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Reposted by Uwe Ohler

Einstein Foundation Berlin @einsteinberlin.bsky.social · Aug 21

☎️ Berlin Calling: Your Research. Our City. A Perfect Match. The Einstein Postdoctoral Grant for early career researchers or the Einstein Visiting Fellowship for distinguished scholars – our funding opportunities offer pathways into Berlin’s research landscape.

berlincalling.einsteinfoundation.de

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Uwe Ohler @uweohler.bsky.social · Aug 6

Awesome work by @prauten.bsky.social who persevered to find out why evaluations looked so strange, where it came from, and how it can be fixed.
(3/3)

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Uwe Ohler @uweohler.bsky.social · Aug 6

We found -70 affected papers in Nature journals alone. So the likely number is in the 100s.
How much it affects conclusions depends on which reliable metrics were also used.

Please stop using it. Choose proper metrics to help you understand whether your tool is doing what it is supposed to!
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Uwe Ohler @uweohler.bsky.social · Aug 6

To evaluate computational models, we rely on trusted benchmark data and metrics

So what if a metrics is widely used… but plain wrong? It means that evaluations in dozens of papers are meaningless.

This has happened in single cell genomics…

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Nature Biotechnology @natbiotech.nature.com · Jul 30

Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology

Silhouette score is unsuitable as a metric for single-cell data integration.

go.nature.com

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Uwe Ohler @uweohler.bsky.social · Jul 14

20 year lab anniversary and local reunion last Friday!

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Uwe Ohler @uweohler.bsky.social · Apr 16

Finally!!

“No government — regardless of which party is in power — should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue” Harvard president Alan M. Garber

www.nytimes.com/2025/04/15/u...

Why Harvard Decided to Fight Trump

The Trump administration will freeze over $2 billion in federal funds because Harvard refused to comply with a list of demands. Harvard leaders believed saying no was worth the risk.

www.nytimes.com

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Uwe Ohler @uweohler.bsky.social · Apr 4

Destroying things takes days. Rebuilding things takes decades.
There is only the present moment to prevent the worst.

Reposted by Uwe Ohler

Maureen Barr @barrlab.bsky.social · Apr 4

A friend at NIH received notice that the National Library of Medicine is terminating its bioinformatics program

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Reposted by Uwe Ohler

PLOS Biology @plosbiology.org · Feb 21

PLOS has issued a statement on recent US Executive Orders and scientific integrity.

We are determined to stand firmly behind our mission, our values and our principles, and against any attempt at censorship or undermining of the core principles of scientific inquiry.

plos.io/3D4O8cH

PLOS statement on recent US Executive Orders and scientific integrity - The Official PLOS Blog

Since its founding over twenty five years ago PLOS has been dedicated to advancing open science, ensuring that knowledge is accessible to…

plos.io

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Reposted by Uwe Ohler

Marc Robinson-Rechavi @marcrr.bsky.social · Feb 20

European Federation of Academies of Sciences and Humanities ALLEA Statement Responding to Recent U.S. Restrictions on Academic Freedom: allea.org/allea-publis...

ALLEA Publishes Statement Responding to Recent U.S. Restrictions on Academic Freedom

On 19 February, ALLEA published a new Statement expressing grave concern over recent developments in the U.S. affecting the autonomy of scientific research, including funding freezes and blatant censo

allea.org

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Reposted by Uwe Ohler

nf-core @nf-co.re · Feb 17

❓ What do you think about nf-core ❓

🤔 We want your thoughts on the initiative, whether you are a user, developer, newcomer or veteran.

✏️ Fill out this short and anonymous <5min survey to help us guide the community! seqera.typeform.com/2025-nf-core

#bioinformatics #nextflow #nfcore #pipelines

nf-core community survey 2025

This short 8-question survey aims to gauge the current feelings about the nf-core initiative and community. Say what you love and how we can make the community even better!

seqera.typeform.com

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Reposted by Uwe Ohler

Jeremy Berg @jeremymberg.bsky.social · Feb 15

Many of the NCBI resources and eRA Commons were run by contractors. However, many of these folks were apparently converted to Fed positions at the end of last year to protect them.

This means that many of them were probationary NIH employees...

Trying to run this down...

2/n

a man in a plaid shirt is typing on a keyboard in front of a computer monitor

ALT: a man in a plaid shirt is typing on a keyboard in front of a computer monitor

media.tenor.com

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Uwe Ohler @uweohler.bsky.social · Feb 14

www.sueddeutsche.de/meinung/asyl...

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Uwe Ohler @uweohler.bsky.social · Feb 12

On his album “Da Questa Parte Del Mare” Gianmaria Testa stated:

“Being rooted means not separating yourself from others. If you know where you come from, you can open yourself up to others. That's exactly the opposite of what political parties like [insert local choice] tell us.”

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Uwe Ohler @uweohler.bsky.social · Feb 12

Will share the occasional piece of music that I am listening to. Who knows, maybe someone will discover a new favorite this way…

youtube.com/watch?v=hov0...

youtube.com

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Uwe Ohler @uweohler.bsky.social · Feb 12

This cause is close to my heart - please sign: weact.campact.de/petitions/sa...

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Reposted by Uwe Ohler

Patrick Cramer @patrick-cramer.maxplanck.de · Feb 11

Im Podcast "In aller Ruhe" mit @emcke.bsky.social habe ich über Forschung, Fakten & politische Verantwortung gesprochen – und drei Vorschläge für die nächste Bundesregierung gemacht. 🎙️👇 www.sueddeutsche.de/meinung/podc...

Wissenschaft und Gegenaufklärung: Max-Planck-Präsident Patrick Cramer im Podcast

Im Gespräch mit Carolin Emcke spricht Patrick Cramer über die Bedeutung von Expertise in der Politik, die Vorteile und Risiken internationaler Forschungszusammenarbeit und wie Forscherinnen und Forsch...

www.sueddeutsche.de

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Uwe Ohler @uweohler.bsky.social · Feb 10

Deadline in 10 days!! @mdc-berlin.bsky.social

Uwe Ohler @uweohler.bsky.social · Dec 19

Our institute wide grad school recruitment 2025 is open!
We’d love to see more #computerscience #bioinformatics #machinelearning applicants. Behind the broad biomedical topics below you will find lots of exciting #datascience projects!!

Max Delbrück Center @mdc-berlin.bsky.social · Dec 18

We are now accepting applications for the spring round of our fully-funded #PhD positions at @mdc-berlin.bsky.social‼️

Apply for your #ScienceCareer in:
▶️ Genes, Cells and Cell-based Medicine
▶️ Molecular Processes and Therapies
▶️ Integrative Biomedicine

👉 www.mdc-berlin.de/phd 👈

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Uwe Ohler @uweohler.bsky.social · Feb 6

In which employees of a private company gain total access to files of every citizen, and government offices are stacked with ‚loyals‘.
It makes me wonder, dear friends in the US: do you see it differently? Because from here, it does look like a coup. With a lot of added noise for distraction. 2/2

Uwe Ohler @uweohler.bsky.social · Feb 6

Tonight, the US correspondent of Austrian public broadcasting expressed consternation at the laissez faire of the American public that they are essentially victims to a coup. Not a military coup but one in which a billionaire‘s employees take over the government and fire public servants at will. 1/

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Uwe Ohler @uweohler.bsky.social · Feb 6

Tonight, the US correspondent of Austrian public broadcasting expressed consternation at the laissez faire of the American public that they are essentially victims to a coup. Not a military coup but one in which a billionaire‘s employees take over the government and fire public servants at will. 1/

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Uwe Ohler @uweohler.bsky.social · Feb 2

Klingt dieses Video etwas zu aufgeregt? Für mich ja. Ist es höchste Zeit, das von den Rechten gelenkte Narrativ gerade zu rücken? Absolut.

youtube.com/watch?v=RbxT...

youtube.com

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Uwe Ohler @uweohler.bsky.social · Jan 27

Important study from Pia @prauten.bsky.social in the lab: some popular evaluation metrics for #singlecell analysis #benchmarking are intrinsically flawed and report near optimal scores even when methods completely fail. This issue is found in dozens of papers. Read her thread for the whole story!

Pia Rautenstrauch @prauten.bsky.social · Jan 24

1/4 🧵 Preprint alert: In "Metrics Matter: Why We Need to Stop Using Silhouette in #SingleCell #Benchmarking," we reveal critical flaws in common #Evaluation metrics for #Integration and propose robust alternatives. @uweohler.bsky.social
www.biorxiv.org/content/10.1...

Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking

Current-day single-cell studies comprise complex data sets affected by nested batch effects caused by technical and biological factors, relying on advanced integration methods. Silhouette is an establ...

www.biorxiv.org

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Reposted by Uwe Ohler

Wolfgang Busch @rootstrapping.bsky.social · Jan 21

This is an amazing opportunity for graduate students in #PlantScience who consider a postdoc. 3-day, all-expenses-paid program from July 23-25, 2025 in
San Diego! Check it out and spread the word!
www.salk.edu/about/our-co...

DISCOVER Symposium - Salk Institute for Biological Studies

Applications are open! Program Overview & Goals The Salk Institute for Biological Sciences Symposium for a Diverse Inclusive Scientific Community Offering a Vision for an Ecosystem Reimagined (DISCO...

www.salk.edu

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Uwe Ohler @uweohler.bsky.social · Jan 8

It’s different for Bezos and Zuckerberg. Both have companies that billions use, both have supported science in sometimes amazing and possibly altruistic ways. It’s harder to disengage. EU laws may help a bit, but are there any alternatives to the Australian model to ban social media for minors?

Uwe Ohler @uweohler.bsky.social · Jan 8

I would distinguish between X and Meta. Twitter was always a niche medium and has been even more so since turning X. Bluesky shows that we are not dependent on the ego that Jimmy Kimmel called ‘the Kramer to Trump’s Seinfeld’. 1/