@susiegriggo.bsky.social
PhD Student @ Flinders University | #bioinformatics #phage #microbiome π¦ π»π§¬ | she/her https://github.com/susiegriggo
Excited to re-share work from
@yoakiyama.bsky.social and Zhidian Zhang on MSA pairformer. (1/4)
Finally, thankyou to @gbouras13.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @beardymcjohnface.bsky.social PrzemysΕaw Decewicz and
@linsalrob.bsky.social for your help on this project π Stay tuned for more on phage annotation as I prepare to submit my PhD (really actually quite soon π³)
Phynteny builds on top of existing annotations. For best results, I recommend using the amazing tools Pharokka and Phold from @gbouras13.bsky.social
and then running your phage through Phynteny
github.com/gbouras13/ph...
github.com/gbouras13/ph...
You can run Phynteny here
github.com/susiegriggo/...
(also available on conda and pypi π οΈ)
The resulting tool, Phynteny, works across a range of phage families and improves the number of phage genes with a known PHROG category by 14%!
30.07.2025 06:08 β π 2 π 0 π¬ 1 π 0
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.
30.07.2025 06:00 β π 2 π 0 π¬ 1 π 0
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!
30.07.2025 06:00 β π 1 π 0 π¬ 1 π 0
π¨Β New preprint π¨
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...
Finally, thank you to @gbouras13.bsky.social @npbhavya.bsky.social @beardymcjohnface.bsky.social @linsalrob.bsky.social and PrzemysΕaw Decewicz for your help on this project π . Stay tuned for more on phage annotation as I prepare to submit my PhD (really actually quite soon π³)
30.07.2025 05:33 β π 0 π 0 π¬ 0 π 0
Phynteny builds on top of existing annotations. For best results, I would recommend using the amazing tools Pharokka and Phold from @gbouras13.bsky.social and then running your phage through Phynteny github.com/gbouras13/ph... github.com/gbouras13/ph...
30.07.2025 05:33 β π 0 π 0 π¬ 1 π 0You can try Phynteny here (also available on conda and pypi π οΈ) github.com/susiegriggo/...
30.07.2025 05:33 β π 0 π 0 π¬ 1 π 0
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 leverage synteny to predict these unknown functions!
30.07.2025 05:33 β π 0 π 0 π¬ 0 π 0
In 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.
π Exciting news! Weβre launching three fully-funded postdoc positions for "New Horizons for Synthetic Phagesβ
Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.
π Read on for details!
#Phage
We (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
22.07.2025 15:06 β π 79 π 39 π¬ 2 π 2
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...
π¨ Last chance to register! π¨
πThe countdown is on for the APG Annual Research Symposium
π₯Get ready for a day of cutting-edge science, inspiring talks, and great connections!
ποΈ Donβt miss out β register now: events.humanitix.com/apg-research...
π£ New preprint alert!
Happy to share the first results from our effort to reannotate Pseudomonas #phage proteins of unknown function, using structural bioinformatics.
π doi.org/10.1101/2025...
Logo for the Sandpiper website
Out 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 π§΅
16.07.2025 21:59 β π 126 π 70 π¬ 7 π 9
Preprint: βStructural modeling reveals viral proteins that manipulate host immune signalingβ
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...
25,715 of the 38,880 PHROGs were folded with a mean pLDDT > 70. Here's a distribution :)
07.07.2025 09:03 β π 3 π 0 π¬ 1 π 0
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've folded a lot of proteins! You can see some of them here @linsalrob.bsky.social @gbouras13.bsky.social
07.07.2025 08:49 β π 13 π 5 π¬ 0 π 0Very honoured and excited to have been awarded an ARC Laureate Fellowship today. Exciting things to come!
#FL25
rms.arc.gov.au/RMS/Report/D...
Our new AI approach for deciphering the virosphere. Led by Mang Shi and Zhao-Rong Li: www.biorxiv.org/content/10.1...
24.06.2025 08:00 β π 19 π 11 π¬ 0 π 2
Presenting 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
22.06.2025 17:05 β π 6 π 1 π¬ 1 π 0
Ruth NUSSINOV (RNA folding), Barbara McClintock (transposons), Tomoko Ohta (neutral theory), Jorja Henikoff (BLOSUM), Christine Orengo (CATH), Janet Thornton (CATH), Julie Thompson (CLUSTAL), Theresa Attwood (PRINTS), Tracy Heath (Bayesian), Bonnie Berger (ARACHNE), Kim Pruitt (RefSeq), Tatiana Tatusova (Entrez), Kira Makarova (COGs), Claire Fraiser (TIGR)
π₯οΈπ§¬βοΈI 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
Journal of Open Source Software: GraphBin-Tk: assembly graph-based metagenomic binning toolkit https://joss.theoj.org/papers/10.21105/joss.07713
30.05.2025 00:00 β π 10 π 6 π¬ 0 π 1
Just a nice reminder! π§ͺπ§¬π₯οΈ I found this GitHub very useful: github.com/cxli233/Frie...
25.05.2025 07:05 β π 38 π 15 π¬ 2 π 0
Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests www.biorxiv.org/content/10.1...
20.05.2025 13:16 β π 88 π 31 π¬ 2 π 1
