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Feargal Ryan

@feargalr.bsky.social
665 followers 440 following 74 posts

Head, computational multi-omics at Flinders University. Sci-fi, history and video games nerd 🤓👾

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Feargal Ryan @feargalr.bsky.social · 15/06/2026
That’s the plan! I just need to find some time 😆 right now I just wanted it up online so it’s easier to share
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Feargal Ryan @feargalr.bsky.social · 15/06/2026
I’ve been maintaining a list of shotgun #metagenomics tools and resources which I got Claude to turn into a GitHub repo. It has 300+ entries. Please share and tell me if I’ve missed anything! github.com/feargalr/Met... #microbiota #bioinformatics #microbiome #genomics
github.com
GitHub - feargalr/Metagenomics-tools-atlas: An inventory of tools and resources for short-read shotgun metagenomics.
An inventory of tools and resources for short-read shotgun metagenomics. - feargalr/Metagenomics-tools-atlas
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Feargal Ryan @feargalr.bsky.social · 11/06/2026
Try out some of the tutorials on the site and lemme know if you run into any issues!
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Feargal Ryan @feargalr.bsky.social · 11/06/2026
It converts everything to NCBI taxonomy under the hood so it shouldn't really matter too much. It tends to work best with human associated stuff just because thats what most of there reference DBs cover.
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Feargal Ryan @feargalr.bsky.social · 11/06/2026
Our database includes sets from BugSigDB, GMRepoV2, gutMGene, mBodyMap, MiMeDB and BacDive and some manually curated from the literature. These capture disease signatures, body-site associations, microbe–metabolite links and microbial traits. You can also define custom sets.
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Feargal Ryan @feargalr.bsky.social · 11/06/2026
Our original version focused on the cohort level, identifying microbiome changes with more precision than “dysbiosis”. Now, ssTaxSEA lets you ask which individual samples/patients carry those signatures. See the heat plot below for an example #metagenomics #microbiome
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Feargal Ryan @feargalr.bsky.social · 11/06/2026
TaxSEA v1.4 is now available in the latest Bioconductor release. This adds single-sample TaxSEA (ssTaxSEA), extending enrichment analysis to individual #microbiome samples. feargalr.github.io/TaxSEA/ Examples 👇 #metagenomics #Bioconductor #microbiota #microbiology
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John F. Cryan @jfcryan.bsky.social · 09/04/2026
Pesticides may wreak havoc on the gut microbiome Disruption of intestinal ecosystem could contribute to diabetes & other health issues, scientists say I enjoyed discussing our research on the impact of pesticides on the microbiome with Sanket Jain for @science.org www.science.org/content/arti...
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abacbs.bsky.social @abacbs.bsky.social · 09/04/2026
Very interesting read. www.asimov.press/p/bioinforma... (Thanks to @torstenseemann.bsky.social for sharing over on the #ABACBS slack)
asimov.press
A Brief History of Bioinformatics Software
How computer scientists on the fringes of biology made sense of sequencing data.
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Dr Monique Ryan @mon4kooyong.bsky.social · 12/03/2026
Join my campaign to properly fund medical research in Australia 🔬 www.moniqueryan.com.au/medical_rese...
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Feargal Ryan @feargalr.bsky.social · 10/03/2026
Well done Anna. I hope the weather wasn’t too bad for her. Not sure how the South Australians would cope 😂
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Feargal Ryan @feargalr.bsky.social · 02/03/2026
I had hoped there’d be a mention or update on the timeline in the tracker newsletter today but nothing…
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abacbs.bsky.social @abacbs.bsky.social · 02/03/2026
We are delighted to announce that #ABACBS2026 will be held at RMIT, Melbourne CBD campus from 16th to 20th November 2026. Big thanks to A/Prof. Sonika Tyagi and team for leading this years organising! More details and official conference launch to follow! #bioinformatics @combine1.bsky.social
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Andrew Baillie @andrewbaillie.bsky.social · 27/02/2026
If anyone waiting for NHMRC to announce investigator grants can tolerate a LOTR joke
"You want me to apply for a fellowship? After what happened to Boromir?"
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Zamin Iqbal @zaminiqbal.bsky.social · 25/02/2026
@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n
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Tatiane Yanes @tatyanes.bsky.social · 27/02/2026
#nhmrc Investigator grant anticipated outcomes Feb 202… Also 2pm Friday 27th Feb….waiting….
media.tenor.com
a man wearing a suit and tie is standing in a field of yellow flowers
ALT: a man wearing a suit and tie is standing in a field of yellow flowers
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Feargal Ryan @feargalr.bsky.social · 27/02/2026
So it’s not just me then 😐
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 26/01/2026
▶️ Spotify: open.spotify.com/show/1f4lBWv... ▶️ Apple Podcasts: podcasts.apple.com/us/podcast/m... ▶️ Amazon Music: music.amazon.com/podcasts/81c... ▶️ Youtube Podcasts: www.youtube.com/playlist?lis...
open.spotify.com
Episode 1 - Jack Gilbert: "We are living in a microbial world"
Spotify video
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Feargal Ryan @feargalr.bsky.social · 14/01/2026
New paper out. Great collab with Hannah, Courtney & team bringing multi-omics into supportive care. Faecal and saliva samples show promise for predicting chemo-brain, a common side effect that deserves way more attention. #MultiOmics #SupportiveCare #Oncology www.sciencedirect.com/science/arti...
sciencedirect.com
Pre-treatment Gut Microbiome and Salivary Metabolome Signatures Associate with Chemotherapy-Induced Cognitive Decline in Women with Breast Cancer: A Prospective Pilot Study
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Vijini Mallawaarachchi @vijinim.bsky.social · 02/12/2025
🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n) #bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly
github.com
GitHub - metagentools/graphbin-visualise-wasm-app: GraphBin Visualise WebAssembly App
GraphBin Visualise WebAssembly App. Contribute to metagentools/graphbin-visualise-wasm-app development by creating an account on GitHub.
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Feargal Ryan @feargalr.bsky.social · 01/12/2025
Glad you enjoyed it 😁
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Feargal Ryan @feargalr.bsky.social · 28/11/2025
That’s a wrap! Huge thank you to everyone who joined us for #ABACBS2025 & a big shout-out to the Adelaide bioinfo community who worked their butts off. Couldn’t have asked for a better crew or a better venue than Adelaide Oval. @wessidepraxis.bsky.social @linsalrob.bsky.social
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Feargal Ryan @feargalr.bsky.social · 26/11/2025
What an amazing crew!!! #ABACBS2025
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Feargal Ryan @feargalr.bsky.social · 25/11/2025
I love all Aliens but yeah some are better than others 😅😂
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Feargal Ryan @feargalr.bsky.social · 25/11/2025
Alien Ressurection fan? 👀
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Monika Mohenska @mmohenska.bsky.social · 23/11/2025
SPECTACULAR first day for #ABACBS2025
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Alistair Forrest @alforrest.bsky.social · 23/11/2025
Heading to Radelaide for #ABACBS2025 . Looking forward to catch up with old friends and nerd out on bioinformatics! Checkout PhD student Peiwen Liu's poster on connectomeDB2025 (Quality matters!) connectomeDB.org
connectomedb.org
– ConnectomeDB2025
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abacbs.bsky.social @abacbs.bsky.social · 24/11/2025
The view in this room is amazing! #ABACBS2025
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Feargal Ryan @feargalr.bsky.social · 23/11/2025
@noraliu.bsky.social @mmohenska.bsky.social 🤣
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Nikeisha Caruana @nikeishacaruana.bsky.social · 23/11/2025
Neglecting the bluesky account lately but that’s going to change with #ABACBS2025 tomorrow! Exciting to see old friends and make new ones! Are you going to be there? Let me know!
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Rob Edwards @linsalrob.bsky.social · 19/11/2025
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
A newpaper clipping from the Adelaide Advertiser showing high school students discovering new phages.
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abacbs.bsky.social @abacbs.bsky.social · 20/11/2025
Swag! #ABACBS2025
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abacbs.bsky.social @abacbs.bsky.social · 13/11/2025
Walkthrough of the conference centre ahead of #ABACBS2025 later this month. Bit overcast in Adelaide today but hoping for clear skies at the conference ☀️🕶️
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abacbs.bsky.social @abacbs.bsky.social · 10/11/2025
Only 13 days, 12 hours, 45 minutes, and 5 seconds until #ABACBS2025! Check out the full program and you can still register (dinner & workshops are almost sold out though!) www.abacbs.org/abacbs2025
abacbs.org
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
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Feargal Ryan @feargalr.bsky.social · 03/11/2025
What’s next? Happy to take requests for new databases or features. Let me know what would make TaxSEA more useful for your work. I’m also putting together workshop materials & tutorials, so stay tuned if you’d like to learn how to use TaxSEA in your own microbiome analyses.
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Feargal Ryan @feargalr.bsky.social · 03/11/2025
Automated BugSigDB integration. TaxSEA now talks more directly to the BugSigDB API and returns a table of PubMed IDs for microbiome signatures most similar to your results, instantly linking your findings to published studies.
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Feargal Ryan @feargalr.bsky.social · 03/11/2025
New curated signature collections from the literature added: • Urbanisation-associated microbiomes • Mucin utilisation • Gut–brain axis relevant taxa All available as built-in gene sets for enrichment testing.
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Feargal Ryan @feargalr.bsky.social · 03/11/2025
TaxSEA now integrates data from BacDive, the Bacterial Diversity Metadatabase, which contains curated phenotypic + metabolic traits for thousands of bacteria. You can test whether your metagenome is enriched for taxa with traits like nitrate reduction, enzyme production etc.
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Feargal Ryan @feargalr.bsky.social · 03/11/2025
🚀 TaxSEA v1.2 is now live in #Bioconductor release 3.22! TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵
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Feargal Ryan @feargalr.bsky.social · 23/10/2025
We've rescued two former racers. Not ideal when your vet is on the news www.abc.net.au/news/2025-10...
abc.net.au
Vet sent greyhounds home with 'open wounds', SA parliament told
Staff at Greyhound Racing SA accuse the organisation of suppressing complaints about its preferred vet, according to documents and graphic photos tabled in state parliament.
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Jeremy Barr @jeremyjbarr.bsky.social · 15/10/2025
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.
nature.com
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
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Feargal Ryan @feargalr.bsky.social · 16/10/2025
Well done! Look forward to reading it 🎉
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Feargal Ryan @feargalr.bsky.social · 11/10/2025
Awesome but brief trip to Dublin for #ICSB2025
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Darren Dahly @statsepi.bsky.social · 01/10/2025
Carefully reading the papers you cite is like a superpower. You might be surprised what you actually find! 😜
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Feargal Ryan @feargalr.bsky.social · 01/10/2025
Fascinating! Genetic risk factors for disease susceptibility show little association with disease progression/mortality. Important as most individuals only approach the health care system after developing symptoms. #genomics www.nature.com/articles/s41...
nature.com
Limited overlap between genetic effects on disease susceptibility and disease survival - Nature Genetics
Systematic comparison of genome-wide association results for disease risk and disease-specific mortality for nine common diseases across seven biobanks finds limited overlap between genetic effects on disease susceptibility and survival.
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 30/09/2025
#MVIF Season 5!
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Feargal Ryan @feargalr.bsky.social · 08/09/2025
Caught the lunar eclipse up in the Flinders Ranges!
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Altmetric @altmetric.com · 07/09/2025
WANT publishorperish.games
publishorperish.games
Publish or Perish: A Humorous Party Game about Academic Publish
Welcome to the chaotic life of academic publishing. In this game, you are a clueless researcher trying to do the one and only thing that matters in your academic life: churning out publications, fast....
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abacbs.bsky.social @abacbs.bsky.social · 05/09/2025
ECRs, join us on Sept 30th 2025, 3-4:30pm for our online Career Panel Q&A Session on bioinformatics career pathways within academia and industry. Check out our invited speakers below! Register at shorturl.at/Lerzw
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Feargal Ryan @feargalr.bsky.social · 19/08/2025
Replied above with a link to how I did it on GitHub!
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