Alejandra Fernandez

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...

Some exciting #PainResearch / #Neuroskyence from @alexchesler.bsky.social & co!

🤯

Baffling… It’s like cutting off one leg because you find shoes expensive.

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...

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

Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety: @cellpress.bsky.social www.cell.com/cell/fulltex...

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...

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...

Turns out LLMs can’t really write your code for you 🤷🏻‍♀️

We are using CUT&RUN-LoV-U to map effectors of Signaling Pathways across tissue and stages of Mouse #DevBio🐭🧬

Do you want to join forces and collaborate to build the future of the TranscriptionFactorBinding(TFB)-OMICS?
www.biorxiv.org/content/10.1...

NimbusImage

Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!

Documentation here!
docs.nimbusimage.com

Check out my postdoc work at Ariel Levine’s lab, hot and fresh, describing how you build a dorsal horn!

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

🚨 New paper on ArXiv:

“Uncertainty quantification and posterior sampling for network reconstruction”

TL;DR; We present an efficient method to sample the entire ensemble of possible network reconstructions that are compatible with an indirect observation, e.g. a dynamics.

Short thread: 1/N

Harp: Platform Independent Deconvolution Tool www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/spang-lab/harp #Rstats pkg github.com/spang-lab/harp

Very cool!

⭐️ Join us for the 2025 Neurotrophic Mechanisms in Health and Disease GRS/GRC (May 31- Jun 6)⭐️.
I am excited to be co-chairing the GRS and it is a great opportunity for postdocs and grad students. Apply by March 15th to be considered to give a talk. See you all there!

www.grc.org/neurotrophic...

Differential encoding of mammalian proprioception by voltage-gated sodium channels Voltage-gated sodium channels differentially encode mammalian proprioception via distinct cellular localization patterns.

Thrilled to share the most recent pub from the Griffith Lab! We show that sodium channels play unique roles in proprioceptive encoding. We also found some really cool effects on skeletal muscle, and a dev dependent role for Nav1.6 in proprioceptive spinal circuits www.science.org/doi/10.1126/...

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1

I am glad it isn’t just me. I kept thinking the output looked off.

@aliibarry.bsky.social ‘s excellent work on human DRG proteomics is now online. Collaboration between our lab and Manuela Schmidt’s lab in Austria. Ali’s multiomic integration analysis leads to some unique new insight into pain mechanisms with strong proteomic support.

Think this s cool? Keep reading this 🧵
DHARANI
A 3D Developing Human-brain Atlas as a Resource to Advance Neuroscience Internationally
Integrated Multimodal Imaging and High-resolution Histology

BOOM! Identification of a PIEZO2+, KIT+, and TRPM8+ A fiber nociceptor subtype that is responsible for human hair pull pain: www.researchsquare.com/article/rs-5... @saadnagi.bsky.social and colleagues, well done!

can I also be added please?

The local molecular signature of human peripheral... : PAIN nature of neuropathic pain at the lesion site, using Morton's neuroma as a human model system of neuropathic pain (n = 22; 18 women) compared with nerves from participants without nerve injury (n = 11...

Welcome to BlueSky @anninaschmid.bsky.social ! Congrats again on your beautiful paper on human peripheral neuropathy - my current favourite 🧪🥳! #PainResearch #painscience #neuroskyence journals.lww.com/pain/fulltex...

Awesome work! and much needed. How else could people do downstream analysis on publicly available datasets? … Definitively a priority!

Looking much forward to it! 🧪
#devbio #collaborate #evodevo #zebrafish #represent