Hugerth lab

And on the odd chance that they're actually brilliant and I don't get it, it gives them a chance to explain, heh

There's something very satisfying about asking authors that are engaging in wild speculation in their discussion section to please go on. "That's a very bold hypothesis. For the benefit of the readership, please be as specific as possible about this proposed mechanism."

🎉🎉🎉 New preprint to start the new year 🎉🎉🎉

Patients recovering from bowel surgery may have stomas formed to divert the flow of faeces to the opening on the skin, away from healing intestinal tissue. The visible sign of this process is an ileostomy or colostomy bag. /1

#surgerysky #medsky

We found:
- High-dose VOWST enabled rapid, durable engraftment and rescued efficacy in phase 3 vs phase 2
- VOWST shifted the gut toward a healthy-like community, reducing Proteobacteria and C. diff
- Engrafted Firmicutes restored key metabolites (secondary bile acids, SCFAs) that inhibit C. diff

In the foreground, a print of a grant application with an Eppendorf pen on top. In the background, an enormous mug of hot chocolate covered in mini marshmallows with a mountain of whipped cream on the side

Revising a large grant for the last time before submission, and all means are fair

Driven by the pain of endometriosis, this scientist is uncovering clues to its causes Katie Burns is helping reveal the immune system’s role in the long-neglected disease

Fascinating read on the immunological origins of endometriosis - with insights into improved diagnostics and treatment

www.science.org/content/arti...

We concluded that plasmids evolve through a birth-death process, involving fusion (birth of a new "species"),
but also fragmentation (by many processes, such as MGE-mediated recombination). Fusions mostly are removed by selection, but sometimes they survive
16/n

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

3/
Bioinformatics is not just about the data.
It’s about the biology behind the data.
Without that, your code is just noise in a terminal.

Glad to have been a tiny part in this consortium!

An entirely empty lecture hall at a renowned university

I have 44 students enrolled in this course. Class officially started two minutes ago. They have an exam next week. Thoughts and prayers.

In Which The Rube Goldberg Machine Behind Retractions Delivers A Limp Payload A Year Late No, I'm not thinking of a better title.

About fifteen months ago, someone handed me a bad study. Today it was retracted. So far, so normal.

But do I just want to yell at journals and publishers again? Hell no. What could they actually DO to be better at handling this sort of nonsense?

open.substack.com/pub/jamescla...

Svensk forskning: Ingen koppling mellan paracetamol och autism Trots att det finns evidens för att paracetamol under graviditeten inte orsakar autism, pekar Trumpadministrationen ut medlet som en orsak.

The Nordic medical and drug registries are amazing because you not only can tell RFK to fuck off and start making some sense, you have the numbers to back it up

www.dn.se/sverige/sven...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

Finally, the results of my postdoc at the
@bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.

See our new preprint:
www.biorxiv.org/content/10.1...

Fusobacterium nucleatum, a common mouth bacterium, may worsen oral cancer by using waste and changing cell behavior. This study offers clues for better oral cancer prevention！👇
#oral #cancer
@ijosjournal.bsky.social
www.nature.com/articles/s41...

This is a major issue is that the incentives are to output false positives in your tools

If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it!

open.substack.com/pub/luispedr...

The legs-up-in-stirrups position sometimes used in birth or gynaecological procedures is called the lithotomy position.

Etymology fans among you might note that this derives from the Greek for "stone cut". Let's explain why...

FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

Anyone know what happened to hmpdacc.org?

More importantly, does anyone know how to apply for HMP participant data nowadays?

Practice-engaged and practice-critical philosophy of science is needed now more than ever in light of widespread AI-integration into science and its oversight mechanisms.

I do miss when things were called "neural networks" and "principal components analysis" etc instead of lumping everything as "ML" and then "AI"

Bioinformatician - Uppsala University Bioinformatician, Department of Organismal Biology, Uppsala University

The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment:

www.uu.se/en/about-uu/...

Best comment on Jay Bhattacharya that I've read to date.

Nice! I'll add it to my epi syllabus as optional material for interested students

Mathematical modelling for biologists - Modelling concepts in biological research Mathematical modelling for biologists - Modelling concepts in biological research

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...

Including both molecular and epidemiological examples

Niche bloop but:
The endocrine system is the original object-oriented program.

NIH Plans to Cap Publisher Fees, Dilute “Scientific Elite” Director of the National Institutes of Health says that capping research journals’ open-access fees will help rein in the $19 billion academic publishing industry and bolster scientific debate.

NIH Director say journals "bully scientists into paying large fees".

No. Academia is a prestige economy in which scientific leadership chose to make journals the currency & Gold OA was deemed 'the way'. Publishers just cashed in; you don't have to pay $10K

www.insidehighered.com/news/governm...

Mixed feelings when a question I've been musing about for a long time gets answered in a paper. Yes, we have an answer! But also oh no, I wanted to study that!

Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring - Nature Communications SARS-COV-2 wastewater surveillance may enable early identification of emerging variants. Here, authors compare variants detected in wastewater from Stockholm city, its airport, aircraft, the wider air...

Out now in @natcomms.nature.com: we show how wastewater surveillance identifies viral strains several weeks before the clinics, and study the trade-offs between the size of the catchment area for the sewer and the number of unique variants identified
www.nature.com/articles/s41...