sinan malik
@sinanmalik.bsky.social
π€ 551
π₯ 664
π 30
RA
@juliesemmelhack.bsky.social
Lab| systems neuroscience | writes @preLights
pinned post!
Really enjoyed highlighting this work by
@vmsruetten.bsky.social
from
@mishaahrens.bsky.social
lab for preLights. WHOLISTIC! A whole-body functional atlas of cellular dynamics. Lots of cool things in the preprint.
@hhmijanelia.bsky.social
@prelights.bsky.social
add a skeleton here at some point
10 days ago
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sinan malik
Allen Institute
5 days ago
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. π§΅
#neuroskyence
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Joey Tidei
9 days ago
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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Jonas Wietek
9 days ago
Merry Christmas, Hanukkah, et al.
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Really enjoyed highlighting this work by
@vmsruetten.bsky.social
from
@mishaahrens.bsky.social
lab for preLights. WHOLISTIC! A whole-body functional atlas of cellular dynamics. Lots of cool things in the preprint.
@hhmijanelia.bsky.social
@prelights.bsky.social
add a skeleton here at some point
10 days ago
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sinan malik
Ryosuke Tanaka
14 days ago
A paper from my PhD lab is on Science! This is a really cool new way to utilize EM connectome datasets. Congrats to the team!
www.science.org/doi/10.1126/...
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Spatial and morphological organization of mitochondria in neurons across a connectome
Neuronal function depends on mitochondria, but little is known about their organization across neurons. Using an electron microscopy Drosophila connectome, we uncovered quantitative rules governing th...
https://www.science.org/doi/10.1126/science.ads6674
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sinan malik
Current Biology
about 2 months ago
Check out our newest issue where we interview
@juliesemmelhack.bsky.social
, who studies the neural circuits of visual behavior at the Hong Kong University of Science and Technology.
www.cell.com/current-biol...
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Q & A
Interview with Julie Semmelhack, who studies the neural circuits of visual behavior at the Hong Kong University of Science and Technology.
https://www.cell.com/current-biology/fulltext/S0960-9822(25)01258-8
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Adrian Jacobo
19 days ago
It's finally out! Our paper on optogenetic interrogation of the lateral line:
www.cell.com/iscience/ful...
This one involved a lot of sweat and tears, and it was a real tour de force. It was also the last paper we got to write with Jim, so it's a special one (and hence, the tears).
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Optogenetic interrogation of the zebrafish lateral line reveals brain-wide neural circuits involved in pattern separation
Zoology; Neuroscience; Sensory neuroscience
https://www.cell.com/iscience/fulltext/S2589-0042(25)02453-8
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Oded Rechavi
24 days ago
The fun leaving your body the moment you're done with the science and it's time to get it published
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sinan malik
Leibniz-Institut fΓΌr Neurobiologie
24 days ago
We are very excited:
@hannazwaka.bsky.social
has been awarded a Leibniz Best Minds grant as a Junior Research Group Leader! Five years of independent research, tenure track and part of the Best Minds network β a real boost for her career.
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You're not you when you're hungry... and neither is a zebrafish! Our new paper shows that hunger completely overrides the instinct to flee, making zebrafish approach potential threats instead. "Hunger shapes predator avoidance in zebrafish."
@zebrafishrock.bsky.social
π
doi.org/10.1080/0394...
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Hunger shapes predator avoidance behaviour in zebrafish
All organisms, including humans, engage in behavioral choices and complex decision-making processes, which are crucial for survival. The mechanisms underlying behavioral choices require the acquisi...
https://doi.org/10.1080/03949370.2025.2563566
26 days ago
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Abe Goldfarb
28 days ago
when someone tells me not to use em dashes because AI uses em dashes
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sinan malik
Portugues Lab
about 1 month ago
(1/n) We are excited to share our new paper in Nature Communications, by Hagar Lavian (
@hlavian.bsky.social
) and team, revealing how the zebrafish brain integrates visual navigation signals!
www.nature.com/articles/s41...
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Visual motion and landmark position align with heading direction in the zebrafish interpeduncular nucleus - Nature Communications
How are various visual signals integrated in the vertebrate brain for navigation? Here authors show that different spatial signals are topographically organized and align to one another in the zebrafi...
https://www.nature.com/articles/s41467-025-66084-1
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David Schoppik
about 1 month ago
Like most animals, fish move less at night. Underwater, stable posture requires movement. Find out how fish don't fall down at night in: Lighting and circadian cues shape locomotor strategies for balance and navigation in larval zebrafish from
@yunluzhu.bsky.social
doi.org/10.1101/2025...
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Lighting and circadian cues shape locomotor strategies for balance and navigation in larval zebrafish
Most fish are inherently unstable and must swim to stabilize posture. How diurnal fish reduce activity at night while maintaining postural control remains unclear. We defined distinct locomotor strate...
https://doi.org/10.1101/2025.11.18.689084
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sinan malik
Matthew Logie
about 1 month ago
The changes we experience may be the source of our subjective experience of time.
www.nature.com/articles/s41...
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Time, space, memory and brainβbody rhythms - Nature Reviews Neuroscience
Understanding how the brain represents experienced time and how representations of space and time are integrated to form episodic memories has been a goal of much neuroscientific research. In this Per...
https://www.nature.com/articles/s41583-025-00987-2
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Oded Rechavi
about 1 month ago
Going to the lab during the weekend to do cell culture work and trying to do everything at double speed
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sinan malik
Oded Rechavi
about 2 months ago
Writing the βAlternative Plansβ part of the grant
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Caroline Wee
about 2 months ago
Now published in Molecular Metabolism, improved by the helpful reviewers! We hope to continue to leverage the
#zebrafish
to understand the neurometabolic and hormonal regulation of appetite and beyond! Read the full article here:
www.sciencedirect.com/science/arti...
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sinan malik
about 2 months ago
β¨ New preprint β¨ What if we could watch AND control thousands of individual neurons in behaving miceβwith stable access over months? π§ β‘ Our work introduces transgenic all-optical tools that make this possible - and a resulting surprising discovery! ππ‘
www.biorxiv.org/content/10.1...
1/13 π§΅
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Large-scale cellular-resolution read/write of activity enables discovery of cell types defined by complex circuit properties
The complexity of the mammalian brainβs vast population of interconnected neurons poses a formidable challenge to elucidate its underlying mechanisms of coordination and computation. A key step forwar...
https://www.biorxiv.org/content/10.1101/2025.10.21.683734v1
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sinan malik
MPI for Biological Intelligence
about 2 months ago
How does a fish know when to blend in? Scientists identified a key circuit controlling camouflage in zebrafish β from cells in the retina sensing light to nerve cells in the brain controlling the release of a hormone that pales the skin to match bright backgrounds.
www.bi.mpg.de/news/2025-11...
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sinan malik
Chiara Fornetto
about 2 months 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
ππ»
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
about 2 months ago
Thank you so much for featuring our studyπ
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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! π
add a skeleton here at some point
about 2 months ago
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Martin Haesemeyer
2 months 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.
2 months ago
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sinan malik
The Transmitter
2 months ago
Naturalistic approaches such as Ulanovskyβs open up βpotential opportunities to really reveal why the brain is structured in the way itβs structured,β 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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Javier Lazaro - illustration
3 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
2 months ago
Just out in Nature! βThe astrocytic ensemble acts as a multiday trace to stabilize memory.β 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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2 months ago
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My first paper is out! βSocial maintenance masks induced aggression in zebrafishβ β research from my internship in the Neuronal Plasticity Group on how social context can suppress aggression.
#zebrafishrocks
π
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
3 months ago
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sinan malik
Katrin Vogt
3 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
3 months ago
1/8 How can the brain create countless unique memories using a single, universal metric of space? Weβve 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
3 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 βshapingβ 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
3 months ago
In this monthβs βLiftoff,β
@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
3 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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sinan malik
Emre Yaksi
3 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: π
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
4 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
4 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 β¨
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sinan malik
Kanaka Rajan
4 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 π
arxiv.org/abs/2506.14957
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sinan malik
Misha Ahrens
4 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
4 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
4 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
4 months ago
π 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. π
www.eurekalert.org/news-release...
#SciComm
π§ͺ
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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
4 months ago
Extremely proud to have contributed to this monumental effort of recording the entire mouse brain, at cellular resolution, during complex behavior π§ π
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sinan malik
The Transmitter
4 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
4 months ago
First sneak peek into SimFish! π 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
4 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 arenβt 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
4 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
4 months ago
Now published
@natecoevo.nature.com
with
@annika-nichols.bsky.social
, our latest on the evolution of π΄ππ¦π¦π± across π²π¬ ππ½π²π°πΆπ²π 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
4 months ago
We look forward to hosting you in Singapore πΈπ¬ Beyond the science, there will be great food, opportunities for sightseeing, and a unique banquet experience! β€οΈπ Feel free to approach us for more details!
@oehlerslab.org
@shifengxue.bsky.social
Ajay Mathuru Sudipto Roy Yan Chuan etc
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sinan malik
Bahl Lab
4 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 π
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