Cool new study -- they used historical water and well water fluoride levels across Wisconsin counties, and linked these to IQ and cognition from age 16 all the way to age 80. Guess what they found? No association between fluoride levels and cognition - at any age www.pnas.org/doi/full/10....

I'm moving to Purdue University as a tenured professor this summer! Excited to hire postdocs there and get a lab up and running with @runxishen.bsky.social as co-lead. More details: www.linkedin.com/posts/anneca...

Visited Zion National Park for the first time - impossible to convey how beautiful it is

Sean Davis & I are hiring a postdoc to work on turning massive public biological data collections into reusable engines for discovery. #ML / #AI + large-scale omics + open software Details + apply: cu.taleo.net/careersectio... seandavi.github.io | thekrishnanlab.org @cubiomedinfo.bsky.social

I'm generally a fan of AI, but I just don't see how this is going to improve polling. Will just make an already messy data even more biased and problematic

“first drafts of Results, Discussion, and Introduction should be the trainee’s own work. AI can help with grammar…tightening prose…critiquing the logic of an argument you’ve already made. But the hard part of forming the argument needs to be yours.’ blekhman.substack.com/p/you-need-t...

A lab using my recent articles on AI use during PhD training doi.org/10.5281/zeno... & doi.org/10.5281/zeno... to kickstart a discussion and draft guidelines for their group is exactly the kind of use I hoped these articles would inspire! Highly recommend reading Ran's post.

I wrote about why every lab should have AI use guidelines, and how to do it. open.substack.com/pub/blekhman...

After 13 years, the Blekhman Lab has a new website: blekhmanlab.org The old one was hand-coded HTML from my first week as a faculty member. It... showed its age. This one was built with Claude Code. Progress on multiple fronts.

Southern Utah countryside

"AI scientists are building ever-larger models, and then claiming that each model can solve even more than the previous one. Then, model in hand, they go around looking around for problems to solve" stevensalzberg.substack.com/p/ai-is-star...

Layers. Today in Chicago

Predicting host sex from metagenomic data Cool approach that uses the "host contamination" reads in shotgun metagenomic data, and (using as few as 450 reads) can accurately predict host sex. Works well across different host species and body sites www.biorxiv.org/content/10.6...

Project Hail Mary is one of my favorite books of the last few years, but it was hard to suspend disbelief with some of the story lines. Like that the main character is a PhD microbiologist who is also an expert in physics. Impossible

We're searching for the next Director of the Duchossois Family Institute at UChicago The most exciting leadership role in microbiome science right now: lead faculty, cutting-edge cores, and an FDA-approved facility for microbiome therapeutics Email/DM me if interested apply.interfolio.com/182203

Something that keeps happening recently: I open an email (or essay, cover letter, whatever), within 0.5 seconds recognize it's AI-written, then I delete it immediately. Anyone else's brain developed this new pattern recognition skill?

Leipzig U and the MPI for Evolutionary Anthropology (MPI-EVA) have an open faculty position (W2) in evolutionary population genetics! This position is tenured and comes with generous core funding. We are eager to welcome a new colleague! Deadline March 11. www.uni-leipzig.de/en/newsdetai...

Got 5 NIH study section invitations in one week. For 5 different panels in May. Never happened before. Not sure what's going on but feels like there is a serious strain on the system.

AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction. My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed blekhman.substack.com/p/ai-keeps-f...

Last week I took one of my favorite Chicago photos of all time. This city is LONG

Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...

Yes, they can hallucinate papers that don't exist, discuss results that seem to be imaginary, and can be confusing and inconsistent. But talking to tenured professors may still be helpful

Terrible. Still need to see a bit more of the timeline, but based on this trend I don't see how the NIH will fund even 10,000 new awards this fiscal year. Maybe closer to 8000

In 1800 (not that long ago!) the average life expectancy was ~30 years.

I've been hearing from more and more people who received peer reviews that were clearly written by AI. It's frustrating, and no one knows what to do. I have some thoughts. blekhman.substack.com/p/so-your-pa...

Good morning from Chicago

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

We should talk more about the graduate admissions crisis that's taking shape in the US. Talking to colleagues across universities, many graduate programs are slashing admission numbers and reducing class sizes substantially for the upcoming academic year. This is shortsighted

if you're in line to sack drake maye, STAY IN LINE

Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer www.biorxiv.org/content/10.6...

This is not heartbreaking. Keep in mind that the authors perspective: they probably disagree that their paper "needs a lot of work". Instead they find another journal (and another set of reviewers) that agree with them, and save months of expensive, time consuming, unnecessary work.

Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months. Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life: doi.org/10.1038/s414...

I just signed up and read the first of Ran's posts. Excellent stuff, highly recommended.

I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post: substack.com/home/post/p-...

My favorite Chicago photos of 2025

another one bites the dust

Review: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social rdcu.be/etIRy

One month later

Due to the shutdown, NIH cancelled >370 study sections, impacting >24,000 applications Rescheduled meetings will only discuss 30-35% of applications, have simplified summary statements (no narrative paragraph), and a new category - "competitive but not discussed" grants.nih.gov/grants/guide...

Great example of what I call a "grift bag"

I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field open.substack.com/pub/blekhman...

Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology www.cell.com/trends/micro...

🧬 🦠 🏙️ Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host? Excited to share our new paper: www.biorxiv.org/content/10.1...

Indiana Dunes National Park, yesterday

Never seen our campus like this before. Like every single tree decided to turn red at the same moment

So funny that this is still the top search term for biorxiv. Like asking what is the impact factor of pubmed. Or your local library.

UChicago Microbiology is searching for tenured or tenure-track faculty working in host-pathogens interactions, viral and bacterial pathogenesis, and emerging infectious diseases. Come join our vibrant Department! microbiology.uchicago.edu Apply here apply.interfolio.com/174404