Walkthrough of the conference centre ahead of #ABACBS2025 later this month. Bit overcast in Adelaide today but hoping for clear skies at the conference ☀️🕶️

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

🚀 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 👇 🧵

We've rescued two former racers. Not ideal when your vet is on the news www.abc.net.au/news/2025-10...

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.

Awesome but brief trip to Dublin for #ICSB2025

Carefully reading the papers you cite is like a superpower. You might be surprised what you actually find! 😜

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...

#MVIF Season 5!

Caught the lunar eclipse up in the Flinders Ranges!

WANT publishorperish.games

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

🚨 Less than 48 hours left! 🚨 Abstract submissions for #ABACBS2025 close midnight Friday, Aug 15 — no extensions. www.abacbs.org/abacbs2025

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

🚨 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

@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

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 🤣

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

⭐️Microtalks: 🇺🇸 @michaelwasney.bsky.social 🇯🇵 Yiting Liu ⭐️Keynote: 🇦🇺 Emad El-Omar ⭐️Selected talks: 🇦🇺 Chaoran Yang 🇦🇺 @feargalr.bsky.social‬ 🇨🇦 @vdumeaux.bsky.social

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/...

argNorm is published now academic.oup.com/bioinformati...

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

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....

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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...

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)

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.

We've just joined Bluesky 🎉 Follow us for research, news, comment and opinion from Nature journal 🧪

A story that brings together calorie restriction, the gut microbiome and red wine. All my favourite things www.nature.com/articles/d41...

This fearless science sleuth risked her career to expose publication fraud Anna Abalkina @abalkina.bsky.social is part of Nature’s 10, a list of people who shaped science in 2024. Holly Else reports at Nature. www.nature.com/articles/d41...

Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon (mBio) journals.asm.org/doi/full/10.... Fungi with different lifestyles have different levels of bacterial HGT - mycoparasites with the most and ectomycorrhizal fungi with the fewest:

🚨 PhD Opportunity @halllab.bsky.social! 🔬 Decoding Early Life Microbiota & Host Interactions 🧬 Ideal for those with bioinformatics/microbiome experience 🌍 Open to international candidates (MSCA mobility rules apply). 📅 Deadline: 18th Dec 🌐 Apply now: www.findaphd.com/phds/project...

Oswalds Australian summer face 😂🐶 #dogsofbluesky #greyhounds #dogs

If you want to get better at naming files, there are tons of useful resources out there! I've compiled a few in the thread below!

The writing is the part of the job I’m (probably?) the worst at. I know what’s good, but getting there used to take me a while. LLMs have been such an unlock. www.nature.com/articles/d41...

Reupping this since the explosion in members here. I’m looking to recruit PhD candidates to work with me in #Bioinformatics and thr human #microbiome Details 👇 Please share 😁 www.flinders.edu.au/scholarships...

I nominate this for #bioinformatiocs tool name of the year. I love it when Aussie home grown software have some "Australiana" in them! 🇦🇺 github.com/AroneyS/binc...

lots of bangers on the site today www.theverge.com/2024/11/25/2...

ARC says they’ll release the Discovery Projects 2025 outcomes tomorrow. Recently, outcomes announcements have tended to happen at/around 11am Canberra time. My bot will pick up the announcement in RMS’s database and post immediately. Good luck!

Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics. 14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell www.sciencedirect.com/science/arti...

🧬 New preprint: TaxSEA, an R package for taxon set enrichment analysis—like GSEA, but for microbiome WMS data. Interesting new tool from @feargalr.bsky.social #Microbiome #Bioinformatics #Preprint

A cell atlas foundation model for scalable search of similar human cells | Nature Develops SCimilarity which they use to query 23.4M cell atlas to find similar cell profiles. #Genomics #SingleCell www.nature.com/articles/s41...

Lit searches are probably the one part of my job where I don’t routinely use LLMs. Burned too many times by hallucinations producing a fake papers. www.nature.com/articles/d41...

Working with a collaborator on a dataset, and we think we might have hit a sample mislabeling issue. It got me thinking about all the ways we evaluate #metagenomics & #microbiome data quality—not just pos/neg controls or read PHRED scores, but other approaches I’ve found helpful. 👇

This is awesome. I'd been down on #metagenomics lately, working in host-microbiome association analyses you realise its limitations pretty quickly. But its utility for infectious disease has a long way to go. www.nature.com/articles/s41...

Jimmy Breen presenting at EpicSA and reminding everyone that Sam Buckberry is hiring as part of Black Ochre Data Labs

Interesting. retractionwatch.com/2024/11/13/e...

Chenxin Li's opinionated essay on practices in data visualization. github.com/cxli233/Frie...

NIAID releases alternative to BioRender, all illustrations freely available in public domain bioart.niaid.nih.gov