...but we're not there yet and at Arc Institute we are putting together all the pieces to make this happen! Check out: State: arcinstitute.org/manuscripts/St… cell-eval: github.com/ArcInstitute/c… scBaseCount: biorxiv.org/content/10.110…

#SpatialOmics The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs 15 M cells 100 donors 10 organs Liver Pancreas Bone marrow Lymph node PBMC Prostate Stomach ILeum Colon Appendix CosMX 1k 6k WTA Xenium GeoMx RNAscope

The FUTURE is NOW! 🚨 Whole-Transcriptome Spatial Genomics with OUT-OF-THE-BOX analysis starring Helena Lucia Crowell. 🔬 Spatial genomics has now reached FULL-transcriptome resolution, enabling spatially resolved single-cell analysis at million cell scale. With this, we’re rethinking how

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery nature.com/articles/s4159…

Very excited to share our preprint on #AI directed Deep Visual Proteomics (DVP) on #PancreaticCancer precursor lesions (PanINs), in collaboration with OmicVision Andreas Mund Thousands of proteins from as few as ~100 precisely microdissected cells in archival samples!

(1/n) Can we disentangle the effects of multiple covariates (e.g., sex, age, disease) to predict multiple counterfactual outcomes at the single-cell level? We introduce CellDISECT, a causal generative model that addresses this by learning to generate synthetic counterfactuals

Temporal and spatial omics technologies for 4D profiling nature.com/articles/s4159…

Meet RESOLVE, our new method for mutational signature analysis just published in Nucleic Acids Research! Applied to 20,000 adult and pediatric cancers, it reveals key links to driver mutations and clinical outcomes. 🔗 doi.org/10.1093/nar/gk… #CancerGenomics #MutationalSignatures

The discussion around virtual cell models has primarily focused on algorithms and metrics. What about the training data? Is scRNA-seq good enough? A key challenge is distinguishing direct vs indirect effects on gene expression. 1/5

Neuron programming! Pro-neural TFs + 480 morphogen conditions + scRNA-seq --> Diverse iN subtypes of forebrain, midbrain, hindbrain, spinal cord, and PNS. science.org/doi/10.1126/sc… Hsiu-Chuan Lin Jasper Janssens Treutlein lab Science Magazine D-BSSE, ETH Zurich #NGN2 #ASCL1

1/11 Our study on subclonal immune evasion in non-small cell lung cancer has just been published in Cancer Cell cell.com/cancer-cell/fu…

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets dlvr.it/TLyB5j

I’m happy to share our latest work on tumour necrosis! During my time in the Mikala Egeblad lab, we found that tumour necrosis is not a passive phenomenon secondary to tumour growth, but an active phenomenon driven by neutrophils and NETs! Thread below: (1/13) nature.com/articles/s4158…

This work was led by stellar postdoc Aditya Pratapa, co-supervised by @tatalab-duke.bsky.social , and with fantastic collaborators @kevinmbyrd and Rajkumar Savai! Here's the preprint: biorxiv.org/content/10.110… The code will be here: github.com/rohitsinghlab/…

One Section, Two Worlds: Single-Cell Integration of MALDI-MSI and Spatial Transcriptomics on the Same Single Tissue Section biorxiv.org/content/10.110…

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: nature.com/articles/s4225… 📖 News & Views: nature.com/articles/s4225… 💻 Code: corneto.org 🧵 Thread 👇

Fuck ML tutorials. This is a collection of 300 ML system design case studies in real world, from Stripe, Spotify, Netflix, Meta, etc. Perfect for interviews and to learn how it’s done in the battlefield. Wish there was a similar thing for agents!

🎉 Thrilled to share our latest paper in Nature Methods on GeneAgent, a next‑generation AI agent designed for gene‑set analysis with built‑in self‑verification against biological databases to minimize LLM hallucinations. 🔬 Key Highlights 📍 Gene‑set analysis helps researchers

(1/12) Over a year ago, we launched a new project to explore whether the tissue microenvironment could predict cellular behaviour and whether reprogramming might unlock new therapeutic avenues. 🧬 Spatial transcriptomics provides deep insights into tissue organisation. We

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.