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Hugerth lab @h-mel.bsky.social · 10d

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

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

Reposted by Hugerth lab

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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Ming Tommy Tang @tommytang.bsky.social · 12d

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.

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Hugerth lab @h-mel.bsky.social · 11d

Glad to have been a tiny part in this consortium!

Geo Santiago-Martínez @geosantiagom.bsky.social · 11d

A roadmap for equitable reuse of public microbiome data by The Data Reuse Consortium @natmicrobiol.nature.com

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Hugerth lab @h-mel.bsky.social · 14d

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

An entirely empty lecture hall at a renowned university

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Reposted by Hugerth lab

JAMES HEATHERS @jamesheathers.bsky.social · 15d

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 Today it was retracted.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...

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

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Reposted by Hugerth lab

Luisa Hugerth @luhugerth.bsky.social · 15d

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...

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

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Reposted by Hugerth lab

Anna Cusco @annacusco.bsky.social · 15d

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...

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

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Reposted by Hugerth lab

IJOS_Editorial Office @ijosjournal.bsky.social · Aug 22

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...

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Reposted by Hugerth lab

Luis Pedro Coelho @luispedrocoelho.bsky.social · Aug 22

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...

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Reposted by Hugerth lab

Vagina Museum @vaginamuseum.bsky.social · Aug 22

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...

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Reposted by Hugerth lab

Rosa Fernández @rosafernandez.bsky.social · Aug 15

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...

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

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Reposted by Hugerth lab

Sean Gibbons 🦠💩 @gibbological.bsky.social · Jul 31

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/...
🧵

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

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Hugerth lab @h-mel.bsky.social · Aug 21

Anyone know what happened to hmpdacc.org?

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

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Reposted by Hugerth lab

Mel Andrews @bayesianboy.bsky.social · Aug 19

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.

Carl T. Bergstrom @carlbergstrom.com · Aug 19

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.

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Reposted by Hugerth lab

Larry R. Nittler 🚀🎹🌖☄️ @larrynittler.bsky.social · Aug 15

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

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Reposted by Hugerth lab

Torsten Günther @trstngnthr.bsky.social · Aug 12

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/...

Bioinformatician - Uppsala University

Bioinformatician, Department of Organismal Biology, Uppsala University

www.uu.se

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Reposted by Hugerth lab

Angie Rasmussen @angierasmussen.bsky.social · Aug 15

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

Carl T. Bergstrom @carlbergstrom.com · Aug 14

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.

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Hugerth lab @h-mel.bsky.social · Aug 16

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

Reposted by Hugerth lab

John Lees @bacpop.org · Aug 15

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

Mathematical modelling for biologists - Modelling concepts in biological research

www.ebi.ac.uk

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Reposted by Hugerth lab

Luisa Hugerth @luhugerth.bsky.social · Aug 15

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

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Reposted by Hugerth lab

Richard Sever @richardsever.bsky.social · Jul 11

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...

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

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Hugerth lab @h-mel.bsky.social · Jun 27

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!

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Hugerth lab @h-mel.bsky.social · Jun 18

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...

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

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