computational-immunology

Dry-lab computational pipeline for prioritizing viral CD8+ T-cell epitopes by predicted immunogenicity across nine viral pathogens (CMV, EBV, HBV, HCV, HPV, HIV-1, IAV, DENV, SARS-CoV-2). RF/XGBoost production track; GINEConv+ESM-2 GNN research track. OpenSSF Passing.

• Updated Sep 7, 2026
• Python

TCR embedding expressivity evaluation framework.

• Updated Jan 1, 2025
• Python

About me (Soumya Banerjee)

• Updated Oct 2, 2025

Curriculum Vitae

• Updated Aug 9, 2026
• TeX

Inverting the antibody affinity-maturation selection operator f = sigma . phi . a: design archive of two orthogonal lines, phi simulation-based inference + sigma analytic inversion, with a three-line progress presentation

• Updated Jun 26, 2026
• Jupyter Notebook

End-to-end clinical shotgun metagenomic pipeline investigating microbial triggers (NOD2/TLR4) of metabolic inflammation, disproving barrier failure and supporting the Host Autonomy model in Type 2 Diabetes.

• Updated Apr 25, 2026
• R

A multi-language bioinformatics pipeline (Bash, R, Python) for single-cell RNA-seq analysis of the Melanoma tumor microenvironment. Identifies CD8+ T-cell exhaustion signatures and statistically validates them as predictive biomarkers for Immune Checkpoint Blockade (ICB) therapy response.

• Updated Mar 15, 2026
• Python

• Updated Apr 20, 2017
• Jupyter Notebook

A Mathematical and Computational Model for simulating immune regulation of Type 1 Diabetes.

• Updated Sep 17, 2025
• Python

An in-silico transcriptomic pipeline employing single-sample Gene Set Enrichment Analysis (ssGSEA) to quantify and characterize MSigDB Hallmark pathway-level host responses to acute and chronic HIV-1 infection

• Updated Apr 11, 2026
• R

EpitopePred — An integrated immunoinformatics web server for automated multi-epitope vaccine engineering against viral, bacterial, protozoal, and fungal pathogens. Combines 30+ bioinformatics tools with deep learning (ESMFold, ESM-1b) and asynchronous pipeline orchestration.

• Updated Sep 1, 2026
• Python

HLA-A*02:01 nine-mer peptide binding prediction from sequence, with grouped validation and fully traceable metrics.

• Updated Aug 16, 2026
• Python

Systems immunology workflow for reconstructing cell–cell communication networks in lupus nephritis using CellChat and single-cell RNA sequencing.

• Updated Jul 25, 2026
• R

TCR-Epitope-MHC Binding Prediction with Metric Learning

• Updated Oct 31, 2025
• Jupyter Notebook

This project analyzes spinal fluid immune cells and tumor DNA to find hidden matches that may explain why some cancers trigger the immune system to mistakenly attack the brain and nerves.

• Updated Jul 6, 2026
• Python

Executable Cell Runtime (ECR) is a modular research framework for exploring how dynamic cellular states, intracellular regulation, cell behaviors, and multicellular interactions can be represented as executable biological systems. The current demo illustrates a simplified antiviral immune response as an initial proof of concept.

• Updated Aug 25, 2026
• Python

Computational pipeline for antigen-specific tolerogenic vaccine design—predicting MHC-II epitopes, scoring tolerance potential, and assembling candidate multi-epitope mRNA constructs (starting with ITP).

• Updated Apr 20, 2026
• Jupyter Notebook

HPV-anchored computational systems-immunology analysis of primary induction, long-term persistence, and heterologous recall in the Fiji HPV systems-serology study.

• Updated Aug 18, 2026
• Python