Alejandra Fernandez
@alefdzphd.bsky.social
Assistant Professor at The University of Texas Rio Grande Valley. Studying development of somatosensory circuits in autism spectrum disorders. Opinions are my own.
Reposted by Alejandra Fernandez
Also, here’s an accessible video intro:
November 15, 2025 at 5:33 PM
Also, here’s an accessible video intro:
Reposted by Alejandra Fernandez
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...
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...
www.cell.com
November 13, 2025 at 3:17 PM
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...
Reposted by Alejandra Fernandez
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.
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...
www.biorxiv.org
November 7, 2025 at 11:16 AM
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.
Reposted by Alejandra Fernandez
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
November 4, 2025 at 10:15 PM
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
Reposted by Alejandra Fernandez
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...
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...
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...
www.biorxiv.org
May 29, 2025 at 12:08 PM
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...
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...
Reposted by Alejandra Fernandez
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...
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...
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...
www.biorxiv.org
October 26, 2025 at 5:15 PM
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...
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...
Reposted by Alejandra Fernandez
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
October 4, 2025 at 8:34 AM
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
Reposted by Alejandra Fernandez
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
October 4, 2025 at 1:31 AM
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
Reposted by Alejandra Fernandez
Ultrasensitive proteomics uncovers nociceptor diversity and novel pain targets https://www.biorxiv.org/content/10.1101/2025.09.20.677124v1
September 21, 2025 at 10:04 PM
Ultrasensitive proteomics uncovers nociceptor diversity and novel pain targets https://www.biorxiv.org/content/10.1101/2025.09.20.677124v1
🤯
Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...
HDAC3 prevents enhancer hyperactivation to enable developmental transitions
Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate tra...
www.biorxiv.org
September 18, 2025 at 11:46 PM
🤯
Reposted by Alejandra Fernandez
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...
September 17, 2025 at 3:14 PM
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...
Reposted by Alejandra Fernandez
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/...
onlinelibrary.wiley.com/doi/10.1002/...
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....
onlinelibrary.wiley.com
September 17, 2025 at 12:17 AM
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/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Alejandra Fernandez
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...
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...
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...
www.biorxiv.org
July 12, 2025 at 12:50 AM
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...
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...
Reposted by Alejandra Fernandez
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
#MustRead
June 8, 2025 at 8:03 AM
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
#MustRead
Reposted by Alejandra Fernandez
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
#DevBio #scRNAseq #NeuralCrest #EvoDevo
May 27, 2025 at 9:00 AM
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
#DevBio #scRNAseq #NeuralCrest #EvoDevo
Reposted by Alejandra Fernandez
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...
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…
www.sciencedirect.com
May 17, 2025 at 10:49 PM
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...
Reposted by Alejandra Fernandez
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...
www.nature.com/articles/s41...
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...
www.nature.com
May 14, 2025 at 11:47 PM
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...
www.nature.com/articles/s41...
Reposted by Alejandra Fernandez
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...
May 5, 2025 at 4:52 PM
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...
Reposted by Alejandra Fernandez
🤯
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics
Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...
doi.org
April 17, 2025 at 4:31 PM
🤯
Baffling… It’s like cutting off one leg because you find shoes expensive.
The plan for NIH is in, source with full 64 page proposal for all of HHS is linked. Reported in WaPo. This is catastrophic. Reduction to 8 centers. 40% cut in budget. 15% IDC cap. This will decimate science across America open.substack.com/pub/insideme...
April 17, 2025 at 3:39 AM
Baffling… It’s like cutting off one leg because you find shoes expensive.
Reposted by Alejandra Fernandez
Hey #deconvolution fans! 👀 We’ve got an exciting new publication for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬
Now out in Genome Biology: doi.org/10.1186/s130...
@lieberinstitute.bsky.social @jhubiostat.bsky.social
Now out in Genome Biology: doi.org/10.1186/s130...
@lieberinstitute.bsky.social @jhubiostat.bsky.social
Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex - Genome Biology
Cellular deconvolution of bulk RNA-sequencing data using single cell/nuclei RNA-seq reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as the h...
doi.org
April 11, 2025 at 2:35 PM
Hey #deconvolution fans! 👀 We’ve got an exciting new publication for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬
Now out in Genome Biology: doi.org/10.1186/s130...
@lieberinstitute.bsky.social @jhubiostat.bsky.social
Now out in Genome Biology: doi.org/10.1186/s130...
@lieberinstitute.bsky.social @jhubiostat.bsky.social
Reposted by Alejandra Fernandez
Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety: @cellpress.bsky.social www.cell.com/cell/fulltex...
April 7, 2025 at 2:42 PM
Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety: @cellpress.bsky.social www.cell.com/cell/fulltex...
Reposted by Alejandra Fernandez
How is the input of the different kinds of primary sensory neurons responding to heat and mechanical stimuli summarized in the spinal cord? Check out our recent study.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord - Nature Neuroscience
Zhang et al. identify unimodal neural representations in the spinal cord of cutaneous mechanical and heat stimuli gated by a shared feed-forward local inhibitory neuron type and a neural transition du...
www.nature.com
March 24, 2025 at 4:07 PM
How is the input of the different kinds of primary sensory neurons responding to heat and mechanical stimuli summarized in the spinal cord? Check out our recent study.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Turns out LLMs can’t really write your code for you 🤷🏻♀️
“If you don’t know what you’re doing, you’ll just do it worse. But faster.”
I just can’t stop reading Pivot to AI!
I just can’t stop reading Pivot to AI!
AI coding tools ‘fix’ bugs by adding bugs
LLMs regurgitate a version of whatever they were trained on. If you train them on typically buggy code, that suggests you’ll get back typically buggy code. In a new preprint, “LLMs are …
pivot-to-ai.com
March 23, 2025 at 5:55 AM
Turns out LLMs can’t really write your code for you 🤷🏻♀️