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That’s a wrap on the 18th Berlin Summer Meeting – Sequencing Planet Earth! 🌍🧬 3 days of cutting-edge science, from hands-on workshops on June 18 to an inspiring symposium on June 19–20, 2025. Thank you to all speakers, participants & organizers for making #BSM2025 a success! @mdc-berlin.bsky.social

submitted 4 days ago • 0 comments

I learnt about Malva yesterday thanks to a fantastic talk by @danilexn.bsky.social (malva.mdc-berlin.de/faq): early access is available if you want to test a user-experience based, v large scale sc and spatial RNA-seq index to explore patterns.

submitted 5 days ago • 1 comment

🌍18th Berlin Summer Meeting: Sequencing Planet Earth 🧬Session 1: Sequencing at Scale – Tools to Decode Life’s Molecular Code From ultra-sensitive molecular tools to real-time sequence search and scalable k-mer analysis — Day 1 opens with cutting-edge tech for decoding life. @mdc-berlin.bsky.social

submitted 6 days ago • 1 comment

See you there next week! So many new things coming…

submitted 5 days ago • 0 comments

Super inspiring morning - and lots more happening until tomorrow! It is a pleasure to share stage with these amazing scientists. (Special thanks to @camillemrcht.bsky.social for the great explanation of k-mers and their analysis)

submitted 6 days ago • 1 comment

🔬Hands-on workshops kick off the Berlin Summer Meeting 2025 #BSM2025! Attendees dove into real-time sequence search, nucleic acid analysis of environmental samples, spatial transcriptomics for infectious diseases, AI-assisted genomics, and a behind-the-scenes tour of single-cell omics 🧬🧑‍🔬 #mdcBerlin

submitted 6 days ago • 1 comment

🌬️ Bacteria and fungi found 10,000 feet up in Japan – likely from over 1,200 miles away. Researchers now use eDNA to trace biodiversity, detect pathogens, and monitor ecosystem health. More about the Berlin Summer Meeting (June 19–20): 👉 www.mdc-berlin.de/news/news/be... 👈 #mdcBerlin | #mdcBIMSB

submitted 12 days ago • 1 comment

This is incredible. The deployed AI models have finally managed the impossible: becoming utterly worse at image recognition than anything from the past 15 years.

submitted 11 days ago • 3 comments

DeepGFT: identifying spatial domains in spatial transcriptomics of complex and 3D tissue using deep learning and graph Fourier transform #Drosophila

submitted 21 days ago • 0 comments

We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.

submitted 21 days ago • 0 comments

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

submitted 33 days ago • 37 comments

AI does not make discoveries. People do. AI is just a tool – that gets dumber and dumber by the minute.

submitted 34 days ago • 0 comments

"The positive results that get published tend to be overly optimistic about AI’s potential. As a result, I’ve come to believe that AI has generally been less successful and revolutionary in science than it appears to be." An excellent firsthand account: www.understandingai.org/p/i-got-fool...

submitted 35 days ago • 3 comments

If you ever feel like you’re late to the game, just remember the EU is only now noticing the genocide in Gaza.

submitted 35 days ago • 1 comment

📢Register for the Berlin symposium #Biology_of_Health Towards a Molecular Approach to Preventive Medicine! 🗓️ 19-20 May 2025 🎤 Inspiring line-up of speakers! Keynotes by Amos Tanay, Elvira Mass, Aleksejs Sazonovs, and Nikolaus Rajewsky ✏️Register & full program: rb.gy/kos81e 📌 Registration: 16May 2025

submitted 42 days ago • 0 comments

We aim to create a meeting venue for interactive discussions among scientists who rarely attend the same meetings. It stimulates creativity & new research directions.

submitted 42 days ago • 0 comments

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

submitted 46 days ago • 8 comments

>:(

submitted 50 days ago • 2 comments

The list of proceedings papers for #ISMB2025 is up on the website www.iscb.org/ismbeccb2025... ! It's an exciting collection of papers, as always :).

submitted 56 days ago • 0 comments

Day 1 of #Biovaria 2025 was filled with engaging presentations of innovative #technologies and #startups, insightful conversations, and lasting connections - but it's not over yet! We are looking forward to a #bavarian night at a Biergarten to wrap up a successful first day 🥳🍻 #biotech #networking

submitted 57 days ago • 0 comments

Bueno. ¿Os ha gustado la performance?

submitted 57 days ago • 49 comments

When RAG systems hallucinate, is the LLM misusing available information or is the retrieved context insufficient? In our #ICLR2025 paper, we introduce "sufficient context" to disentangle these failure modes. Work w Jianyi Zhang, Chun-Sung Ferng, Da-Cheng Juan, Ankur Taly, @cyroid.bsky.social

submitted 61 days ago • 1 comment

The STIM paper is out! We build on established computer vision techniques to automatically create 3D volumes of spatial transcriptomics datasets with human-level accuracy, and useful, interactive visualizations. www.sciencedirect.com/science/arti... @hhmijanelia.bsky.social @mdc-bimsb.bsky.social

submitted 63 days ago • 0 comments

Starting #RECOMBseq with @rayanchikhi.bsky.social 's keynote. Here stressing our responsibility as scientists to enable access to a common good: genomic data

submitted 62 days ago • 1 comment

+ How much RAM do you need? - yes

submitted 65 days ago • 1 comment

Treating cells as sentences is not all you need.

submitted 65 days ago • 1 comment

Our PhD student Louis Romette is optimizing long-term live-cell imaging. He just casually dropped this 65-hour movie of a growing neuron (div 3 to 6) with knocked-in actin 🔥🕶️ #realtimemicroscopy

submitted 68 days ago • 14 comments

Soon we are releasing a search engine (Malva) that, among many other things, allows to reproduce something like Figure 3 of this preprint in less than 1 second across the whole Human Cell Atlas (>100TB raw data).

submitted 68 days ago • 1 comment

New preprint out! This is probably my most important paper. To my deep chagrin, it has no math. XIST is a non-coding RNA exclusive to XX females. It silences one of the X chromosomes. So what is it doing in male heart Schwann cells?

submitted 70 days ago • 1 comment

Male XIST expression in cardiac pseudo-glia does not induce X chromosome inactivation https://www.biorxiv.org/content/10.1101/2025.04.09.648005v1

submitted 70 days ago • 0 comments

I taught LASSO the other day and one student asked "But surely I can't just go throw all the variables I have into LASSO and expect it to pick all the correct ones" and I just wanna say bless his innocent heart

submitted 69 days ago • 8 comments

Check out this fantastic work on neighbourhood preference in spatial omics data from the Schapiro lab 🚀! Congratulations @chiaraschiller.bsky.social and team on a wonderful project! 👏🤩

submitted 69 days ago • 0 comments

Our 3D study of the tumor microenvironment is finally out! Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 ) Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!

submitted 69 days ago • 2 comments

submitted 71 days ago • 1 comment

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search. rdcu.be/eg4OA w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/

submitted 74 days ago • 3 comments

Excited to introduce Malva publicly for the first time - our sequence-centric search engine for instant exploration of spatial and single-cell data at unprecedented scale. #bioinformatics #singlecell

submitted 75 days ago • 0 comments

From an #AI-powered search engine for omics data to a scalable drug screening platform for neuromuscular diseases – 4 of our labs present their projects at @biovaria.bsky.social #techtransfer networking event! www.biovaria.org/ @[email protected] @garyrlewin.bsky.social

submitted 75 days ago • 0 comments

Scholar.archive.org

submitted 77 days ago • 3 comments