Posts on X

Excited to listen to @deboramarks talking at #ECCB2020 on the prediction & design of biological sequences using neural machines. It's an "exciting time to be a computational biologist" - agreed :)

scArches let's you easily query reference atlases. To demo online sharing, @marenbuettner has uploaded the first annotated single-cell intestine atlas in collab with @lickertlab to scArches models, which you can query with own gut data. Sharing demo at scarches.readthedocs.io/en/latest/zeno…

Great keynote by @GAlmouzni from @Institute_Curie at #ECCB2020, amongst others on her coordinating activity for the @LifeTimeIni project, aiming to 'revolutionise healthcare' using single-cell *omics and machine learning, see lifetime-initiative.eu

Working outside - fun meeting, and one of the first f2f ones since April with colleagues @helmholtz_en, discussing about communication in @helmholtz_ai 🤓🤗

Excellent two minute paper video on @OpenAI’s recent GPT-3 NLP engine🤖 - with so many diverse, creative, unexpected and sometimes scary applications youtu.be/_x9AwxfjxvE

Happy that TcellMatch is now out in @MolSystBiol: Led by @davidsebfischer, we predict antigen specificity of single T cells from multimodal single‐cell experiments, modeling dextramer binding as func of receptor seq, RNA state etc. embopress.org/doi/full/10.15… github.com/theislab/tcell…

Great that @le_and_er got a best poster award at #ICML2020’s Comp Bio workshop #WCB20202 for our work on studying more expressive priors for variational autoencoders when applied to single cell genomics. Congrats!

@OlgaTroyanskaya talking at #WCB2020 #ICML2020 about her seminal DeepSea model and SeqWeaver, to model genomic code using neural networks. Impressive applications to discover noncoding disease signals eg in autism.

Will talk about scArches at #ICML2020 Comp Bio workshop today, looking forward to that meeting! icml-compbio.github.io

Want to map #scRNA-seq data on a reference atlas without sharing raw data? Plz check out single-cell architectural surgery (scArches) - led by @MohammadLotfol1, we use transfer learning for efficient query to reference integration. biorxiv.org/content/10.110… github.com/theislab/scarc…

Excited to listen to @c_drosten talking (by VC of course) in @HelmholtzMunich townhall meeting now on #SARSCoV2 detection and implications for outbreak control.

Just read about this (2019) beautiful work from @OpenAI on reinforcement learning to efficient play hide&seek and use tools: openai.com/blog/emergent-… Check out this nice summary video here: youtu.be/Lu56xVlZ40M Hilarious, how those agents find exploits in the physics engine.

"We do research, but protection is only possible together." Please download #CoronaApp, and join us in fighting #COVID19. @helmholtz_en @HelmholtzMunich bundesregierung.de/breg-de/themen…

Hilarious 🍪 intro by @MDLuecken in a #sparse2big consortium progress report - cookies being baked in batches and selected by users in biased fashion lead to batch effect similar to those in #scRNA-seq, hence the need for benchmarking 🤓 manuscript here: biorxiv.org/content/10.110…

Really happy that our paper on the proteome landscape across 100 species is out @Nature. Led by @labs_mann, we contributed a machine-learning based exploration of that landscape using a bidirectional LSTM, and robustly predicted a peptide's retention time. rdcu.be/b41a6

Back in the office after 3 months of completely virtual group existence. Feels strange, like coming back after a strenuous vacation, or as a colleague called it, like first day at school. A twice per week school but still. 🥳

With #COVID19 looking increasingly controlled in Germany, many places start coming back to offices - our lab is planning to do this ^slowly^ and only for ~a day/week initially. Organisation difficult though. Does anyone have tips for scheduling socially distanced desks and rooms?

GIF, plays on X

Happy diversity day 2020! IMHO diversity is a crucial asset for successful research and organizations, hope our science systems improve (and don’t turn the dial back as is currently happening). charta-der-vielfalt.de/diversity-tag

Excited to share our work on benchmarking large-scale data integration in single-cell genomics. Led by @MDLuecken and starting from an internal hackathon with @colomemaria_epi, we compare methods & preprocessing using a series of metrics and scenarios, see biorxiv.org/content/10.110…

MorphoSeq, really impressive integration of scRNA-seq and imaging for gastrulation, good resource, too! Not so sure why another clustering algorithm (‚SCECTION’) is needed though, so many already - would have been nice to see some comparisons at least. sciencedirect.com/science/articl…

Great work on #singlecell tracing to study memory in yeast from Schneider-lab @HelmholtzMunich in @MolecularCell - they found that single cells pass on life experience to their progeny. cell.com/molecular-cell…

Just gave talk @singlecellomics and got ‚zoom-bombed‘. Kind of annoying trolling but cute how persistently tried. In any case recommend to everyone setting up public lectures to read up on this, and to @zoom_us to remove audio hijack bug. Good reference medium.com/pcmag-access/h…

To our #AI overlords: got this ad served today, which seems a tad off-target for a vegetarian. Let’s see if you improve after mining this tweet 😂

Interview with @melindagates @SZ on her contributions to master the global #COVIDー19 crisis, impressive! I haven’t seen philanthropy on this level of engagement & professionalism in Germany - a ray of hope that US will pull through despite current leadership vacuum.

Before our virtual @ICBmunich seminar yesterday, I asked around what positive #COVID19 take-aways people could see for how we work in science and @Helmholtz_MUC in the future, see word cloud attached. 👍 for home office & digitalization!

Did my first virtual lecture today @TUM_Mathematics (statistical learning). >100 students joined via zoom, and I tried to make it a bit interactive via mentimeter Q&As but really missed the direct interaction. Any suggestions for better virtual seminars? 🤔

Excited to contribute to the @humancellatlas lung biological network study, with first ever single-cell meta analysis, showing cell-type specific association of SARS-CoV-2 entry genes with age, gender and smoking. Well done, Chris, @MDLuecken +all! biorxiv.org/content/10.110…

Currently playing the online game 'CODENAMES' in the group @ICBmunich with ~10 people via group chat and this shared webpage - horsepaste.com - lot's of fun! Goal is to associate a clue with a wordlist. Attached, @g_palla1 asked for "bioinformatics" @Bioconductor 🤓

I joined the Scientific Committee of the @EuroJedi GrandChallenge, aiming to make a major breakthrough in structural biology & machine learning. Now starts a 1w phase where we call upon input of all for def of robust success metrics, please contribute! http://covid19.jedi.groupit

Want to know how to select #samples, #cells and sequencing depth in your #scRNAseq experiment? Please check out our recent contribution to experimental design, led by Katharina Schmid from @heinig_matthias lab. Great collab with @LickertHeiko, @Binder_Lab. biorxiv.org/content/10.110…