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Reposted by Simon Wengert

Stegle Lab @steglelab.bsky.social · Aug 5

We're seeking a PhD student passionate about ML, biology, and driving impact in healthcare!

You'll be working on multi-omics factorization models for personalized medicine, co-supervised by @junyanlu.bsky.social.

👉 Project: www.helmholtz.de/assets/hidss...
✍️ Apply: hidss4health.de/application

Application - Helmholtz Information & Data Science Academy

hidss4health.de

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Reposted by Simon Wengert

Jolien Rietkerk @jolienrietkerk.bsky.social · Jul 24

‘Genetic Risk Effects on Psychiatric Disorders Act in Sets’, the title of our new preprint on
@medrxivpreprint.bsky.social! This huge collaborative effort advances our understanding of psychiatric genetic architecture and emphasizes the importance of looking beyond additive effects. 🧵1/n; 🧪👩🏽‍🔬🧬

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Simon Wengert @simon-wengert.bsky.social · Jul 9

Finally - please do reach out and let's grab a coffee if you happen to be in beautiful Copenhagen! :)

Simon Wengert @simon-wengert.bsky.social · Jul 9

..and, of course, to all my fellow student and friends who were with me all the way - true science is a team sport and I would never have been able to climb so high without all of you.

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Simon Wengert @simon-wengert.bsky.social · Jul 9

Above all though, a genuine and heartfelt thanks to my doctoral advisors @caina89.bsky.social and Matthias Heinig for their invaluable guidance, training and countless opportunities!

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Simon Wengert @simon-wengert.bsky.social · Jul 9

While leaving, I am deeply greatful to everyone at @pioneercampus.bsky.social for making the last five years such a wonderful adventure. Special and many thanks to everyone at HPC, #MUDS and ‪@jherzstiftung.bsky.social‬ for their continued support and making our research possible.

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Simon Wengert @simon-wengert.bsky.social · Jul 9

I will exploring the capabilities of patient level multi-model foundation models to large-scale human data sets to learn the molecular basis of human disease - stayed tuned for exciting news on this front! :)

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Simon Wengert @simon-wengert.bsky.social · Jul 9

After an immensely enriching and rewarding PhD in @caina89.bsky.social lab at @pioneercampus.bsky.social, I am excited to announce that I moved to beautiful Copenhagen for my postdoc in Simon Rasmussen's group @cbmr.science!

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Reposted by Simon Wengert

Tuuli Lappalainen @tuuliel.bsky.social · May 20

Postdoc opportunity! At National Genomics Infrastructure in Uppsala we're looking for a postdoc in genomics R&D. Cutting-edge methods dev in an excellent, international environment at the junction between academia and infrastructure. Deadline May 23!
www.uu.se/en/about-uu/...

Postdoctoral Researcher, NGI Uppsala, SNP&SEQ Technology Platform - Uppsala University

Postdoctoral Researcher, NGI Uppsala, SNP&SEQ Technology Platform, Department of Medical Sciences, Uppsala University

www.uu.se

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Simon Wengert @simon-wengert.bsky.social · May 1

Thank you, very encouraging indeed!

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Simon Wengert @simon-wengert.bsky.social · Apr 30

Absolutely! Any chance of a reprint coming?

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Simon Wengert @simon-wengert.bsky.social · Dec 19

Thanks so much @anavinuela.bsky.social, glad you like it!! :)

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Reposted by Simon Wengert

Na Cai @caina89.bsky.social · Dec 19

Very happy to share *two* new projects from my group now on @biorxivpreprint.bsky.social on mtDNA variation effects on tissue-specific gene expression conducted using RNAseq data in 49 tissues in the GTEx project! 🧵
1/n

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Simon Wengert @simon-wengert.bsky.social · Dec 18

...and here is the big, big thanks to all co-authors in full: @xenophong.bsky.social, Peter Kreitmaier, Pauline Kautz, Leif S. Ludwig, Holger Prokisch, Paolo Casale, Matthias Heinig and
@caina89.bsky.social !!! Thank you for this amazing journey!!! 🤩

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Simon Wengert @simon-wengert.bsky.social · Dec 18

Huge shout out to @caina89.bsky.social & Matthias Heinig for their guidance, to all co-authors and acknowledgements for invaluable contributions, to @pioneercampus.bsky.social for support, and to @tuuliel.bsky.social, @alanjhodgkinson.bsky.social & @bhattaarjun2p.bsky.social for stellar prior work!

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Simon Wengert @simon-wengert.bsky.social · Dec 18

7/7 Taken together, we provide the first deep dive into mtDNA heteroplasmy across 49 human tissues: exploring its age-related changes, its impact on gene expression, mediation of age-related gene expression changes, and the biological mechanism underlying variations in mtRNA mod.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

6/7 Finally, we zoom in on p9 mt-tRNA mod levels to test their impact on mitochondrial transcript processing. We replicate prev assocs between them in blood, test this in all 48 tissues, and further test whether cuts on the 5’ of p9 mods mediate this effect using read-level data.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

5/7 There are 10 sites (9 mtDNA het, 1 mtRNA mod) linked to both donor age and mtDNA gene exp. To learn how age, gene exp and het/mod are related, we perform a mediation analysis using partial corr, and find the variations are consistently mediating the effect of age on gene exp.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

4/7 Next, we apply the framework to test for relationships with mtDNA encoded poly-A transcript levels, and find 784 effects across tissues (# 576 mtDNA hets; # 208 mtRNA mods). We find that 18 of these are cell type specific, suggesting potentially common effects across cells.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

3/7 Since the detection of both variations are affected by RNAseq coverage, we develop a calibrated association testing framework that accounts for coverage effects. Using it, we identify 109 assocs of mtDNA hets and mtRNA mods with donor age, 7 of which are cell type specific.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

2/7 We first assess the landscape of both types of variations across tissues: for mtDNA heteroplasmy, we identify those with putatively somatic and inherited origins, and for mtRNA modifications, we find significant enrichments in CNS as compared to other tissues.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

1/7 How much does mtDNA heteroplasmy vary between tissues? How much of it is
transcribed to RNA and how much are mtRNAs modified post-transcription? We investigate how these variations change with age, and how they affect mtDNA gene expression in a tissue-specific manner.

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Simon Wengert @simon-wengert.bsky.social · Dec 18

After 4 fantastic years of research, together with @caina89.bsky.social & Matthias Heinig, I’m thrilled to share the first tissue specific map of apparent mtDNA heteroplasmy in humans and their relationships with donor age and mtDNA gene expr across 49 tissues!

www.biorxiv.org/content/10.1...

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