A unified cell atlas of vascular plants reveals cell-type foundational genes and accelerates gene discovery www.cell.com/cell/fulltex...

A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito www.cell.com/cell/fulltex...

Sperm sequencing reveals extensive positive selection in the male germline www.nature.com/articles/s41...

Generation of modified cows and sheep from spermatid-like haploid embryonic stem cells go.nature.com/42wdD05

RAEFISH - Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution www.cell.com/cell/fulltex...

Mind blowing mechanotherapy of aged embryo 🤯👹

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights. 🔗 www.biorxiv.org/content/10.1...

The creator of the NumPy and SciPy libraries reflects on their supporting role in the story of Python, now the subject of a documentary go.nature.com/4gHDSGF

🗳️ Election results are in! Join ASN in congratulating Benjamin D. Humphreys, MD, PhD, FASN, as Executive Councilor and Rasheed A. Gbadegesin, MBBS, MD, FASN, as At-Large Councilor. Their terms begin January 1, 2026.

1. Bluesky doesn’t downrank links 2. You can choose your own algorithm from among thousands 3. The whole app is open source This keeps it a free and open platform by design, leading to better click-throughs and traffic to your site. We 💙 the open web.

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes. www.nature.com/articles/s41...

A prototype of bifocal eyeglasses uses liquid crystals and electric fields to switch between modes that aid in nearby and distance vision

Stereoseq v2 works on ffpe samples www.cell.com/cell/fulltex...

Target sequence-conditioned design of peptide binders using masked language modeling - @pranam.bsky.social go.nature.com/3UtVc7N

www.nature.com/articles/s41... Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues

Nature research paper: A diverse and distinct microbiome inside living trees go.nature.com/3Hl3D2h

Just out in @science.org Silencing mitochondrial gene expression in living cells | Science www.science.org/doi/10.1126/...

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

📢ONLINE @natgenet.nature.com 📰Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy. By Jie Liu, @kellybolton.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...

Topological velocity inference from spatial transcriptomic data www.nature.com/articles/s41...

📢ONLINE @natgenet.nature.com 📰Single-cell and spatial transcriptomics of stricturing #Crohn’s disease highlights a fibrosis-associated network. By Lingjia Kong, ‪@thexavierlab.bsky.social‬ and colleagues. ⬇️ www.nature.com/articles/s41...

First came AlphaFold. Now comes AlphaGenome for DNA.

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model storage.googleapis.com/deepmind-med...

An AI model developed by Google DeepMind could help scientists make sense of the non-protein-coding part of the genome https://go.nature.com/3HYwJEu

Single-Cell Spatial Mapping of Human Kidney Development Reveals the Critical Role of the Local Microenvironment in Cell Fate Decisions www.biorxiv.org/content/10.1...

scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration link.springer.com/article/10.1...

Elevations in local complement are linked with kidney fibrosis that progressively impairs renal function. Portilla et al. highlight the potential for complement-targeted therapeutics to slow fibrosis progression in CKD and other kidney diseases. buff.ly/5YDT6jM

Nephron segmentation and patterning in kidney organoids can be modulated by distinct FGF subfamily members www.biorxiv.org/content/10.1...

Spatial long read seq at near single cell resolution www.biorxiv.org/content/10.1...

How adding mRNA to code for interleukin-12 markedly increased T cell immune response which could be used for vaccines vs infectious diseases and cancer @sciimmunology.bsky.social www.science.org/doi/10.1126/...

Atkinson’s gleeful brilliance helped people draw on computer screens and access information via links. www.wired.com/story/bill-a...

An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day www.biorxiv.org/content/10.1...

Maternal iron deficiency causes male-to-female sex reversal in mouse embryos www.nature.com/articles/s41...

EpiTrace infers cell mitotic age and evolution from single-cell ATAC-seq data go.nature.com/3QHBfc3 rdcu.be/em31W

Manufacturing CAR T cells in the laboratory is expensive and time-consuming. A feature in Nature explores how an in vivo approach could get the cancer therapy to more people. #medsky 🧪

A visual–omics foundation model to bridge histopathology with spatial transcriptomics www.nature.com/articles/s41...

I cannot believe I didn't post about dark sectioning! I can only blame my crazy travel schedule. Check out this amazing tool for background removal in fluorescence microscopy. An important new concept, not 'just another' denoising algorithm.

SUM-seq out @natmethods.nature.com !
 🚀 Ultra-high-throughput Multiplexed snATAC+RNA Used to: ⏳ link temporal macrophage GRNs to immune disease genetics 🩸 map T cell regulatory landscapes 🧬✂️ dissect TF function in hiPSC differentiation via CRISPRi/a screens doi.org/10.1038/s41592-025-02700-8 🧵

cell seg tool for spatial omics github.com/dcjones/proseg

Proseg is a segmentation tool for single-cell spatial transcriptomics data that uses unsupervised probabilistic modeling of transcript spatial distribution, for accurate segmentation without multimodal staining. www.nature.com/articles/s41...

My Penn Biostatistics colleague Mingyao Li & two of our Biostatistics PhD students, Kyle Coleman & Shunzhou Jiang, have helped co-lead a new article published in Nature presenting spatial single cell transcriptomic characterization of brains of developing fetuses www.nature.com/articles/s41...

New online! Cell-type deconvolution methods for spatial transcriptomics

Spatial transcriptomics reveals human cortical layer and area specification ->Nature | More info from EcoSearch

Today we’re sharing an early look at our latest Gemini model update for I/O! Introducing the updated Gemini 2.5 Pro (I/O edition), which ranks #1 on WebDev Arena and surpasses our previous 2.5 Pro model by +147 Elo points. 🏆 blog.google/products/gem...

A neoantigen vaccine generates antitumour immunity in renal cell carcinoma www.nature.com/articles/s41...

Dear AI, Deep learning models trained using DNA sequence to predict gene expression really struggle to accurately predict counterfactual effects such as effects of genetic variants. Why is this the case? platform.futurehouse.org/trajectories...

Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies www.cell.com/cell/fulltex...

Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.

#SpatialTranscriptomics Stereo-seq 👤Carotid #Atherosclerosis IntraPlaque #TertiaryLymphoidOrgan😎 CD138+ Plasma cells +diverse B cells ❎ #GerminalCenter ✅ #Lymphangiogenesis ✅#HEV Col5A1+ fibroblast-like #SmoothMuscleCell as #LymphoidTissueOrganizer #NatCVR 2025 www.nature.com/articles/s44...