Susie Grigson
Postdoc @ DOE JGI Berkeley Lab 🇺🇸 | Former PhD Student @ Flinders University 🇦🇺 | #bioinformatics #phage #microbiome 🦠💻🧬 | she/her
github.com/susiegriggo
- Reposted by Susie GrigsonDeath & Chemotaxis: Bacterial chemotaxis enables collective escape from phage predation biorxiv.org/content/10.64898/20…
- Reposted by Susie GrigsonPhold'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/...
- 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...
- Reposted by Susie Grigson
Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance medrxiv.org/content/10.64898/20… - Reposted by Susie Grigson🦠🧪🧬🚨 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-...
- Reposted by Susie Grigson🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106 • 💻 Github: github.com/Vini2/agtools 📄 Preprint: biorxiv.org/content/10.110…
- Reposted by Susie GrigsonKeeping the naming convention - PholdAPhage - great work Renee github.com/reneegreen81... #ABACBS2025
- Reposted by Susie Grigson
- Reposted by Susie Grigson🚀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 (🧵)
- Reposted by Susie GrigsonExcited 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/...
- Reposted by Susie GrigsonI 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
- Reposted by Susie Grigson🚨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...
- Reposted by Susie Grigson🎉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
- Reposted by Susie GrigsonVery 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.
- Reposted by Susie GrigsonIsolates 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)
- Reposted by Susie GrigsonDear 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)
- Reposted by Susie GrigsonOur quiz night is happening TONIGHT! Remember to get your tickets through the link and we'll see you there!😁
- 💡The APG Quiz Night is back for 2025!💡 Join us on the 3rd of October at The University of Adelaide for a night of trivia, laughs, pizzas, and drinks! 🍕🍺 🎟️Tickets: $5 (ASBMB members FREE entry + chance to win the door prize!) ⚡Only 100 spots available – register now! bit.ly/4p2KSlp
- Reposted by Susie GrigsonDiscovery of phage defense systems through component modularity networks | bioRxiv biorxiv.org/content/10.1101/202…
- Reposted by Susie GrigsonNew 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....
- Reposted by Susie GrigsonExcited 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
- Reposted by Susie Grigsonagtools: a software framework to manipulate assembly graphs biorxiv.org/content/10.1101/202…
- Reposted by Susie Grigson🚨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/...
- Reposted by Susie GrigsonFor 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...
- Reposted by Susie GrigsonPreprint: 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 🧵
- Reposted by Susie GrigsonThree 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
- Reposted by Susie GrigsonNew 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...
- Reposted by Susie GrigsonThird 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
- Reposted by Susie GrigsonNew 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....
- Reposted by Susie Grigson💡The APG Quiz Night is back for 2025!💡 Join us on the 3rd of October at The University of Adelaide for a night of trivia, laughs, pizzas, and drinks! 🍕🍺 🎟️Tickets: $5 (ASBMB members FREE entry + chance to win the door prize!) ⚡Only 100 spots available – register now! bit.ly/4p2KSlp
- Reposted by Susie Grigson
- Thrilled to share our new review just published in Microbiology and Molecular Biology Reviews (@asm.org #MMBR): “Computational Function Prediction of Bacteria and Phage Proteins” with @gbouras13.bsky.social @linsalrob.bsky.social @bedutilh.bsky.social 🔗 journals.asm.org/doi/10.1128/...
- Plus, it's heaps good timing with preprints for our phage annotation tools Phynteny and Phold coming out in the past few weeks! www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
- Finally, a huge thank you to the entire community of developers whose tools and methods made this review possible, you’re the reason this field is moving forward so quickly 🙌
- Reposted by Susie Grigson🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12
- Reposted by Susie GrigsonOnly 2 more days to submit an abstract for ABACBS 2025 in Adelaide! www.abacbs.org/abacbs2025
- Reposted by Susie GrigsonThe notebook uses Pharokka, Phold and @susiegriggo.bsky.social's Phynteny to comprehensively annotate your phage - please also check out the related very recent preprint for Phynteny www.biorxiv.org/content/10.1...
- Reposted by Susie GrigsonStoked 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...
- Reposted by Susie GrigsonProtein Structure Informed Bacteriophage Genome Annotation with Phold biorxiv.org/content/10.1101/202…
- Reposted by Susie GrigsonA novel approach to Caudoviricetes taxonomy utilising whole proteome structure-structure comparison biorxiv.org/content/10.1101/202…
- Reposted by Susie Grigson🚀 I just released agtools – a Python API + CLI for working with assembly graphs! ⚙️ Convert, filter, clean, visualise & more. 📦 Install with pip or conda 📖 Docs & code: github.com/Vini2/agtools ⭐ Feedback, contributions, and stars are welcome! #bioinformatics #python #genomics #opensource
- 🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...
- Phage genomes follow specific ordering patterns (synteny), where gene functions are often related to their order. Given that 60-80% of phage genes remain functionally uncharacterised, it seemed like a fantastic opportunity to use AI to predict phage protein functions!
- So... I built a Transformer model that uses synteny to annotate phage genomes. This model is trained on over 280,000 genes from the PhageScope database and uses ESM2 protein language model embeddings to predict the PHROG category of unknown genes.
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View full threadFinally, thankyou to @gbouras13.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @beardymcjohnface.bsky.social Przemysław Decewicz and @linsalrob.bsky.social for your help on this project 🙌 Stay tuned for more on phage annotation as I prepare to submit my PhD (really actually quite soon 😳)
- Reposted by Susie GrigsonIn 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known. Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.
- Reposted by Susie Grigson🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages” Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide. 👇 Read on for details! #Phage
- Reposted by Susie GrigsonWe (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt
- Reposted by Susie GrigsonFold first, ask later: structure-informed function annotation of Pseudomonas phage proteins Structural predictions to improve #phage genome annotation! @hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social www.biorxiv.org/content/10.1...
- Reposted by Susie Grigson🚨 Last chance to register! 🚨 🎉The countdown is on for the APG Annual Research Symposium 💥Get ready for a day of cutting-edge science, inspiring talks, and great connections! 🗓️ Don’t miss out — register now: events.humanitix.com/apg-research...
- Reposted by Susie Grigson📣 New preprint alert! Happy to share the first results from our effort to reannotate Pseudomonas #phage proteins of unknown function, using structural bioinformatics. 📄 doi.org/10.1101/2025...
- Reposted by Susie GrigsonOut in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
- Reposted by Susie GrigsonPreprint: “Structural modeling reveals viral proteins that manipulate host immune signaling” Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules Congrats Nitzan Tal! www.biorxiv.org/content/10.1...
- Reposted by Susie GrigsonPhD opportunities at @flindersuniversity.bsky.social in Adelaide, Australia's most liveable city, to study genetics in #phage We will also have genetics #postdoc positions too! #microsky #phagesky www.linkedin.com/pulse/phd-pr...
- We've folded a lot of proteins! You can see some of them here @linsalrob.bsky.social @gbouras13.bsky.social
- We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB. 💻🧬 #phagesky linsalrob.github.io/PHROG_struct...
- Reposted by Susie GrigsonVery honoured and excited to have been awarded an ARC Laureate Fellowship today. Exciting things to come! #FL25 rms.arc.gov.au/RMS/Report/D...
- Reposted by Susie GrigsonOur new AI approach for deciphering the virosphere. Led by Mang Shi and Zhao-Rong Li: www.biorxiv.org/content/10.1...
- Reposted by Susie GrigsonPresenting our latest research on Achromobacter Phage Therapy in individuals with Cystic Fibrosis! Come check out my poster and chat if you're interested in innovative approaches to tackling multidrug-resistant infections. #PhageTherapy #CysticFibrosis #Microbiology #ASM
- Reposted by Susie Grigson🖥️🧬♀️I overheard a conversation guilty of youth and arrogance, saying there were not many women in bioinformatics besides Margaret Dayhoff (PAM). That is not only stupid but also wrong. Since my foundation years bioinformatics was always very female: #WomenInBioinformatics #WomenInStem
