13. Hence our dismal conclusion: rather than finding that LLMs free us to do a better job of what we were doing before they came along, they shift scientific incentives (and the playing field of academic competition) in ways that compel us to do more and more, faster and faster, less and less well.

Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/

I'm hiring a #postdoc 🥳 and applications are open 🤩 Candidates with interests in EITHER statistical methodology or microbial ecology / microbiome are welcome to apply. The position / projects will be tailored to the candidate 🌟📈🎤 Thank you for sharing widely! apply.interfolio.com/188571

I'm hiring a #postdoc!! 🥳 Official ad is making its way through HR but If you have interests in statistical methodology OR microbial bioinformatics, please reach out via my UW email. I'll share the description with you when it's available. 🔥😻

radEmu took the cake today. I'm looking at a dataset where the truth is known (a complex spike-in, spiked-in at varying intensities). All taxa should be unchanging in abundance except for the spike-ins... True "positives": 6 / 1505 radEmu score tests identifies 7 CLR + linear model identifies 517

Are you doing prediction using microbial community data as input? Please report accuracy as *average percentage error* of the prediction relative to the measurement. I'm not interested in their correlation -- I want to know how many orders magnitude you're off by. Thx! #microbiome #deeplearning

I am delighted to share that the radEmu manuscript was accepted today to Biometrika 🥳 Sending gratitude to our users and reviewers for their enthusiasm and support!! Huge congrats to @davidandacat.bsky.social and Sarah Teichman on all their hard work and brilliance 😻❗ 1/

Thanks for corroborating!! We've seen again and again that ALDEx2's p-values can be either very conservative (= underpowered) or very anticonservative (= wrong), but this points to something more problematic, such as a mistake in how they're being calculated.

ALDEx2's p-values are unusually strongly correlated with its effect sizes. Has anyone else noticed this? That... shouldn't happen. Data is actual shotgun coverages, ~8000 "taxa", 57 samples.

I had this conversation again with someone today, so posting a screenshot of an old t**** for those who missed it the first time around -- or want a refresher! 1/n

With much gratitude to everyone who supported the wonderful #STAMPS summer course at the MBL, I share that STAMPS will not be offered in 2026. 💔😿

pixi is awesome. That is all. @titus.idyll.org you're all over this, right?

Are you looking for a #tenuretrack or #openrank job in #biostatistics or #statistics? @fredhutch.org is hiring! Seattle is a wonderful place to grow your career; the bio/stat & science scene here is world-class; and you will work w/ amazing UW Biostat students. Apply! apply.interfolio.com/176402

In other news, I just had the great pleasure of teaching at #EBAME10 in Brittany 🇫🇷🥐. For this workshop, I made a tutorial showing how to use radEmu with the taxonomic profiling output of #anvio 😍😻 Workflow available for everyone on our blog: statdivlab.github.io/blog/article... ❤️❤️

Happy Friday from the StatDivLab! We just made updates to radEmu to make it faster & more stable than ever. Thanks to all our users -- we're excited to keep supporting it. github.com/statdivlab/r... Interpretable and robust microbial differential abundance, woohoo!

GitHub - statdivlab/radEmu

Contribute to statdivlab/radEmu development by creating an account on GitHub.

github.com

Wisdom from @titus.idyll.org on the final day of #STAMPS2025: "There's free as in beer, and there's free as in kittens. #Bioinformatics software is free as in kittens. You have to love and care for them or they... well... yeah."

The StatDivLab is getting excited for #STAMPS2025 and working on our lectures for 🤩 Stats Day 😻. We ran this think-pair-share activity last year and, wow, the ensuing discussion was *very* engaged 😹😅 Reach out if you'd like to attend! Woods Hole, MA, July 14-24 2025. #microbiome #dataanalysis

Best workshop you can ever follow

Amy D Willis@amydwillis.bsky.social · last yr.

We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025. If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!! Thx for sharing widely! 🤞❤️

We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025. If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!! Thx for sharing widely! 🤞❤️

Titus Brown@titus.idyll.org · last yr.

Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at ctbrown@ucdavis.edu. Thx!

The StatDivLab is *fully* reliant on our NIGMS #MIRA R35 to bring you top-quality statistical methods for microbiome research. #NIH They are quietly taking MIRAs away from this year's applicants. It's sneaky and scary. Fight back! Call your reps and tell them to protect science!

Mark Peifer (He, him)@peiferlabunc.bsky.social · last yr.

The fantastically successful NIGMS MIRA R35 "expired" on May 17, after the most recent deadline--these removals are the most aggressive attack on American science in the current series of devastating actions 🧪

It only takes 2 minutes to help defend our amazing program officers (and many other federal employees) and allow them to keep serving all Americans instead of responding to the whims of a single person

Leslie Rissler@ljrissler.bsky.social · last yr.

You have 2 days left to comment (by May 23 at 11:59 pm)! Go to the link if you don’t want your NSF or NIH program officers who took an oath to the constitution (not a political party) to instead be subject to the whims of a president and fired if they don’t “conform”.

Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6

How are DOGE & Trump planning to permanently decrease the NIH budget, and how do we fight back? -- by a courageous NIH whistleblower. Thank you to this brave person for their clear analysis and constructive suggestions. #NIH #DOGE donmoynihan.substack.com/p/the-nih-bu...

The NIH budget is on a fast track to disaster

An NIH insider explains what Republicans are likely to do next, and what we can do

donmoynihan.substack.com

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025. A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay! Apply here until June 1: maignienlab.gitlab.io/ebame

Please take 2 minutes to log that the ACA should be protected and expanded, and that trans healthcare is both the right thing to do and a great investment in Americans and America (or however you want to put it!) 💙💓🤍🤎🖤

emily sunshine@threnody.northsky.social · last yr.

and if you're like "but trump doesn't listen to courts" or "it'll eventually pass," i have this to say: every single day a trans person can access the lifesaving, essential healthcare they need is worth fighting for. it's worth court battles & protests & especially 2 minutes of your time.🧵

We've just released radEmu v2.0.0 🥳🦤😻 `remotes::install_github("statdivlab/radEmu")` A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment! Release notes: github.com/statdivlab/r...

Hello everyone, the STAMPS course on microbiome data analysis at @mblscience.bsky.social is open until Mar 11, 2025! Join us for a great experience! Please ALSO check out my co-Director @amydwillis.bsky.social excellent post on how to write a great application: statdivlab.github.io/blog/article...

Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) | Marine Biological Laboratory

The STAMPS course promotes dialogue and the exchange of ideas between experts in environmental and microbiome analysis and offers interdisciplinary bioinformatics and statistical training to practitio...

go.mbl.edu

I wrote a blog post about how to write a great #STAMPS2025 application!🙋❓🧑‍💻 Please share with anyone you know who is applying!!!! 🙏🤩 statdivlab.github.io/blog/article...

The latest from the StatDivLab -- guidance for your #microbiome data analysis with a focus on the #statistics. Planning, deciding, modeling, justifying, communicating, visualizing... "Papers Need Friends" blog post coming shortly.

Nature Microbiology@natmicrobiol.nature.com · last yr.

A must-read for any microbiome researcher 🦠📐and a new addition to our #bestpractices series Planning and describing a microbiome data analysis by @amydwillis.bsky.social and @davidandacat.bsky.social www.nature.com/articles/s41...

AND, I wrote a blog post about how to write a great application!🙋❓🧑‍💻 TL;DR: ✅ We care about whether you can benefit from the course 🥱(not how much you've already achieved) 😻Tell us about your data and what you want to learn! statdivlab.github.io/blog/article...