Daniel Podlesny

Excited to release metaTraits.embl.de! 🦠 Explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Paper at NAR: doi.org/10.1093/nar/gk… 🧵 1/9

full thread at bsky.app/profile/podles…

This thread was originally posted on 🦋. It is partially broken here. Consider switching.

Excited to release metaTraits.embl.de! 🦠 Explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Paper at NAR: doi.org/10.1093/nar/gk… 🧵 1/9

@FrankRHutter is there a solution for wide data? pm

4/4 We’re currently working directly with customers to run TabPFN-2.5 Scaling Mode on their data. If you’re interested, please contact sales@priorlabs.ai to get on the waitlist.

The tabular data science revolution is really here now! I’m thrilled to introduce *TabPFN Scaling Mode*, removing TabPFN’s previous limit on dataset size. The plot below shows scaling results for the biggest dataset we have tried so far (subsamples of 100k and 1M, and the full 10M rows / data points). While we’ve only benchmarked up to 10M rows (a 100x increase in the 3 weeks since the release of TabPFN-2.5!), the results indicate that we can just scale to any dataset size now 🚀 🧵1/4

For somebody working on the gut #microbiome, the responses ("gross", "embarrassment", "pseudoscience", etc.) to this @Nature article on the treatment of C-section babies with their mother’s poo are quite sobering. So, I thought I would provide a perspective in the thread below.

Sign for Europe: eu-inc.org

@vsbuffalo You can use webhooks on @SlackHQ

Is there a service to get push notifications to your phone when a command line task finishes?

After a high dose of psilocybin, the brain desynchronizes at a massive scale, causing loss of our sense of self, time, and space. This may drive the burst of plasticity caused by psychedelics. The next day, brain activity has largely returned to normal, but an echo remains – a reset of circuits critical to the sense of self. Our study is out today in @Nature nature.com/articles/s4158…

Thrilled to share our new preprint. A thread 🧵 biorxiv.org/content/10.110…

Immensely proud to share our four papers on #SingleCell dissection of #Alzheimers Disease coming out in @CellCellPress today, reporting 2.3M #scRNA profiles and 850k #scATAC profiles across 427 post-mortem human brain samples from AD and non-AD donors in a wonderful #interdisciplinary collaboration with @DrLiHueiTsai between @MIT @MIT_Picower @MIT_CSAIL @BroadInstitute @RushUniversity Paper 1: scRNA + vulnerability + resilience cell.com/cell/fulltext/… Paper 2: scATAC + GWAS + Epigenome Erosion cell.com/cell/fulltext/… Paper 3: Microglia States + reprogramming cell.com/cell/fulltext/… Paper 4: DNA damage + gene fusions cell.com/cell/fulltext/… MIT News: news.mit.edu/2023/decoding-… Issue: cell.com/cell/current News & Views: cell.com/cell/fulltext/…

New preprint with @delafuenteupenn : The antimicrobial peptides (AMPs) of the global microbiome! From 72 diffferent habitats (the best current sampling of the global microbiome) we obtained almost 1 million candidate AMPs biorxiv.org/content/10.110…

Greengenes2 unifies microbial data in a single reference tree nature.com/articles/s4158…

1/ 🤰What can we learn about pregnancy form 45 million lab tests? We present a dynamic atlas of pregnancy and postpartum based on measurements from over half a million pregnancies at a one-week resolution. @biorxivpreprint @AlonBar10

This is awesome (new genetic code acting as a bidirectional firewall for infection and gene transfer) and a bit frightening (potentially higher fitness): I am glad they added a proper biocontainment (stable dependency on non-standard amino acid). nature.com/articles/s4158…

Our new @NatureMedicine study aims to improve our understanding of obesity & its impact on health. Although useful, classical BMI misclassifies ~30% of people. To capture the heterogeneity of obesity, we developed blood-omics-based biological BMI (bBMI). nature.com/articles/s4159…

Necrotizing enterocolitis (#NEC) is a devastating disease, affecting up to 11% of all very-low birthweight (<1500g) infants. In our newest paper @Naturecomms we look at NEC prophylaxis regimens in clinics that are highly successful in preventing NEC (average NEC rate: 2.9%).

I am thrilled to share with you our recently published paper showing that the microbiota-derived metabolite 3-IAA influences chemotherapy efficacy in #PancreaticCancer @Nature nature.com/articles/s4158…

Forget losing jobs to AI, look to the sky! Flocks of pigeons detect cancer in scans with 99% accuracy & “are suitable surrogates for human observers in certain medical image perception studies, thus avoiding the need to recruit, pay & retain clinicians...”journals.plos.org/plosone/articl…