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Alejandra Fernandez

@alefdzphd.bsky.social
310 followers 614 following 16 posts

Assistant Professor at The University of Texas Rio Grande Valley. Studying development of somatosensory circuits in autism spectrum disorders. Opinions are my own.

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Reposted by Alejandra Fernandez
Lukas Groschner @lukasgroschner.bsky.social · 29/09/2026
Single-neuron computations depend on the subcellular distribution and voltage sensitivity of ion channels. | @pnas.org #HorizonEU @erc.europa.eu (1/5) www.pnas.org/doi/10.1073/...
pnas.org
Distribution and voltage dependence of ion channels shape single-neuron computations | PNAS
Voltage-gated ion channels do not distribute evenly in the plasma membrane of a neuron; they localize to distinct domains where they govern the exc...
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Tony Kelly @tonykellyeu.bsky.social · 13/09/2026
Very happy our work on a weird new nanoscale morphological feature is out in @science.org. A massive effort involving different high resolution microscopy techniques, multiple institutes, & years of work to convince ourselves DENDRITIC NARROWINGS EXIST #neuroskyence 🧪 doi.org/10.1126/scia...
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Dendritic shaft constrictions shape synaptic integration in neurons
For nearly 150 years, textbooks have described dendritic morphology as optimized for efficient synaptic voltage transfer from spines to the soma, implemented as a tubular design respecting Rall’s 3/2…
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Tomás Ryan @tjryan.bsky.social · 13/09/2026
"MIT wants to rebuild education around the things AI can't replace. That means oral exams, semester portfolios, in-person project work, and a required social component in every subject. The report even floats the idea of rethinking grades entirely..." This is the way forward @tcddublin.bsky.social
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Jieyu Zheng @jieyusz.bsky.social · 10/09/2026
An acortical mouse — born without hippocampus and most of its neocortex — learns the Manhattan Maze: a 30× improvement in 5 hours, 18 rewards! Now a question for everyone: How can an acortical brain do this? Leave a comment! Preprint w/ @mameister4.bsky.social: www.biorxiv.org/content/10.6...
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Matteo Carandini @carandinilab.net · 09/09/2026
If you thought "everything is everywhere" in the brain: inactivations reveal a clear distinction of labor. Sensory areas sense, colliculus promotes eligible actions (!), and prefrontal cortex integrates. The role of superior colliculus in a logistic decision www.biorxiv.org/content/10.6...
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Tom McCoy @rtommccoy.bsky.social · 01/09/2026
🤖🧠NEW PAPER🧠🤖 (The result of an 8-year project!) LLMs seem very different from symbolic systems. Yet LLMs excel in symbolic domains (e.g., language/code/math). How do they do it? Our finding: LLM representations have implicit symbolic structure! Link in thread ⬇️ 1/n
Overview of the paper. 
Title: The Emergent Symbolic Structure of Artificial Neural Networks
Authors: Tom McCoy, Paul Soulos, Tal Linzen, Paul Smolensky
Left: Neural networks encode information in vectors (there is then an image of a vector), yet they excel at tasks long thought to require symbolic structure (there is then an image of a symbolic representation, specifically a syntax tree). How do LLMs do it?
Right: We find that LLM representations can be closely approximated with symbolic structures. This approximation lets us edit the structure of an LLM’s output by editing the structure of its internal representations, as shown. There is then an image of two edits to LLMs. In the first one, the original input is 3 + 6 * 8, with an answer of 51. But if we swap the positions of the 3 and the 6, the output becomes 30. In the second one, the original input is a Python command repeating the list [Z, U] three times, producing [Z, U, Z, U, Z, U]. But if we edit the input in a way that adds a Q at the end of the input, the output becomes [Z, U, Q, Z, U, Q, Z, U, Q].
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James Briscoe @jamesbriscoe.bsky.social · 27/08/2026
Our latest: We develop a dynamical landscape modelling framework based on time resolved single-cell data Applied to neural tube fate decisions it shows cell fate decisions as flip bifurcations, a circular topology & it predicts unseen signalling regimes @plosbiology.org doi.org/10.1371/jour...
doi.org
Dynamic Landscape Analysis of cell fate decisions provides predictive models of neural development from single-cell data
Applying dynamical systems theory to single-cell data can provide a detailed picture of the cellular states observed during cell fate decisions. This study presents a dynamic landscape analysis (DLA) ...
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Gan Lab @liganlab.bsky.social · 30/07/2026
Our study is out today in @NatureNeuro! We show that stressed neurons release DNA, activating cGAS–type I interferon signaling and driving inflammation, seizures and mortality in Dravet syndrome. Blocking cGAS disrupts this immune cascade and improves outcomes. www.nature.com/articles/s41...
nature.com
cGAS-mediated type I IFN signaling contributes to disease progression in drug-refractory epilepsy - Nature Neuroscience
Huang et al. found that stressed neurons release DNA that activates the immune sensor cGAS, driving inflammatory responses that worsen seizures and mortality in Dravet syndrome. Blocking cGAS interrup...
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The Transmitter @thetransmitter.bsky.social · 30/07/2026
The brain’s sensorimotor-association axis may emerge as a result of competing sets of genetic blueprints—a dynamic process described in a paper published this month. By Holly Barker www.thetransmitter.org/spectrum/cor...
thetransmitter.org
Cortical territories compete in developmental space race
Sensory and association regions are established through a reciprocal process, according to a new model of cortical development.
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Satpreet (Sat) Singh @satpreetsingh.bsky.social · 29/07/2026
How do you "see" with electric eyes? How does collective behavior emerge from individual interactions? Nocturnal weakly electric fish evolved to do this, but studying naturalistic social behavior is very hard. Our solution? Virtual 'fish' 🤖🐟⚡ 📄 arxiv.org/abs/2511.08436
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Lorenzo Posani @lorenzoposani.com · 15/07/2026
Out today on @nature.com! Connecting neural specialization, population geometry, and their functional implications across the cortical hierarchy. So grateful for this beautiful and fun collaboration with @shuqiw.bsky.social, S Muscinelli, L Paninski, and @stefanofusi.bsky.social!
nature.com
Rarely categorical, highly separable representations along the cortical hierarchy - Nature
Cortical circuits prioritize diversity over categorical structure, supporting a computational regime geared towards high-dimensional, highly separable neural representations.
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Paul Francois @pfrancois.bsky.social · 14/07/2026
New paper 🧵 What if the "landscape" that guides cell differentiation isn't fixed, but is sculpted, in real time, by the very cells moving through it? We call this a 'sandscape' : grains of sand that carve dunes as they move, while the dunes' shape simultaneously steers where the grains go next.
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Vinny Costa @vincentcostaphd.bsky.social · 15/07/2026
Just listening to Nelly Furtado’s song Promiscuous while reading that Nature paper about how there is no neuronal specialization in the mouse brain outside visual cortex, with this paper from @rudebecklab.bsky.social & @zachzeisler1.bsky.social open in the background www.cell.com/current-biol...
cell.com
Comparative basolateral amygdala connectomics reveals dissociable single-neuron projection patterns to frontal cortex in macaques and mice
Zeisler et al. compare the projection patterns of single BLA neurons from mice and macaques using MAPseq. They reveal that BLA projections, particularly to frontal cortex, exhibit a number of differen...
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Reposted by Alejandra Fernandez
Jake Watson @jakefwatson.bsky.social · 11/07/2026
We have a new preprint! By studying neuronal heterogeneity in CA3, we found a weird but powerful new feature in the hippocampal circuitry! 🧠 #neuroskyence 🧵.. Morse-Mora et al. | Hippocampal CA3 forms a two-layer network of molecularly distinct cell types in mice and humans doi.org/10.64898/202...
Mouse hippocampal slice with deep cells labelled blue, patch-clamp recorded cells in yellow, and deep CA3 projections labelled purple
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Ashley Watts @ashleylwatts.bsky.social · 09/07/2026
Excited to share a paper recently accepted at Nature Mental Health! 😄 For decades, we've assumed that covariance among psychopathology informs comorbidity. What if we’ve been wrong?
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Earl K. Miller @earlkmiller.bsky.social · 05/07/2026
Individual variability of neural computations underlying flexible decisions www.nature.com/articles/s41... #neuroscience
nature.com
Individual variability of neural computations underlying flexible decisions - Nature
Behavioural experiments to study decision-making in response to context-dependent accumulation of evidence provide testable models that are consistent with the heterogeneity in neural signatures among...
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Reza Kalhor @rezakalhor.bsky.social · 01/07/2026
Our weirdly fresh 4D map of hair follicle genesis is finally out in @cp-cell.bsky.social . It'll make you see spatial more temporally! Brilliant tour-de-force by my PhD student Soichiro Asami, with great support from @jef.works and Luis Garza #devbio #spatialomics www.cell.com/cell/fulltex...
cell.com
Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis
A deep-tissue spatial transcriptomics method simultaneously captures hundreds of hair follicles spanning organogenesis in mouse skin. Ordering follicles by molecular age transforms this snapshot into ...
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Blake Richards @tyrellturing.bsky.social · 01/07/2026
New in PLOS Comp Bio, cool work from @timothyoleary.bsky.social showing that representational "drift" (lol, sorry for the scare quotes, Tim!), follows non-Gaussian statistics that can be beneficial for adaptive decoding: journals.plos.org/ploscompbiol... #neuroscience 🧪
journals.plos.org
Statistics of cortical representational drift can enable robust readout
Author summary Percepts, actions and experiences, such as the appearance of an apple and its flavour, are represented in the activity of populations of neurons in various parts of the brain. For decad...
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Prisca Liberali @priscaliberali.bsky.social · 30/06/2026
It is out 😍 check it out!! Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. @cschwayer.bsky.social @silviabarbiero.bsky.social @davidbrueckner.bsky.social @ehannezo.bsky.social www.cell.com/cell/fulltex...
cell.com
Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning
During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...
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Aaron Milstein @neurosutras.bsky.social · 28/06/2026
Excited to share this preprint from @ianoldenburg.bsky.social . To evoke movement with holo stim, you need the right pattern at the right time! Interestingly, the preparatory state before spont motion is not the same as the state permissive for evoked motion. Dig in! www.biorxiv.org/content/10.6...
biorxiv.org
The Importance of Synchrony in the Neural Control of Movement
Throughout the mammalian cortex, populations of neurons must work together to enact behaviors. While population recordings in motor cortex have revealed many aspects of when neurons fire during behavi...
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Lena Schindler @lena-schindler.bsky.social · 23/06/2026
I am thrilled to share my PhD work with @nicolettapetridou.bsky.social @embl.org: www.biorxiv.org/cgi/content/... A fun collaboration with Bernat Corominas-Murtra, Adrián Aguirre-Tamaral, @bart-smeets.bsky.social , Jef Vanghel and Tom Belpaire! Read the story in the comments below ⤵️
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Allan-Hermann Pool @allanhpool.bsky.social · 22/06/2026
Thrilled to share the latest pre-print from the lab – TLDR: we identified the (near) full ascending spinal projection neuron repertoire that gives rise to central itch/touch/pain/temperature sensation as well as sex specific neuron types in the mouse spinal cord. Thread below (1/n):
biorxiv.org
Deep Cellular and Spatial Profiling of the Mouse Spinal Cord Reveals Sex-Specific Neuron Types and the Ascending Projection Neuron Repertoire
The spinal cord gives rise to central somatosensation and orchestrates autonomic and motor control. How its cellular diversity achieves functions across sex, longitudinal axis and links the spinal cor...
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Rui Ponte Costa @somnirons.bsky.social · 18/06/2026
Our latest story is finally in preprint! 🧠✨ How does the brain solve the (hierarchical) credit assignment problem efficiently? Cell-type-specific cortical feedback holds the key, closely approximating backprop. Paper: doi.org/10.64898/202...
doi.org
Cell-type-specific cortical feedback coordinates hierarchical credit assignment
Learning is thought to arise from synaptic modifications embedded in brain-wide circuits, yet how such circuits coordinate plasticity to support complex behaviour is not known. Inspired by deep learni...
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Elena Dvoretskova @elena-dvoretskova.bsky.social · 14/06/2026
New preprint from our lab on bioRxiv: “Stoichiometric transcription factor partnerships control GABAergic neuron fate allocation” www.biorxiv.org/content/10.6... A great collaboration with @annrosebright.bsky.social, Connor Lynch, @chr-mayer.bsky.social, and many others.
biorxiv.org
Stoichiometric transcription factor partnerships control GABAergic neuron fate allocation
Combinatorial transcription factor (TF) codes specify neuronal fates, yet how quantitative differences in interacting TFs shape these decisions remains unresolved. We address this in the developing ba...
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Lorena A Barba @labarba.bsky.social · 12/06/2026
Last spring I taught a graduate course built on the idea that 𝘧𝘭𝘶𝘦𝘯𝘤𝘺 𝘸𝘪𝘵𝘩 𝘈𝘐 𝘪𝘴 𝘢 𝘳𝘦𝘴𝘦𝘢𝘳𝘤𝘩 𝘴𝘬𝘪𝘭𝘭, not a novelty: 𝗚𝗲𝗻𝗲𝗿𝗮𝘁𝗶𝘃𝗲 𝗔𝗜 𝗳𝗼𝗿 𝗘𝗻𝗴𝗶𝗻𝗲𝗲𝗿𝗶𝗻𝗴 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵—all the course materials are now public. Take it, use it, adapt it for your own students or your own research. barbagroup.github.io/mae6291-genai/
barbagroup.github.io
Generative AI for Engineering Research (MAE-6291) — Lorena A. Barba group
MAE-6291, Spring 2026. A graduate course teaching engineering PhD students to use generative AI as a research accelerator. Lecture notes and slides, openly shared.
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James Briscoe @jamesbriscoe.bsky.social · 08/06/2026
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
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Alejandra Fernandez @alefdzphd.bsky.social · 09/06/2026
Pretty cool!!
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Cedric Boeckx @cedricboeckx.bsky.social · 20/05/2026
Great paper on developmental gene expression patterns underlying species-specific cortical features (with a nice combination of tools and datasets) By @itsmeawais.bsky.social @estherkli.bsky.social @djabaudon.bsky.social @silvianeuro.bsky.social @mveronicapravata.bsky.social and colleagues 🧪🧠🧬
nature.com
Developmental gene expression patterns driving species-specific cortical features - Nature
Machine learning analysis of cell-type-specific gene expression in mouse and human neocortex and human cortical organoids reveals human-specific cell-type and temporal variations in expression control...
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Zebrafish Rock! @zebrafishrock.bsky.social · 03/05/2026
First 22 hours of zebrafish development. Credit to @zebrafish007.bsky.social at #WeinsteinLab. #ZebrafishZunday 🧪
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Stephen Turner @stephenturner.us · 03/05/2026
Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪
doi.org
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Melanie D. White @melaniedwhite.bsky.social · 27/04/2026
I'm SO excited to see this new paper from our lab's first PhD graduate @wangjianxiong.bsky.social. An outstanding student with a promising career ahead! A PCP-independent role for Prickle1 in junctional neural tube formation. 🧪🐣 Check it out: www.nature.com/articles/s41...
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Jan Żylicz @jzylicz.bsky.social · 25/04/2026
New paper out in @cp-cellstemcell.bsky.social. We uncover unexpected complexity in how metabolism changes when the embryo implants or when stem cells exit naive pluripotency, revealing a central role for dynamic TCA cycle rewiring in cell fate decisions. www.cell.com/cell-stem-ce...
cell.com
TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency
Using carbon tracing and functional experiments, Kafkia, Pladevall-Morera, et al. show that TCA cycle rewiring underlies mouse embryo implantation and the exit from naive pluripotency. In this context...
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sverregr.bsky.social @sverregr.bsky.social · 17/04/2026
1/ 97% of cortical PNNs are on PV interneurons. But PNN-positive and PNN-negative PV cells don't split into two groups — they sit at different ends of a transcriptional continuum of fast-spiking specialization. New preprint 🧵
Expansion microscopy image of perineuronal nets (unpublished).
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Matt Banghart @mattbanghart.bsky.social · 16/04/2026
Excited to share our new study on how the brain generates placebo pain relief! We developed a mouse model that recapitulates key features of human placebo analgesia, then used it to identify causal circuitry. www.sciencedirect.com/science/arti... today.ucsd.edu/story/neurob... 1/n
today.ucsd.edu
Neurobiologists Hack Brain Circuits Tied to Placebo Pain Relief
Scientists have identified the brain circuits tied to placebo pain relief. Researchers have known that placebo effects can be a powerful treatment, yet the underlying neurological mechanisms have not ...
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Xin Jin @xinjin.bsky.social · 09/04/2026
Form follows function, or function dictates form? 📢Preprint: we build Perturb-CLEAR, in vivo screen of neuroanatomy! Disease perturbations produce selective morphology-RNA changes that RNA impact alone cannot predict. Was led by the invincible grad student Boli Wu! www.biorxiv.org/content/10.6...
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Yoav Gilad @ygilad.bsky.social · 04/04/2026
For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.
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@LaBonneLaB @labonnelab.bsky.social · 22/03/2026
💯@newyorker.com @paulnoth.bsky.social
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Alfred Nobel @alfrednobel.bsky.social · 15/03/2026
@ravenwallace.bsky.social @themindwanders.bsky.social This study provides elegant evidence that motor learning is associated with the re-instatement of large-scale neural manifold structures. However, interpreting these manifolds as the retrieval of a stored motor plan may not be necessary.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/03/2026
A latent space thermodynamic model of cell differentiation www.biorxiv.org/content/10.64898/20…
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Ardem Patapoutian @ardemp.bskyverified.social · 04/03/2026
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...
nature.com
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.
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Pascal Mamassian @mamassian.bsky.social · 24/09/2025
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...
An array of 9 purple discs on a blue background. Figure from Hinnerk Schulz-Hildebrandt.
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Konrad Kording @kordinglab.bsky.social · 26/02/2026
This paper on how the brain may do gradient descent is very cool: www.nature.com/articles/s41...
nature.com
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.
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ᴅʀ. ᴍᴏᴡɪɴᴄᴋᴇʟ'ꜱ @drmowinckels.io · 09/02/2026
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
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.
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Alex Pollen @brainevodevo.bsky.social · 23/01/2026
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...
nature.com
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...
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Alejandra Fernandez @alefdzphd.bsky.social · 20/12/2025
I don’t worry about AI taking my job. I worry about AI destroying the very thing that makes my job make sense.
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Patrik Ernfors @patrikernfors.bsky.social · 13/06/2025
A read only for the DRG nerd: "Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons". www.nature.com/articles/s42...
nature.com
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...
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Marcin Szczot @szczotml.bsky.social · 14/12/2025
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...
biorxiv.org
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....
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paveltomancak.bsky.social @paveltomancak.bsky.social · 13/12/2025
#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...
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Andrew Bass @ajbass.bsky.social · 25/11/2025
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 ...
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