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Uwe Ohler

@uweohler.bsky.social
1.8K followers 366 following 47 posts

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 www.mdc-berlin.de/ohler Baritone at www.byrdland.org

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Uwe Ohler @uweohler.bsky.social · 30/09/2026
Our #genome still holds many mysteries… Want to help figuring out what is actually translated into proteins and how it is regulated? Our research network #ORFeus is looking for motivated #PhD students to join projects across Europe. Deadline is soon (Oct 22), have a look! www.orfeus-dn.eu/apply/
orfeus-dn.eu
Apply to ORFeus — 15 fully funded PhD positions
15 fully funded PhD positions across Europe, starting 2027. Applications open 1 October and close 22 October 2026. Rank up to three projects.
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Uwe Ohler @uweohler.bsky.social · 07/08/2026
Join the 40th anniversary symposium on the Eukaryotic Promoter Database #EPD at #ECCB26 in Geneva on Sep 4! We have a great lineup of speakers - more info here: eccb2026.org/communities-... There is still time to register and submit an abstract for poster/flash talk!
eccb2026.org
Communities Day
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Uwe Ohler @uweohler.bsky.social · 11/06/2026
#HEIBRiDS, our graduate school for #data_science in the natural sciences, is looking for #PhD students to join! lnkd.in/dpscUjqz Our project is on using #explainableAI and generative models for regulatory DNA sequence design. Interested? Apply by June 24, 2026: lnkd.in/dX_rWVsV
lnkd.in
HEIBRiDS - Helmholtz International Berlin Research School in Data Science | LinkedIn
HEIBRiDS - Helmholtz International Berlin Research School in Data Science | 878 followers on LinkedIn. Interdisciplinary doctoral program on data science applications within a broad range of natural s...
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Uwe Ohler @uweohler.bsky.social · 22/05/2026
What a way to go. Take care, Stephen Colbert… youtube.com/watch?v=zG0H...
youtube.com
"Jump Up / Hello Goodbye" Paul McCartney, Elvis Costello, Jon Batiste, Louis Cato & Stephen Colbert
YouTube video by The Late Show with Stephen Colbert
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Uwe Ohler @uweohler.bsky.social · 22/01/2026
#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!
linkedin.com
#jobalert | Uwe Ohler
#jobalert Humboldt-Universität zu Berlin   @mdcberlin Open position/s in explainable AI for genomics! https://lnkd.in/dwcMkN4e couple of things for context: Out of formal reasons, the position’s ...
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Uwe Ohler @uweohler.bsky.social · 22/11/2025
Deadline is coming up soon!! www.mdc-berlin.de/career/jobs/...
mdc-berlin.de
Six AI Fellowships in Human Health
Six Independent Fellow Positions in Artificial Intelligence for Human Health in Berlin
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Max Delbrück Center @mdc-berlin.bsky.social · 09/10/2025
🚀 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/...
Job announcement: The image has a solid dark blue background with a clean, minimal layout. In the top left corner, the word “JOBS” appears in all-capital red sans-serif text. Below, large white sans-serif text spans several lines and reads: “Three Independent Group Leaders in Bioengineering Approaches to Human Health m/f/d.” Near the bottom left, smaller white sans-serif text reads: “Apply by November 16, 2025,” followed by “Max Delbrück Center (Berlin-Buch)” in lighter gray. In the bottom right corner is the Max Delbrück Center logo in white and blue.
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Uwe Ohler @uweohler.bsky.social · 10/10/2025
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-...
cell.com
Issue: Cell Genomics
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Einstein Foundation Berlin @einsteinberlin.bsky.social · 21/08/2025
☎️ 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 · 06/08/2025
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/)
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Uwe Ohler @uweohler.bsky.social · 14/07/2025
20 year lab anniversary and local reunion last Friday!
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Uwe Ohler @uweohler.bsky.social · 16/04/2025
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...
nytimes.com
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.
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Uwe Ohler @uweohler.bsky.social · 04/04/2025
Destroying things takes days. Rebuilding things takes decades. There is only the present moment to prevent the worst.
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Maureen Barr @barrlab.bsky.social · 04/04/2025
A friend at NIH received notice that the National Library of Medicine is terminating its bioinformatics program
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PLOS Biology @plosbiology.org · 21/02/2025
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.io
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…
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Marc Robinson-Rechavi @marcrr.bsky.social · 20/02/2025
European Federation of Academies of Sciences and Humanities ALLEA Statement Responding to Recent U.S. Restrictions on Academic Freedom: allea.org/allea-publis...
allea.org
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
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nf-core @nf-co.re · 17/02/2025
❓ 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
seqera.typeform.com
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!
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Jeremy Berg @jeremymberg.bsky.social · 15/02/2025
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
media.tenor.com
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
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Uwe Ohler @uweohler.bsky.social · 14/02/2025
www.sueddeutsche.de/meinung/asyl...
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Uwe Ohler @uweohler.bsky.social · 12/02/2025
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 · 12/02/2025
This cause is close to my heart - please sign: weact.campact.de/petitions/sa...
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Patrick Cramer @handle.invalid · 11/02/2025
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...
sueddeutsche.de
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...
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Uwe Ohler @uweohler.bsky.social · 10/02/2025
Deadline in 10 days!! @mdc-berlin.bsky.social
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Uwe Ohler @uweohler.bsky.social · 06/02/2025
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
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Uwe Ohler @uweohler.bsky.social · 06/02/2025
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 · 02/02/2025
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 · 27/01/2025
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!
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Wolfgang Busch @rootstrapping.bsky.social · 21/01/2025
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...
salk.edu
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...
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Uwe Ohler @uweohler.bsky.social · 08/01/2025
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?
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Uwe Ohler @uweohler.bsky.social · 08/01/2025
Happy to have you visit! For anyone in Berlin - the seminar is Tues 14th at 4pm.
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Max Delbrück Center @mdc-berlin.bsky.social · 17/12/2024
“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...
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.
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Uwe Ohler @uweohler.bsky.social · 19/12/2024
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!!
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René Ketting @reneketting.bsky.social · 14/12/2024
We 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...
imb.de
Jobdetail
IMB Mainz
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Uwe Ohler @uweohler.bsky.social · 11/12/2024
Hugely deserved award for my colleague…
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Anshul Kundaje @anshulkundaje.bsky.social · 11/12/2024
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
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Uwe Ohler @uweohler.bsky.social · 07/12/2024
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...
bifold.berlin
BIFOLD is a Research Assistant (salary grade E 13 TV-L Berliner Hochschulen)
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Anthony Mathelier @amathelier.bsky.social · 04/12/2024
We 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.
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Uwe Ohler @uweohler.bsky.social · 04/12/2024
#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...
biorxiv.org
Cell-type specific prediction of RNA stability from RNA-protein interactions
RNA-binding proteins (RBPs) are important contributors to post-transcriptional regulatory processes. The combinatorial action of expressed RBPs and non-coding factors bound to the same transcript dete...
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Uwe Ohler @uweohler.bsky.social · 01/12/2024
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/...
dagstuhl.de
Dagstuhl Seminar 24491: Deep Learning for RNA Regulation and Multidimensional Transcriptomics
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Markus Landthaler @landthalerm.bsky.social · 21/11/2024
Our 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
embopress.org
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting | Molecular Systems Biology
imageimageTranscriptome-wide measurement of subcellular mRNA dynamics in mouse ES cells reveals that nuclear retention is the rate-limiting step in the life-cycle of most mRNAs and provides a resource for understanding spatiotemporal gene ...
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Stefan Haufe @sparsity.bsky.social · 24/09/2024
Happy 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 .
alphaxiv.org
Explainable AI needs formal notions of explanation correctness | alphaXiv
The use of machine learning (ML) in critical domains such as medicine poses risks and requires regulation. One requirement is that decisions of ML systems in high-risk applications should be human-und...
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Uwe Ohler @uweohler.bsky.social · 19/11/2024
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...
jobs.tu-berlin.de
Stellenausschreibung IV-618/24: Research Assistant - salary grade E13 TV-L Berliner Hochschulen - For qualification – Stellenausschreibungen der Technischen Universität Berlin
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Anthony Mathelier @amathelier.bsky.social · 18/11/2024
🧵 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...
Illustration comparing the improvement process in software writing to rock climbing.
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Carsen Stringer @computingnature.bsky.social · 14/11/2024
Janelia 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
AI at hhmi, link ai.hhmi.org; theory fellows, link janelia.org/theoryfellow
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Uwe Ohler @uweohler.bsky.social · 14/11/2024
Joanne Chory, 1955-2024
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Uwe Ohler @uweohler.bsky.social · 14/11/2024
www.salk.edu/news-release...
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Daniel Ibrahim @danielibrahim.bsky.social · 14/11/2024
JOBS! JOBS!! JOBS!!! 3 open positions in my lab (PhD & 2Postdoc). 2 in collaborative projects. if you're interested in using synthetic genomics to program gene regulation (or in #HIV latency) & could imagine a working in #Berlin. Apply/DM/email me! Find details below - spread the word please
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Igor Ulitsky @igorulitsky.bsky.social · 13/11/2024
Let's make a thread of RNA-related conferences in 2025 🧵 (add missing!)
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Uwe Ohler @uweohler.bsky.social · 12/11/2024
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:
biorxiv.org
Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation
Transcriptional enhancers are non-coding DNA elements that regulate gene transcription in a temporal and tissue-specific manner. Despite advances in computational and experimental methods, identifying...
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Lionel Christiaen, PhD (he/him/his) @lionlchristiaen.bsky.social · 10/11/2024
At the Michael Sars Centre, 📢 We are hiring Group Leaders! 🌊 Come join our team @UiB to lead innovative research in molecular, cellular and organismal biology using marine/aquatic organisms! ⌛️ Application deadline Dec. 15. Share this exciting opportunity ⤵️ tinyurl.com/4bwn8u3n @embl @EMBRC_EU
tinyurl.com
Group Leader Positions&nbsp;(Researcher I, code 1110) (270380) | University of Bergen
Job title: Group Leader Positions&nbsp;(Researcher I, code 1110) (270380), Employer: University of Bergen, Deadline: Sunday, December 15, 2024
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