Hugerth lab
@h-mel.bsky.social
Human molecular ecology lab at Uppsala University. Microbiota as a modifiable risk factor in women's health. Bloops by @luhugerth.bsky.social
Revising a large grant for the last time before submission, and all means are fair
October 13, 2025 at 1:33 PM
Revising a large grant for the last time before submission, and all means are fair
Fascinating read on the immunological origins of endometriosis - with insights into improved diagnostics and treatment
www.science.org/content/arti...
www.science.org/content/arti...
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
www.science.org
September 28, 2025 at 5:48 AM
Fascinating read on the immunological origins of endometriosis - with insights into improved diagnostics and treatment
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by Hugerth lab
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
but also fragmentation (by many processes, such as MGE-mediated recombination). Fusions mostly are removed by selection, but sometimes they survive
16/n
September 25, 2025 at 9:39 PM
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
but also fragmentation (by many processes, such as MGE-mediated recombination). Fusions mostly are removed by selection, but sometimes they survive
16/n
Reposted by Hugerth lab
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
Thread 1/n
September 25, 2025 at 9:29 PM
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
Thread 1/n
Reposted by Hugerth lab
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.
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.
September 26, 2025 at 1:15 PM
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.
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!
A roadmap for equitable reuse of public microbiome data by The Data Reuse Consortium @natmicrobiol.nature.com
September 27, 2025 at 5:58 PM
Glad to have been a tiny part in this consortium!
I have 44 students enrolled in this course. Class officially started two minutes ago. They have an exam next week. Thoughts and prayers.
September 24, 2025 at 7:18 AM
I have 44 students enrolled in this course. Class officially started two minutes ago. They have an exam next week. Thoughts and prayers.
Reposted by Hugerth lab
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...
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...
In Which The Rube Goldberg Machine Behind Retractions Delivers A Limp Payload A Year Late
No, I'm not thinking of a better title.
open.substack.com
September 23, 2025 at 10:48 PM
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...
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...
Reposted by Hugerth lab
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...
www.dn.se/sverige/sven...
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.
www.dn.se
September 23, 2025 at 5:14 AM
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...
www.dn.se/sverige/sven...
Reposted by Hugerth lab
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...
@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...
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...
www.biorxiv.org
September 23, 2025 at 11:24 AM
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...
@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...
Reposted by Hugerth lab
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...
#oral #cancer
@ijosjournal.bsky.social
www.nature.com/articles/s41...
August 22, 2025 at 5:09 AM
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...
#oral #cancer
@ijosjournal.bsky.social
www.nature.com/articles/s41...
Reposted by Hugerth lab
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...
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...
August 22, 2025 at 4:35 PM
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...
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...
Reposted by Hugerth lab
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...
Etymology fans among you might note that this derives from the Greek for "stone cut". Let's explain why...
August 22, 2025 at 11:20 AM
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...
Etymology fans among you might note that this derives from the Greek for "stone cut". Let's explain why...
Reposted by Hugerth lab
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...
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
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...
www.nature.com
August 15, 2025 at 12:05 AM
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...
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
Reposted by Hugerth lab
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/...
🧵
Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.
journals.asm.org/doi/10.1128/...
🧵
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, ...
journals.asm.org
July 31, 2025 at 3:33 PM
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/...
🧵
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?
More importantly, does anyone know how to apply for HMP participant data nowadays?
August 21, 2025 at 1:57 PM
Anyone know what happened to hmpdacc.org?
More importantly, does anyone know how to apply for HMP participant data nowadays?
More importantly, does anyone know how to apply for HMP participant data nowadays?
Reposted by Hugerth lab
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.
1. The philosophy of science sometimes gets an unearned reputation as a purely academic exercise that offers little by way of concrete tools for advancing research.
This is wrong.
And today, as we grapple with how AI is changing the nature of scientific activity, it's desperately wrong.
This is wrong.
And today, as we grapple with how AI is changing the nature of scientific activity, it's desperately wrong.
August 19, 2025 at 5:27 AM
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.
Reposted by Hugerth lab
I do miss when things were called "neural networks" and "principal components analysis" etc instead of lumping everything as "ML" and then "AI"
August 15, 2025 at 6:51 AM
I do miss when things were called "neural networks" and "principal components analysis" etc instead of lumping everything as "ML" and then "AI"
Reposted by Hugerth lab
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/...
www.uu.se/en/about-uu/...
Bioinformatician - Uppsala University
Bioinformatician, Department of Organismal Biology, Uppsala University
www.uu.se
August 12, 2025 at 7:10 AM
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/...
www.uu.se/en/about-uu/...
Reposted by Hugerth lab
Best comment on Jay Bhattacharya that I've read to date.
Motherfucker wrote one sloppy paper in April 2020 and instead of being like oops, shit, my bad, he has kept doubling down until now he's killing most promising medical technology of the past quarter century rather than going to therapy.
August 15, 2025 at 12:25 AM
Best comment on Jay Bhattacharya that I've read to date.
Reposted by Hugerth lab
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
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Mathematical modelling for biologists - Modelling concepts in biological research
Mathematical modelling for biologists - Modelling concepts in biological research
www.ebi.ac.uk
August 15, 2025 at 10:39 AM
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
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Reposted by Hugerth lab
Niche bloop but:
The endocrine system is the original object-oriented program.
The endocrine system is the original object-oriented program.
August 15, 2025 at 2:08 PM
Niche bloop but:
The endocrine system is the original object-oriented program.
The endocrine system is the original object-oriented program.
Reposted by Hugerth lab
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...
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...
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.
www.insidehighered.com
July 11, 2025 at 1:30 PM
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...
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!
June 27, 2025 at 1:26 PM
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!
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...
www.nature.com/articles/s41...
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...
www.nature.com
June 18, 2025 at 6:03 AM
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...
www.nature.com/articles/s41...