Haojia Wu

Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...

Universal consensus 3D segmentation of cells from 2D segmented stacks

www.nature.com/articles/s41...

A unified cell atlas of vascular plants reveals cell-type foundational genes and accelerates gene discovery A cross-species single-cell atlas highlights a core subset of cell-type foundational genes associated with major vascular plant cell types, enabling the identification of hidden cell types and the dev...

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 A comprehensive single-nucleus RNA-seq atlas of >367,000 nuclei from male and female Aedes aegypti mosquitoes reveals sexual dimorphism in sensory systems and brain cell types and widespread co-expres...

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 - Nature A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.

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 - Nature Biotechnology Haploid embryonic stem cells for cattle and sheep are produced, opening new reproductive possibilities.

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

Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution RAEFISH delivers whole-transcriptome (>20,000 genes) imaging at single-molecule resolution in cells and tissues and enables direct gRNA detection for high-content, image-based CRISPR screens.

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...

Python, the movie! The programming language’s origin story comes to the silver screen The creator of the NumPy and SciPy libraries reflects on their supporting role in the story of Python, now the subject of a documentary.

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/

Translon: a single term for translated regions - Nature Methods Nature Methods - Translon: a single term for translated regions

A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes.

www.nature.com/articles/s41...

Liquid crystal lenses could make better bifocal glasses A prototype of bifocal eyeglasses uses liquid crystals and electric fields to switch between modes that aid in nearby and distance vision

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

Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune reperto...

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

Target sequence-conditioned design of peptide binders using masked language modeling - Nature Biotechnology PepMLM designs peptide binders against diverse targets using masked language modeling.

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

Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues - Nature Methods This work presents MAPIT-seq, an antibody-guided RNA editing method that enables co-profiling of RBP-RNA interactions and gene expression at single-cell resolution and in tissue contexts.

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

A diverse and distinct microbiome inside living trees - Nature Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minimal similarity to other tissues or ecosystem components.

Nature research paper: A diverse and distinct microbiome inside living trees

go.nature.com/3Hl3D2h

Silencing mitochondrial gene expression in living cells Mitochondria fulfill central functions in metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, the central mechanis...

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

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

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.

Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy - Nature Genetics The relationship between pathogenic germline variation, clonal hematopoiesis (CH) and risk of hematologic malignancy is explored in 731,835 individuals across 6 cohorts. Carriers of variants in certai...

📢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 - Nature Biotechnology TopoVelo infers cell differentiation stages and rate parameters of gene expression using spatially coupled differential equations.

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

Single-cell and spatial transcriptomics of stricturing Crohn’s disease highlights a fibrosis-associated network - Nature Genetics Single-cell and spatial transcriptomics analysis of stricturing Crohn’s disease highlights cellular heterogeneity in fibrotic tissue and identifies neighborhoods of fibroblasts and immune cells contri...

📢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...

Google’s new AI will help researchers understand how our genes work First came AlphaFold. Now comes AlphaGenome for DNA.

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...

DeepMind’s new AlphaGenome AI tackles the ‘dark matter’ in our DNA Tool aims to solve the mystery of non-coding sequences — but is still in its infancy.

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 - Genome Biology Single-cell RNA sequencing has revolutionized cellular heterogeneity research, but analyzing the abundance of unannotated public datasets remains challenging. We present scExtract, a framework leverag...

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 Human pluripotent stem cell-derived kidney organoids replicate embryonic nephrogenesis in a 3D-culture system. Recent advances suggest that refining the culture environment to replicate spatiotemporal...

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