CMVividly

Welcome! I’m Damon May, a lead author of a preprint describing ECOclusters: groups of T-cell receptors (TCRs) that represent humanity’s collective T-cell responses to viruses, bacteria, and other prevalent immune exposures. Conceptually, and in several cases verifiably, each ECOcluster represents the response to a single immune exposure. Its TCRs are more likely to be sequenced in people who’ve had the exposure. For more background, see About.

The CMV ECOcluster (download here) is a sensitive, specific, quantitative biomarker of response to Cytomegalovirus (CMV). Each of its 52,447 TCRs is associated with the Human Leukocyte Antigen (HLA) allele that presents the CMV peptide it binds. Here, I’m exploring the CMV ECOcluster to help the AIRR community and others get the most from this new resource. I’ll post updates here and on my LinkedIn. All the code is in the GitHub repo, easily runnable by anyone.

So, those 52,447 TCRs: let’s see ’em, vividly.

Posts (newest first)

Individual HLA-COclusters as CMV biomarkers

The different HLA-COclusters in the CMV ECOcluster range widely in diagnostic value. Let’s see if we can figure out why.

Jul 25, 2026

CMV ECOcluster basics

Download the CMV ECOcluster (using code from this repo), explain the columns. Break it down by HLA-COcluster, HLA allele and HLA class. Look at HLA alleles with more than one HLA-COcluster, and at TCR generation probability.

Jul 24, 2026

--- listing: contents: posts/*/index.qmd sort: "date desc" type: default categories: false sort-ui: false filter-ui: false page-layout: full number-sections: False format: html: body-classes: home-posts-sidebar include-in-header: text: | <script> document.addEventListener("DOMContentLoaded", () => { const sidebar = document.querySelector("#quarto-margin-sidebar"); if (!sidebar || document.getElementById("posts-sidebar-menu")) return; const links = Array.from(document.querySelectorAll("#listing-listing .listing-title a")) .map((link) => ({ href: link.getAttribute("href"), title: link.textContent.trim(), })) .filter((item) => item.href && item.title); if (!links.length) return; const menu = document.createElement("nav"); menu.id = "posts-sidebar-menu"; menu.className = "posts-sidebar-menu"; menu.setAttribute("aria-label", "Posts"); const heading = document.createElement("h5"); heading.textContent = "Posts"; menu.appendChild(heading); const list = document.createElement("ul"); links.forEach(({ href, title }) => { const item = document.createElement("li"); const anchor = document.createElement("a"); anchor.href = href; anchor.textContent = title; item.appendChild(anchor); list.appendChild(item); }); menu.appendChild(list); sidebar.appendChild(menu); }); </script> --- <img src="resources/cmvividly_logo.png" alt="CMVividly" style="display: block; margin: 0 auto" /> Welcome! I'm [Damon May](https://www.linkedin.com/in/damonhmay){target="_blank" rel="noopener noreferrer"}, a lead author of a [preprint](https://www.biorxiv.org/content/10.1101/2024.03.26.583354){target="_blank" rel="noopener noreferrer"} describing **ECOclusters**: groups of T-cell receptors (TCRs) that represent humanity's collective T-cell responses to viruses, bacteria, and other prevalent immune exposures. Conceptually, and in several cases verifiably, each ECOcluster represents the response to a single immune exposure. Its TCRs are more likely to be sequenced in people who've had the exposure. For more background, see [About](about.html). The **CMV ECOcluster** ([download here](https://www.biorxiv.org/content/10.1101/2024.03.26.583354v3.supplementary-material){target="_blank" rel="noopener noreferrer"}) is a sensitive, specific, quantitative biomarker of response to Cytomegalovirus (CMV). Each of its 52,447 TCRs is associated with the Human Leukocyte Antigen (HLA) allele that presents the CMV peptide it binds. Here, I'm exploring the CMV ECOcluster to help [the AIRR community](https://www.antibodysociety.org/the-airr-community/){target="_blank" rel="noopener noreferrer"} and others get the most from this new resource. I'll post updates here and on my [LinkedIn](https://www.linkedin.com/in/damonhmay){target="_blank" rel="noopener noreferrer"}. All the code is in [the GitHub repo](https://github.com/dhmay/CMVividly){target="_blank" rel="noopener noreferrer"}, easily runnable by anyone. So, those 52,447 TCRs: let's **see 'em, vividly**. #### Posts (newest first)