@brianfclarke.bsky.social
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!
Welcome, Steffi!
Please join me in welcoming Stefanie Mantz to our lab! 👋
Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
November 17, 2025 at 9:32 AM
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!
Welcome, Steffi!
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!
Welcome, Gesa!
Welcome to our team, Gesa Voigt! 👋
During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
November 17, 2025 at 9:31 AM
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!
Welcome, Gesa!
Reposted
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
Due date: Monday, Nov 3, 2025 at 11:59pm (PT)
Please help spread the news.
aprecruit.berkeley.edu/JPF05144
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!
aprecruit.berkeley.edu
October 14, 2025 at 9:53 PM
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
Due date: Monday, Nov 3, 2025 at 11:59pm (PT)
Please help spread the news.
aprecruit.berkeley.edu/JPF05144
Reposted
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.
October 10, 2025 at 2:49 AM
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.
Reposted
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
📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
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.
October 10, 2025 at 1:35 PM
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
📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
Reposted
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.
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.
EMBL scientists have created a more sensitive single-cell sequencing tool for genomic variants and RNA in the same single cell.
Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.
www.embl.org/news/science...
Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.
www.embl.org/news/science...
New tool offers single-cell study of specific genetic variants | EMBL
Scientists developed a more sensitive single-cell sequencing tool linking genomic variants & RNA in the same cell uncover links to disease.
www.embl.org
October 10, 2025 at 2:42 PM
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.
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.
Grateful to have been included in this interesting and sure to be very impactful work!
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 23, 2025 at 8:39 AM
Grateful to have been included in this interesting and sure to be very impactful work!
Reposted
📢 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
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
September 1, 2025 at 9:07 AM
📢 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
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
Reposted
Deadline in 9 days - apply now!
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/de-DE/EMBL/d...
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...
embl.wd103.myworkdayjobs.com
July 4, 2025 at 9:36 AM
Deadline in 9 days - apply now!
Reposted
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/de-DE/EMBL/d...
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...
embl.wd103.myworkdayjobs.com
June 26, 2025 at 10:00 AM
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/de-DE/EMBL/d...
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!
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!
PhD Student in Deep Learning for Rare Variant Genetics
jobs.dkfz.de
June 2, 2025 at 10:05 AM
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!
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!
Reposted
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...
bsky.app/profile/manu...
🧠 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🧵👇
May 16, 2025 at 3:57 PM
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...
bsky.app/profile/manu...
Reposted
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 🧵
May 16, 2025 at 11:44 AM
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 🧵
Reposted
🧠 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🧵👇
May 16, 2025 at 10:05 AM
🧠 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🧵👇
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.
March 18, 2025 at 2:56 PM
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.
Reposted
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...
@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...
March 18, 2025 at 2:48 PM
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...
@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...
Reposted
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...
Exciting collab with Alexander Aivasidis in Bayraktar & @steglelab.bsky.social
www.nature.com/articles/s41...
March 4, 2025 at 11:34 PM
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...
Exciting collab with Alexander Aivasidis in Bayraktar & @steglelab.bsky.social
www.nature.com/articles/s41...
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.
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.
📢 Bring your computational expertise to our cutting-edge research team at @embl.org! Join us together with experts from GSK to explore the effects of rare variants using population-scale cohorts and single-cell readouts.
Please share 🙏
🔗 Apply now: embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Please share 🙏
🔗 Apply now: embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
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...
embl.wd103.myworkdayjobs.com
February 19, 2025 at 12:29 PM
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.
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.