sinan malik
@sinanmalik.bsky.social
📤 545
📥 657
📝 26
RA
@juliesemmelhack.bsky.social
Lab| systems neuroscience | writes @preLights
pinned post!
My first paper is out! “Social maintenance masks induced aggression in zebrafish” — research from my internship in the Neuronal Plasticity Group on how social context can suppress aggression.
#zebrafishrocks
🐟
www.nature.com/articles/s41...
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Social maintenance masks induced aggression in zebrafish - Scientific Reports
Scientific Reports - Social maintenance masks induced aggression in zebrafish
https://www.nature.com/articles/s41598-025-17318-1
about 1 month ago
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sinan malik
Chiara Fornetto
7 days ago
Excited to share our paper now published in Cell! 'Zebrafish use spectral information to suppress the visual background' Huge thanks to
@neurofishh.bsky.social
&
@teuler.bsky.social
@cellpress.bsky.social
@cp-cell.bsky.social
👇🏻
www.cell.com/cell/fulltex...
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Zebrafish use spectral information to suppress the visual background
Vertebrate eyes first evolved in water, where spectral content rapidly fades with distance. Zebrafish exploit this loss by antagonizing cone signals to suppress the background, pointing to distance es...
https://www.cell.com/cell/fulltext/S0092-8674(25)01138-9
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Fumi Kubo
11 days ago
Thank you so much for featuring our study🙏
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Found them: the brain's specific "go" neurons for swimming.
@fumikubo.bsky.social
team discovers the inhibitory pretextal cells essential for optomotor response, dissociating it from eye movements. A stunning map from function to molecular identity. Thrilled to highlight this work! 🐟
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13 days ago
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Martin Haesemeyer
18 days ago
Out now in
@currentbiology.bsky.social
led by Kaarthik A Balakrishnan: We identify medullary circuits that represent the valence of thermal stimuli and control both long-term strategies of cold-avoidance and short term hot avoidance behaviors to enable thermoregulation.
www.cell.com/current-biol...
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Behavioral and circuit principles of temperature gradient navigation
Behavioral thermoregulation is critical for survival across animals. Balakrishnan and Haesemeyer discover that thermoregulatory behavior in larval zebrafish is organized into longer-term swim modes. T...
https://www.cell.com/current-biology/fulltext/S0960-9822%2825%2901253-9
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Witnessed an Orchestra for the first time 'Silk Notes From Pipa'. Simply beautiful. Definition of teamwork and synchronicity.
20 days ago
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sinan malik
The Transmitter
22 days ago
Naturalistic approaches such as Ulanovsky’s open up “potential opportunities to really reveal why the brain is structured in the way it’s structured,” says Iain Couzin. By
@claudia-lopez.bsky.social
#neuroskyence
www.thetransmitter.org/neuroetholog...
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Diving in with Nachum Ulanovsky
With an eye toward realism, the neuroscientist, who has a new study about bats out today, creates microcosms of the natural world to understand animal behavior.
https://www.thetransmitter.org/neuroethology/diving-in-with-nachum-ulanovsky/?utm_source=bluesky&utm_medium=org-social&utm_campaign=20251020-profile-nachum-ulanovsky
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sinan malik
Javier Lazaro - illustration
about 2 months ago
"Fishman", proposal for a journal cover. Commissioned by MY Dennis' lab
@mydennis.bsky.social
for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model.
@dcsoto.bsky.social
#art
#digitalart
#sciart
#fish
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Jun Nagai
27 days ago
Just out in Nature! “The astrocytic ensemble acts as a multiday trace to stabilize memory.” We identified astrocytic ensembles that link experiences across days to stabilize memory
nature.com/articles/s41...
. New astrocyte tools are openly available at Addgene:
addgene.org/Jun_Nagai/
. 1/8
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Cool work! from Engert Lab
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27 days ago
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My first paper is out! “Social maintenance masks induced aggression in zebrafish” — research from my internship in the Neuronal Plasticity Group on how social context can suppress aggression.
#zebrafishrocks
🐟
www.nature.com/articles/s41...
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Social maintenance masks induced aggression in zebrafish - Scientific Reports
Scientific Reports - Social maintenance masks induced aggression in zebrafish
https://www.nature.com/articles/s41598-025-17318-1
about 1 month ago
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sinan malik
Katrin Vogt
about 2 months ago
How is valence computed in the brain? Check out our new preprint about a single cell that integrates excitatory and inhibitory input across modalities according to valence and impacts behavioral decisions. An exciting collaboration across many labs. Enjoy reading!
www.biorxiv.org/content/10.1...
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A multisensory, bidirectional, valence encoder guides behavioral decisions
A key function of the brain is to categorize sensory cues as repulsive or attractive and respond accordingly. While we have some understanding of how sensory information is processed in the sensory pe...
https://www.biorxiv.org/content/10.1101/2025.09.26.678749v1
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sinan malik
about 2 months ago
1/8 How can the brain create countless unique memories using a single, universal metric of space? We’ve been waiting for the answer to this for two decades! Read it here:
www.biorxiv.org/content/10.1...
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Venki Murthy
about 2 months ago
(edited repost) Thrilled to see our computational work on adaptive shaping of behavior (we call it outcome-based curriculum learning) in PLoS Comp Biol!
@wl-tong.bsky.social
,
@gautamreddy.bsky.social
& I formalize curricula in any RL task that can be framed as sequential simple-to-complex behavior.
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Adaptive algorithms for shaping behavior
Author summary Animals are commonly trained by ‘shaping’ their behavior using a sequence of simpler tasks towards a complex behavior. Numerous schools of thought have proposed heuristics for shaping b...
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013454
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sinan malik
The Transmitter
about 2 months ago
In this month’s “Liftoff,”
@matthiasnau.bsky.social
talks about the importance of making quick decisions as a PI, and
@kmcostalab.com
shares how lab members being mad at a PI can sometimes be a good thing. By
@franciscorr25.bsky.social
#neuroskyence
www.thetransmitter.org/liftoff-new-...
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Liftoff: New lab alerts
Learn about early-career scientists starting their own labs.
https://www.thetransmitter.org/liftoff-new-lab-alerts-early-career-neuroscientists/?utm_source=bluesky&utm_medium=org-social&utm_campaign=20250917-liftoff-sept
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sinan malik
bioRxiv Neuroscience
about 2 months ago
Hierarchical processing of sensory information across topographically organized thalamocortical-like circuits in the zebrafish brain
https://www.biorxiv.org/content/10.1101/2025.09.15.675867v1
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Emre Yaksi
about 2 months ago
Check out this exciting study led by Anh-Tuan Trinh from our lab, where we investigated how thalamocortical-like circuits in the zebrafish pallium receive, represent, and integrate sensory information: 🔗
doi.org/10.1101/2025...
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Hierarchical processing of sensory information across topographically organized thalamocortical-like circuits in the zebrafish brain
Thalamocortical projections contribute to the spatial organization and functional hierarchies of the mammalian cortex. Primary sensory cortices receive topographically segregated information from firs...
https://doi.org/10.1101/2025.09.15.675867
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sinan malik
bioRxiv Neuroscience
about 2 months ago
Beyond Locomotion: How Specialized Motor Rhythms Enable Vertebrate Escape from Capture
https://www.biorxiv.org/content/10.1101/2025.09.08.674955v1
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sinan malik
Kanaka Rajan
about 2 months ago
(4/8) Beyond neural predictions, POCO's learned unit embeddings independently reproduce brain region clustering without any anatomical labels. That means at single-cell resolution across entire brains, POCO mimics biological organization purely from neural activity patterns ✨
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sinan malik
Kanaka Rajan
about 2 months ago
(1/8) New paper from our team! Yu Duan & Hamza Chaudhry introduce POCO, a tool for predicting brain activity at the cellular & network level during spontaneous behavior. Find out how we built POCO & how it changes neurobehavioral research 👇
arxiv.org/abs/2506.14957
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sinan malik
Misha Ahrens
2 months ago
Preprint - Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten
@vmsruetten.bsky.social
, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
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Parichy Lab | Dave Parichy
3 months ago
Nemo needs gap junctions, too. New preprint with Marleen Klann, Vincent Laudet, et al. showing anemonefish Snowflake mutant due to E42K substitution in Connexin Gja5b. Found exact same E42K in zebrafish gja5b (= leopard) by ENU, to the nucleotide! Details, inferences:
www.biorxiv.org/content/10.1...
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sinan malik
Patricia Ramos
2 months ago
I am thrilled to share the main result of our work at
@nordenlab.bsky.social
with
@liormoneta.bsky.social
and
@carldmodes.bsky.social
. We bridged DevBiology + theoretical physics to understand how the eye becomes round
#morphogenesis
#devbio
#biophysics
#zebrafish
www.biorxiv.org/content/10.1...
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The Optic cup is actively shape programmed by independently patterned apical forces
During morphogenesis, initially flat tissues often must transition into complex 3D shapes, reminiscent of shape-programmable systems in physics and engineering. One key question in developmental biolo...
https://www.biorxiv.org/content/10.1101/2025.08.21.671431v1
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Prof Sam Illingworth
2 months ago
🐟 Autism, genes and setting Zebrafish with an autism-linked mutation acted less social in a stressful Styrofoam tank but less so in clear Plexiglass. This shows how environment can shape social behaviour in genetically predisposed animals. 🔗
www.eurekalert.org/news-release...
#SciComm
🧪
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Tiny fish open new horizons for autism research.
This study demonstrated that environment influences autism-like behaviours in genetically predisposed zebrafish. By altering perceived safety and anxiety levels, the study revealed that lack of social...
https://www.eurekalert.org/news-releases/1097002
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sinan malik
Guido Meijer
2 months ago
Extremely proud to have contributed to this monumental effort of recording the entire mouse brain, at cellular resolution, during complex behavior 🧠🐭
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sinan malik
The Transmitter
2 months ago
The mouse brain lights up during decision making, showing widespread activity across both predictable as well as unexpected areas. By
@claudia-lopez.bsky.social
#neuroskyence
www.thetransmitter.org/decision-mak...
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Everything everywhere all at once: Decision-making signals engage entire brain
The findings, gleaned from the most comprehensive map yet of brain activity during decision-making in mice, show that the process is even more distributed than previously thought.
https://www.thetransmitter.org/decision-making/everything-everywhere-all-at-once-decision-making-signals-engage-entire-brain/?utm_source=bluesky&utm_medium=org-social&utm_campaign=20250903-news-decision-making-signals-engage-entire-brain
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sinan malik
Asaph Zylbertal
2 months ago
First sneak peek into SimFish! 🐟 Long in development with
@isaacbianco.bsky.social
and Sam Pink, our fish-on-chips now captures key aspects of larval
#zebrafish
sensory processing and motor control.
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Shane Liddelow
2 months ago
Great story in the
@thetransmitter.bsky.social
today by
@callimcflurry.bsky.social
. It was fun chatting about
@melcooperphd.bsky.social
's new research on astrocyte networks. Read the story here:
www.thetransmitter.org/astrocytes/a...
Read the preprint here:
www.biorxiv.org/content/10.1...
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Astrocyte networks span large swaths of brain
The networks are plastic, connect brain regions that aren’t connected by neurons and may enable long-distance communication between astrocytes, a new preprint shows.
https://www.thetransmitter.org/astrocytes/astrocyte-networks-span-large-swaths-of-brain/?utm_source=The%20Transmitter%20newsletters&utm_campaign=c0081d57a9-DAILY%2020250903%20WEDNESDAY&utm_medium=email&utm_term=0_-434a84391f-169252482
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sinan malik
bioRxiv Neuroscience
2 months ago
Zebrafish sleep displays distinct sub-states
https://www.biorxiv.org/content/10.1101/2025.08.28.672887v1
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sinan malik
Maxwell Shafer
3 months ago
Now published
@natecoevo.nature.com
with
@annika-nichols.bsky.social
, our latest on the evolution of 𝘴𝘭𝘦𝘦𝘱 across 𝟲𝟬 𝘀𝗽𝗲𝗰𝗶𝗲𝘀 of cichlid fishes!
doi.org/10.1038/s415...
with members of the
@schierlab.bsky.social
and Salzburger labs, as well as the burgeoning Shafer lab
@uoftcellsysbiol.bsky.social
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Caroline Wee
2 months ago
We look forward to hosting you in Singapore 🇸🇬 Beyond the science, there will be great food, opportunities for sightseeing, and a unique banquet experience! ❤️🐟 Feel free to approach us for more details!
@oehlerslab.org
@shifengxue.bsky.social
Ajay Mathuru Sudipto Roy Yan Chuan etc
add a skeleton here at some point
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sinan malik
Bahl Lab
3 months ago
How do brains make decisions when faced with multiple, potentially conflicting cues? In our latest preprint, we show how
#zebrafish
use an additive strategy and process multiple visual features through anatomically distinct parallel pathways
tinyurl.com/mvkn8em9
Thread 👇
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sinan malik
Rick Betzel
3 months ago
This is fucking amazing.
add a skeleton here at some point
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Isaac Bianco
3 months ago
Latest from the lab. Beautiful work from Joanna Lau and a fantastic collaboration with James Fitzgerald.
www.cell.com/current-biol...
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Supraspinal commands have a modular organization that is behavioral context specific
Lau et al. use calcium imaging and statistical modeling to comprehensively survey reticulospinal activity during diverse locomotor behaviors. They find that a small set of functional modules act combi...
https://www.cell.com/current-biology/fulltext/S0960-9822(25)01003-6
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sinan malik
Ann Kennedy
3 months ago
Can't wait to read this preprint from Misha Ahrens and team. Calcium imaging in larval zebrafish, in every cell in the body! Amazing.
www.biorxiv.org/content/10.1...
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sinan malik
FocalPlane
3 months ago
#FocalPlaneFeatures
meets
@prelights.bsky.social
@fadelvalle.bsky.social
& Vibha Singh have picked 2 fantastic
#cellbio
preprints & will be presenting their preLights alongside research talks from
@probablycarmen.bsky.social
& Eva Mejia-Ramirez. Register:
focalplane.biologists.com/2025/08/20/f...
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sinan malik
Journal of Cell Science
3 months ago
Why would anyone want to be a scientist? Check out our new Essay from Martin Schwartz:
journals.biologists.com/jcs/article/...
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Needhi Bhalla 💅🏽
3 months ago
"Some might argue that personal growth is a fine thing, but not enough to justify the investment that goes to support educating a scientist. Rather, we'd argue that our current focus on professionalization runs the risk of homogenizing science, to its detriment...Science is done by whole people."
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The importance of character development in scientific research
One of the fundamental pleasures of our jobs as professors running university research labs is to see young people come, not quite knowing who they are, and grow into scientists. They acquire knowledg...
https://journals.biologists.com/jcs/article/136/13/jcs261405/322682/The-importance-of-character-development-in
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sinan malik
Bertoglio lab (FMC/UFSC)
3 months ago
New
idtracker.ai
: rethinking multi-animal tracking as a representation learning problem to increase accuracy and reduce tracking times
elifesciences.org/reviewed-pre...
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idtracker.ai — idtrackerai 6.0.7 documentation
https://idtracker.ai
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Is
@zebrafishrock.bsky.social
slack group working for everyone?
@mads100tist.bsky.social
3 months ago
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sinan malik
Itai Yanai
3 months ago
The creative process in science has a set of thinking tools that we could do a better job teaching. Here are the 12 articles that Martin and I wrote about them, including "It takes two to think", "A hypothesis is a liability" and "The two languages of science".
night-science.org/home/learn/r...
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Ciarán Murphy-Royal
3 months ago
Excellent paper from
@emreyaksi.bsky.social
@manumameli.bsky.social
labs. So much gold in the supplementary figures!
www.nature.com/articles/s42...
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Calcium dynamics in habenular astrocytes regulate active coping within behavioral transitions - Communications Biology
Tracking of astrocytes dynamics in habenula reveals their contribution to behavioral transitions across species.
https://www.nature.com/articles/s42003-025-08535-5#MOESM1
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Predicting individual learning trajectories in zebrafish via the free-energy principle
www.biorxiv.org/content/10.1...
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Predicting individual learning trajectories in zebrafish via the free-energy principle
The free-energy principle has been proposed as a unified theory of brain function, and recent evidence from in vitro experiments supports its validity. However, its empirical application to in vivo ne...
https://www.biorxiv.org/content/10.1101/2025.08.06.668947v1
3 months ago
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Caroline Wee
3 months ago
Our preprint is out: following up on our previous work on the zebrafish lateral hypothalamus, we do a deep dive into the molecular identities of
#zebrafish
LH cell types and compare them to mice. We found a novel conserved population expressing the growth hormone receptor, read to find out more!
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sinan malik
Tomer Ullman
3 months ago
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sinan malik
David Sussillo
3 months ago
Coming March 17, 2026! Just got my advance copy of Emergence — a memoir about growing up in group homes and somehow ending up in neuroscience and AI. It’s personal, it’s scientific, and it’s been a wild thing to write. Grateful and excited to share it soon.
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Wei-Chung Allen Lee
3 months ago
How is the nervous system organized to coordinate behavior? To approach this massive question, a team led by
@asbates.bsky.social
,
@jasper-tms.bsky.social
,
@mindyisminsu.bsky.social
, & Helen Yang present the BANC: a Brain and Nerve Cord connectome. Preprint:
doi.org/10.1101/2025...
🧪#Neuroskyence
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Dr. Krissy Lyon
4 months ago
Cool astrocyte paper!
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Astrocyte specification in the mouse septum is shaped by both developmental origin and local signals - Nature Neuroscience
The relative contribution of intrinsic and extrinsic factors to astrocyte heterogeneity is unknown. Using heterotropic transplantation of septal astrocytes with distinct lineage origins, we show that ...
https://www.nature.com/articles/s41593-025-02007-z
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sinan malik
Katja Reinhard
4 months ago
Finally it's out!
www.nature.com/articles/s41...
How flexible are essential innate behaviours and their underlying neural circuits?
@felixbaier.bsky.social
& I, with Hopi Hoekstra and
@farrowlab.bsky.social
, addressed this by studying the
#evolution
of threat avoidance in Peromyscus mice.
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The neural basis of species-specific defensive behaviour in Peromyscus mice - Nature
Visual threat triggers contrasting freeze and escape defensive responses in two species of deer mice as a result of different activation thresholds downstream of the superior colliculus in the do...
https://www.nature.com/articles/s41586-025-09241-2
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I just wrapped up an amazing summer at RIKEN’s Center for Brain Science and University of Tokyo (IRCN‐Chen Institute Joint Course on Neuro‐inspired Computation) in Tokyo, where I presented my poster and had countless inspiring scientific conversations! 🧠
4 months ago
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sinan malik
eLife
4 months ago
Using high-speed video and neural networks, researchers have compared hunting behaviours across five species of larval fish. The study uncovers both shared strategies and striking differences in how fish move, see, and strike during prey capture.
buff.ly/T2o9JJp
#EvoBio
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