I carry out research into the evolution of viruses and their impact on host species. Open science.https://bsky.app/profile/robjgifford.bsky.socialhttps://bsky.app/profile/robjgifford.bsky.social/post/3mfgkb5qwxk24Most bioinformatics tools put software first and data second. GLUE does the opposite. In this blog post (link in reply), I provide a plain-language explanation of its data-oriented philosophy, and why that matters for reproducible virology. https://gluetools.substack.com/p/data-oriented-virology-glues-philosophy22 Feb 2026 06:49 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mfgkb5qwxk24https://bsky.app/profile/robjgifford.bsky.social/post/3melm2cvlt22jGenomics has a data rot problem. Pipelines change. Alignments are regenerated. Assumptions disappear. Context is lost. This post explains why GLUE was built around data immutability and durable scientific objects. https://gluetools.substack.com/p/data-immutability-and-longevity-in11 Feb 2026 13:39 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3melm2cvlt22jhttps://bsky.app/profile/robjgifford.bsky.social/post/3me4oervxhc2rComparative genomics generates results fast - but preserving the context needed to understand them over time is much harder. I’ve written a perspective on GLUE as a long-lived, data-oriented knowledge base: projects as persistent scientific objects rather than disposable pipelines. sl1nk.com/Y0O4H https://gluetools.substack.com/p/a-long-lived-data-oriented-knowledge05 Feb 2026 15:11 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3me4oervxhc2rhttps://bsky.app/profile/robjgifford.bsky.social/post/3mdsnuafw5s2nStudying immune gene evolution is rarely about a lack of data, it’s about keeping data, biology, and interpretation aligned as everything changes. New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study. https://gluetools.substack.com/p/glue-resources-for-gene-families01 Feb 2026 15:35 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mdsnuafw5s2nhttps://bsky.app/profile/robjgifford.bsky.social/post/3mdum5q6zbc2vRecovery of viral RNA from centuries old human tissue is genuinely exciting. This changes the horizons for recovery of ancient virus genomes. [contains quote post or other embedded content]02 Feb 2026 10:10 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mdum5q6zbc2vhttps://bsky.app/profile/robjgifford.bsky.social/post/3mdsnuafw5s2nStudying immune gene evolution is rarely about a lack of data, it’s about keeping data, biology, and interpretation aligned as everything changes. New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study. https://gluetools.substack.com/p/glue-resources-for-gene-families01 Feb 2026 15:35 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mdsnuafw5s2nhttps://bsky.app/profile/robjgifford.bsky.social/post/3mddv56gfsc2mI’ve just published a new Substack post explaining how MLCA genotyping works in GLUE, and how to run it yourself locally using Docker. It covers the evolutionary logic behind MLCA and the practical workflow for using it. https://gluetools.substack.com/p/how-mlca-genotyping-works-and-how26 Jan 2026 18:35 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mddv56gfsc2mhttps://bsky.app/profile/robjgifford.bsky.social/post/3mcruoriu3c2jAs virus discovery accelerates, integrating new sequences meaningfully is becoming a central challenge. Flavivirus-GLUE provides an open framework for multi-scale comparative genomic analyses of flaviviruses. https://gluetools.substack.com/p/flavivirus-glue19 Jan 2026 14:39 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mcruoriu3c2jhttps://bsky.app/profile/robjgifford.bsky.social/post/3mc5uhpbo522qHCV-GLUE is best known as a web-based tool for HCV genotyping and drug resistance analysis. Less well known is that the same analysis can be run entirely offline and integrated into pipelines. I’ve written a short guide on running HCV-GLUE offline using Docker and GLUE scripts. shorturl.at/bvm3d https://shorturl.at/bvm3d11 Jan 2026 15:42 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mc5uhpbo522qhttps://bsky.app/profile/robjgifford.bsky.social/post/3mc5uhpbo522qHCV-GLUE is best known as a web-based tool for HCV genotyping and drug resistance analysis. Less well known is that the same analysis can be run entirely offline and integrated into pipelines. I’ve written a short guide on running HCV-GLUE offline using Docker and GLUE scripts. shorturl.at/bvm3d https://shorturl.at/bvm3d11 Jan 2026 15:42 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mc5uhpbo522qhttps://bsky.app/profile/robjgifford.bsky.social/post/3mbohsa7hws2oVirus taxonomy increasingly rests on phylogenetic hypotheses, but the trees, alignments, and assumptions behind them are often ephemeral. This post explores what it might look like to make that phylogenetic basis transparent and reproducible, using retroviruses as a case study. shorturl.at/s9aft https://shorturl.at/s9aft05 Jan 2026 12:45 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3mbohsa7hws2ohttps://bsky.app/profile/robjgifford.bsky.social/post/3m7h4tgqk522jThe translational potential of bat immune traits is wildly overstated. These aren’t modular switches we can port into humans; They’re parts of tightly integrated systems that don’t travel. https://www.sciencedirect.com/science/article/pii/S147149062400007308 Dec 2025 03:50 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m7h4tgqk522jhttps://bsky.app/profile/robjgifford.bsky.social/post/3m76apfsrqc24Gardening in the Viral Genome Wilderness: Why virus genomics needs structure, not pipelines. https://gluetools.substack.com/p/the-sequence-data-problem-and-the04 Dec 2025 15:06 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m76apfsrqc24https://bsky.app/profile/robjgifford.bsky.social/post/3m765sa6s5c2zStellenbosch University Botanical Garden04 Dec 2025 14:13 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m765sa6s5c2zhttps://bsky.app/profile/robjgifford.bsky.social/post/3m765dz5ytc2tThis article by Linda Geddes reproduces every structural flaw I described in my recent Substack essay. Every narrative device, every logical inconsistency, and every evidentiary shortcut that sustains the ‘bat specialness’ story. https://www.gavi.org/vaccineswork/bat-paradox-what-natures-night-flyers-could-teach-us-about-pandemics-and-ourselves04 Dec 2025 14:05 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m765dz5ytc2thttps://bsky.app/profile/robjgifford.bsky.social/post/3m73jhk7oo22yMost viral workflows are fragile pipelines. GLUE turns them into structured, shareable projects: curated sequences, alignments, features, phylogenies, metadata & scripts all in one reproducible environment. https://gluetools.substack.com/p/glue-a-flexible-software-system-for03 Dec 2025 13:04 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m73jhk7oo22yhttps://bsky.app/profile/robjgifford.bsky.social/post/3m725yknjws27Introducing the GLUE Genomics Blog: https://gluetools.substack.com/p/welcome-to-the-glue-blog03 Dec 2025 00:06 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m725yknjws27https://bsky.app/profile/robjgifford.bsky.social/post/3m6ho53xpg227"The hyperreal bat: more vivid, more coherent, and more narratively satisfying than any bat in nature." Why does the idea of bats as special viral reservoirs endure? New Substack post: https://robertjgifford.substack.com/p/bats-and-viruses-rumour-intrigue25 Nov 2025 15:35 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m6ho53xpg227https://bsky.app/profile/robjgifford.bsky.social/post/3m56tjkq6ds2qGrounded and thought-provoking reflections on LLMs. [contains quote post or other embedded content]09 Nov 2025 09:52 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3m56tjkq6ds2qhttps://bsky.app/profile/robjgifford.bsky.social/post/3lm56d2ekwk25Macduff, Scotland06 Apr 2025 09:51 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3lm56d2ekwk25https://bsky.app/profile/robjgifford.bsky.social/post/3llo6ma7ou22gThe Ghost in the Culture Flask: Did Cold War virologists accidentally alter the evolution of a ubiquitous virus? shorturl.at/HSke331 Mar 2025 10:47 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3llo6ma7ou22ghttps://bsky.app/profile/robjgifford.bsky.social/post/3llo6ma7ou22gThe Ghost in the Culture Flask: Did Cold War virologists accidentally alter the evolution of a ubiquitous virus? shorturl.at/HSke331 Mar 2025 10:47 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3llo6ma7ou22ghttps://bsky.app/profile/robjgifford.bsky.social/post/3lftzlrwscs2uDiscover GLUE: a versatile framework for virus genomics and beyond. Explore adaptable tools, resources, and projects developed in our lab using GLUE: https://github.com/giffordlabcvr/gluetools/wiki/Gifford-Lab-GLUE-Projects #Genomics #Bioinformatics #OpenScience16 Jan 2025 10:02 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3lftzlrwscs2uhttps://bsky.app/profile/robjgifford.bsky.social/post/3lfnfyholhc2zI've been comparing annual publication trends across different viruses The vast difference in the number of publications for SARS-CoV-2 compared to other viruses like Ebola, Dengue, and Influenza A is striking.13 Jan 2025 18:55 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3lfnfyholhc2zhttps://bsky.app/profile/robjgifford.bsky.social/post/3lfhitdk62c24Personally, I have a lot of sympathy for Jens Kuhn. He's dealing with a fundamental and increasingly pressing issue in virology, one that might otherwise be neglected without the intense dedication of someone so earnestly committed to the cause. [contains quote post or other embedded content]11 Jan 2025 10:30 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3lfhitdk62c24https://bsky.app/profile/robjgifford.bsky.social/post/3lfcthwssgk2tIntroducing HMPV-GLUE: a comprehensive, open-source resource for human metapneumovirus (HMPV) research. With the recent rise in HMPV cases in China, this tool offers timely support for the scientific community. https://github.com/giffordlabcvr/HMPV-GLUE09 Jan 2025 13:57 +0000at://did:plc:m3qhtafpnhttprtwtkblpmr4/app.bsky.feed.post/3lfcthwssgk2t