My department at UTK is hiring! 🧪🧫 We are hiring two Assistant Professors, one in Microbial Drivers of Chronic Disease and one in Quantitative Microbe-Plant-Environment Interactions! Come join our growing department of microbiologists. Knoxville is a great place to live!

Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist! aprecruit.ucsf.edu/JPF05807

Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...

some cool papers on the challenge of creating train-test splits for protein deep learning models Constructing benchmark test sets... journals.plos.org/ploscompbiol... Cracking the black box of deep sequence-based protein–protein interaction prediction: pmc.ncbi.nlm.nih.gov/articles/PMC...

At 88%, it's hard to find a topic that more Americans agree with each other on than the benefits of routine vaccinations. And with 62% for COVID vaccines (while sadly low), that is also something of a supermajority consensus as policies go in American politics www.pewresearch.org/science/2023...

Hey all! Now that i've left my position at UQ, I thought I would leverage my network here to see if anyone has leads on environmental genomics, biotech, marine policy positions in the US/Canada/Australia/Europe. I'd love to speak with anyone in those fields re openings, worthwhile recruiters, etc.

📝New preprint! #MicroSky 🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy. 🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation. www.biorxiv.org/content/10.1...

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life. www.nature.com/articles/s41...

President Trump said he demolished USAID to reduce waste. In fact, my reporting finds that the demolition of USAID has wasted billions of dollars--and the lives of children like 8-year-old Gy Gael. Sec. Rubio, you still claim aid cuts haven't killed anyone? www.nytimes.com/2025/09/24/o...

There seems to quite a few new faces lately, so if I haven’t already added you, but you’d like added please let me know and for anyone interested in following more microbial natural products folks, then our starter pack is now 100 strong go.bsky.app/72NeGsT

With this, the last bit of my PhD at @embl.org is finally out! We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models. Paper: nature.com/articles/s42256-… Code: github.com/mjendrusch/salad Data: zenodo.org/records/14711580 1/🧵

“Everyone should read it”: Nature reviews Human Nature www.nature.com/articles/d41...

Happy to share the published version of our genetic toolbox, EASY-edit, for simple, flexible and efficient targeted editing in E. coli! Feel free to to try it, we can send strains and plasmids! academic.oup.com/nar/article/...

It's absolutely astonishing: In just about 13 years, Norway has skyrocketed from virtually no sales of zero-emission battery electric vehicles to nearly 100% of all new passenger car purchases.

The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...

Useful polling data: In 2025, confidence in public health institutions has steeply declined among Democrats, but hasn't gained under Republicans. MAHA public health takeovers appear very unconvincing, even to supporters. www.annenbergpublicpolicycenter.org/public-confi... (h/t @tgof137.bsky.social)

Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology. www.nature.com/articles/s41...

California researchers take heart from nuanced ruling in suit to get grants reinstated www.science.org/content/arti...

New PrePrint from the Vecchiarelli and Mosalaganti (@shyamalm.bsky.social) labs! 🧵 Collaboration with the Giessen and Pi labs Congratulations to co-first authors Y Hoang (@hoanghamyy.bsky.social) and Pankaj Jadhav! www.biorxiv.org/content/10.1...

In a UN speech today, President Trump said that "all of these [climate] predictions were wrong". Back in 2019 I led a research effort to digitize old climate model projections and assess how well they did. Turns out they got future warming pretty spot on!

Microbiome sequencing has come so far in 2 decades. In my PhD— I used TRFLP…. am now doing long read sequencing of entire soil metagenomes! This review was great fun- thanks Gitta Szabó @emileyeloe-fadrosh.bsky.social Tanja Woyke of @jgi.doe.gov www.nature.com/articles/s41...

Fecal filtrate is less effective than donor stool (FMT) for the treatment of C. difficile recurrence. Now shown in a multicentre trial, out today in @lancetgastrohep.bsky.social . Congratulations to Dina Kao @ualberta.bsky.social & team! Gift link: authors.elsevier.com/c/1lphg8nByr...

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

Let's go to some of the main messages: 🧬We recovered 2,676 MAGs from Shanghai dogs, ~72% were near-finished (high-quality regarding MIMAG criteria) & highly contiguous. ⭕We recovered 185 circular extrachromosomal elements like plasmids and viruses from the same dogs.

Relabeling drugs on Vibes is a 4-alarm fire that can collapse the entire framework of pharmacology safety and confidence.

How much of selection in human microbiomes is driven by phage? Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important: Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin www.biorxiv.org/content/10.1... 🧵

So please don’t both sides the critique of the truly terrible NY Times piece this morning. As Daniel Patrick Moynihan said once: you are entitled to your own opinions but not your own facts. The piece is garbage.

I was today years old when I learned what Newick trees were named for... "Newick trees, named after a meeting of several scientists in Newick’s restaurant in Dover, New Hampshire, in 1986 (Archie, Day, Maddison, Meacham, Rohlf, Swofford, and Felsenstein;" doi.org/10.1093/jher...

Intersting to see where Myloasm sits. These new assemblers like MetaMDBG,HFiasm, Myloasm, show really impressive benchmarks for MAG recovery, but also higher error rates, often much higher, and substantial misassembly rates (ref below). Curious to know how the community is viewing these assemblers?

Lineage tracking using methylation states from longitudinal bulk sampling. Sounds 🆒 and given recent work by @trevorgraham.bsky.social and colleagues, looks real. Wondering about other applications like 🦠🧫 👉🏻News and views: www.nature.com/articles/d41... 👉🏻Paper www.nature.com/articles/s41...

‼️Don’t miss the September issue of @asm.org Journals #ApplEnvMicrobiol (#AEM), with a record number of articles. A 🧵 about my Spotlight picks journals.asm.org/doi/10.1128/...

And a 4th reminder that a transition to 100% WindWaterSolar reduces the annual total tonnes of mining in the world by >84% despite the need for precious metals, which are a trivial component of total mining tonnage.

Want to be able to start micro-editing on Wikipedia in a few minutes – and know why you could be very glad you did? Then my new post @plos.org is just what you need! absolutelymaybe.plos.org/2025/09/21/w... #Wikipedia

Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater https://www.biorxiv.org/content/10.1101/2025.09.19.676942v1

Eight states and New York City officially announced the Northeast Public Health Collaborative this week, while the West Coast Health Alliance released its first vaccination guidelines. My latest: www.theguardian.com/us-news/2025...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

Excited to share our recent paper @newphyt.bsky.social where we describe evidence of a Jurassic nurse log from Scotland! Great work led by @anajusagasti.bsky.social Sophie Burne and @jeremywyman.bsky.social @instmolplantsci.bsky.social 🧵 👇 1/6 nph.onlinelibrary.wiley.com/doi/10.1111/...

Multiplexed DIA enabled multimodal proteomics of ~ 10³ single cells, including quant of protein synthesis & degradation rates. Our technologies can increase the multiplexing along different dimensions (mass, time) and thus scale up throughput further to ~ 10⁴ - 10⁵ single cells. 🔽

Our latest review is now live! Check out our thoughts on how the filamentous lifestyle of Actinomycetes and their ability to make a diverse array of natural products may be connected 👇: www.annualreviews.org/content/jour...

I've been reporting in East Africa on the impact of President Trump's USAID cuts, and I find that not only are children dying in large numbers but the pace is accelerating as stockpiles run out and people grow weaker. www.nytimes.com/2025/09/20/o...

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range. @rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social www.nature.com/articles/s41...

Despite RFK’s ACIP leaning towards pushing back newborn HepB vax—again, based on no evidence—they have voted unanimously to postpone the vote on the decision. Public pressure likely doing its job. Lots of brave voices showed up yesterday and today.

we wrote about this WH tactic recently. they’re asking journalists for expert source names and then using them to look up political donations in FEC records to try to discredit those sources as biased. www.npr.org/2025/08/18/n...

Newborn lives are on the line. The hepatitis B birth dose is safe, effective, and lifesaving yet it’s under attack at ACIP this week. Weakening this policy would be a grave mistake. Read why we must defend it. open.substack.com/pub/bktitanj...

Who would have thought we will see the day that the #ACIP meeting sounds like a plenary at an anti-vaccine convention? The primary emotion I feel is sadness. We are losing so much in real time.

This isn't even a slight exaggeration. He is actively working on destroying the US's entire vaccine infrastructure. The HepB vote will be tomorrow, where they will get rid of the birth dose and recommend it at 30 days, dooming a bunch of infants to chronic infection ft. cirrhosis, cancer, and death.

New issue of Works in Progress!! • A blueprint for far-UVC to disinfect the air • How antibody manufacturing scaled up • Magical systems thinking • Hydropower, dams and water conflict • How France built nuclear • Science needs outsiders • Sunscreen for the planet Read it here: worksinprogress.co

Great and nuanced thread. But I think we can expand further. As noted, phage selected for synthesis, and that worked, were significantly less novel. In Fig 4D, there's a very strong correlation between novelty and not working. The phage that worked were much less novel. This is nucleotide ID!

at the same time, we need to stay grounded about what has been achieved and the extent to which these techniques could be pushed to generate highly diverse or even totally novel sequences. we can't be too impressed with how the sequences were designed and ignore how many changes were made

What is the current preferred hybrid genome assembler for mammalian genomes? We have Illumina and ONT data. There is a draft reference genome from a different population, but no complete one.