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Jacob Ratliff

@jacobmratliff.bsky.social
86 followers 94 following 14 posts

Neuroscientist postdoc at UCL Harris and Carandini lab Studying cell types and decision making

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Anthony Ramnauth @philoneurosci.bsky.social · 09/09/2026
New publication from @lukesjulson.bsky.social lab and collaborators! #Neocortical long-range #inhibition promotes #cortical #synchrony and #sleep doi.org/10.1038/s415...
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Neocortical long-range inhibition promotes cortical synchrony and sleep - Nature
In mice, a sparse population of sleep-active long-range inhibitory neurons in the neocortex promote widespread cortical synchronization and sleep, revealing a cortical mechanism that co...
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Eliezyer de Oliveira @eliezyer.bsky.social · 14/09/2026
After a long journey through review, our paper is finally out in Nature Communications. We started with a simple problem: The visual cortex is strongly modulated by movement. So how can it represent the visual world without movement interfering with everything? www.nature.com/articles/s41...
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Jacob Ratliff @jacobmratliff.bsky.social · 14/09/2026
Many long years after the project started, I am really happy to announce that the main paper from my PhD is out! Below there is brief summary about what we learned about Sst-Chodl cells driving sleep Or you can check out the full paper www.nature.com/articles/s41...
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Jacob Ratliff @jacobmratliff.bsky.social · 04/09/2026
It always struck me when Enny was presenting this great work just how un-special the hippocampus is with representing spatial information (though I'm not sure she would say it as strongly)
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Anyi Liu @anyiliu.bsky.social · 29/07/2026
Pyramidal cells in the cortex send a long apical dendrite to layer 1. What is its role? What happens when it's gone? ✂️ A causal spatial role for apical dendrites in the cortex Out today with @kenneth-harris.bsky.social, @carandinilab.net and @fedrossi.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
A causal spatial role for apical dendrites in the cortex
Cortical pyramidal neurons project a long apical dendrite to layer 1 (L1), to receive synaptic inputs that are thought to provide contextual and possibly suppressive modulation. In visual cortex, thes...
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Matteo Carandini @carandinilab.net · 31/07/2026
The apical dendrite looks great, and does wonders in a slice. What does it do in the living cortex? It depends on the cell. A causal spatial role for apical dendrites in the cortex www.biorxiv.org/content/10.6... by @anyiliu.bsky.social with @kenneth-harris.bsky.social and @fedrossi.bsky.social
A cartoon providing a graphical summary of the paper. It is divided in 3 rows.

The top row shows a pyramidal cell and its apical tuft, and shows the two experiments that we ran: optical dendritic pruning (chopping off the apical tuft), and synaptic imaging done in the same neurons where we do somatic imaging. 

The middle row shows the results pertaining to neurons that prefer large stimuli (this is visual cortex): pruning reduced their responses, and the receptive fields of apical synapses are far away from the that of the soma. 

The bottom row shows the results pertaining to neurons that prefer small stimuli: pruning seemed to do nothing to the responses, and the receptive field of apical synapses are right around that of the soma.
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Yao Chen @yaochen20.bsky.social · 09/07/2026
How does the brain track how much sleep has occurred, and gauge the likelihood of waking at each moment? Check out our new preprint: “A molecular integrator of sleep duration and interruption” www.biorxiv.org/content/10.6... (1/10)
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shijiegu @shijiegu.bsky.social · 03/06/2026
Last week, we finally submitted my first paper during my PhD (bioRXiv: www.biorxiv.org/content/10.6...). The paper is about change-of-mind (COM) behavior. You know when you're taking a test and switch your answer after second-guessing yourself? We studied what happens in the brain at that moment.
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John Tuthill @tuthill.bsky.social · 30/06/2026
My department, Neurobiology and Biophysics at the University of Washington (nbio.uw.edu), is hiring a new tenure-track Assistant Professor, application deadline 09/30/26. It's a broad search — molecular to organismal, all of neuroscience/physiology/biophysics welcome. apply.interfolio.com/187735
NBIO department logo
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Zhiwen Ye @zhiwenneuron.bsky.social · 19/06/2026
1/ Complex behavior demands the sequential coordination of hundreds of muscle groups. The body is mapped topographically in the brain, but does neural activity actually propagate across these maps to organize sequential action? Our new paper in Science: doi.org/10.1126/scie... 🧵
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Kenneth Harris @kenneth-harris.bsky.social · 19/05/2026
New method for identifying the fine transcriptomic types of thousands of neurons recorded in vivo!
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Blake Richards @tyrellturing.bsky.social · 20/04/2026
1/2) Just out from @alexkwan.bsky.social's group, a study showing that psilocybin silences SST interneurons but activates PV interneurons: www.biorxiv.org/content/10.6... #neuroscience 🧪
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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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Jeremiah Cohen @jeremiahycohen.bsky.social · 13/04/2026
Delighted to share our discoveries about one of the brain's neurotransmitter systems: www.biorxiv.org/content/10.6... Together with colleagues at the @alleninstitute.org, we have learned a lot about a tiny cluster of neurons in the brainstem locus coeruleus (LC) that releases norepinephrine (NE). 1
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Julie Fabre @juliefabre.bsky.social · 08/04/2026
How do the basal ganglia turn what you see into what you do? New preprint w/ @kenneth-harris.bsky.social, @flickerfusion.bsky.social & @carandinilab.net: we recorded across striatum, GPe & SNr in a Go/NoGo task. Striatum encodes which stimulus, GPe & SNr encode action. 🧵 biorxiv.org/content/10.6...
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Arkarup Banerjee @arkarupbanerjee.bsky.social · 02/04/2026
This is a really insightful piece. Highly recommend 👇🏽
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Nima Dehghani @neurovium.bsky.social · 16/03/2026
Check our recent preprint (with Yáñez, Messore,Qi,Meyer, Feldmeyer, Bert Sakmann, Oberlaender) Presented @cosynemeeting.bsky.social 2025 #cosyne2026 Morphoelectric properties of inhibitory neurons shift gradually and regardless of cell type along the cortical depth share.google/GYGGquVAHyow...
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Morphoelectric properties of inhibitory neurons shift gradually and regardless of cell type along the depth of the cerebral cortex
How can we understand the enormous diversity of the GABAergic inhibitory neurons in the cerebral cortex? To address this question, we quantify the electrophysiological and morphological properties of inhibitory neurons across the depth of an entire cortical column in the rat barrel cortex. We find properties that shift gradually with the cortical depth of the cell bodies across all inhibitory neurons, regardless of their cell types. By isolating morphoelectric variations from their shifts along the cortical depth, we find that the same simple relationships between morphoelectric properties distinguish between the four main molecular cell types of inhibitory neurons at any cortical depth, and in both the rat barrel cortex and mouse primary visual cortex. We provide converging evidence from dense electron-microscopic reconstructions of inhibitory neurons in the mouse visual cortex, and observe comparable depth-dependent shifts in additional datasets from the mouse primary motor cortex and the middle temporal gyrus of the human cortex. Our findings indicate that two different sources of morphoelectric variations can account for the diversity of cortical inhibitory neurons. The first source is molecular cell type-specific, but cortical depth-independent. The second source is cortical depth-dependent, but affects inhibitory neurons similarly across all cell types. We propose that intrinsic developmental specification vs. extrinsic environmental modulation leads to such a decoupling of inhibitory type-specific properties from gradual shifts of these properties with cortical depth. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 633428 Deutsche Forschungsgemeinschaft, SFB 1089, SPP 2041, Fe472/2-1 Bundesministerium für Bildung und Forschung, 01GQ1002, 01IS18052 Neuroscience Network North Rhine-Westphalia, iBehave National Institutes of Health, https://ror.org/01cwqze88, R24MH117295 The Kavli Foundation, NeuroData Discovery Award
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Scott Thompson, PhD @sthom003.bsky.social · 25/02/2026
Let’s not forget his co-director. If you’re not a mad scientist, you’re not paying attention.
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Nancy Parmalee @nparmalee.bsky.social · 25/02/2026
Gift link from the NYT story about Axel and Epstein. When I was at Columbia he ran a lab where sexual harassment of women was business as usual. We all knew. We all warned each other. www.nytimes.com/2026/02/25/n...
nytimes.com
Leader of Columbia Brain Institute Quits Over Friendship With Epstein
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Gord Fishell @gordfishell.bsky.social · 22/01/2026
Excited for the publication of our recent work on how pyramidal cells shape the identity of interneurons in the Cortex! Big shout out to @artofbiology and Sherry Jingjing wu! www.nature.com/articles/s41...
nature.com
Pyramidal neurons proportionately alter cortical interneuron subtypes - Nature
Pyramidal neuron-driven mechanisms actively promote the survival and terminal differentiation of their associated interneuron subtypes.
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Nicole Rust @nicolecrust.bsky.social · 21/01/2026
Let's talk about "grumpy lab person". Many labs have them. With an eye to keeping science at its most rigorous, they cross the line into criticism that's too harsh. They are the ones who risk killing your scientific spirit. They are reviewer 2. /1
Grumpy from Disney's Snow White and the 7 dwarves.
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Pierre Le Merre @pierrelemerre.bsky.social · 20/01/2026
Main postdoc study out! We can redefine prefrontal cortex regions with single-unit activity! Grateful to @carlenlab.bsky.social and @weltgeischt.bsky.social who made this crazy project real. Thanks to all co-authors, collaborators, and reviewers. www.nature.com/articles/s41...
nature.com
A prefrontal cortex map based on single-neuron activity - Nature Neuroscience
The authors mapped spontaneous and choice activity across mouse prefrontal cortex. The activity maps aligned with intrinsic connectivity rather than anatomical subregions, suggesting that connectivity...
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Ben Hayden @benhayden.bsky.social · 23/12/2025
New Perspective from myself, Sarah Heilbronner and @myoo.bsky.social . “Rethinking the centrality of brain areas in understanding functional organization” in Nature Neuroscience. 🧵 rdcu.be/eVZ1A
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Rethinking the centrality of brain areas in understanding functional organization
Nature Neuroscience - Parcellation of the cortex into functionally modular brain areas is foundational to neuroscience. Here, Hayden, Heilbronner and Yoo question the central status of brain areas...
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Matteo Carandini @carandinilab.net · 22/12/2025
Sequences are everywhere! In every brain region. And are written in stone. Invariant Activity Sequences Across the Mouse Brain. Out today, by Célian Bimbard, with @kenneth-harris.bsky.social. Based on data by Célian and by @intlbrainlab.bsky.social. www.biorxiv.org/content/10.6...
Examples of sequences of activity seen in multiple regions of the brain
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Luke Sjulson @lukesjulson.bsky.social · 17/12/2025
It’s horrifying that the NIH director’s collaborators are publishing opinions as uninformed and flat out stupid as this. Let’s save American science by removing incentives for foreign researchers to come here! Science isn’t competitive enough! Underreliance on standardized testing is the problem!
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Jure Majnik @juremaj.bsky.social · 18/12/2025
My first paper just got published last week! *Longitudinal tracking of neuronal activity from the same cells in the developing brain using Track2p* elifesciences.org/articles/107...
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Mark Histed @markhisted.org · 14/11/2025
Hearing a rumor that NIH/HHS may now plan to retaliate against other Bethesda Declaration signers. I am one, but it’s not about me: we have been speaking out because of the ongoing damage to US medical research, cancer and Alzheimer’s research. As @jenna-m-norton.bsky.social put well: 1/
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Kenneth Harris @kenneth-harris.bsky.social · 14/11/2025
1. New preprint resolving a conundrum in systems neuroscience with an AI scientist, and humans Reilly Tilbury, Dabin Kwon, @haydari.bsky.social, @jacobmratliff.bsky.social, @bio-emergent.bsky.social, @carandinilab.net, @kevinjmiller.bsky.social, @neurokim.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
Characterizing neuronal population geometry with AI equation discovery
The visual cortex contains millions of neurons, whose combined activity forms a population code representing visual stimuli. There is, however, a discrepancy between our understanding of this code at ...
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Valentin Schmutz @bio-emergent.bsky.social · 19/09/2025
🎉 "High-dimensional neuronal activity from low-dimensional latent dynamics: a solvable model" will be presented as an oral at #NeurIPS2025 🎉 Feeling very grateful that reviewers and chairs appreciated concise mathematical explanations, in this age of big models. www.biorxiv.org/content/10.1... 1/2
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