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sinan malik

@sinanmalik.bsky.social
558 followers 676 following 33 posts

RA @juliesemmelhack.bsky.social Lab| systems neuroscience | writes @preLights

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Reposted by sinan malik
Rainer Friedrich @rainerfriedrichlab.bsky.social · 26/09/2026
Precise structural and functional organization of the olfactory bulb neuropil early in development, revealed by volume EM, dense reconstruction and 2P calcium imaging in zebrafish. Great work by Ruth and others in collaboration with @michalwj.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Fine ultrastructural organization of glomerular neuropil in the developing zebrafish olfactory bulb
Across animal phyla, odor information is represented in the first olfactory processing center by combinatorial activation of discrete glomeruli. To examine how this organization of olfactory processin...
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Matt Lovett-Barron @mlovettbarron.bsky.social · 26/09/2026
New lab preprint: @grace-padilla.bsky.social studied how zebrafish respond to chemical cues of death and decay. Brief exposure initiated a persistent state, but not through olfaction. Instead, these cues' basic pH was detected by trigeminal neurons and TrpA1 channels www.biorxiv.org/content/10.6...
biorxiv.org
Decay chemicals activate a pH-sensing pathway to initiate a persistent state
Animals use multiple sensory systems to identify signs of danger, including dead conspecifics. Fish can identify decaying conspecifics from chemosensory cues, which prompt a long-lasting avoidance; th...
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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 21/09/2026
Our Google Summer of Code participants have been writing up their projects. First up, Anna Teruel-Sanchis who built an interactive GUI in @napari.org for correcting pose estimation tracks directly within the movement framework. Read more in Anna's blog: neuroinformatics.dev/blog/gsoc_20...
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Ashrit Mangalwedhekar @ashritocyte.bsky.social · 12/08/2026
Excited to share the first paper from my PhD work! Read it to find out how larval zebrafish don't let go of the past.
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Phoebe Reynolds @pheereynolds.bsky.social · 23/06/2026
I’m very excited to share that our paper is now out in Neuron! 🎉
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Dan Levenstein @dlevenstein.bsky.social · 01/09/2026
Have spent more brain juice than I want to admit thinking about this question. Turns out the answer is still “it depends”, on so many things. www.jneurosci.org/content/43/7...
jneurosci.org
On the Role of Theory and Modeling in Neuroscience
In recent years, the field of neuroscience has gone through rapid experimental advances and a significant increase in the use of quantitative and computational methods. This growth has created a need for clearer analyses of the theory and modeling approaches used in the field. This issue is particularly complex in neuroscience because the field studies phenomena that cross a wide range of scales and often require consideration at varying degrees of abstraction, from precise biophysical interactions to the computations they implement. We argue that a pragmatic perspective of science, in which descriptive, mechanistic, and normative models and theories each play a distinct role in defining and bridging levels of abstraction, will facilitate neuroscientific practice. This analysis leads to methodological suggestions, including selecting a level of abstraction that is appropriate for a given problem, identifying transfer functions to connect models and data, and the use of models themselves as a form of experiment.
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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 26/08/2026
Day 3 of Week 2 is underway at our summer school! In the @brainglobe.info track, Igor Tatarnikov is introducing deep learning to analyse whole-brain images. In Extracellular Electrophysiology, Chris Halcrow is teaching the @spikeinterface.bsky.social GUI for visualisation and curation. #NIU_OSSS_26
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Alex Schier @schierlab.bsky.social · 19/08/2026
What regulates the urge to sleep? William Joo and colleagues identified brain regions that reflect how long mice have been awake. Strikingly, inhibiting one of these regions reduces sleep by 70%, without the major behavioral deficits associated with sleep deprivation. www.nature.com/articles/s41...
nature.com
Wake-activated neuronal populations that regulate sleep drive - Nature
Whole-brain activity mapping, targeted cell manipulations and electrophysiology in mice identify wake-activated neuronal populations that are crucial for sleep drive and can persistently red...
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Tom Baden @neurofishh.bsky.social · 18/08/2026
New primer on Danionella cerebrum, with @xinwei-wang.bsky.social . What a fun little fish :) Free access here: authors.elsevier.com/a/1ndEe_LsQS...
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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 17/08/2026
The Neuroinformatics Unit Open Software Summer School starts today! Week one starts with: - Animals in Motion, how to use open source tools to quantify animal behaviour - Large Array Data, working with very large scientific datasets neuroinformatics.dev/open-softwar... #NIU_OSSS_26
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Margarita Parada-Kusz @margaritapk.bsky.social · 09/08/2026
Amygdala astrocyte primary cilium mechanisms contribute to stress behaviours www.nature.com/articles/s41...
nature.com
Amygdala astrocyte primary cilium mechanisms contribute to stress behaviours - Nature
Amygdala astrocyte primary cilia are disrupted during stress, and their restoration leads to improvements in stress-related behaviour in mice.
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Peter Rupprecht @ptrrupprecht.bsky.social · 07/08/2026
Excited to share our work now in Nature Methods! We wrote this manuscript to help others better analyze and interpret calcium imaging data. As a central aspect, we show why nonlinear behavior of calcium indicators matters in practice. Very happy about this work!
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Florian Engert @engertlab.bsky.social · 20/07/2026
Yet another cool story just came out of the ever-so-capable hands of Roy Harpaz (@royharpaz.bsky.social). www.nature.com/articles/s41... Roy showed that larval zebrafish will adapt and get used to crowded conditions, and that they are then, later on, less sensitive about their personal space.
nature.com
Experience-dependent modulation of collective behavior in larval zebrafish - Nature Communications
How does social experience shape collective behavior? Here, authors show that larval zebrafish use visual-social encounters in crowded or sparse environments to dynamically retune social interactions,...
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May-Britt Moser @m-bmoser.bsky.social · 03/07/2026
Congratulations to @emreyaksi.bsky.social and his team at @kavlintnu.bsky.social! Beautiful story! 💐🎉🍀
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Emre Yaksi @emreyaksi.bsky.social · 17/07/2026
🧠 A new paper from our lab is out! In this study, we explore how dorsal raphe nucleus (DRN) circuits modulate forebrain activity and behavior. www.nature.com/articles/s41...
nature.com
Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors - Nature Communications
Functional heterogeneity of dorsal raphe nucleus is not fully understood. Here authors show topographically organized sensory and locomotor responses from the zebrafish dorsal raphe and its forebrain ...
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 20/07/2026
Deep anatomical and ultrastructural classification of neurons in the zebrafish olfactory bulb www.biorxiv.org/content/10.64898/20…
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Jonas Wietek @jwietek.bsky.social · 30/06/2026
bssst bssst CU @ #FENS26
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Wataru Koyama @watarukoyama.bsky.social · 30/05/2026
My PhD paper is out in Science Advances! We found that the adult zebrafish cerebellum encodes both positive and negative valence during GO/NOGO task learning, and teaching signals sent to Purkinje cell update internal models of task rules. www.science.org/doi/10.1126/...
science.org
The cerebellum implements structured representation of valence to support adaptive behavior control
Cerebellar circuits identify danger and safety to guide flexible, adaptive behavior.
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Roxana Zeraati @roxana-zeraati.bsky.social · 01/04/2026
Many thanks to @klaus-tschira-stiftung.de and @gso-forresearchers.bsky.social for this wonderful opportunity to study the mechanisms underlying naturalistic decision processes in the context of foraging behavior! We’ll also soon have openings for PhD students, stay tuned!
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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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Martin Haesemeyer @haesemeyerlab.bsky.social · 13/05/2026
New preprint from the lab, led by Bradley Cutler. With the @james-gagnon.bsky.social lab we use zebrafish to show that fever is not a reduction in the perception of warmth. Immune signals instead increase the valence of warming stimuli while cooling turns aversive. www.biorxiv.org/content/10.6...
Conceptual model of how PGE2 signaling alters temperature encoding in medullary circuits to change the valence of heating and cooling stimuli.
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Rory Cooper @rorylcooper.bsky.social · 12/05/2026
Having a lovely time using the incredible imaging facilities at @clf-stfc.bsky.social 🦈🔬
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James Gagnon @james-gagnon.bsky.social · 28/04/2026
Using light-activated CRISPR in zebrafish, we triggered synchronized DNA breaks and track the repair process. ⚡🐟⚡ 

 Well ... DNA repair is very different in embryos compared to tissue culture cells. Embryos repair DNA breaks incredibly fast - within minutes! www.biorxiv.org/content/10.6...
A cartoon showing how a caged guide RNA poises CRISPR cleavage until release by light. Below, a cartoon of injection of "light-activated CRISPR" into the embryo, followed by activation.
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Nature @nature.com · 23/04/2026
Nature research paper: Astrocytes connect specific brain regions through plastic networks go.nature.com/4eBe8fV
go.nature.com
Astrocytes connect specific brain regions through plastic networks - Nature
Communication between distant brain regions is mediated by plastic networks of gap junction-coupled astrocytes.
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Fumi Kubo @fumikubo.bsky.social · 17/04/2026
Happy to share our new paper published in Nature Communications! www.nature.com/articles/s41... We developed CaMPARI-seq to link neural activity with molecular profiles and revealed how the brain distinguishes optic flow to guide behavior. Congratulations to our postdoc Koji Matsuda!
rdcu.be
Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors
Nature Communications - In this study, the authors develop CaMPARI-seq to link neural activity with molecular profiles in larval zebrafish. They identify inhibitory pretectal neurons required for...
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Dayu Lin @moccalin.bsky.social · 15/04/2026
What has changed in mama bear brain (well, actually mice) to make her risk her life to attack a potential threat and protect her young? Oxytocin is the key! Happy to share our new study led by two awesome postdocs: Takashi Yamaguchi and Rongzhen Yan. www.nature.com/articles/s41...
nature.com
The neural mechanisms supporting the rise and fall of maternal aggression - Nature
In mice, female aggression is governed by an amygdala–to–medial hypothalamus circuit that is strengthened during pregnancy and is dynamically amplified by oxytocin during lactation.
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Yale Kavli Institute for Neuroscience @kavliatyale.bsky.social · 13/04/2026
In a new study, @yale.edu researchers led by @yaleschoolofmed.bsky.social's @ehoffmanlab.bsky.social, MD, PhD 🥼 identified a promising candidate to rescue disrupted brain activity in zebrafish carrying mutations in autism risk genes 🦓🐠
news.yale.edu
Zebrafish reveal new insights into the biology of autism
In a new study, Yale researchers identified drug candidates that reverse disrupted behaviors in zebrafish carrying mutations in autism risk genes.
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Constantinople lab @constantinoplelab.bsky.social · 25/03/2026
Thrilled to share our new paper, which shows that the relative timing of cholinergic and dopamine release dynamically gates whether dopamine acts as an RPE for in vivo plasticity and reinforcement learning. www.nature.com/articles/s41...
nature.com
Acetylcholine demixes heterogeneous dopamine signals for learning and moving
Nature Neuroscience - Jang et al. measured dopamine and acetylcholine release in the striatum of rats performing a decision-making task and found that the relative timing of cholinergic and...
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Natalie Schaworonkow @nschawor.bsky.social · 25/03/2026
a while ago, I made this feed for neuroscience/cognitive science summer schools. after some tuning, it generally manages to find cool events. 🙂 bsky.app/profile/did:...
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Emily Troyer @fishfetisher.bsky.social · 17/03/2026
Out now in Science: The Truman Show, but with killifishes! "Continuous recording of a vertebrate’s adult life from adolescence until death would provide a complete view into the behavioral architecture of aging." www.science.org/doi/10.1126/...
science.org
Lifelong behavioral screen reveals an architecture of vertebrate aging
Mapping behavior of individual vertebrate animals across lifespan could provide an unprecedented view into the lifelong process of aging. We created a platform for high-resolution continuous behaviora...
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Benjamin Judkewitz @benjulab.bsky.social · 16/03/2026
How do fish localize sound without interaural cues? @johve.bsky.social et al. found a behavioral algorithm for directional hearing that predicts behavior from a pressure/motion phase comparison and accounts for how this relationship varies with distance. www.cell.com/current-biol...
cell.com
An algorithm underlying directional hearing in fish
Veith et al. show how a fish—Danionella cerebrum—can reliably startle away from sound. It uses the relative phase between particle motion and pressure to infer the direction of sound. This sensorimoto...
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Benjamin Judkewitz @benjulab.bsky.social · 05/03/2026
First whole-brain recording of social sound processing in a vertebrate. Surprises start in the hindbrain; thalamus gates conspecific calls; male and female brains diverge downstream. Work by @joerghenninger.bsky.social, @mh123.bsky.social sky.social and team. www.biorxiv.org/content/10.6...
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The Transmitter @thetransmitter.bsky.social · 04/03/2026
“Astrocytes in the lateral septum may explain, or be at the basis of, the sex differences we observe in terms of social fear.” –Alexandre Charlet. By Holly Barker www.thetransmitter.org/spectrum/ast...
thetransmitter.org
Astrocytes orchestrate oxytocin’s social effects in mice
The cells amplify oxytocin—and may be responsible for sex differences in social behavior, two preprints find.
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Ahmed El Hady @zamakany.bsky.social · 03/03/2026
An exciting study with Roberto Garza and Armin Bahl biorxiv.org/content/10.6... We combine high-throughput behavioral assays in larval zebrafish with drift-diffusion modeling studying integration dynamics across development and a variety of mutants . Give it a read :D
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Florian Engert @engertlab.bsky.social · 26/02/2026
Check this out! Latest collaborative work from my and Mark Fishman's labs - led by Roy Harpaz, with help from Pedro Piquet and Yasuko Isoe (@yasukoisoe.bsky.social)
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Portugues Lab @portugueslab.bsky.social · 08/02/2026
Have you ever wondered how the brain should represent the sensory world in order to generate behavior? Read our new preprint: work by Shuhong Huang shuhonghuang.bsky.social with our long-standing collaborator James Fitzgerald at Northwestern.
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Oded Rechavi @odedrechavi.bsky.social · 29/01/2026
“ok so this is embarrassing but just for the record and just so we have it, your C.V says "Nature Scientific Reports"? sorry to have to even ask”
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Peter Rupprecht @ptrrupprecht.bsky.social · 19/01/2026
Excited to share our new preprint! We explore the link between the locus coeruleus (LC) and arousal for astrocytes, pyramidal cells, interneurons in the hippocampus. A fantastic collaboration with @sianduss.bsky.social @bohaceklab.bsky.social, and many others: www.biorxiv.org/content/10.6... 1/5
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Oded Rechavi @odedrechavi.bsky.social · 10/04/2025
Supplementary figure 16
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Simon Schultz @simonschultz.bsky.social · 10/01/2026
Lu, Schultz, Kozlov, Astrocytes and neurons exhibit partially shared but distinct composite receptive fields for natural stimuli Now published in J Neurophys journals.physiology.org/doi/abs/10.1...
journals.physiology.org
Astrocytes and neurons exhibit partially shared but distinct composite receptive fields for natural stimuli | Journal of Neurophysiology | American Physiological Society
Astrocytes are increasingly recognized as active participants in sensory processing, but whether they show selective responses to stimulus features, analogous to neuronal receptive fields, is not yet ...
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samuelsy20.bsky.social @samuelsy20.bsky.social · 09/01/2026
In @elife.bsky.social: Pallium-encoded valence-specific chemosensory amplification of eye-body coordination in larval zebrafish doi.org/10.7554/eLif...
doi.org
Pallium-encoded valence-specific chemosensory amplification of eye-body coordination in larval zebrafish
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Portugues Lab @portugueslab.bsky.social · 07/01/2026
1/6: New publication from the lab: “Plastic landmark anchoring in zebrafish compass neurons” by Ryosuke Tanaka (@ryosuketanaka.bsky.social) and Ruben is available here: rdcu.be/eX1L4
rdcu.be
Plastic landmark anchoring in zebrafish compass neurons
Nature - Using two-photon microscopy with a panoramic virtual reality setup, how head direction cells in larval zebrafish integrate visual landmarks and optic flow to track orientation is revealed.
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Artologica aka Michele Banks @artologica.net · 03/01/2026
Okay, well, I painted some new neurons in burnt sienna and black #sciart
Pattern of pyramidal neurons in brown and black with white lines
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Portugues Lab @portugueslab.bsky.social · 02/01/2026
1/n: A new collaborative preprint from the lab to start the year: "A multi-ring shifter network computes head direction in zebrafish" together with Siyuan Mei, Martin Stemmler and Andreas Herz from the LMU, Munich.
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BWJones @bwjones.bsky.social · 01/01/2026
Surprise mother$#@%er! Q: What does this mean for neural systems to understand them? A: We absolutely need the wiring diagram. All synapses, chemical and electrical. #Connectomics
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Mackenzie Weygandt Mathis @trackingactions.bsky.social · 31/12/2025
Interested in the latest advances in neuroscience (neural dynamics and internal models) and how they can be leveraged to build smarter, adaptive AI? ➡️ My first real solo piece 🖤🫶 @natneuro.nature.com rdcu.be/eWVmA
rdcu.be
Leveraging insights from neuroscience to build adaptive artificial intelligence
Nature Neuroscience - Adaptive intelligence envisions AI that, like animals, learns online, generalizes and adapts quickly. This Perspective reviews biological foundations, progress in AI and...
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Ann Kennedy @antihebbiann.bsky.social · 30/12/2025
"My New Year's Resolution is to find a principled way to think about all those cell types in the brain" Why friend, you are in luck, because @rgast.bsky.social has just the perspective for you: www.sciencedirect.com/science/arti...
sciencedirect.com
How heterogeneity shapes dynamics and computation in the brain
Much effort has been spent clustering neurons into transcriptomic or functional cell types and characterizing the differences between them. Beyond sub…
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allen institute @alleninstitute.org · 23/12/2025
Glutamate is the primary molecule that neurons use to communicate with each other. Previously, scientists have mostly recorded when neurons fire output signals, but now with a new glutamate indicator, they can record the many inputs that causes cells to fire. 🧵 #neuroskyence
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Joey Tidei @j-today.bsky.social · 19/12/2025
I don't always get pretty, isolated, AND transfected primary neurons in culture, but when I do I take advantage.... Rat hippocampal neuron overexpressing ThymosinB4-mScarlet and imaged for 16hr on a @zeiss-microscopy.bsky.social LSM880 with Airyscan. #FluorescenceFriday #Microscopy
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