Uwe Ohler
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
mdc-berlin.de/ohler
Baritone at www.byrdland.org
- #jobalert We have open position/s in genomics and explainable/generative AI @mdc-bimsb.bsky.social @humboldtuni.bsky.social www.hu-berlin.de/universitaet... More info also on linkedin: www.linkedin.com/posts/uwe-oh... please share!
- Deadline is coming up soon!! www.mdc-berlin.de/career/jobs/...
- 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/... - 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-...
- I am so happy to share that our paperis officially published in Cell Genomics! In this paper, we describe TESLA-seq, which combines pooled CRISPR activation with targeted single-cell RNA-seq to map enhancer-gene connections at high sensitivity. Link to the full story: www.cell.com/cell-genomic...
- 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
- 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/)
- 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
- 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! (2/)
- 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)
- 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...
- Destroying things takes days. Rebuilding things takes decades. There is only the present moment to prevent the worst.
- Reposted by Uwe OhlerA friend at NIH received notice that the National Library of Medicine is terminating its bioinformatics program
- Reposted by Uwe OhlerPLOS 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
- Reposted by Uwe OhlerEuropean Federation of Academies of Sciences and Humanities ALLEA Statement Responding to Recent U.S. Restrictions on Academic Freedom: allea.org/allea-publis...
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- 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...
- 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.”
- This cause is close to my heart - please sign: weact.campact.de/petitions/sa...
- Reposted by Uwe OhlerIm 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!!
- 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
- 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...
- 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...
- Reposted by Uwe OhlerThis 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...
- 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?
- Happy to have you visit! For anyone in Berlin - the seminar is Tues 14th at 4pm.
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- 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!!
- Reposted by Uwe OhlerWe are looking for new group leaders. If RNA is your thing, and/or computational biology and you want to start your own group, check out these links. Feel free to contact me about these! And, please help me spread this. Thanks! www.imb.de/jobs/jobdeta... www.imb.de/jobs/jobdeta...
- Hugely deserved award for my colleague…
- Congrats, Ana Pombo! The #mdcBerlin scientist receives Germany's most important science prize: the Gottfried Wilhelm Leibniz Prize by the German Research Foundation #DFG. About @apombo1.bsky.social and her work: www.mdc-berlin.de/news/news/an... #mdcBIMSB @www.helmholtz.de @humboldtuni.bsky.social
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- Reminder #jobalert for a starting postdoc or PhD position (for someone with strong ML background)! Joint project with Gregoire Montavon’s lab at #BIFOLD @xtraexer.bsky.social - explainable AI for self supervised LLMs in gene regulation. Apply until Dec 13! www.bifold.berlin/about-us/opp...
- Reposted by Uwe OhlerWe want to make JASPAR even better for our users! Please share your experience and ideas to help us enhance the database by taking a quick survey at nettskjema.no/a/467839. Your insights make a difference! Thank you so much for your participation.
- #paperalert! In our new study, we ask the question: Can we predict RNA stability across conditions and protocols, based solely on experimental and/or computationally predicted RNA binding protein target sites? Read the paper to find out ! www.biorxiv.org/content/10.1...
- On the way to #Dagstuhl for a week full of amazing RNA & ML - co-organizing w/ @igorulitsky.bsky.social #KathiZarnack #AnnalisaMarsico #GeneYeo. First time since 2019! www.dagstuhl.de/en/seminars/...
- Reposted by Uwe OhlerOur fantastic collaboration with the lab of Nils Blüthgen @molsysbio.bsky.social has been published: www.embopress.org/doi/full/10.... #RNASky #RNAbiology @mdc-berlin.bsky.social
- Reposted by Uwe OhlerHappy to share our perspective preprint on the state of explainable AI. XAI needs to shift from algorithm- to problem-driven development to make sure methods can serve meaningful purposes. We are looking forward to discuss, here or on alphaxiv.org/abs/2409.14590 .
- First #jobalert on Bluesky! Postdoc (or PhD position with strong ML background), for a joint project with Gregoire Montavon’s lab at #BIFOLD #TU-Berlin . Topic is explainable AI /ML for self supervised LLMs in multi/spatial omics & gene regulation. www.jobs.tu-berlin.de/stellenaussc...
- Reposted by Uwe Ohler🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices. In our latest paper, we advocate for improving software quality in bioinformatics through teamwork. academic.oup.com/bioinformati...
- Reposted by Uwe OhlerJanelia is recruiting AI scientists and theory fellows to collaborate with experimental scientists on hard biological problems - these positions have a considerable level of independence and very competitive salaries. Join our great community! Ai.hhmi.org janelia.org/theoryfellow #neuroscience #AI
- Joanne Chory, 1955-2024
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- Re-Posting our recent preprint, the last one I wrote up on The X That Must Not Be Named: www.biorxiv.org/content/10.1... Targeted single cell CRISPR dissection of complex enhancer landscapes - among the most intricate wet lab work we have attempted so far:
- It’s really great to see how quickly this is taking off here. Thanks to @johnprensner.bsky.social and @anshulkundaje.bsky.social and others who nudged me a few weeks ago! (I will post a new RNA regulation preprint here soon :-)
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- Hello World.. ehm.. Bluesky! Great to find many familiar faces on here! Also nice to see the @biorxivpreprint.bsky.social presence … To get more traction - let’s get journals and conferences to move over here! @ritastrack.bsky.social #EMBL #keystone #GRC #cshl #wellcome
