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... 🧬🖥️🧪

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.

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 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.

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!

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

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 🧬🖥️ 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

📍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! 📍

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...

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.

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

The whole DaiSyBio team wishes you happy holidays - more to come in 2025 ✨ (Nota bene: This is not an AI generated picture)

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

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...

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!

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...

🧬🖥️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

🧬💻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 🧵

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...

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-...

Nice to see our review highlighted on bluesky!

I'm excited to visit the German University in Cairo next week as a speaker of the GEM-CAP symposium on Microbiome and Bioinformatics. Participation is free and registration open until Nov. 25th if you happen to be around: www.guc.edu.eg/Conference/G...

These starter packs are a really great feature I would have wished for back when I had joined twitter. Great way to (re)grow your network.

Predicting treatment response is a complex task and NovumRNA can illuminate one key facet of anticancer immunity: the dynamics of noncanonical neoantigens. If applied to perturbed tumor RNA-seq, it can unveil drugs that might boost tumor-cell immunogenicity and facilitate T-cell recognition. 🧬 🖥️

We're looking for a full professor Plant Breeding (Kiel University, Germany). The position comes with good labs, glasshouses, technical and administrative staff and one or two permanent postdoc positions to be filled freely. Questions? Feel free to contact me!

Great collaboration with @itisalist.bsky.social ✨ We hope our study and set of tools and resources can be helpful to the scientific community 💫 📝 preprint: doi.org/10.1101/2024... 🛠️ omnideconv ecosystem: omnideconv.org Please repost and help us spread the word! 6/6

Had great fun attending the #gcb2024 in Bielefeld. Our group had the honor of contributing 2 talks (Judith Bernett on guiding questions to avoid data leakage and Johannes Kersting on GRN inference with DysRegNet. A surprise at the end: Alex Dietrich won the poster prize with the project omnideconv!

Looking for a postdoc: Project on Quantitative Disease Resistance. Use high-throughput phenotyping & transcriptomics to find QDR regulators in quinoa. Think spj.science.org/doi/10.34133... plus bmcplantbiol.biomedcentral.com/articles/10.... Experience w/ scripting req'd! DM for details.

Nice to see that Bluesky is getting some traction.

Hello world!