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Markus List

@itisalist.bsky.social
332 followers 544 following 33 posts

Assistant Professor for Data Science in Systems Biology at the Technical University of Munich (daisybio.de). Mostly posting about bioinformatics and systems / network biology research. Views are my own. he / him.

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REPO4EU @repo4eu.bsky.social · 01/09/2026
Meet the #RExPO26 Speakers | S2: REPO4EU Platform: Introducing Beta Release 🟣 Balázs Orbán & Janos Dallos (@egnosis.bsky.social) 🟣 Shu-Min Kao (BioLizard) 🟣 Markus List @itisalist.bsky.social (@daisybio.de / @tum.de) Check the full conference agenda ⤵️ repo4.eu/rexpo26/agen...
RExPO26 Speakers | Session 2: REPO4EU Platform, introducing the beta release. Balázs Orbán and Janos Dallos (Egnosis), Shu-Min Kao (BioLizard) and Markus List (TUM).
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REPO4EU @repo4eu.bsky.social · 27/08/2026
Meet the #RExPO26 Speakers | S1: REPO4EU Core Framework 🟣 Hermann Mucke (H.M. Pharma) 🟣 Sabine Grimm (MUMC+) 🟣 Ana Sofia Carvalho (University of Porto) 🟣 @itisalist.bsky.social (@daisybio.de / @tum.de) 🟣 Frank Ruwe (3D-PharmXchange) Check the conference agenda ⤵️ repo4.eu/rexpo26/agen...
RExPO26 Speakers: Hermann Mucke (H.M. Pharma Consultancy), Sabine Grimm (Maastricht UMC+), Ana Sofía Carvalho (University of Porto), Markus List (DaiSyBio, Technical University of Munich) and Frank Ruwe (3D-PharmXchange).
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Markus List @itisalist.bsky.social · 11/08/2026
The last MOPITAS autumn school in Garching was a lot of fun, great participants and great instructors. I'm really looking forward to join this second installment in Copenhagen. Don't miss the deadline and sign up if your interested in taking your spatial data analysis to the next level. Vi ses i DK!
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REPO4EU @repo4eu.bsky.social · 30/07/2026
What does it take to build effective AI-powered tools and systems to accelerate #DrugRepurposing? Find out in the latest episode of RExPO Voices with Markus List (@itisalist.bsky.social), Assistant Prof for Data Science in Systems Biology at @tum.de & Head of @daisybio.de 🎬 👉 youtu.be/XQA30xnayZw
youtu.be
AI-powered tools for drug repurposing | RExPO Voices ft Markus List (Technical University of Munich)
YouTube video by REPO4EU
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DaiSyBio @daisybio.de · 13/07/2026
🚀 Great news from DaiSyBio: our new manuscript, “Inferring and Evaluating Network Medicine-Based Disease Modules with Nextflow”, has been published in Bioinformatics (Oxford) as part of the ISMB 2026 proceedings.
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DaiSyBio @daisybio.de · 08/06/2026
📅 Join the upcoming Munich Data Science Institute (MDSI) research talk of Francesca Finotello on Wednesday, 24 June 2026 at 01:00 pm at the MDSI in Garching. 🔗 Further information on the talk and the registration can be found on the MDSI website. www.mdsi.tum.de/mdsi/bildung...
mdsi.tum.de
Research Talk: Decoding tissue complexity via deconvolution of transcriptomic data
The investigation of the cellular composition and architecture of tissues is key to understanding mechanisms that underlie tissue function and its disruption during disease. Deconvolution is a computa...
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DaiSyBio @daisybio.de · 11/06/2026
Yesterday, we took part in the Weihenstephaner Berglauf 2025 and enjoyed much better weather than at the last Campus Lauf. 🏃‍♂️‍➡️🏃‍♀️‍➡️
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DaiSyBio @daisybio.de · 12/05/2026
🚀 Excited to share that our latest publication, "Drugst.One DREAM, Drug Repurposing through Expert Annotation and Modification" is now published in the British Journal of Pharmacology.
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DaiSyBio @daisybio.de · 28/04/2026
Amazing news from DaiSyBio! As the first official DaiSyBio PhD student, Alexander Dietrich successfully defended his thesis, “Advanced Methods for Cellular Composition Inference from Bulk Molecular Profiles,” on February 24th and, as of yesterday, can officially be called Dr. Dietrich.
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DaiSyBio @daisybio.de · 29/04/2026
Today @fabiantheis.bsky.social has been visiting the campus of the TUM School of Life Sciences for giving an inspiring TUM Life Science Talk. We fully share his view that the decades-old vision of systems biology is finally within our reach. Exciting times ahead!
Lecture hall showing the talk of Prof. Fabian Theis and the audience.
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DaiSyBio @daisybio.de · 15/04/2026
🚀 New publication from the MOPITAS project Very happy to share our latest publication in Briefings in Bioinformatics, presenting a benchmarking and analysis platform for spatial transcriptomics simulations.
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Markus List @itisalist.bsky.social · 20/03/2026
I really enjoyed our DyHealthNet.ai workshop in Erlangen this week. It was especially amazing to meet our IHEC collaborator @guillaumebourque.bsky.social in person again after many years!
dyhealthnet.ai
DyHealthNet
DyHealthNet is a DFG-funded research project run by FAU (Biomedical Network Science Lab), TUM (Big Data in Biomedicine Group), Eurac (Institute for Biomedicine), and UNIBZ (Database Systems Group).
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DaiSyBio @daisybio.de · 17/03/2026
✨ Call for abstracts for the "AI and Bioinformatics" satellite workshop at the 55th Annual Meeting of the German Society for Immunology ✨
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Markus List @itisalist.bsky.social · 24/01/2026
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
ls.tum.de
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.
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Markus List @itisalist.bsky.social · 17/01/2026
Sad news for the whole bioinformatics community and science at large. My condolences to Peer's family, former and current members of his team.
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REPO4EU @repo4eu.bsky.social · 18/12/2025
"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?...
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Christina Steidele @steidele.bsky.social · 10/12/2025
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!
doi.org
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...
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DaiSyBio @daisybio.de · 04/12/2025
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...
makerworld.com
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...
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Markus List @itisalist.bsky.social · 03/12/2025
Welcome Ryu, it's a pleasure having you in our @daisybio.de lab!
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Markus List @itisalist.bsky.social · 18/09/2025
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 :-)
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Stephen Turner @stephenturner.us · 15/09/2025
Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing academic.oup.com/nargab/artic... 🧬🖥️🧪
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Markus List @itisalist.bsky.social · 10/09/2025
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.
Rhein in Basel
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Markus List @itisalist.bsky.social · 07/09/2025
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.
Park bench in a misty morning
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REPO4EU @repo4eu.bsky.social · 03/09/2025
#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
RExPO25 Session in focus: AI/ML in systems medicine and drug repurposing.
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Gregor Sturm @grst.bsky.social · 13/08/2025
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
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Markus List @itisalist.bsky.social · 28/06/2025
A flowery surprise at our @tum.de campus Freising yesterday. Congratulations to all students who celebrated their graduation.
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Markus List @itisalist.bsky.social · 05/06/2025
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...
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Markus List @itisalist.bsky.social · 03/06/2025
🧬🖥️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.
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Markus List @itisalist.bsky.social · 28/05/2025
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!
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Markus List @itisalist.bsky.social · 27/05/2025
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
webinar description
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Markus List @itisalist.bsky.social · 27/05/2025
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!).
Colorful liquid flowing from one bottle into another, as an illustration for (data) leakage.
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Victor Javier @vjsanchez.bsky.social · 30/04/2025
Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics 🧬🖥️ academic.oup.com/bioinformati...
academic.oup.com
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
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DaiSyBio @daisybio.de · 03/04/2025
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 😉
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Ana Conesa @anaconesa.bsky.social · 28/03/2025
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
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DaiSyBio @daisybio.de · 20/03/2025
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
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DaiSyBio @daisybio.de · 13/02/2025
📍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! 📍
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Markus List @itisalist.bsky.social · 31/01/2025
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...
linkedin.com
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...
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DaiSyBio @daisybio.de · 30/01/2025
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...
blog.scienceopen.com
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...
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Markus List @itisalist.bsky.social · 27/01/2025
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.
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Markus List @itisalist.bsky.social · 23/01/2025
Hey young investigators, use this opportunity to learn about the COST action MyeInfoBank and listen to a nice talk by our fabulous @a-dietrich.bsky.social
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DaiSyBio @daisybio.de · 19/12/2024
The whole DaiSyBio team wishes you happy holidays - more to come in 2025 ✨ (Nota bene: This is not an AI generated picture)
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Markus List @itisalist.bsky.social · 14/12/2024
Incredibly happy to finally see our manuscript "Emergence of power-law distributions in protein-protein interaction networks through study bias" published in @elife.bsky.social. doi.org/10.7554/eLif... It's been a long but fun journey with @dbblumenthal.bsky.social and @martinschaefer.bsky.social
doi.org
Emergence of power-law distributions in protein-protein interaction networks through study bias
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Dominic Grün @dominicgrun.bsky.social · 06/12/2024
NiCo is out! Our new algorithm for spatial transcriptomics data analysis predicts the crosstalk of cell types co-localized in tissue niches and sheds light on signalling mediators and downstream effects of cell-cell interactions by inferring covarying gene programs. www.nature.com/articles/s41...
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Anshul Kundaje @anshulkundaje.bsky.social · 05/12/2024
Looks like yet another case of overhyped results due to poor #bioMLeval evaluation of deep learning models -this time deep docking methods - specifically DiffDock. Look forward to the DiffDock authors response. But dont see any major flaws in this critique. Conclusion is REALLY worth reading!
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Rita Strack @ritastrack.bsky.social · 06/12/2024
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
nature.com
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
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Judith Bernett @judith-bernett.bsky.social · 02/12/2024
🧬🖥️Tranferring my papers, Pt. 2: "Guiding questions to avoid data leakage in biological machine learning applications" doi.org/10.1038/s41592-024-02362-y, which I published with @itisalist.bsky.social @dbblumenthal.bsky.social @romanjoeres.bsky.social, D. Grimm, F. Haselbeck, and O.V. Kalinina. 🧵1/20
Overview figure of the seven guiding questions addressed in manuscript regarding (1) Study bias, (2) Label distribution, (3) Data shift, (4) Inter-sample similarities, (5) Unavailable features, (6) Features as illegitimate surrogates, (7) Pretraining
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Judith Bernett @judith-bernett.bsky.social · 28/11/2024
🧬💻Transferring my paper posts here, starting off with "Cracking the black box of deep sequence-based protein-protein interaction prediction" doi.org/10.1093/bib/..., which I published together with @itisalist.bsky.social and @dbblumenthal.bsky.social. So what was it about? 1/13 🧵
Overview figure summarizing the major analyses of the paper. In the setting employed by published methods, performances are strongly inflated regardless of model and dataset. When the positive training dataset is randomly rewired, there is only a slight decrease in performance. When the models are evaluated on unseen proteins that are unsimilar to the training proteins, performances become random.
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Mitch Guttman @mitchguttman.bsky.social · 27/11/2024
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...
nature.com
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
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Oxford Nanopore @nanoporetech.com · 27/11/2024
We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them. Read more: nanoporetech.com/news/oxford-...
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