A venn diagram with a small circle that says "Software That Works" and a much larger circle that says "Software that looks like it works"

A slide from my upcoming PyTexas talk about vibe coding and AI. PyTexas is in beautiful Austin this year, April 17 to 19. www.pytexas.org/2026/

Flexible ensheathment of axons enables myelination of complex CNS networks - Nature The rate of axon ensheathment varies within individual myelinating processes, resulting in chains of myelin sheaths connected by bridges consisting of thin cytoplasmic processes that provide&nbsp...

Latest offering. How myelin ensheathes axons!

Born from chat with Dwight Bergles on "weird things" we saw oligodendrocytes do, like making "bridges" between sheaths.

Driven forward by Cody Call, Kelly Monk, and myelin folks @edinburgh-uni.bsky.social

Enjoy!
www.nature.com/articles/s41...

This is my favorite climate change chart. Japanese monks, aristocrats, and emperors kept meticulous records of cherry blossom festivals for 1,200 years and accidentally built the world's longest climate dataset.

ChromSMF preprint is out!🚀
tinyurl.com/ChromSMF

We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting!

In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬

What does this unlock? ⬇️

One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!

Single-molecule peptide sequencing through reverse translation of peptides into DNA - Nature Biotechnology Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.

Would I have called it reverse translation? No. Do I think it is? Also no. Is it cool? Heck yes.

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

Gene regulatory networks: from correlative models to causal explanations - Nature Reviews Genetics In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without compromising explanatory power.

"GRNs, which should provide mechanistic explanations, are increasingly reduced to statistical correlations — ‘hairballs’ that fail to capture molecular causation"

By Maizels and @jamesbriscoe.bsky.social

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

Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus www.nature.com/articles/s4...

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

"Here, we present SPAtial Cell Exploration (SPACE), a spatial CRISPR screening platform that integrates whole-transcriptome profiling (~18,000 genes), multiplexed protein detection (~68 markers), and CRISPR perturbation mapping at subcellular resolution"

www.biorxiv.org/content/10.1...

R is slow in plotting tens of thousands of points. How to speed up for a million cell scRNAseq data?
check out scattermore github.com/exaexa/scat...

Cross-species cellular mapping and humanization of Fcγ receptors to advance antibody modeling Preclinical modeling of human IgG–based drugs is enhanced through humanized Fcγ receptor and FcRn expression in a murine knockin model.

A new #ScienceImmunology study highlights the limitations of preclinical models for human antibody-based drugs, and demonstrates how a humanized mouse model may improve study outcomes. https://scim.ag/4t2ye7T

Human cortical organoids recapitulate inter-individual variability in infant brain-growth trajectories Glass, Matoba, et al. demonstrate that human cortical organoid cell-type proportions, cross-sectional area growth, and cell cycle genes in early neural progenitors are associated with inter-individual variability in infant cortical surface area measurements, supporting the fidelity of organoids as a model system.

Human cortical organoids recapitulate inter-individual variability in infant brain-growth trajectories

From bulk RNA sequencing to spatial transcriptomics: a comparative review of differential gene expression analysis methods - Human Genomics Human Genomics - Transcriptome analysis is essential to dissect the molecular mechanisms underlying phenotypic differences and disease mechanisms. Traditionally, microarrays were used, but RNA...

Review | From bulk RNA sequencing to spatial transcriptomics: a comparative review of differential gene expression analysis methods link.springer.com/article/10.1...

Paternal exercise confers endurance capacity to offspring through sperm microRNAs Yin et al. show that paternal exercise improves offspring endurance capacity and metabolic health via sperm microRNAs that reprogram gene expression in early embryos, revealing how exercise benefits c...

This is a very new study and needs to be replicated further, but I found it interesting. As a physiotherapist and neuroscientist, what caught my attention more was whether this alleged epigenetic change on the mitochondria has an effect on infants' brain health, www.cell.com/cell-metabol...

Neuronal PARIS-STAT3 axis drives tau pathology and glial activation in Alzheimers disease www.biorxiv.org/content/10.64898/2025.12...

Motif-based models accurately predict cell type-specific distal regulatory elements www.nature.com/articles/s4...

"BOM outperforms more complex deep-learning models while using fewer parameters." simplicity is a beauty.

CellWhisperer

From Transcriptome to Text

A great LLM-Chatbot explorer for CELLxGENE & GEO & your own data!

Contrastive language image pretraining
Geneformer
BioBERT
>1 million bulk/pseudo-bulk transcriptomes

cellwhisperer.bocklab.org

#NatBiotech 2025
www.nature.com/articles/s41...

VRK2 targeting potentiates anti-PD-1 immunotherapy in hepatocellular carcinoma through MYC destabilization www.nature.com/articles/s4...

The pitfalls of class prediction in omics 🧵
1/ You think you’ve built the perfect omics predictor.
The accuracy is high. The p-value is low.
But is it real—or just a story your data whispered back?

Oligodendrocyte progenitor cell responses to inflammatory demyelination with aging www.biorxiv.org/content/10.1101/2025.09....

A host organelle integrates stolen chloroplasts for animal photosynthesis Sea slugs steal foreign chloroplasts and store them in specialized organelles that facilitate photosynthesis and eventual digestion to mediate starvation resistance.

www.cell.com/cell/abstrac...

A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis

tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment

Now 90% of what I need from IGV can be done in the terminal.

Some interesting behind-the-scenes:

Single-cell transcriptomic and genomic changes in the ageing human brain - Nature Sequencing analyses of human prefrontal cortex from donors ranging in age from 0.4 to 104 years show that ageing correlates with an accumulation of somatic mutations in short housekeeping genes and a reduction in the expression of these genes.

Nature research paper: Single-cell transcriptomic and genomic changes in the ageing human brain

go.nature.com/4mRVCl0

H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells H3K79me and H3K36me3 synergistically dampen gene expression to facilitate cellular differentiation.

H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells

www.science.org/doi/10.1126/...

Check it out, Chromatin Kids!

Chromatin remodeller does stuff to Transcription Factors!

Functions where it is seldom seen!

Both decreases and increases chromatin accessibility!

How cool is that?

EBV induces CNS homing of B cells attracting inflammatory T cells - Nature Epstein–Barr virus infection generates a neuroinvasive B cell subset, which recruits activated T cells to the central nervous system, promoting multiple sclerosis.

How does Epstein- Barr virus induce multiple sclerosis?
The infection leads to B cells that get into the brain, attracting pro-inflammatory T cells (mouse model)
www.nature.com/articles/s41...

Coming back to a 2 year old script...

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

I've been to two bars tonight and both had feels so good playing