Markus List

New lecture series: TUM Life Science Talks foster interdisciplinary discourse New lecture series: TUM Life Science Talks in Freising-Weihenstephan promote exchange with renowned scientists.

On Wednesday, @rnakato.bsky.social gave an excellent talk in our new @tum.de Life Science Talks series: www.ls.tum.de/en/ls/public.... It was nice to see so many people join to hear about the role of multi-omics data in elucidating gene-regulatory mechanisms. Well done @rnakato.bsky.social

Sad news for the whole bioinformatics community and science at large. My condolences to Peer's family, former and current members of his team.

"There's no denial that AI has had a big impact on all scientific fields, including drug repurposing."

#RExPO25 highlights with Markus List (@itisalist.bsky.social), Group Leader at @daisybio.de & Associate Professor at TUM.

Watch the full video for more insights ⤵️
youtu.be/iz7PisP_n08?...

Network Inference Reveals Distinct Transcriptional Regulation in Barley against Drought and Fusarium Head Blight We analyzed transcriptional networks in barley under single and combined Fusarium head blight (FHB) and drought stress. We applied complementary Weighted Gene Correlation Network Analysis (WGCNA) to i...

My barley transcriptional network preprint is officially out!
Started as my Bachelor’s thesis — now it’s online:
doi.org/10.64898/202...
Huge thanks to @itisalist.bsky.social, @daisybio.de, @huckelhovenr.bsky.social , Felix Hoheneder & Johannes Kersting for all their help and support!

Histone Display by user_506892605 MakerWorld: Download Free 3D Models This is a histone display that illustrates a nucleosome. The DNA is wrapped around a histone octamer consisting of H3, H4, H2A, and H2B. The model includes methylated cytosines, as well as histone tai...

One of our students, EliasAlbrecht, went the extra mile in his project and created an educational 3D-printed model of a nucleosome. We're stunned by the level of detail and excited to use this in our lectures and public events. The model is open to the community makerworld.com/en/models/20...

Welcome Ryu, it's a pleasure having you in our @daisybio.de lab!

We're getting ready for Maustag 2025 www.mdsi.tum.de/en/mdsi/late... at the @tum.de Munich Data Science Institute, where we @daisybio.de plan to show children why AI and bioinformatics are important for studying the code of life. I dare say that our first practice session went quite well :-)

Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing academic.oup.com/nargab/artic... 🧬🖥️🧪

And for those who enjoyed our tutorial on network medicine and drug repurposing: if you are spontaneous, consider joining us for the RExPO conference organized by @repo4eu.bsky.social repo4.eu/rexpo25/ later this month.

Rhein in Basel

I enjoyed visiting the BC2 conference: cool talks,
great networking, beautiful location. Thanks to the organizers at @sib.swiss I appreciated especially today's session on startups in bioinformatics, that was insightful.

Park bench in a misty morning

En route to Basel for the @sib.swiss #BC2 conference. We're contributing to a workshop on 🕸️ network medicine and 💊 drug repurposing, with tools developed in @repo4eu.bsky.social incl. drugst.one for which we've just released the DREAM extension doi.org/10.58647/DRU... simplifying expert annotation.

RExPO25 Session in focus: AI/ML in systems medicine and drug repurposing.

#RExPO25 Speakers | S7: AI/ML in #SystemsMedicine & #DrugRepurposing

🟣 @itisalist.bsky.social & Lisa Spindler (@daisybio.de)

🟣 Jan Baumbach & Fernando Delgado Chavez (@cosybio-uhh.bsky.social)

Check the full conference agenda ⤵️
repo4.eu/rexpo25/agen...

🇪🇺 #EUfunded #DrugRepurposing

Our benchmark + guidelines for atlas-level differential gene expression of single cells is online:

academic.oup.com/bib/article/...

Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings.

Collab w/ @leonhafner.bsky.social @itisalist.bsky.social

A flowery surprise at our @tum.de campus Freising yesterday. Congratulations to all students who celebrated their graduation.

Yes indeed, are you here as well :-)

En route to visit the @cosybio-uhh.bsky.social lab in Hamburg who are kindly organizing the latest @repo4eu.bsky.social WP2 workshop. Looking forward to discussing the refinement of our computational pipelines for drug repurposing. Hope the train will not be too much delayed...

🧬🖥️Drug response prediction is a machine learning challenge with immense potential for precision medicine. Our latest preprint introduces DrEval, a comprehensive benchmarking framework to evaluate state-of-the-art methods, uncover widespread issues, and guide the development of more robust models.

Had a great time in Innsbruck. The scenery here with the mountains in the background is always impressive, even when the weather is not so nice. Thanks @francescafinotello.bsky.social for inviting me!

webinar description

For those of you who are not in Innsbruck to see me today, you might instead listen to @judith-bernett.bsky.social at the @iscb.bsky.social NetBio webinar!

🔗 Attend at ISCB Nucleus: iscb.junolive.co

📍 If you’re not an ISCB member, register for access to ISCB Nucleus: lnkd.in/gMhrKGJz

Guiding questions to avoid data leakage in biological machine learning applications - Nature Methods This Perspective discusses the issue of data leakage in machine learning based models and presents seven questions designed to identify and avoid the problems resulting from data leakage.

I believe the seminar is offline only. My focus is not data privacy (also very important!), but on inflated performance estimates due to methods learning illegitimate shortcuts. If you'd like to know more, we have written a perspective article with guiding questions: www.nature.com/articles/s41...

Colorful liquid flowing from one bottle into another, as an illustration for (data) leakage.

Traveling to Innsbruck by invitation of @francescafinotello.bsky.social to talk about data leakage, a widespread issue in biomedical machine learning applications. I'll talk about challenges in protein-protein interaction (doi.org/10.1093/bib/...) and drug response prediction (upcoming preprint!).

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics AbstractMotivation. The rapid development of spatial transcriptomics has underscored the importance of identifying spatially variable genes. As a fundament

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics 🧬🖥️ academic.oup.com/bioinformati...

Weihenstephan Bioinformatics Symposium 2025: More than 75 scientists from Bavaria and the world came together to share talks and create new synergies. It was great to host this event, for those who missed it: The next edition is planned for 2027 😉

I am so happy to see this manuscript finally out!!! We review and discuss all analysis steps in long reads transcriptomics. Hope the community finds this useful! Hugo thanks to @carolinamonzo.bsky.social and @tianyuanliu.bsky.social for the huge work!!! @longtrec.bsky.social @hitseq.bsky.social

Greetings from Palermo! @en-coding.bsky.social, @a-dietrich.bsky.social, @itisalist.bsky.social, Serafina Reif, Nico Trummer & Kamila Kwiecien are united here at the occasion of the MyeInfoBank COSTAction: Converting Molecular Profiles of Myeloid Cells into Biomarkers for Inflammation and Cancer

It was a pleasure having you, Ryu! Thanks so much for your talk and visit.

📍Welcome to our presentation round of the DaiSyBio members! Every week, you will get to know someone from our lab.
The start is done by @itisalist.bsky.social who heads the group. Markus joined TUM in 2018 and became a W2 tenure track associate professor in 2023. More members are about to follow! 📍

DaiSyBio | LinkedIn DaiSyBio | 323 followers on LinkedIn. DaiSyBio is a research group created in December 2023 as part of the TUM School of Life Sciences. Cutting-edge expertise in biology, medicine and computer scienc...

By the way, we also have a lab account on bluesky now. Follow @daisybio.de to get more news about our activities. We are also on LinkedIn: www.linkedin.com/company/dais...

Johannes Kersting Awarded an ASAPBio Poster Prize for RExPO Contribution The ASAPBio poster competition is an initiative that champions open science by highlighting innovative research and the early sharing of results. This year’s competition emphasized transparency, colla...

Congrats to our PhD student Johannes Kersting for winning the ASAPbio poster prize for his contribution to the @repo4eu.bsky.social #REXPO24: blog.scienceopen.com/2025/01/joha...

We followed up on our previous work, where we showed that predicting protein-protein interactions from sequence alone yields random performance when data leakage is accounted for. In this new preprint, we show that ESM2 embeddings raise the bar to 0.65 accuracy independent of the model architecture.