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Feargal Ryan

@feargalr.bsky.social
664 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
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
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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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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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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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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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
🚀 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 · 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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abacbs.bsky.social @abacbs.bsky.social · 14/08/2025
🚨 Less than 48 hours left! 🚨 Abstract submissions for #ABACBS2025 close midnight Friday, Aug 15 — no extensions. www.abacbs.org/abacbs2025
abacbs.org
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
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Feargal Ryan @feargalr.bsky.social · 07/08/2025
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
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abacbs.bsky.social @abacbs.bsky.social · 05/08/2025
🚨 Abstract deadline extended! 🚨 You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only! Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more. 🔗 www.abacbs.org/abacbs2025
abacbs.org
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
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mmarchin.bsky.social @mmarchin.bsky.social · 24/07/2025
@hubertr.bsky.social‬ presented during #bioinfocore about GEO uploader, trying to simplify the upload process for researchers (I kinda hate doing this, so I'll be looking at it) github.com/fgcz/geo-upl... #ISMBECCB2025
github.com
GitHub - fgcz/geo-uploader: A Python GUI for the upload of NGS data to GEO
A Python GUI for the upload of NGS data to GEO. Contribute to fgcz/geo-uploader development by creating an account on GitHub.
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Feargal Ryan @feargalr.bsky.social · 23/07/2025
Tomorrow at 9:40am I’ll be speaking at #ISMBECCB2025 about how we can speed up microbiome data interpretation using taxon sets Paper: academic.oup.com/bib/article/... R package on #Bioconductor: TaxSEA #RStats #Microbiome Come say hi, I flew from Australia for this 🤣
academic.oup.com
TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases
Abstract. Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most curre
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abacbs.bsky.social @abacbs.bsky.social · 02/07/2025
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
abacbs.org
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 19/05/2025
⭐️Microtalks: 🇺🇸 @michaelwasney.bsky.social 🇯🇵 Yiting Liu ⭐️Keynote: 🇦🇺 Emad El-Omar ⭐️Selected talks: 🇦🇺 Chaoran Yang 🇦🇺 @feargalr.bsky.social‬ 🇨🇦 @vdumeaux.bsky.social
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Feargal Ryan @feargalr.bsky.social · 22/04/2025
Manuscript out now in Briefings in Bioinformatics! TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases. #microbiome #metagenomics academic.oup.com/bib/article/...
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 17/04/2025
argNorm is published now academic.oup.com/bioinformati...
academic.oup.com
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
AbstractSummary. Currently available and frequently used tools for annotating antimicrobial resistance genes (ARGs) in genomes and metagenomes provide resu
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Feargal Ryan @feargalr.bsky.social · 17/04/2025
My first R package is officially out Bioconductor 3.21 today 🎉 TaxSEA adapts GSEA-style methods for metagenomic data— useful for interpreting differential abundance results. Manuscript accepted & in-press. Check it out bioconductor.org/packages/rel... #Bioinformatics #Metagenomics #RStats
bioconductor.org
TaxSEA
TaxSEA is an R package for Taxon Set Enrichment Analysis, which utilises a Kolmogorov-Smirnov test analyses to investigate differential abundance analysis output for whether there are alternations in ...
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Feargal Ryan @feargalr.bsky.social · 11/04/2025
Excellent editorial in Microbiome this week including lots of practical advice for analysis (and lots of what not to do!) #microbiome #bioinformatics microbiomejournal.biomedcentral.com/articles/10....
microbiomejournal.biomedcentral.com
A blueprint for contemporary studies of microbiomes - Microbiome
This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...
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Feargal Ryan @feargalr.bsky.social · 03/04/2025
😆
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Feargal Ryan @feargalr.bsky.social · 03/04/2025
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...
nature.com
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...
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 06/03/2025
We're looking for a postdoc on the Computational Analysis of Environmental #Microbiome Data! embl.wd103.myworkdayjobs.com/en-US/EMBL/j... In the past two years, @embl.org scientists have gathered more than 3000 soil, sediment & water samples from Europe's coastlines within the #TREC expedition (1/2)
embl.wd103.myworkdayjobs.com
Postdoctoral Fellow - Computational Analysis of Environmental Microbiome Data
We are seeking a highly motivated computational biologist to join the research group of Peer Bork within the Molecular Systems Biology Unit as a postdoctoral fellow. This bioinformatics group works on...
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Markus Eichhorn @markuseichhorn.bsky.social · 31/03/2025
It's getting to the point as an editor where if you receive a long, clearly-written reviewer's report before the deadline that you start to become suspicious.
nature.com
AI is transforming peer review — and many scientists are worried
Artificial intelligence software is increasingly involved in reviewing papers, provoking interest and unease.
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Nature @nature.com · 19/12/2024
We've just joined Bluesky 🎉 Follow us for research, news, comment and opinion from Nature journal 🧪
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Feargal Ryan @feargalr.bsky.social · 19/12/2024
A story that brings together calorie restriction, the gut microbiome and red wine. All my favourite things www.nature.com/articles/d41...
nature.com
A bile acid could explain how calorie restriction slows ageing
Lithocholic acid might mediate calorie restriction’s health benefits.
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