Don't forget, we'll be live later for our Variant Effects Seminar. Today's talk is with @sarahgurev.bsky.social. Find your time zone and join us at 4.00 pm (UTC): www.varianteffect.org/seminar-seri...

NEW stuff for Monday morning! Get your new stuff here! Pandemic risk is going up. Can we bring it back down? Probably not - unless we radically reimagine our relationship with nature, food, and each other. First preprint led by the brilliant @torrelavelle.bsky.social: www.medrxiv.org/content/10.6...

🚨 Ever wonder why some viral reassortants establish and spread while others disappear? Us too! Led by @ricardoriveroh.bsky.social, we studied drivers of viral reassortment across hantaviruses and found that it varies dramatically among lineages (1/3) Preprint: doi.org/10.64898/202...

1/7 New #ecology preprint out. We’ve spent half a century searching for Arenavirus and Hantavirus reservoirs, but it turns out global surveillance is essentially just us looking under the nearest streetlight. It is decoupled from actual host biodiversity.🧵 doi.org/10.64898/202...

🔥Preprint fresh off the press🔥 Hello Bluesky! I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social. It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵

Most benchmark papers are boring but this is a masterpiece. Authors present a comprehensive breakdown of different inference strategies on variant effect prediction (VEP) in viruses. There were two surprising results that IMO deserve more attention🧵

Sarah Gurev@sarahgurev.bsky.social · 12mo ago

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...

This was fun work and a remarkable effort across the computational and wet-lab teams! Strategies for in-silico filtering and ranking of antibody designs have been under-discussed in the literature, e.g. in most technical reports on antibody design that I've seen. Let's talk about these here! [1/n]

AI x Bio Discovery@aixbiobot.bsky.social · 7mo ago

Origin-1: a generative AI platform for de novo antibody design against novel epitopes [new] GenAI designs novel Ab targeting. It uses structure, sequence, & co-folding for binding.

We’ve updated the EVEREST benchmark to include real-world viral evolution! www.biorxiv.org/content/10.1... Co-led by Noor Youssef and me, along with co-authors Navami Jain, Aarushi Mehrotra, Sarrah Leung, Abigail Jackson, @deboramarks.bsky.social, and with @cepi.net @futurehousesf.bsky.social!

Sarah Gurev@sarahgurev.bsky.social · 12mo ago

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

The fundamental problem with GISAID is this - data on the platform are neither open, nor FAIR. Such data - key for combating infectious diseases - are, by a large margin, paid for by taxpayers and hence must be openly available to all. With GISAID, they are not. www.science.org/content/arti...

Fresh conflicts erupt around giant database for flu and COVID-19 sequences

Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic

science.org

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon. 🌐 evedesign.bio

Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org 🧬Code and notebooks will be released by the end of this week. 🎧Golden- Kpop Demon Hunters

Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome. A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants. 1/2

In new study led by @ckikawa.bsky.social, we provide near real-time data on human neutralizing antibody landscape to influenza by measuring ~26,000 titers to >100 recent viral strains Data can inform vaccine selection & evolutionary/epidemiological modeling www.biorxiv.org/content/10.1...

Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025

The hemagglutinin of human influenza virus evolves rapidly to erode neutralizing antibody immunity. Twice per year, new vaccine strains are selected with the goal of providing maximum protection again...

biorxiv.org

There’s been a bunch of new approaches looking at deep viral evolutionary history. We’ve put together a mini review highlighting some recent advancements in structural phylogenetics and time-dependent rate models and what they could do for the field 🦠 🔗 journals.asm.org/doi/full/10....

Recent advances in the inference of deep viral evolutionary history | Journal of Virology

Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourishing field of genomic epidemiology. This, in part, reflects the ability of viruses, particularly those with RNA genomes, to evolve at rates much greater than their cellular counterparts (1). The rapid rate at which viruses evolve and accumulate mutations enables evolutionary signals to be identified through comparative genomics at short timescales relevant for outbreak investigation and response. The integration of phylogenetics and epidemiology, known as phylodynamics, has become a vital tool in response to numerous viral outbreaks, epidemics, and pandemics, including Ebola (2), Zika (3), and, more recently, COVID-19 (4) and mpox (5).

journals.asm.org

Excited to share our new preprint co-led by @jnoms.bsky.social! Here we reveal an exceptional diversity of viral 2H phosphodiesterases (PDEs) that enable immune evasion by selectively degrading oligonucleotide-based messengers. This 2H PDE fold has evolved striking substrate breath & specificity.

Divergent viral phosphodiesterases for immune signaling evasion

Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase...

biorxiv.org

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

biorxiv.org

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Scaling down protein language modeling with MSA Pairformer

Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

biorxiv.org

Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...

Pathoplexus | Pathoplexus July Update

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9

End-to-end differentiable homology search for protein fitness prediction. @yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social arxiv.org/abs/2506.089...

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!