Lightnews — Scholar-powered news

Eva Holtkamp @evaholtkamp.bsky.social · 3h

Staying active during this time #ASHG25 is important🏋️‍♀️, so go and check out Shubhankar’s poster! Really happy to be part of this project!

Shubhankar Londhe @slondhe.bsky.social · 1d

Excited to share UKBBGym at #ASHG25, a new benchmark for variant effect predictors using WGS, proteomics and phenotypes from 500K UKBiobank participants. Stop by for insights on the impact of non-coding variants and how computational scores stack up against exp assays.
Poster 5022W, Wed 2:30-4:30.

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Eva Holtkamp @evaholtkamp.bsky.social · 19h

DeepRVATv2 is in the making! We learn from >60M WGS variants, >90 features, and 500k UKB participants to predict gene impairment beyond coding regions and showcase how DeepRVAT can advance rare disease diagnostics and gene constraint measurement.

Learn more at my Poster 5058W, Wed 2:30pm #ASHG25

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Eva Holtkamp @evaholtkamp.bsky.social · Jul 31

This was such a special event! So grateful that I could be part of it, learning about great science, making truly unique connections with amazing fellow students and tutors, and even learning how to punt 🛶 Huge thanks to everyone who helped bring this unique school back to life!

Andrea Ganna @andganna.bsky.social · Jul 30

Leena Peltonen School of Human Genetics in full-swing!

@gosiatrynka.bsky.social
@dgmacarthur.bsky.social
@bpasaniuc.bsky.social
@tuuliel.bsky.social
@hilarycmartin.bsky.social
@sashagusevposts.bsky.social
@zkutalik.bsky.social
@mashaals.bsky.social
@alemedinarivera.bsky.social

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Reposted by Eva Holtkamp

Stegle Lab @steglelab.bsky.social · Jul 19

@thbec.bsky.social is going to share preliminary results on Meta-DeepRVAT, a new approach for deep learning based meta-analysis improving the power of rare variant association studies using population scale external control cohorts. #MLCSB
📅 July 21 |📍 Poster A-312

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Reposted by Eva Holtkamp

Oliver Stegle @oliverstegle.bsky.social · Jun 26

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...

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

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Reposted by Eva Holtkamp

Gagneur lab @gagneurlab.bsky.social · Jun 5

Update of our protein outlier caller PROTRIDER. We now handle missing values, a widespread issue for mass spec where missing values are not a random -- and this improves outlier detection on non-missing data! Thumbs up to Daniela and George for the great work.
doi.org/10.1101/2025...

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Reposted by Eva Holtkamp

Kipoi @kipoizoo.bsky.social · May 28

Join us for our next Kipoi Seminar with Katherine Pollard, Gladstone Institute of Data Science & Biotechnology,UCSF, Biohub
@gladstoneinst.bsky.social @czbiohub.bsky.social
👉Human variant interpretation with sequence-to-activity models
📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social

https://kipoi.org/seminar/🦋kipoizoo.bsky

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Eva Holtkamp @evaholtkamp.bsky.social · May 25

Excited to be back at #eshg2025! Come by my poster today to check out fresh results on how rare high impact variants influence gene expression across immune cells—analyzed in 5,000 UK Biobank participants

Gagneur lab @gagneurlab.bsky.social · May 24

Eva Holtkamp @evaholtkamp.bsky.social shares insights on rare variant effects on cell type-specific gene expression in immune cells across 4,978 UK Biobank participants - catch poster P18.066.A (Sunday, 1pm)

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Reposted by Eva Holtkamp

Kipoi @kipoizoo.bsky.social · May 2

Join us for our next Kipoi Seminar with Laura Martens, Gagneur lab, TUM @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de
🐕scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
📅Wed May 7, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky

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Reposted by Eva Holtkamp

brianfclarke.bsky.social @brianfclarke.bsky.social · Mar 18

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
•
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 Eva Holtkamp

Gagneur lab @gagneurlab.bsky.social · Mar 6

Hello #probgen25! We have 3 contribs this year @lauradmartens.bsky.social starts today, poster 87, presenting scooby modeling scRNA-seq and sc-ATAC-seq profiles from DNA and applications. Shhh... don't tell it further... rumour says there are awesome cute scooby stickers to win ;-)

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Reposted by Eva Holtkamp

Kipoi @kipoizoo.bsky.social · Mar 1

Join us for our next Kipoi Seminar with with Alexander Sasse
@lxsasse.bsky.social
@zmbh.uni-heidelberg.de

👉Advanced training strategies for genomic sequence-to-function models
📅 Wed March 5, 5:30pm CET
🧬 kipoi.org/seminar/
🦋 @kipoizoo.bsky.social

Kipoi

kipoi.org

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Reposted by Eva Holtkamp

Kipoi @kipoizoo.bsky.social · Feb 3

Join us for our next Kipoi Seminar with with Pedro Tomaz da Silva @pedrotomazdasilva.bsky.social @gagneurlab.bsky.social @TU_Muenchen!
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky

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Reposted by Eva Holtkamp

Gagneur lab @gagneurlab.bsky.social · Dec 23

Hey reg genomics folks, here is our little x-mas present: Flashzoi. Borzoi. Just as good. 3x faster. Thumbs up to @johahi.bsky.social for the great initiative, conception & implementation. Big thanks to Johannes Linder, David Kelley and colleagues to have created Borzoi and shared it freely.

bioRxiv Genomics @biorxiv-genomic.bsky.social · Dec 22

Flashzoi: An enhanced Borzoi model for accelerated genomic analysis https://www.biorxiv.org/content/10.1101/2024.12.18.629121v1

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Reposted by Eva Holtkamp

bioRxiv Genomics @biorxiv-genomic.bsky.social · Dec 22

Flashzoi: An enhanced Borzoi model for accelerated genomic analysis https://www.biorxiv.org/content/10.1101/2024.12.18.629121v1

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