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Brian Clarke

@brianfclarke.bsky.social
66 followers 58 following 16 posts

Group Leader and Deputy Division Head at German Cancer Research Center (DKFZ). Mechanistic AI in Genomics – maigegroup.github.io

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Reposted by Brian Clarke
Yun S. Song @yun-s-song.bsky.social · 23/09/2026
Please help spread the word! We are recruiting multiple Postdoctoral Fellows as part of the recently launched Bakar Computational Biomedicine Initiative (BCBI) at UC Berkeley and UCSF. BCBI website: bcbi.berkeley.edu Apply by Nov 1, 2026: berkeley.infoready4.com#freeformComp... (1/n)
bcbi.berkeley.edu
Bakar Computational Biomedicine Initiative | Bakar Computational Biomedicine Initiative
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Reposted by Brian Clarke
Yun S. Song @yun-s-song.bsky.social · 26/09/2026
We are excited to announce a new faculty position in AI for Biology at UC Berkeley. Please repost & share this opportunity with outstanding early-career researchers in your networks. Apply by Nov 9, 2026: aprecruit.berkeley.edu/JPF05560
aprecruit.berkeley.edu
Assistant Professor - AI for Biology - Electrical Engineering & Computer Sciences and Center for Computational Biology
University of California, Berkeley is hiring. Apply now!
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Reposted by Brian Clarke
Yun S. Song @yun-s-song.bsky.social · 09/09/2026
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)
doi.org
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
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Brian Clarke @brianfclarke.bsky.social · 17/08/2026
1/4 Job alert: Our group is looking for a postdoc for a three-year position in an international collaboration with Marc Jan Bonder and @science-wallet.bsky.social. Recruiting is through the DKFZ International Postdoc Program: www.dkfz.de/en/karriere/... Deadline: September 8
dkfz.de
DKFZ Postdoctoral Fellowships - German Cancer Research Center
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Brian Clarke @brianfclarke.bsky.social · 29/07/2026
Our division is recruiting a PhD student through the Helmholtz Information and Data Science School for Health (HIDSS4Health). The supervision will be joint between me, @oliverstegle.bsky.social and @junyanlu.bsky.social. www.hidss4health.de/application/ → Project ID03 Deadline August 18
hidss4health.de
Application - Helmholtz Information & Data Science Academy
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Reposted by Brian Clarke
Yun S. Song @yun-s-song.bsky.social · 06/07/2026
I am thrilled to share that UC Berkeley and UCSF have launched a joint initiative in Computational Biomedicine! cdss.berkeley.edu/news/uc-berk... We will soon be recruiting new faculty and postdoctoral fellows. Please repost to help spread the word.
cdss.berkeley.edu
UC Berkeley and UCSF Launch Computational Biomedicine Initiative
UC Berkeley and UCSF have launched a joint program called the Bakar Computational Biomedicine Initiative to develop the frontier of AI and biomedicine, tremendously accelerating advances in clinical c...
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Brian Clarke @brianfclarke.bsky.social · 12/06/2026
#ESHG attendees: Hope to see you at my presentation about our Nature Genetics paper on deep learning for rare variant genetics. Sunday 8:30-9:15am in session E02. It's an educational session for non-experts in AI, so I'll start from the basics and explain the principles behind the model in detail.
nature.com
Integration of variant annotations using deep set networks boosts rare variant association testing - Nature Genetics
Deep rare variant association testing (DeepRVAT) is a deep set neural network model that flexibly integrates rare variant annotations into a trait-agnostic gene impairment score. These scores improve ...
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Reposted by Brian Clarke
Tami Gjorgjieva @tamigj.bsky.social · 18/05/2026
Hi Genetics/Comp-Bio community 👋 Interested in mentoring a comp-bio research student in East Africa over the summer? Do you have any experience in bioinformatics, biostats, genome/RNA-seq analyses, ML, or metagenomics? We'd love to have you as a mentor in our new program! 🧵 (1/n)
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Reposted by Brian Clarke
Ran Blekhman @blekhman.bsky.social · 17/05/2026
Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted at UChicago. Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia open.substack.com/pub/blekhman...
open.substack.com
Seven points on the current state of AI in genomics
A grounded take from the messy middle of an AI revolution
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Brian Clarke @brianfclarke.bsky.social · 01/04/2026
This was a great conference, and exciting to see Katharina and Dominik's work (with many other great collaborators) presented!
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Reposted by Brian Clarke
Stegle Lab @steglelab.bsky.social · 31/03/2026
Join us for a postdoc in AI in human genetics at @embl.org in close collaboration with Adrian Cortes (GSK) and @brianfclarke.bsky.social - exploring the effects of rare variants using population-scale cohorts and single-cell readouts. 🔗 Apply now: embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
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Reposted by Brian Clarke
Deutsches Krebsforschungszentrum (DKFZ) @dkfz.bsky.social · 27/03/2026
Dreaming of a career in cancer research? Join the International PhD Program at DKFZ - Germany’s largest biomedical research center. Explore #cancerresearch including #cancerbiology, #bioinformatics, #epidemiology & #medicalphysics. The Summer Selection is open now 👉 apply here: t1p.de/hl56b
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Brian Clarke @brianfclarke.bsky.social · 24/03/2026
This is a great opportunity, with recruiting by many excellent DKFZ PIs, including yours truly. If you'd like to know more about what kinds of projects we work on, check out our group website: www.dkfz.de/en/computati...
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Reposted by Brian Clarke
EMBL @embl.org · 02/03/2026
📢 Last call for the EMBL International PhD Programme summer recruitment! This is a fully funded PhD programme fostering creative approaches to questions in the molecular life sciences. Join us promoting scientific excellence throughout Europe. Apply now! www.embl.org/about/info/e...
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Reposted by Brian Clarke
Danai Vagiaki @danaivagiaki.bsky.social · 08/02/2026
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
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Brian Clarke @brianfclarke.bsky.social · 11/12/2025
This is an exciting paper, highly recommend it!
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Brian Clarke @brianfclarke.bsky.social · 17/11/2025
Steffi wrote a fantastic master's thesis with us and I'm very happy she decided to stay on for her PhD. She's already made some intriguing discoveries (stay tuned!) and I can't wait to see what's next. Welcome, Steffi!
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Brian Clarke @brianfclarke.bsky.social · 17/11/2025
Really great to have Gesa join the team! She's already shown a ton of enthusiasm, and I'm impressed by her keen analytical insights. Excited to see what she'll develop in her time here! Welcome, Gesa!
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Reposted by Brian Clarke
Yun S. Song @yun-s-song.bsky.social · 14/10/2025
An open-rank faculty search in AI + Engineering (Bioengineering included) at UC Berkeley. Due date: Monday, Nov 3, 2025 at 11:59pm (PT) Please help spread the news. aprecruit.berkeley.edu/JPF05144
aprecruit.berkeley.edu
Assistant/Associate/Full Professor – Engineering + Artificial Intelligence - College of Engineering (host academic department(s) to be determined)
University of California, Berkeley is hiring. Apply now!
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Manu Saraswat @manusaraswat.bsky.social · 10/10/2025
Excited to be at #ASHG2025 in Boston next week. On Thursday, I will be presenting a poster (1007T) on our latest work on Personalised sequence to expression modelling. Looking forward to meeting new folks and reconnecting with old friends and colleagues.
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Reposted by Brian Clarke
Stegle Lab @steglelab.bsky.social · 10/10/2025
Don’t miss Manu’s poster on DeepGenoXcan, our new personalized and interpretable sequence-to-expression model, at #ASHG2025! 📅 October 16, 2:30pm-4:30pm 📍 Poster 1007T
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Reposted by Brian Clarke
Stegle Lab @steglelab.bsky.social · 10/10/2025
Do you want to link genomic variants to functional gene expression - cell by cell? SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells. Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
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Brian Clarke @brianfclarke.bsky.social · 23/09/2025
Grateful to have been included in this interesting and sure to be very impactful work!
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Reposted by Brian Clarke
EMBL @embl.org · 01/09/2025
📢 Recruitment for the EMBL International PhD Programme is officially open! At EMBL, we train young scientists to become skilled and creative future leaders in academia and other sectors. Join us and get a head start on your career in life sciences! bit.ly/47mmiFF
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Reposted by Brian Clarke
Stegle Lab @steglelab.bsky.social · 04/07/2025
Deadline in 9 days - apply now!
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Reposted by Brian Clarke
Oliver Stegle @oliverstegle.bsky.social · 26/06/2025
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
embl.wd103.myworkdayjobs.com
Postdoctoral Researcher in Computational Genetics
The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...
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Brian Clarke @brianfclarke.bsky.social · 02/06/2025
We're hiring! Want use deep learning to discover genetic disease mechanisms and therapeutic targets? Like the sound of applying Bayesian deep learning, DNA language models and federated learning to this exciting problem? Then this position in our group is for you!
jobs.dkfz.de
PhD Student in Deep Learning for Rare Variant Genetics
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Reposted by Brian Clarke
Moritz Mall @moritzmall.bsky.social · 16/05/2025
An insightful thread for the second study by the one and only @manusaraswat.bsky.social that spearheaded this superstar team effort together with @lauraruedag.bsky.social and Elisa Heinzelmann in the labs of @oliverstegle.bsky.social and me: bsky.app/profile/manu...
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Reposted by Brian Clarke
Omer Ali Bayraktar @bayraktarlab.bsky.social · 16/05/2025
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵
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Reposted by Brian Clarke
Manu Saraswat @manusaraswat.bsky.social · 16/05/2025
🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
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Brian Clarke @brianfclarke.bsky.social · 18/03/2025
The next selection round for the DKFZ International PhD Program has started. Please consider applying to this really excellent program! I'll be proposing projects, as will many other outstanding PIs.
PHD POSITIONS IN
COMPUTATIONAL RESEARCH, DATA SCIENCE
AND ARTIFICIAL INTELLIGENCE

Are you interested in solving fascinating biological or medical questions computationally?
At the German Cancer Research Center (DKFZ), Germany’s largest biomedical research institute with
its core site in Heidelberg, computational scientists work at the forefront of artificial intelligence
and cancer research. They combine inter­ disciplinary approaches from computer science, medical
informatics, physics, biology, bioinformatics and statistics to analyze and understand complex
biological and medical data.

Main activities at the DKFZ involving big data:
•
Development and application of machine
learning and computa­ tional methods for
multi-modal data integration, including
integrative analysis of genomic, epigenomic,
transcriptomic, proteomic, meta­ bolomic and
radiomic imaging data
•
Development of methods for modeling and
simulation of biological and medical processes
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Medical Informatics

•
•
•
•
DNA mutation analysis and machine learning to
decipher cancer genome variation
Application and development of state-of-the-art
technologies for single-cell omics and life cell
imaging
Computer-assisted radiology and surgery
Biostatistical evaluation of experimental and
clinical data
More information at www.dkfz.de/datascience. Full funding is provided for the duration of the PhD.

To apply online to the International PhD Program visit
To apply online to the International PhD Program visit
www.dkfz.de/phd
Application deadline
24 April 2025

We support and value diversity and encourage applications from individuals
from underrepresented groups. If you require assistance during the application
process, please contact phd@dkfz.de.
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Reposted by Brian Clarke
Stegle Lab @steglelab.bsky.social · 18/03/2025
1/ New preprint! 🍳 @elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins! doi.org/10.1101/2025...
Segger logoMessage passing intuition behind the segger’s link-prediction model and the network architecture
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Vitalii Kleshchevnikov, PhD @vitaliikl.bsky.social · 04/03/2025
Cell2fate learns which genes have co-regulated transcription rates => spatially mapping velocity modules & improved robustness. Bayesian modelling => easier to add biological realism. Exciting collab with Alexander Aivasidis in Bayraktar & @steglelab.bsky.social www.nature.com/articles/s41...
Fig 4.
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Brian Clarke @brianfclarke.bsky.social · 19/02/2025
Exciting job opportunity!👇 A great chance to work on an application of machine learning in human genetics which will make an impact on our understanding of disease and has real potential for future translation to the clinic.
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