Alejandra Fernandez

A latent space thermodynamic model of cell differentiation https://www.biorxiv.org/content/10.64898/2026.03.04.709512v1

The molecular basis of force selectivity by PIEZO2 Nature - PIEZO2 is intrinsically more rigid than PIEZO1, and disparate mechanical stimuli paradoxically evoke opposite conformational and gating responses in each channel.

New paper from the lab led by @ericmulhall.bsky.social addresses how PIEZO1 and PIEZO2 are tuned to different types mechanical forces. From nanometer-scale super-resolution microscopy to in vivo experiments, links single-molecule observations to physiological function.
www.nature.com/articles/s41...

An array of 9 purple discs on a blue background. Figure from Hinnerk Schulz-Hildebrandt.

A nice shift in perceived colour between central and peripheral vision. The fixated disc looks purple while the others look blue.

The effect presumably comes from the absence of S-cones in the fovea.

From Hinnerk Schulz-Hildebrandt:
arxiv.org/pdf/2509.115...

Vectorized instructive signals in cortical dendrites - Nature Mice learning a neurofeedback brain–computer interface task show neuron-specific teaching signals in cortical dendrites, consistent with a vectorized solution for credit assignment in the brain.

This paper on how the brain may do gradient descent is very cool: www.nature.com/articles/s41...

Dark blue hexagon, with a light blue frame. Features a brain facing the left, with the front half as a wire-frame mesh of light blue, and the back half with several polygon segments of different colours. Below is written "ggseg" in light blue.

The ggseg ecosystem finally has a proper home! 🧠

For those who don't know, ggseg is an R package ecosystem for visualizing brain atlas data. Think ggplot2, but for brains.

#rstats #neuroimaging #openscience

Dissecting gene regulatory networks governing human cortical cell fate - Nature Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...

A chicken broccoli taco for 3 dlls? that one other thing better be salsa.

I don’t worry about AI taking my job. I worry about AI destroying the very thing that makes my job make sense.

Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons - Communications Biology Single cell RNA-sequencing, spatial transcriptomics and chromatin analyses of sensory neurons provide insights into cell type organization of the dorsal root ganglion and the enhancer-driven co-regula...

A read only for the DRG nerd: "Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons". www.nature.com/articles/s42...

Hierarchical organization of mechano-nociceptive pathways revealed by activity labeling Noxious mechanical stimuli give rise to distinct percepts, from sharp cutaneous pain to diffuse visceral discomfort, yet the nociceptor ensembles that underlie these differences remain poorly defined....

Not all pain is created equal: stepping on a nail feels different from a stomachache. We know there are many nociceptor types, but a key question remains: how is mechanical pain encoded across the body by those sensory neurons? Our new work helps answer this. 1/8
www.biorxiv.org/content/10.6...

#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you.

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

Happy to see this out w/ @epsteinstatgen.bsky.social and @davecutler.bsky.social (paper: doi.org/10.1093/bioi...)! We tackled the problem of identifying dysregulated pathways (i.e. differentially co-expressed) in gene expression studies. We show that differential co-expression arises ...

Also, here’s an accessible video intro:

An enteric-DRG pathway for interoception and visceral pain in mice Wang et al. reveal a neuroanatomical and functional crosstalk between cholinergic enteric neurons and sensory neurons of the dorsal root ganglia that mediates colonic interoception. While this pathway...

Enteric neurons join the pain conversation! New paper shows that cholinergic circuits in the colon signals through DRG pathways, especially after inflammation. www.cell.com/neuron/fullt...

A Reference Atlas of the Human Dorsal Root Ganglion Somatosensory perception largely emerges from diverse peripheral sensory neurons whose cell bodies reside in dorsal root ganglia (DRG). Damage or dysfunction of DRG neurons is a major cause of chronic...

The BIG DRG paper is now up on @biorxiv-neursci.bsky.social www.biorxiv.org/content/10.1... so many people worked so hard to make this happen. Props to the whole PRECISION Human Pain Network.

Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus https://www.biorxiv.org/content/10.1101/2025.11.03.686433v1

Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding dise...

Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"

A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making

Applied to ventral neural tube development

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

Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...

Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social

We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇

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

Labelled axons of calb1+ spinal projection neurons innervate multiple brain targets associated with cold sensation and thermoregulation. Darkfield images of different brain areas including the postal parabrachial and periaqueductal grey are shown with axons of ascending cells in yellow.

New preprint from the spinal cord group at Glasgow. Anatomical and functional characterisation of spinal circuits for cold, from sensory neurons to the brain…..https://www.biorxiv.org/content/10.1101/2025.10.03.680240v1

Dynamic and non-uniform expression of key transcription factors provides novel insights into the emergence of neural crest cells at the neural plate border https://www.biorxiv.org/content/10.1101/2025.10.03.680132v1

Ultrasensitive proteomics uncovers nociceptor diversity and novel pain targets https://www.biorxiv.org/content/10.1101/2025.09.20.677124v1

🤯

Now out in @nature.com: Our study discovering a neural circuit in Drosophila that predictively inhibits proprioceptor axons during voluntary leg movements, such as walking and grooming. www.nature.com/articles/s41...

Altered Primary Somatosensory Neuron Development in a Pten Heterozygous Model for Autism Spectrum Disorder Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder characterized by deficits in social interactions, repetitive behaviors, and hyper- or hyposensitivity to sensory stimuli. The c....

Newest paper from the lab, looking at how somatosensory neuron development and function is altered in a Pten haploinsufficient model of ASD. Work was all done by @alefdzphd.bsky.social, who just started an independent position at UTRGV.

onlinelibrary.wiley.com/doi/10.1002/...

H2AK119ub Safeguards Against Ectopic Transcription Factor Mediated Gene Activation in the Developing Forebrain The PRC1 complex regulates developmental gene expression in mammals by ubiquitinating histones (H2AK119ub) and nucleating repressive chromatin interactions. Human genetic data and functional experimen...

Excited to share our hot-off-the-press @biorxivpreprint.bsky.social
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...

Very important @nicolettapetridou.bsky.social‬ report #mechanochemical signalling control fate transitions www.biorxiv.org/content/10.1... w/ wide/significant implications. Perhaps the clearest indication so far of HOW #NotInTheGenes cell interactions mechanical pattern gene expression
#MustRead

We developed a transgene-free method to isolate neural crest cells using antibody labelling + FACS — tested in Podarcis muralis. It works as well as transgenic tools, opening doors for NCC research in non-model species! Link in comment.
#DevBio #scRNAseq #NeuralCrest #EvoDevo

Truncated TrkB: The predominant TrkB isoform in nociceptors Truncated TrkB (TrkBT1), traditionally considered a dominant-negative regulator of full-length TrkB (TrkBTK+), remains poorly understood in peripheral…

Our paper in Journal of Pain challenges old labels: TrkB isnt just an A-LTMR marker. Its truncated isoform is expressed and functional in trigeminal nociceptors, opening new avenues for studying the receptor in pathological pain #painresearch www.sciencedirect.com/science/arti...

Spatial transcriptomics reveals human cortical layer and area specification - Nature Multiplexed error-robust fluorescence in situ hybridization (MERFISH) together with deep-learning-based nucleus segmentation enabled the construction of a highly detailed and informative spatially res...

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...

Why does the forebrain expand dramatically while other neural regions grow less? Our new publication reveals progenitor metabolism critically shapes region-specific brain growth. Thread below. authors.elsevier.com/a/1k-udL7PXu...