It’s official! I am a doctor 🎓

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

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...

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...

For any hoping to submit workshop proposals for ABACBS25/BiocAsia, EOIs close today. We understand how busy everyone is, so if your EOI is a day or so late, it'll still be considered. We've already had some fantastic proposals too, so it looks like being a really beneficial couple of days.

🧬 🖥️

🌟 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

Synteny-aware functional annotation of bacteriophage genomes with Phynteny Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

🚨 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...

Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins Phages, the viruses of bacteria, harbor an incredibly diverse repertoire of proteins capable of manipulating their bacterial hosts, inspiring many medical and biotechnological applications. However, t...

Fold 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...

ABACBS 2025 Conference Adelaide, South Australia. Nov. 24-

🚨 Reminder: Key #ABACBS2025 deadlines are fast approaching in the next few weeks! 🚨
📝 Abstract submissions
🎤 EOI to host a Workshop
🏆 Award nominations

All now open! Full details + dates here 👉 www.abacbs.org/abacbs2025

#Bioinformatics #ABACBS #COMBINE2025

Expressions of Interest Paid Internship in Indigenous Genomics

The 2025 South Australian Internship in Indigenous Genomics is open 🎉

EOI for Indigenous Australian students, researchers & professionals for a 12- week paid internship 👇

sahmri.org.au/careers-and-...

#GenomicsEquality #IndigenizeScience #IndigenousGenomics

PhD Project: Discovering Novel Mechanisms of Phage Genome Evolution We are looking for an awesome PhD student to join our research team to investigate how bacteriophages (phages) generate targeted mutations that enable them to evolve and infect new bacterial hosts. Yo...

PhD 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 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...

ABACBS 2025 Conference Adelaide, South Australia. Nov. 24-

Finally joined Bluesky! Follow along to stay connected with ABACBS. Keep an eye out in the coming days, we’ll be releasing more details for 2025 conference, including opening abstract submissions and announcing invited speakers!

www.abacbs.org/abacbs2025

Bifidobacteria support optimal infant vaccine responses - Nature Neonatal antibiotic use is shown to reduce immune response to infant vaccines, accompanied by reduced abundance of Bifidobacteria in the gut microbiota, with experiments in mice indicating that probio...

Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...

🎥 Supercomputing vs Superbugs 💻🦠
Antibiotic resistance is a growing threat, but Sphae—a genomic toolkit developed with help from Pawsey Supercomputing—helps scientists discover new bacteriophage therapies. Learn how this powerful tool is transforming health: hubs.ly/Q03c_VC70
#PhageTherapy #Setonix

Excited to see our tool, Sphae, gaining attention! #PhageTherapy #Bioinformatics #Sphae #phagesky

GitHub - shandley/awesome-virome: A listing of software, tools and databases useful for virome analysis A listing of software, tools and databases useful for virome analysis - shandley/awesome-virome

Check out this list of awesome #virome tools and be sure to add yours!

github.com/shandley/awe...

#phagesky #microsky

Helping viruses deliver a knockout blow to killer bacterial infections In the face of rising concerns about antibiotic resistant infections, an international group of microbial experts have launched a powerful and flexible free online genomic toolkit for more rapid devel...

Helping viruses deliver a knockout blow to killer bacterial infections!

Great work by @npbhavya.bsky.social

phys.org/news/2025-02...

GitHub - linsalrob/sphae: Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing! - linsalrob/sphae

New paper out!

I'm excited to share our latest work in Bioinformatics Advances! We've developed Sphae, a bioinformatics pipeline to evaluate phage therapeutic potential. doi.org/10.1093/bioa...

Try it here: github.com/linsalrob/sp...

#PhageTherapy #AMR #Bioinformatics #phagesky

Check out Nora's amazing postdoc project on phage species coexistence!

Sphae workflow can be run on any bacteriophage dataset, host species will not impact the workflow.

Great, saves me time 😀

Will give this a try

Interesting we have come across only a few cases of the miss assembling so I didn’t bother to add an option to change the assembler.

Like George mentioned, I just fix the assembly by running a different assembler and run it through sphae again for annotation.

GitHub - linsalrob/sphae: Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing! - linsalrob/sphae

github.com/linsalrob/sp...

Trying to purify and sequence #phage for phage therapy?

Try #sphae a new approach to identify if your phage could be useful for treatment

#phagesky

Honoured to have been voted as President-elect of the International Society for the Viruses of Microbes (ISVM) and excited to work with the Executive Board over the next few years

#phagesky

phagesociety.org

🎉🎉

The final talk at the #combine24 protein structure session on predicting the effect of mutations on protein structures by Emily Zhou

@gbouras13.bsky.social presenting his tool PHOLD to use protein structure information for assigning a function to unknown proteins #COMBINE24