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Reposted by Michael Kuhn

Erick Ratamero @erickratamero.com · 9h

The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Scientific Community Manager

EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and teams performing scientific research in disci...

embl.wd103.myworkdayjobs.com

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Reposted by Michael Kuhn

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 6d

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns https://www.biorxiv.org/content/10.1101/2025.10.01.679725v1

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Reposted by Michael Kuhn

Anna Mankowski @oceanna.bsky.social · 8d

Had a great time yesterday presenting my efforts to use large-scale computational analyses to better understand marine microbes and their impact on carbon cycling. Thanks #SAME18 for the opportunity!

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Reposted by Michael Kuhn

Ákos T Kovács @evolvedbiofilm.bsky.social · 12d

Cool PNAS paper by @jordivangestel.bsky.social and colleagues
Contributed by Carol Gross
[reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social]

Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation

www.pnas.org/doi/10.1073/...

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Reposted by Michael Kuhn

Matt Rockman @wormsrock.bsky.social · 13d

C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

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Reposted by Michael Kuhn

Pamela Ferretti @pamferretti.bsky.social · 11d

If you generate or reuse #microbiome data, check out these guidelines for equitable sequence data reuse. Grateful to @alexjprobst.bsky.social and his team for leading this important work and for bringing together 160+ microbiome scientists (myself included) to contribute!

doi.org/10.1038/s415...

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Reposted by Michael Kuhn

DSMZ Digital Diversity @dsmzd3.bsky.social · 12d

❗New publication📑

Read all about #StrainInfo - the central database for linked microbial strain identifiers 🧫🖥️

👉 academic.oup.com/database/art...

#DSMZDigitalDiversity #science 🧪 #databases #FAIRdata @nfdi4microbiota.bsky.social 🧬

StrainInfo—the central database for linked microbial strain identifiers

Abstract. Throughout scientific literature and databases, microbial strains are often distinguished using either non-standardized designations or one of se

academic.oup.com

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Reposted by Michael Kuhn

Arnau Sebé-Pedrós @arnausebe.bsky.social · 14d

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...

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Reposted by Michael Kuhn

Michael Zimmermann Lab @zimmermannlab.bsky.social · 14d

📍Paper alert 📍

Our new preprint is available on: chemrxiv.org/engage/chemr...

Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.

Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites

The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....

chemrxiv.org

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Reposted by Michael Kuhn

Freya Harrison @friendlymicrobe.bsky.social · 14d

A colleague received proofs of an accepted manuscript, and the "proofing process" clearly involved running the text through ChatGPT. Their voice has been erased, and errors introduced. This is from a supposedly reputable publisher. Anyone else been put through this particular form of hell? #MicroSky

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Reposted by Michael Kuhn

Infect-Net @infect-net.bsky.social · 15d

🏆 Fighting the Gender Award Gap: Microbiologist Prof Dr Lisa Maier from @unituebingen.bsky.social received the main award of the German Association for #Microbiology and Hygiene at the #DGHM meeting in Jena. Congratulations to @lisamaierlab.bsky.social we are proud of you! 💜
📸 Gabriele Pradel

Bildschirmpräsentation mit der Vita von Prof. Dr. Lisa Maier, Mikrobiologin an der Uni Tübingen, zur Verleihung des Hauptpreises der DGHM in Jena.

Mikrobiologin Prof. Dr. Antje Flieger liest die Laudatio für Prof. Dr. Lisa Maier zur Verleihung des Hauptpreises der DGHM in Jena. Preisträgerin Lisa Maier steht links neben ihr.

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Reposted by Michael Kuhn

Pamela Ferretti @pamferretti.bsky.social · 15d

My commentary article, featuring the work of Aasmets et al. on the long-lasting effects of medications on the gut microbiome, is now out in mSystems @asm.org
#microbiome #microsky

doi.org/10.1128/msys...

The gut remembers: the long-lasting effect of medication use on the gut microbiome | mSystems

Over the past decades, medication use has steadily increased worldwide, with individuals frequently taking multiple medications (polypharmacy), often repeatedly over extended periods of time (1). Yet,...

doi.org

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Reposted by Michael Kuhn

EMBL Events @events.embl.org · 22d

Our scientific organisers opened ‘The human microbiome’ symposium by giving us a brief update on their most recent work 🦠 #EESMicrobiome

🔹Mani Arumugam, University of Copenhagen
🔹Ami Bhatt, Stanford University School of Medicine
🔹Peer Bork, EMBL Heidelberg
🔹Nicola Segata, University of Trento

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Michael Kuhn @biocs.bsky.social · 22d

Da ich in Leipzig aufgewachsen bin muss ich doch zur Ehrenrettung der Stadt schreiben, dass die tatsächlich einen Plan hat um die Wärmeversorgung zu Dekarbonisieren, u.a. eine neue Fernwärmeleitung nach Leuna um Abwärme zu nutzen

zukunft-fernwaerme.de

Leipziger Wärme

Leipzig hat beste Voraussetzungen, die kommunale Wärmewende erfolgreich zu gestalten. Dazu hat der Stadtrat den Auftrag erteilt, eine kommunale Wärmeplanung zu erstellen. Ziel der Stadt Leipzig ist es...

zukunft-fernwaerme.de

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Michael Kuhn @biocs.bsky.social · 24d

Wahrscheinlich ist @garbageday.email gemeint

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Reposted by Michael Kuhn

Thomas Lin Pedersen @thomasp85.com · 27d

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.

It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.

Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

ggplot2 4.0.0

A new major version of ggplot2 has been released on CRAN. Find out what is new here.

www.tidyverse.org

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Reposted by Michael Kuhn

Lior Pachter @lpachter.bsky.social · Sep 5

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

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Reposted by Michael Kuhn

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

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Reposted by Michael Kuhn

Pat Schloss @patschloss.bsky.social · Aug 30

My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to...

genomebiology.biomedcentral.com/articles/10....

Closure of the NCBI SRA and implications for the long-term future of genomics data storage - Genome Biology

genomebiology.biomedcentral.com

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Reposted by Michael Kuhn

Alex Crits-Christoph @acritschristoph.bsky.social · Aug 21

Soo.... the last time it was online was April 1 2025 (consistently offline April 4 onwards)
web.archive.org/web/20250401...

My (limited) understanding is that hmpdacc.org is recently run by a team at IGS UMD, and the website being offline may or may not relate to changes at the NIH

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Reposted by Michael Kuhn

Brendel @brendelbored.bsky.social · Aug 19

This is in the replies and it demonstrates a real issue which is if you find profundity from an AI, you’re responding to something profound a human being wrote that was vacuumed up and what ends up happening is you thank AI and not only don’t thank the person, you have no idea they were involved

Michael Love@elkmovie.bsky.social • 6m
I thought this sounded familiar and it turns out it literally just found an old George RR
Martin quote and wrote a short story out of it:
George R.R. Martin > Quotes > Quotable Quote (?)
"I think there are two types of writers, the architects and the gardeners.
The architects plan everything ahead of time, like an architect building a house. They know how many rooms are going to be in the house, what kind of roof they're going to have, where the wires are going to run, what kind of plumbing there's going to be. They have the whole thing
designed and blueprinted out before they even nail the first board up. The gardeners dig a hole, drop in a seed and water it. They kind of know what seed it is, they know if planted a fantasy seed or mystery seed or whatever. But as the plant comes up and they water it, they don't know how many branches it's going to have, they find out as it grows. And I'm much more a gardener than an architect."
ALT
- George R.R. Martin

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Michael Kuhn @biocs.bsky.social · Aug 15

We hope many of you will find it useful, and will continue to add data. Here's the preprint: www.biorxiv.org/content/10.1... - hopefully coming soon to a NAR Database Issue near you 😅 Thanks to everyone in the @borklab.bsky.social @embl.org who contributed to this! 7/7

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

www.biorxiv.org

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Michael Kuhn @biocs.bsky.social · Aug 15

Going from an internal database to a public resource required a lot of work in the past year to enforce consistency, and I'm sure there are still some inconsistencies left. But such is life with >100k entries! 6/7

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Michael Kuhn @biocs.bsky.social · Aug 15

We have already made good use of part of the data in publications, e.g. doi.org/10.1136/gutj... doi.org/10.1038/s415... doi.org/10.7554/eLif... doi.org/10.1016/j.ce... doi.org/10.1101/2024... to study biomarkers for pancreatic cancer, associations with microbial load, or the spread of C. diff 5/7

Figure 3 from Kartal et al. 2022, showing that the proposed signature of pancreatic duct carcinoma mainly has a low false-positive rate for other diseases

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Michael Kuhn @biocs.bsky.social · Aug 15

The database grew from human data to animal and environmental data, and now covers the whole globe (and even the International Space Station). I'm still fascinated by the tracks of expeditions across the oceans and samples from Antarctica to Greenland 4/7

A map of the globe showing the distribution of samples in Metalog

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