Seth Blackshaw
@sethblackshaw.bsky.social
Professor of Neuroscience. Studying neural development, regeneration, and control of innate behaviors at Johns Hopkins.
This perspective piece reviews new omics, developmental genetic, and cell lineage studies to critically review current models of developing forebrain organization. Spoiler: there are _serious_ problems with the prosomere model.
Elizabeth Manning@emmanning.bsky.social · 2mo agoWell done to @elsieplace.bsky.social, Marysia Placzek and @sethblackshaw.bsky.social for this beautifully clear overview of a very complex history of brain developmental models www.sciencedirect.com/science/arti...
Proud to have been part of this work.
Bob Johnston@bobbyjeyeguy.bsky.social · 5mo agoI'm excited to share our PNAS paper from 1st author Kasia Hussey. We study how the foveola, the high acuity region of the retina, is patterned by RA and TH. We were surprised to find that cone subtypes appear to convert fates. Our studies are important for AMD sufferers. www.pnas.org/doi/10.1073/...
Happy to announce that our latest paper is now out! Have you ever wondered how neural tissues control their size? In this paper, we show that cell division orientation is critical in both the cortex and retina. www.science.org/doi/10.1126/...
Oriented cell divisions induce basal progenitors and regulate neural expansion across tissues and species
A fundamental role for division orientation in progenitor output driving cortical and retinal growth is revealed.
science.org
Indeed.
OneNeuro Initiative@oneneurojhu.org · 6mo ago"Choose your training environment carefully. Lab culture and institutional culture will significantly impact your happiness and success, so choose carefully." - OneNeuro Profile: Seth Blackshaw, PhD @sethblackshaw.bsky.social www.oneneurojhu.org/2026/01/29/o...
Excited to finally share the final/final.doc version of our paper. It's been a journey, but very proud of the result. Well done to all involved, especially @elsieplace.bsky.social @kchinnaiya.bsky.social , @thomasdwkim.bsky.social, @sethblackshaw.bsky.social 👏👏 www.nature.com/articles/s41...
Resolving forebrain developmental organisation by analysis of differential growth patterns - Nature Communications
Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and offering an updated view of ho...
nature.com
Second paper is a collaboration with Jim Handa's lab at Hopkins. Cigarette smoke exposure induces aging-related molecular changes in both mouse and human retinal pigment epithelium. www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
pnas.org
The lab's first paper of the new year is out. In it, we investigate the role of the late stage retinal progenitor-enriched SoxE family factors Sox8 and Sox9 in controlling retinal development./1 www.biorxiv.org/content/10.6...
Sox8 and Sox9 regulate differentiation and nuclear positioning of retinal Müller glia
Temporal patterning of retinal progenitor cells governs the sequential generation of retinal cell types, with gliogenesis occurring late in development. Sox8 and Sox9, members of the SoxE transcription factor family, are highly expressed in late-stage retinal progenitor cells and mature Müller glia, yet their functional roles remain incompletely defined. Here we employed gain- and loss-of-function approaches, single-cell multiomic profiling, and injury models to investigate Sox8/9 function. Overexpression of SOX8 and/or SOX9 in early-stage retinal progenitor cells suppressed early-born cell fates and promoted photoreceptor generation, consistent with a role in late-stage temporal identity. Conversely, conditional deletion of Sox8 and/or Sox9 in late-stage progenitors did not impair Müller glia specification, but caused radial displacement of Müller glia nuclei into the outer retina and modest changes in glial gene expression. Loss of Sox8/9 in mature Müller glia modestly increased proliferation post-injury without inducing neurogenic competence. These findings suggest that Sox8/9 are dispensable for gliogenesis and repression of neurogenic competence, but are essential for proper laminar positioning and maturation of retinal Müller glia. ### Competing Interest Statement S.B. is a cofounder, shareholder, and scientific advisory board member of CDI Labs LLC, and receives research support from Genentech. National Eye Institute, https://ror.org/03wkg3b53, R01EY036173
biorxiv.org
We’re thrilled to share that CSHL Associate Professor Jeremy Borniger (@jborniger.bsky.social) has received the 2026 Bakewell Emerging Leader Award from The Mark Foundation. His lab is exploring synthetic torpor—a hibernation-like state—as a novel way to slow cancer growth. #ScienceMakesLifeBetter
New featured article! Resolving forebrain developmental organisation by analysis of differential growth patterns @emmanning.bsky.social @elsieplace.bsky.social @kchinnaiya.bsky.social @sethblackshaw.bsky.social @thomasdwkim.bsky.social http://dlvr.it/TQLWh5
Nice summary on our paper on mechanisms controlling development and evolution of the cone-dominant ground squirrel retina, which is now in final form at eLife. www.lifescienceeditors.com/2026/01/06/h...
How ground squirrels enhanced their retinas - Scientific editing and writing experts - Life Science Editors
Scientific editing and writing experts for manuscripts and grants
lifescienceeditors.com
rdcu.be/eX8JD DRN new publication alert: Manning et al., 2025, @emmanning.bsky.social, co-led by Marysia Placzek and Elsie Place @elsieplace.bsky.social, in collaboration with Seth Blackshaw @sethblackshaw.bsky.social
Resolving forebrain developmental organisation by analysis of differential growth patterns
Nature Communications - Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and...
rdcu.be
A new paper from my lab. I will have a full description soon. rdcu.be/eX1Ld
ipRGC properties prevent light from shifting the SCN clock during daytime
Nature - The inability of intrinsically photosensitive retinal ganglion cells to shift the circadian clock in the suprachiasmatic nucleus during daytime is caused by light-dependent depolarization...
rdcu.be
It's been quite a year for hypothalamic development. With this heroic analysis of developmental cell lineage, coupled with earlier multimode-based gene regulatory network analysis, the prosomere model looks like it has passed into history. www.nature.com/articles/s41...
Resolving forebrain developmental organisation by analysis of differential growth patterns - Nature Communications
Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and offering an updated view of ho...
nature.com
On our evolutionary branch, a few genes got an update unique to humans. Some used to think those variants might have been difference that made all the difference: the key to becoming human. This month's Q&A with Barbara Molz @mpi-nl.bsky.social gets into new results that tell a different story. 🧪
There's no gene for being human
A Q&A on genetics and human evolution with Barbara Molz
reviewertoo.com
Simon Fisher@profsimonfisher.bsky.social · 8mo agoHow did DNA changes that alter protein structures impact evolution on the branch that led to modern humans? As we demonstrate today in Science Advances, biobanking initiatives offer ways to directly assess biological effects of rare archaic variants in living people, & (re)evaluate their roles. 🧬🧪
Second, not only does Ptpb1 not repress neurogenesis in adult glia, it doesn't do much in the developing CNS either. Scratch another master regulator off the list. doi.org/10.7554/eLif...
Ptbp1 is not required for retinal neurogenesis and cell fate specification
Loss of function of Ptbp1 in retinal progenitors leads to changes in RNA splicing but does not affect neurogenesis and cell fate specification.
doi.org
A couple of papers are finally out too. First, Meis factors are (unfortunately) not sufficient to respecify temporal identity in retinal progenitor cells. www.nature.com/articles/s41...
Overexpression of Meis factors in late-stage retinal progenitors yields complex effects on temporal patterning and neurogenesis - Scientific Reports
The vertebrate retina serves as a model for studying neurogenesis and cell fate specification, with retinal progenitor cells following a tightly regulated temporal sequence to generate distinct cell t...
nature.com
Recent Hopkins Hub article highlighting our work on optic nerve regeneration in axolotl. Congratulations to Ted! hub.jhu.edu/2025/12/11/s...
Could axolotls hold the key to restoring human vision?
Axolotls can regenerate optic nerves, retinas, and parts of their brain. Provost's Undergraduate Research Award-winner Ted Chor wants to understand how.
hub.jhu.edu
Very proud to have Leah working with us.
Jane Coffin Childs Fund for Medical Research@jcchildsfund.bsky.social · 10mo agoLeah Elias, Ph.D., is our Featured Fellow! Elias' postdoctoral research in @sethblackshaw.bsky.social's lab is dissecting how the need for restorative sleep is encoded into our brains at the level of cellular circuits and molecular signals. Her findings may reveal novel therapeutic targets ... 1/
Leah Elias, Ph.D., is our Featured Fellow! Elias' postdoctoral research in @sethblackshaw.bsky.social's lab is dissecting how the need for restorative sleep is encoded into our brains at the level of cellular circuits and molecular signals. Her findings may reveal novel therapeutic targets ... 1/
Exciting new study shows that organoid-derived human retinal ganglion cells survive when apoptosis is genetically inhibited.
Jingliang (Simon) Zhang@simonomisz.bsky.social · 10mo agoExcited to share my PhD work! We characterize waves of cell death during human retinal development, and show how blocking apoptosis promotes RGC long-term survival and alters their developmental dynamics in organoids. These findings will improve future organoid design for retinal disease modeling‼️
Our latest manuscript is out, and this one tackles the problem of cellular aging in the retina, using comparative multiomic analysis of zebrafish, mouse, and humans. What led us to work on aging after studying development and regeneration? Explainer follows./1 www.biorxiv.org/content/10.1...
Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging.
Biological age is a major risk factor in the development of common degenerative retinal diseases such as age-related macular degeneration and glaucoma. To systematically characterize molecular mechani...
biorxiv.org
👁️The retina — strikingly conserved across vertebrates, but an oddity among bilaterians! So how did it evolve? With @mikebok.bsky.social, @neurofishh.bsky.social and @denilsson.bsky.social, we argue that retinal complexity may 𝑝𝑟𝑒𝑑𝑎𝑡𝑒 𝑡ℎ𝑒 𝑒𝑦𝑒 𝑖𝑡𝑠𝑒𝑙𝑓. www.biorxiv.org/content/10.1... 1/n
a black and white dog is sitting on a couch with its tongue sticking out .
ALT: a black and white dog is sitting on a couch with its tongue sticking out .
media.tenor.com
Fantastic workshop !!!! Thank you again Seth and Michel !!!
Our latest preprint is out, focusing on characterizing the response of Lhx6-positive neurons of the zona incerta (ZI) to naturally-occurring and experimentally-induced changes in the need to sleep, also known as sleep pressure. www.biorxiv.org/content/10.1...
Sleep pressure is differentially regulated by molecularly distinct subtypes of Lhx6-positive and Lhx6-negative neurons of the zona incerta
Sleep pressure, the accumulating drive towards sleep during wakefulness, is shaped by Lhx6-positive GABAergic neurons in the zona incerta (ZI). Here, we show that these neurons are broadly activated b...
biorxiv.org
Now up, positively our lab's last word on Ptbp1. Developmental loss of function Ptbp1 turns out not to regulate neurogenesis or cell fate specification at all, but does alter splicing patterns and slightly accelerates expression of photoreceptor-specific genes./1 www.biorxiv.org/content/10.1...
Ptbp1 is not required for retinal neurogenesis and cell fate specification.
The RNA-binding protein Ptbp1 has been proposed as a master regulator of neuronal fate, repressing neurogenesis through its effects on alternative splicing and miRNA maturation. While prior studies us...
biorxiv.org
Job alert ‼️ @thomasdwkim.bsky.social and I are recruiting a postdoc in single-cell genomics via the NORPOD program of the @nordicembl.bsky.social. Collaboration between @fimm-uh.bsky.social and @dandrite.bsky.social on multimodal data integration in neurodevelopment. jobs.helsinki.fi/job/Helsinki...
Postdoctoral Researcher in Single-Cell Genomics through the NORPOD program
Postdoctoral Researcher in Single-Cell Genomics through the NORPOD program
jobs.helsinki.fi
New collaborative study out with Mark Wu’s group identifies a thalamic reuniens-zona incerta circuit as both responsive to induced sleep deprivation and essential for mediating recovery sleep. Further perspective on this work follows./1 www.science.org/doi/epdf/10....
Sleep need–dependent plasticity of a thalamic circuit promotes homeostatic recovery sleep
Prolonged wakefulness leads to persistent, deep recovery sleep (RS). However, the neuronal circuits that mediate this process remain elusive. From a circuit screen in mice, we identified a group of th...
science.org
Our paper on gene regulatory networks controlling hypothalamic and prethalamic development is now out in Cell Reports./1 www.cell.com/cell-reports...
Decoding gene networks controlling hypothalamic and prethalamic neuron development
Kim et al. map gene regulatory networks of the developing mouse hypothalamus and prethalamus using single-cell multiomics, identifying regulators of regionalization and neurogenesis. They further show...
cell.com
Meis1/2 are transcription factors that are predicted to regulate early-stage temporal identity in retina based on single-cell multiomic analysis. We tested whether Meis1/2 were sufficient to confer early temporal identity./1 www.biorxiv.org/content/10.1...
Overexpression of Meis factors in late-stage retinal progenitors yields complex effects on temporal patterning and neurogenesis.
The vertebrate retina serves as a model for studying neurogenesis and cell fate specification, with retinal progenitor cells following a tightly regulated temporal sequence to generate distinct cell t...
biorxiv.org
OK everyone, you know what to do, particularly if you live in a red state with a major medical school. donmoynihan.substack.com/p/the-nih-bu...
The NIH budget is on a fast track to disaster
An NIH insider explains what Republicans are likely to do next, and what we can do
donmoynihan.substack.com