Uwe Ohler
@uweohler.bsky.social
Scientist and music nerd. All things machine learning and genomics for gene regulation.
Faculty at Max Delbruck Centrum and Humboldt University Berlin
@mdc-berlin.bsky.social
http://www.mdc-berlin.de/ohler
Baritone at www.byrdland.org
Faculty at Max Delbruck Centrum and Humboldt University Berlin
@mdc-berlin.bsky.social
http://www.mdc-berlin.de/ohler
Baritone at www.byrdland.org
Reposted by Uwe Ohler
🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
October 9, 2025 at 11:00 AM
🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Dusa’s study is on the cover of this month’s #CellGenomics! Check it out if you haven’t had the chance yet!
www.cell.com/issue/S2666-...
www.cell.com/issue/S2666-...
October 10, 2025 at 9:32 AM
Dusa’s study is on the cover of this month’s #CellGenomics! Check it out if you haven’t had the chance yet!
www.cell.com/issue/S2666-...
www.cell.com/issue/S2666-...
Reposted by Uwe Ohler
☎️ 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
berlincalling.einsteinfoundation.de
August 21, 2025 at 8:32 AM
☎️ 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
berlincalling.einsteinfoundation.de
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…
(1/)
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…
(1/)
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
August 6, 2025 at 8:07 AM
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…
(1/)
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…
(1/)
20 year lab anniversary and local reunion last Friday!
July 14, 2025 at 7:15 PM
20 year lab anniversary and local reunion last Friday!
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...
“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
April 16, 2025 at 6:40 AM
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...
“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...
Destroying things takes days. Rebuilding things takes decades.
There is only the present moment to prevent the worst.
There is only the present moment to prevent the worst.
April 4, 2025 at 7:37 PM
Destroying things takes days. Rebuilding things takes decades.
There is only the present moment to prevent the worst.
There is only the present moment to prevent the worst.
Reposted by Uwe Ohler
A friend at NIH received notice that the National Library of Medicine is terminating its bioinformatics program
April 4, 2025 at 7:00 PM
A friend at NIH received notice that the National Library of Medicine is terminating its bioinformatics program
Reposted by Uwe Ohler
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
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
February 21, 2025 at 3:41 PM
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
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
Reposted by Uwe Ohler
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
February 20, 2025 at 3:55 PM
European Federation of Academies of Sciences and Humanities ALLEA Statement Responding to Recent U.S. Restrictions on Academic Freedom: allea.org/allea-publis...
Reposted by Uwe Ohler
❓ 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
🤔 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
February 17, 2025 at 10:49 AM
❓ 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
🤔 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
Reposted by Uwe Ohler
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
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
February 15, 2025 at 12:05 PM
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
This means that many of them were probationary NIH employees...
Trying to run this down...
2/n
February 14, 2025 at 5:10 PM
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/watch?v=hov0...
youtube.com
February 12, 2025 at 9:39 PM
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/watch?v=hov0...
This cause is close to my heart - please sign: weact.campact.de/petitions/sa...
February 12, 2025 at 8:47 PM
This cause is close to my heart - please sign: weact.campact.de/petitions/sa...
Reposted by Uwe Ohler
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
February 11, 2025 at 8:37 AM
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...
Deadline in 10 days!! @mdc-berlin.bsky.social
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!!
We’d love to see more #computerscience #bioinformatics #machinelearning applicants. Behind the broad biomedical topics below you will find lots of exciting #datascience projects!!
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 👈
Apply for your #ScienceCareer in:
▶️ Genes, Cells and Cell-based Medicine
▶️ Molecular Processes and Therapies
▶️ Integrative Biomedicine
👉 www.mdc-berlin.de/phd 👈
February 10, 2025 at 4:13 PM
Deadline in 10 days!! @mdc-berlin.bsky.social
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
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
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/
February 6, 2025 at 11:02 PM
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
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
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/
February 6, 2025 at 10:58 PM
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/
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/watch?v=RbxT...
youtube.com
February 2, 2025 at 11:34 AM
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/watch?v=RbxT...
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!
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...
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
January 27, 2025 at 3:23 PM
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!
Reposted by Uwe Ohler
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...
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
January 21, 2025 at 10:28 PM
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...
San Diego! Check it out and spread the word!
www.salk.edu/about/our-co...
So.
the cowardly abandonment of fact checking and content moderation at #Meta makes it more urgent -
how can we let our children use any social media? How can we educate to make use of the good things and support facts while not promoting fascism, autocrats, xenophobia, lgbtqia+phobia etc?
the cowardly abandonment of fact checking and content moderation at #Meta makes it more urgent -
how can we let our children use any social media? How can we educate to make use of the good things and support facts while not promoting fascism, autocrats, xenophobia, lgbtqia+phobia etc?
January 8, 2025 at 6:34 PM
So.
the cowardly abandonment of fact checking and content moderation at #Meta makes it more urgent -
how can we let our children use any social media? How can we educate to make use of the good things and support facts while not promoting fascism, autocrats, xenophobia, lgbtqia+phobia etc?
the cowardly abandonment of fact checking and content moderation at #Meta makes it more urgent -
how can we let our children use any social media? How can we educate to make use of the good things and support facts while not promoting fascism, autocrats, xenophobia, lgbtqia+phobia etc?
Happy to have you visit!
For anyone in Berlin - the seminar is Tues 14th at 4pm.
For anyone in Berlin - the seminar is Tues 14th at 4pm.
Very excited to visit the Berlin Institute of Health/Max Planck next week and give some updates about what I've been working on at the BIMSB seminar! Looking forward to seeing any of you who happen to be around.
Any recommendations on things to do in Berlin?
Any recommendations on things to do in Berlin?
January 8, 2025 at 6:26 PM
Happy to have you visit!
For anyone in Berlin - the seminar is Tues 14th at 4pm.
For anyone in Berlin - the seminar is Tues 14th at 4pm.
Reposted by Uwe Ohler
“Onconaut,” an #AI-based online tool that #mdcBerlin's @al2na.bsky.social has developed, helps oncologists and patients to find the most up-to-date and tailored treatment possible. @helmholtzai.bsky.social has now recognized it as the “Best digital resource.”
More: www.mdc-berlin.de/news/news/na...
More: www.mdc-berlin.de/news/news/na...
![Graphic with text: The title "ONCONAUT" is at the top, featuring an illustration of a space helmet with a DNA strand in the background [icon of the "onconaut.ai" program]. Below, the text reads 'ALTUNA AKALIN' with a small portrait of a person [Altuna Akalin] in the bottom left corner.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:xe7uchirikbpccf37pu52pz2/bafkreiadjx3fknmcyxpfiy3pt2fy2x7v6eosuzgec4vb6pugmo47r4jn4y@jpeg)
December 17, 2024 at 4:25 PM
“Onconaut,” an #AI-based online tool that #mdcBerlin's @al2na.bsky.social has developed, helps oncologists and patients to find the most up-to-date and tailored treatment possible. @helmholtzai.bsky.social has now recognized it as the “Best digital resource.”
More: www.mdc-berlin.de/news/news/na...
More: www.mdc-berlin.de/news/news/na...