iiinova — where your digital self keeps evolving

Reposted by Simon Wengert

Ana Viñuela @anavinuela.bsky.social · 08/09/2026

Please share! Fully funded PhD position (UK home fees) at U. of Dundee for someone interested in combining wet-lab (Dr Murdoch) and computational approaches (🙋‍♀️ 2nd supervisor), with plenty of scope for learning new skills across both areas. 🧪🧬 Deadline 21 September

findaphd.com

Redox Control of RNA Splicing in Cardiovascular Disease at University of Dundee on FindAPhD.com

PhD Project - Redox Control of RNA Splicing in Cardiovascular Disease at University of Dundee, listed on FindAPhD.com

048

Reposted by Simon Wengert

Kaessmann Lab @kaessmannlab.bsky.social · 31/08/2026

We’re hiring! Experimental #Postdoc and computational and/or experimental #PhD positions in evolutionary genomics are available in our lab in Heidelberg: home.kaessmannlab.org/openPositions Please repost and spread the word!

home.kaessmannlab.org

Kaessmann Lab

02632

Reposted by Simon Wengert

Juuso Koponen @juusokoponen.bsky.social · 24/07/2026

📊 My and @jhilden.bsky.social’s book has been out of print for some time, as our publisher closed down its general publishing arm. We are working on a 2nd edition, but it is not going to be ready anytime soon, so we’re making the current edition available as an e-book for €9.90. payhip.com/b/zbl43

payhip.com

Data visualization handbook

The Data visualization handbook by Juuso Koponen and Jonatan Hildén is a practical guide for creating compelling graphics to explain and explore data. It is primarily aimed at designers, journalists, ...

44212

Simon Wengert @simon-wengert.bsky.social · 29/05/2026

Midway through the CSHL Symposium on AI in Biology and this far it's been a blast! Tomorrow I will be presenting our work on genomic foundation models for large-scale biomedical data analysis in poster session #3, 4:30 pm, poster #291. Come find me to connect and discuss :) #cshlsymp26

021

Reposted by Simon Wengert

Uri Alon @urialonlab.bsky.social · 06/05/2026

Identify. Attack. Resolve. The immune system follows a perfect defense program: ignore weak/self signals, attack true threats with force, then shut down to avoid damage. (1/2) www.science.org/doi/10.1126/...

science.org

Excitability as a design principle in the immune system

A simple pulse-and-rest circuit may explain how immune cells strike hard at threats yet avoid self-destruction.

2187

Simon Wengert @simon-wengert.bsky.social · 04/02/2026

*Biology background moved to the data side here. I think there's a good chapter on this in MSMB by Wolfgang with references (www.huber.embl.de/msmb/13-chap...). Also, I really liked this one here which focuses on causal thinking: designexptr.org

designexptr.org

Welcome | Design and Analysis of Experiments and Observational Studies using R

Online version of Design and Analysis of Experiments and Observational Studies using R

120

Reposted by Simon Wengert

Stegle Lab @steglelab.bsky.social · 02/02/2026

We are hiring a Research Software Engineer at @embl.org Heidelberg to enhance and maintain open-source infrastructure for spatial omics. 🔗 Deadline: 15/02/2026 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

embl.wd103.myworkdayjobs.com

Research Software Engineer - Spatial-omics

The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...

031

Reposted by Simon Wengert

Jonathan Pritchard @jkpritch.bsky.social · 11/12/2025

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

nature.com

Causal modelling of gene effects from regulators to programs to traits - Nature

Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

318682

Reposted by Simon Wengert

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 09/12/2025

I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students. I will record lectures & all will be found at this link: github.com/rmcelreath/s...

course schedule as a table. Available at the link in the post.

12660233

Reposted by Simon Wengert

Gosia Trynka @gosiatrynka.bsky.social · 04/12/2025

Hiring Senior Computational Postdoc to lead large-scale scRNAseq analysis for Project JAGUAR, one of the world’s most comprehensive single-cell immune resources from Latin American ancestries. If big data, global partnerships, human diversity and immune regulation excite you, apply! bit.ly/3XyFWrW

sanger.wd103.myworkdayjobs.com

Senior Postdoctoral Fellow

Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...

078

Reposted by Simon Wengert

Wolfgang Huber @wkhuber.bsky.social · 01/12/2025

Join EMBL's Interdisciplinary Postdoc Programme! 3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states. In particular: AI&Theory, use mathem. models, physics principles and AI www.embl.org/about/info/p...

embl.org

EIPOD-LinC Fellowship Programme – Postdoctoral Programme

22021

Reposted by Simon Wengert

loic-yengo.bsky.social @loic-yengo.bsky.social · 12/11/2025

First time on Bsky and first big announcement! I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature. Our manuscript is here: www.nature.com/articles/s41....

nature.com

Estimation and mapping of the missing heritability of human phenotypes - Nature

WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...

821870

Reposted by Simon Wengert

Bastian Grossenbacher-Rieck @pseudomanifold.topology.rocks · 29/10/2025

Want to generate point clouds? Our (w/ Ernst Röell) #NeurIPS2025 paper shows a topology-driven method that is fast, simple, and high-quality. 🔥 1/n

1174

Reposted by Simon Wengert

Stegle Lab @steglelab.bsky.social · 05/08/2025

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

hidss4health.de

Application - Helmholtz Information & Data Science Academy

064

Reposted by Simon Wengert

Jolien Rietkerk @jolienrietkerk.bsky.social · 24/07/2025

‘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; 🧪👩🏽‍🔬🧬

1118

Simon Wengert @simon-wengert.bsky.social · 09/07/2025

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

000

Simon Wengert @simon-wengert.bsky.social · 09/07/2025

..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.

100

Simon Wengert @simon-wengert.bsky.social · 09/07/2025

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!

110

Simon Wengert @simon-wengert.bsky.social · 09/07/2025

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.

110

Simon Wengert @simon-wengert.bsky.social · 09/07/2025

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! :)

110

Simon Wengert @simon-wengert.bsky.social · 09/07/2025

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!

241

Reposted by Simon Wengert

Tuuli Lappalainen @tuuliel.bsky.social · 20/05/2025

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/...

uu.se

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

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

12418

Simon Wengert @simon-wengert.bsky.social · 01/05/2025

Thank you, very encouraging indeed!

010

Simon Wengert @simon-wengert.bsky.social · 30/04/2025

Absolutely! Any chance of a reprint coming?

120

Reposted by Simon Wengert

Na Cai @caina89.bsky.social · 19/12/2024

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

196

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

...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!!! 🤩

020

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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!

120

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

110

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

130

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

110

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

110

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

110

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

110

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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.

110

Simon Wengert @simon-wengert.bsky.social · 18/12/2024

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...

284