Gene regulatory networks: from correlative models to causal explanations Nature Reviews Genetics, Published online: 09 March 2026; doi:10.1038/s41576-026-00939-1In 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.

FYI: New online! Gene regulatory networks: from correlative models to causal explanations

FGF8-expressing embryonic body Organizer fusion induced rostral-caudal arealization of elongated hPSC-derived cortical assembloids (15-mm long😎)

Modeling FGFR3-related temporal lobe dysgenesis

#NatMeth 2024
www.nature.com/articles/s41...

Transient molecular chimerism for exploiting xenogeneic organelles - Nature Communications Kleptoplasty, the transient integration of foreign organelles, could illuminate organellogenesis. Here, using the flagellate, Rapaza viridis, the authors show that host nuclear proteins are imported i...

www.nature.com/articles/s41... #protistsonsky

Hao's Preprint Reading List
March 25 2026

Pericyte loss in🧠small vessel disease

Single-cell atlas of postnatal👤🫁development

Substrate microtrench confers Endothelial cell resilience to >200 dyn/cm2 shear

SuperFocus Single-cell spatial multi-omics

Zebrafish ZMAP

docs.google.com/document/d/e...

The coordinated action of UFMylation and the RQC pathways clears arrested polypeptides at the ER - The EMBO Journal Clearance of arrested nascent polypeptides resulting from ribosomal stalling is essential for proteostasis. Stalled endoplasmic reticulum (ER)-bound ribosomes are marked by ubiquitin-fold modifier 1 (...

Congrats Milica @alessandrick.bsky.social & everyone @gekaragoz.bsky.social lab. Glad we could contribute to this awesome story on #UFMylation & #RQC crosstalk @embojournal.org link.springer.com/article/10.1...

Genetic influences on haematopoiesis Nature Reviews Genetics, Published online: 23 March 2026; doi:10.1038/s41576-026-00947-1Haematopoiesis is a classic process for understanding the genetic basis of human health and disease. In this Review, Poeschla and Sankaran discuss this history and more recent advances in our understanding of the roles of rare variants in monogenic blood diseases, germline and somatic variants in population-level variation, as well as emerging therapeutic applications.

New online! Genetic influences on haematopoiesis

Happy to share this work from @alexneaverson.bsky.social where she has dissected the timing and relative contribution of the organiser and its derivates to multiple aspects of early neural development:

www.biorxiv.org/content/10.6...

Evidence for chronological diversification of spinal neuron subtypes by a shared sequence of transcription factors Molecular and functional diversification of spinal cord output neurons by a conserved sequence of transcription factors.

New work by @sagnera.bsky.social & co

A conserved sequence of TFs: OC2 → Pou2f2 → Pou3f1 drives chronological diversification of spinal neuron subtypes across multiple cardinal domains

Spinal neuron diversity is generated by integrating spatial & temporal programs

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

Delighted to share that our study is now out @cp-cellstemcell.bsky.social www.cell.com/cell-stem-ce... Congrats to Dr. @federicamosti.bsky.social for the culmination of a beautiful thesis!

Unstructured transcription factor interactions enable emergent specificity How intrinsically disordered regions (IDRs) influence chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We employed proximity-assisted photoactivation (PAPA), ...

Unstructured transcription factor interactions enable emergent specificity | @science.org www.science.org/doi/10.1126/...

This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice.

Wild rice is a perennial, creeping plant. The secret to its perennial growth habit lies in a developmental reversal directed by small RNAs. This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice.

Learn more: https://scim.ag/40GOjDb

🤵Artery Super-enhancer (H3K27ac ChIPseq) analysis (127 TFs)▶️
PRDM16 as a positive regulator of Injury-induced (not developmental) Proliferation of Vascular Smooth Muscle Cell😎

Any role in SMC-to-brown adipocyte conversion?😁

@jiliang-zhou.bsky.social #JMCC 2026
www.sciencedirect.com/science/arti...

⭐NAR Breakthrough! ⭐
Back-to-back NAR studies show #Palbociclib binds #HIV TAR RNA with low affinity & striking specificity. Induced-fit RNA refolding creates a #druggable pocket, blocking #SEC recruitment.📖 Read the articles here: doi.org/10.1093/nar/... doi.org/10.1093/nar/... #DrugDiscovery

nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets Hodgetts et al., (2026). nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets. Journal of Open Source Software, 11(119), 9672, https://doi.org/10.21...

If you're analysing Cut&Run or Cut&Tag data here's a nf-core NextFlow pipeline to simplify and standardise data processing

joss.theoj.org/papers/10.21...

Huda Zoghbi in her lab in Houston talking with another researcher

New work from #HHMIInvestigator Huda Zoghbi & colleagues points to a promising new treatment strategy for Rett syndrome, a rare disorder that affects brain development in infants & children, primarily girls: bit.ly/3Np4Ng9.

@bcmhouston.bsky.social | Texas Children’s Hospital

ICYMI

CRISPR-based therapeutic genome editing for inherited blood disorders Nature Reviews Drug Discovery - CRISPR-based technologies provide a diverse set of tools to correct pathogenic mutations. This Review describes the promise and the challenges of genome editing...

Seb will be giving a talk this afternoon @ #KSGenomeEng26
Check out his recent review in @natrevdrugdiscov.nature.com on CRISPR-based therapeutic genome editing for inherited blood disorders rdcu.be/e70WP #Review by Sébastien Levesque & Daniel E. Bauer

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...

New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations"

Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations?

rdcu.be/e7zx7

RNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell Biology Geisterfer, Jalihal et al. show spatially distinct effects of Whi3 condensates on target translation in Ashbya syncytia. In vitro, translation is enriched at condensate–solute interfaces but repressed...

Condensates are powerful ways to break symmetry and cells do remarkable things with them. Here we show that in a multinucleate fungus, a condensate regulates translation of a cyclin and a formin in distinct locations.
www.nature.com/articles/s41...

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Imaging spotlight: the axonal membrane-associated periodic skeleton - FocalPlane Imaging spotlight: the axonal membrane-associated periodic skeleton - News

🔬🔦In our latest Imaging spotlight, Nicholas Boyer takes us through the key results, & offers some top technical tips, from their research on the axonal membrane-associated periodic skeleton with Rohan Sharma, Christophe Leterrier @christlet.bsky.social, Subhojit Roy @roylab-ucsd.bsky.social & team.

Keeping cells fit Fragments of aberrant cytoplasmic mRNA pair with nuclear RNAs to augment transcription

In a new Science study, researchers report on transcriptional adaptation, a dual feedback and feedforward mechanism that uses genetic redundancy to compensate for mutations in protein-coding genes.

Learn more in a new #SciencePerspective: https://scim.ag/4ryeXtN

'Making of BDNF: role of promoters, enhancers, and untranslated regions'

by Eli-Eelika Esvald, Annela Avarlaid, Indrek Koppel, Jürgen Tuvikene & Tõnis Timmusk

www.cell.com/trends/neuro...

Good representation from teleosts 👍

Stress controls heterochromatin inheritance via histone H3 ubiquitylation - Nature A histone ubiquitin-dependent regulatory hub governs stimulus-dependent heterochromatin propagation, with important implications for understanding mechanisms governing rapid changes in the epigen...

Discussed @mrsantosny.bsky.social lit review: Stress controls heterochromatin inheritance via histone H3 ubiquitylation. www.nature.com/articles/s41...

From our new paper out now in @currentbiology.bsky.social: www.cell.com/current-biol... w/ @neurofishh.bsky.social @gkafetzis.bsky.social @denilsson.bsky.social

Looking across animals, the vertebrate eye is an obvious outlier. Why is it so different that other highly visual animals?

LINE-L1, HIV, Ty3 retrotransposons in insects.
several of these genomes are > 40% adenosine!

What is the molecular origin & evolutionary pressure resulting in A-rich genomes of retrotransposons & some retroviruses?

it must be so hardwired that hosts exploit this bias for genome defense

any ideas?

Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formatio...

Out now in @science.org
Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes | Science www.science.org/doi/10.1126/...

Single-cell and isoform-specific translational profiling of the mouse brain - Nature Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hippocampal neuronal and non-neuronal cell types, highlighting functional differences between CA1 and CA3.

Nature research paper: Single-cell and isoform-specific translational profiling of the mouse brain

go.nature.com/4aYPQu7

Accurate predictions of disordered protein ensembles with STARLING - Nature The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.

Nature research paper: Accurate predictions of disordered protein ensembles with STARLING

go.nature.com/4cyskFw