Night heron, spotted at the Garden of the Phoenix

Unrelated to anything, just a cool recent paper jamanetwork.com/journals/jam...

Garden of the Phoenix in Hyde Park is a gem

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

Excellent journal club discussion today of a new paper finding human genetic variants associated with fungi in the gut - interesting results! journals.plos.org/plosbiology/...

Update from Chicago. The situation is dire. Complete anarchy. Please send the national guard asap to put an end to this lawlessness

More foundations should do this: "Funding is exclusively available to applicants who have already received federal funding (e.g., from the NIH, CDC, NSF) for their health equity research, but have since had their funding rescinded due to federal administrative actions" www.rwjf.org/en/grants/ac...

"It's people who will get cancer in 10, 20 or 30 years who will really pay the price." We're literally defunding our future survival.

Cool application of microbiome in food science Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters! www.nature.com/articles/s41...

The second BME UNITE Future Faculty Seminar will be on Monday, August 25th, at 1 pm EST. Come hear from Drs. Mattea Allert, Taj Yeruva, and Said Arévalo Alquichire, PhD to learn more about their science and future research programs! Register here: tinyurl.com/bmeunite25

Chicago ✈️

200 days in, checking in on HHMI funding opportunities: Freeman Hrabowski Scholars Program - not accepting applications Gilliam Fellows Program - not accepting applications Hanna H. Gray Fellows Program - not accepting applications Investigator Program - not accepting applications

Fascinating new paper reveals a new gut microbiome connection to heart disease. Microbes produce imidazole propionate (ImP), which directly triggers atherosclerosis through immune activation - even without high cholesterol. www.nature.com/articles/s41...

Good night from Chicago

New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...

New paper showing that gut bacteria absorb "forever chemicals" (PFAS) at high levels. This bacterial "sponge effect" could influence PFAS levels in our bodies and explain individual differences in PFAS exposure. www.nature.com/articles/s41...

Our article on the challenges and opportunities in studying host-microbe symbioses is now published in Cell Host & Microbe! @cp-cellhostmicrobe.bsky.social www.sciencedirect.com/science/arti...

Some personal news: I was recently promoted to Full Professor at the University of Chicago. This milestone is deeply meaningful, and also feels quite surreal. When I started as a graduate student at UChicago in 2005 I never imagined my journey would lead me here 20 years later as a professor.

New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs. Take home message: don't use the word "Delve" www.science.org/doi/10.1126/...

Today is July 2, 2025, which means we are officially closer to the year 2050 than to the year 2000

Had fun on the Inside Matters podcast with James McIlroy discussing the microbiome as our "second genome"! We dive into how genetics & environment shape our microbial communities, the Human Microbiome Compendium, and the future of microbiome diagnostics 👇 open.spotify.com/episode/135G...

Sending some peace and quiet, from the rocky shores of Lake Michigan

US State Dept restarts student visa interviews, but with a new requirement: all social media accounts must be public for screening. Policy affects F, M & J visas, looking for "hostile attitudes" toward US. Could impact 400K+ applications yearly www.washingtonpost.com/national-sec...

Another review from my lab out this week, on analyzing gut microbiome data from global populations -- tackling computational challenges and providing practical frameworks and resources for the field With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social www.cell.com/trends/micro...

ICYMI: New online! Genomics of host–microbiome interactions in humans

The good news: NIH has published a new funding opportunity today, for the first time since January(!) The bad news: It's this one grants.nih.gov/grants/guide...

Don't tell Trump, but the best revenge on Elon would be to fully restore all the NIH and NSF funding that DOGE cut. Ultimate spite move

Just out in Nature Reviews Genetics! From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome! Fun working together with @pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson www.nature.com/articles/s41...

📣 Happy to share our review on host-microbiome genomics! We synthesize the growing field exploring interactions between human genetics and the microbiome, building a roadmap for mapping the dialogue between our genes and microbes Out now in Nature Reviews Genetics👇 www.nature.com/articles/s41...

I asked this before, but why don't private foundations pick up canceled NIH/NSF fellowships? The science have already been peer-reviewed and deemed high quality, led by promising early-career scientists. It's literally the most low-risk, high-impact funding sitting on a silver platter.

Fascinating new paper. They sequenced Borrelia genomes using DNA from ancient British remains, showing that the pathogen that causes louse-borne relapsing fever evolved ~5,000 years ago in response to humans adopting wool clothing www.science.org/doi/10.1126/...

Silver lining of the NIH funding crisis: Maybe universities will finally rethink the soft money model. Even in normal NIH times, making faculty fundraise their own salaries is questionable. Now it's just unrealistic.

Amazing. The authors found a gene deletion responsible for orange color in domestic cats. But that was not enough -- they then proceeded to create the best graphical abstract ever (not joking) www.cell.com/current-biol...

So they paid $256M for 15 million genomes. If you're a 23andme customer, your genetic data was just sold for $17

Excited to share the Compendium Manager -- our new tool for scaling bioinformatics pipelines! Launch thousands of analyses, track progress, and maintain reproducibility. Developed by @richabdill.com. Check it out: arxiv.org/abs/2505.11385

"NIH funding is gone, so you should pivot to private foundations for funding" Meanwhile, private foundations:

Love this example. In 1981 John Hopfield received this small $283K NSF grant to study an obscure topic -- artificial neural networks: www.nsf.gov/awardsearch/... The results of this NSF grant are the basis of a multibillion-dollar AI revolution, for which Dr. Hopfield won a Nobel prize last year

Spring evening, Hyde Park, Chicago

It's great to see some initiative from the EU, but unfortunately this will not move the needle. $566 million is nothing -- just the cuts to Harvard alone ($2 billion) is 4x this amount. www.nytimes.com/2025/05/05/w...

Why are they trying to kill the goose that lays the golden eggs? #WithoutNSF the US would not be at the forefront of science innovation in the world. #SaveNSF #StandUpForScience www.nsf.gov/policies/doc...

This might be a controversial topic, but as a professor of medicine, I feel that I must speak up: I believe that the germ theory is real

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

I received a surprising and disturbing request from NIH on Friday. They wrote to cancel a subaward to Hong Kong on one of my grants. (This was disturbing but not surprising.) They also ordered us not to interact with our collaborators in Hong Kong on any work under the award:

Sending you all some peace from Chicago

In today's journal club we had a great discussion of this new paper, describing a clinical trial of defined bacterial consortium to treat C. diff recurrence. Exciting times for microbiome therapeutics! www.nature.com/articles/s41...

Keep in mind that this is just the beginning. I wouldn't be surprised to see an "official" NIH page saying that vaccines cause autism next. We're far from the bottom. www.npr.org/sections/sho...

Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics www.nature.com/articles/s42...

Cherry blossoms 🌸 are back at Jackson Park. Fortunate to have this park in our neighborhood

Come and work with me! The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists Link below 👇

Great to see a successful clinical trial for phage therapy! But these p-values are making my eye twitch www.fiercebiotech.com/biotech/biom...