potential TCRs.
Impact: This collaboration was central to addressing reviewers' questions for the manuscript under review at a highly recognized journal, providing novel mechanistic insights connecting tRNA biology to immune recognition and new methodological approaches for linking peptide presentation to T cell responses
A Case to Cover Spatial Approaches in Tissue Immunity
Our collaborative approach consistently delivers results that advance scientific understanding and accelerate discovery. Here's what our research partners say about working with ImmSilico:
Impact Stories
“ImmSilico’s expertise in mapping antigenic peptides to cognate TCRs was exactly what we needed to strengthen our manuscript. Their expertise and analytical approach helped us address critical reviewer questions and provided new mechanistic insights we hadn’t considered. The collaboration was seamless and scientifically rigorous — exactly what you want when working on high‑impact, multidisciplinary research." Professor XXX.