Susie Grigson

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...

AlphaFold Database welcomes community datasets Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.

This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.

Explore the new datasets in the AlphaFold Database.

www.ebi.ac.uk/about/news/u...

Death & Chemotaxis: Bacterial chemotaxis enables collective escape from phage predation https://www.biorxiv.org/content/10.64898/2026.01.28.702367v1

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance https://www.medrxiv.org/content/10.64898/2025.12.28.25342520v1

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106
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💻 Github: github.com/Vini2/agtools
📄 Preprint: biorxiv.org/content/10.110…

Keeping the naming convention - PholdAPhage - great work Renee github.com/reneegreen81... #ABACBS2025

#ABACBS2025

🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)

Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

Excited to share our new review article on Viral Dark Matter led by PhD student @kosmopoulos.bsky.social. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology. pubs.acs.org/doi/10.1021/...

A newpaper clipping from the Adelaide Advertiser showing high school students discovering new phages.

I worked with the Australian Science & Maths School to design new Year 10–12 curricula: phage hunting, of course! The students discovered & sequenced a new jumbo phage, and will present their work at @abacbs.bsky.social in Adelaide next week. Proud of these young scientists!

#phage #ABACBS2025

Congratulations Dr. Papudeshi! 🎉

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

🎉Wrap up 2025 with the APG at Proteins in the Pub!

⚡Lightning talks, networking & good vibes.

📅Nov 19 | 6 PM | Seven Stars Hotel
🎟️Free entry + snacks | $100 prize for best talk

👉Register: events.humanitix.com/proteins-in-...
👉Lightning Talk Registrations: shorturl.at/xMP57

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Isolates or MAGs, we're looking for the worst-annotated genomes, i.e. high fraction of CDS w/o any functional annotation. Any public/shareable bacterial genome is highly welcome!

Please help us to further improve the annotation of bacterial genomes.

Please RT & share

(2/2)

Dear community, Bakta needs your help!

To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)

(1/2)

Our quiz night is happening TONIGHT! Remember to get your tickets through the link and we'll see you there!😁

Discovery of phage defense systems through component modularity networks Phage defense systems in bacteria exhibit high degrees of modularity, with sensing, signal transmission, and effector enzymes frequently being exchanged among phage defense gene clusters. In this study, we capitalized on this modularity to discover phage defense systems by searching for defense-associated modules in new gene contexts. This approach revealed a large and interconnected network of modular components distributed across diverse gene clusters. From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system. Collectively, we demonstrate that leveraging the modular architecture of phage defense systems is an effective approach to their discovery. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, 101003229 Netherlands Organisation for Scientific Research, VI.C.192.027, OCENW.XS23.1.006 Koningin Wilhelmina Fonds, 15602

Discovery of phage defense systems through component modularity networks | bioRxiv https://www.biorxiv.org/content/10.1101/2025.09.30.679545v1

Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬

Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social

www.embopress.org/doi/full/10....

agtools: a software framework to manipulate assembly graphs Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n)

www.biorxiv.org/content/10.1...

#Bioinformatics #genomics #assembly #assemblygraphs #software

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

Reprogramming resistance: phage-antibiotic synergy targets efflux systems in ESKAPEE pathogens | mBio Antimicrobial resistance (AMR) is one of the greatest threats to global health. If unaddressed, it is projected to cause over 39 million cumulative deaths globally by 2050 (1). While resistance is a b...

🚨New Review Out🚨
We explore how phage-antibiotic synergy can dismantle efflux-driven resistance in multidrug-resistant ESKAPEE pathogens. By reprogramming bacterial defences, phages offer a precision strategy to restore antibiotic efficacy.

journals.asm.org/doi/10.1128/...

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵

Three postdoc positions are now open for applications! Live and work on Kaurna land (Adelaide) in sunny South Australia. We have beach views, wineries, kangaroos, and koalas.

Develop new synthetic biology to engineer and understand #phage, and computational tools for #phage and #microbiome analysis

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

Protein Structural Phylogenetics Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his

Third Era of Phylogenetics!

1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️

Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics

academic.oup.com/gbe/article/...

#structuralbiology #evolution #AlphaFold #SciSky

Examples of protein annotations across functional classification schemes. Yellow: hierarchical classification schemes, red: orthologous/homologous groups, and blue: methods using protein domain information. Protein structures were generated using the ColabFold Alphafold MMseqs2 interactive notebook (version 1.5.2) (57) and visualized using ChimeraX (58). (A) Functional labels associated with the glycogen synthase protein in Escherichia coli (UniprotKB P0A6U8). (B) Functional labels associated with Kehishuvirus sp. tikala major capsid protein (NCBI WEU69752.1).

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes

by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob

#phagesky #microsky

journals.asm.org/doi/epub/10....