IMO, medium scale combinatorial regulator perturb expts with diverse measurable stoichiometry are going to be far more informative to learn causal models of cis-trans regulation than genome scale single gene knockouts. Hope we get more of these kinds of datasets at scale. 1/

Single cell and spatial alternative splicing analysis with Nanopore long read sequencing nature.com/articles/s4146…

Pathology-oriented multiplexing enables integrative disease mapping nature.com/articles/s4158… PathoPlex is a highly multiplexed imaging at subcellular resolution with a software package (spatiomic) to interpret protein co-expression patterns (clusters) across biological layers.

1/ Better late than never, here’s a long thread of threads summarizing our MOSAIC preprint. If you’re curious about the process by which a new microscope is conceived and brought into the world, this is the thread for you. If you’ve come for eye candy, there’s plenty of that too

🎉 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 👇

“Single-cell methods in biology are at this point of democratization, which is really exciting.” jonah on our effort to build high-quality, well-annotated datasets across tissues + states so more scientists have what they need to advance discovery bit.ly/3U31D1e

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In Cell, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. sciencedirect.com/science/articl…

#EpigeneticAging DNA Methylation Ageing Atlas Across 17 Human Tissues😎 (Sorry No blood vessels...😣) Meta-analysis of 15k human methylomes with age! 👉#DifferentiallyMethylatedPosition 👉#VariablyMethylatedPosition (only detected in brain buccal epithelia cervix liver lung

The Plot Builder in #JASP 0.95.0 is now powered by #tidyplots 🚀 Kudos to @matyasbukva JASP is an open-source statistical software suite with a graphical user interface for conducting classical and Bayesian analyses. jasp-stats.org #rstats #dataviz #phd

TopoLa: A Universal Framework to Enhance Cell Representations for Single-cell and Spatial Omics through Topology-encoded Latent ... biorxiv.org/content/10.110… #biorxiv_bioinfo

Thrilled to share scverse x Biomni! Biomni agent now supports 10 scverse core packages including scanpy, squidpy, scirpy, pertpy, etc! You can now use natural language to unlock complex single cell, spatial, and perturbation data analysis to generate novel

PUBLICATION ALERT: The African BioGenome Project (AfricaBP) Open Institute has now published the progress of its activities in 2024 in a publication authored by over 100 Africa-based researchers. Article: doi.org/10.1038/s44185… AfricaBP press release: africanbiogenome.org/2025/07/29/afr…

(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

Biological foundation models have hit a plateau. Scaling isn't working as expected. Foundational concepts from evolutionary biology could have predicted this: 🧵 research.arcadiascience.com/pub/idea-phylo… [1/9]

Potato evolved from tomato 9 million years ago. cell.com/cell/fulltext/… Natural History Museum Sandra Knapp University of British Columbia Loren H. Rieseberg Sichuan University Jianquan Liu #CAAS Sanwen Huang @cellcellpress

Interested in studying cell differentiation at the cellular level but don't trust your UMAP plots? Try visualizing your cell differentiation in space with our TopoVelo tool!

After many yrs building internally Arcadia Science, we're now able to partner more with others on cool organisms. You won't hurt my feelings if you don't read my post, but i will cut you if you don't watch our first organismal spotlight animation -- just skip to the bottom! 🧵

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.

✅ Published in nature today, the paper describing the initial whole-genome sequencing analysis of 500,000 UK Biobank participants. nature.com/articles/s4158…

New preprint on a surprising question - with a pangenome reference, *what is a genetic variant?* biorxiv.org/content/10.110… With Pouria Salehi Nowbandani, Shenghan Zhang, Haoyang Hu, and Heng Li Heng Li