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Alexander Shakeel Bates

@asbates.bsky.social
259 followers 195 following 58 posts

Fly Neuroscientist and other good things.

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Alexander Shakeel Bates @asbates.bsky.social · 13/09/2026
Google, but not possible without the academic driving force here from Cambridge and Janelia! We also built a fly CNS connectome (this one female) as an open source project: www.nature.com/articles/s41...
nature.com
Distributed control circuits across a brain-and-cord connectome - Nature
A connectome of the brain and ventral nerve cord of an adult female fruit fly is reconstructed and annotated, providing an open resource that reveals neural control of behaviour to be distri...
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Alexander Shakeel Bates @asbates.bsky.social · 04/09/2026
And now this new beast - the full male fly central nervous system connectome - is out in print! www.cell.com/cell/fulltex... A phenomenal resource, @ukri.org @hhmijanelia.bsky.social, @cellpress.bsky.social
cell.com
Sexual dimorphism in the complete Drosophila male central nervous system connectome
The Drosophila whole male central nervous system connectome enables end-to-end analysis of sensorimotor circuits. Comparison with existing female datasets shows that brain-wide wiring differences betw...
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Greg Jefferis @jefferis.bsky.social · 15/10/2025
Excited to share our new #biorxivpreprint: “Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1... We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
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Alexander Shakeel Bates @asbates.bsky.social · 04/09/2026
One of the coolest fly neuroscience studies this year. We need to think more about all these understudied links from CNS to body.
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Yichen Luo 骆奕辰 @camellyc.bsky.social · 03/08/2026
1/8 Breathing seems automatic. But it's a finely tuned motor behavior that has to be controlled. In this preprint, I map the circuits that match a fly's respiration to the metabolic demands of flight and mitigate the risk of dehydration. 🧵🪰 www.biorxiv.org/content/10.6...
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Greg Jefferis @jefferis.bsky.social · 27/08/2026
Last week to apply for these posts. This a great time to join this project — every week we’re finding out new and exciting things about the organisation of the mosquito brain — with super collaborators @darbly.bsky.social and @megyounger.bsky.social. Pls share!
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Alexander Shakeel Bates @asbates.bsky.social · 29/07/2026
Now published open-access: www.nature.com/articles/s41... The BANC connectome! Go use it: codex.flywire.ai?dataset=banc
nature.com
Distributed control circuits across a brain-and-cord connectome - Nature
A connectome of the brain and ventral nerve cord of an adult female fruit fly is reconstructed and annotated, providing an open resource that reveals neural control of behaviour to be distri...
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Alexander Shakeel Bates @asbates.bsky.social · 10/06/2026
And hopefully there will be more from the #BANC, Chris Salmon and Arie Matsliah plan a nerve cord alignment paper, incoming, and @debivort.bsky.social @mindyisminsu.bsky.social may be able to link this connectome to the sample's real-life movement bias, so stay tuned!
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Justin Ellis-Joyce @justinellis-joyce.bsky.social · 09/06/2026
I was delighted to contribute to this amazing work lead by @asbates.bsky.social, Lee and Wilson labs, and a village of contributors. This is a monument complete with connections to muscles and proprioceptors which will enable us to simulate of the sensorimotor loops of a brain for the first time!!
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
Our thread on the newly published brain and nerve cord #BANC #connectome, and what #neuroscience stories we can tell with it.
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Now published - the #BANC! A full central nervous system (CNS) connectome of a limbed animal at single-synapse resolution, enabling us to follow sensory-motor arcs and understand how the CNS controls the body. rdcu.be/fncjS. #neuroscience. Video by @quorumetrix.bsky.social 1/18
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Jan Drugowitsch @jdrugowitsch.bsky.social · 09/06/2026
We are excited to have been part of the community effort that led to the Brain-and-Nerve-Cord (BANC) connectome.
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Jan Drugowitsch @jdrugowitsch.bsky.social · 09/06/2026
Please check out @darbly.bsky.social & @asbates.bsky.social 's thread at bsky.app/profile/darb..., or HMS News at hms.harvard.edu/news/researc... for a quick overview, or read the full paper at doi.org/10.1038/s415... for details.
hms.harvard.edu
Researchers Publish First Complete Connectome of Fruit Fly Brain and ‘Spinal Cord’
Open-source resource poised to propel research on how nervous systems work
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
I think all this is a big deal. The fly connectomes give the field a strong organizational framework. I think they are making us an “organized system of tunnels”, and really advance the fly as the premier system for mechanistic, cognitive neuroscience. 14/18
neuroscience as many workers tunnelling into one mountain
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
note a high-quality contemporaneous male connectome is preprinted, data available male-cns.janelia.org (Berg et al., @stuartberg.bsky.social erg.bsky.social, @beckett14.bsky.social, @mmcosta.bsky.social, @jefferis.bsky.social), they compare the nervous systems of the sexes neuron by neuron. 13/18
the contemporaneous maleCNS connectome
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
And very importantly, the BANC is a deep, open resource. Browse via FlyWire Codex (codex.flywire.ai/?dataset=banc, by Arie Matsliah) and Neuroglancer (ng.banc.community/view); download everything from the Harvard Dataverse: doi.org/10.7910/DVN/7WTH1N 12/18
Card: where to browse, download and find the code, with addresses
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
The modules influence one another, not a strict hierarchy but a heterarchy, recruiting or suppressing each other. Together it resembles Rodney Brooks’ subsumption architecture from robotics: complex behaviour from layered, semi-autonomous modules, not a central controller. 11/18
modules influencing one another, a heterarchy
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
Let’s look at a specific example. DNg27 drives flight power and, at the same time, recruits the endocrine cells that release the energy flight demands. One cell, matching a behaviour to the body state that supports it. 10/18
DNg27 drives flight power and recruits energy-mobilising endocrine cells
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
We embedded the neck neurons by connectivity, then lit the map up by influence from each sensor and to each effector. They resolve into clusters that, we infer, group controllers by behaviour: walking, flight, grooming, feeding, reproduction, threat and more. 9/18
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
Where are the long-range links that join these local modules? Easiest to find at the neck, because these are definitionally long-ranged and cross module. About 3,600 ascending and descending neurons cross it, wiring the brain to the nerve cord, and one body part to another. 8/18
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
Following influence from sensors to effectors, body part by body part, reveals control built from local sensorimotor loops. Effectors are influenced most by their own body part’s sensors (the diagonal); weaker off-diagonal links join body parts, key for complex behaviour. 7/18
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
How do you read 160,000 neurons when most connections are indirect? Linear dynamics. Influence (with @zakiajabi.bsky.social) estimates how strongly one neuron affects another across the entire network: essentially a scalable measure of network distance. Code: doi.org/10.5281/zenodo.15999929 6/18
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
We saw a chance to build not just a CNS connectome but one that is “embodied” by linking sensors and effectors across the body to the CNS. These peripheral labels are among the most interpretable we have! 5/18
an embodied connectome, sensors and effectors tied to body parts
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
We linked the BANC to other connectomes mainly by morphology: e.g. the steering neuron DNa02 matches closely between FAFB and BANC (tools with @jefferis.bsky.social). With @helenhyang.bsky.social we refined classification into literature-consistent groupings, with rich metadata. 4/18
a DNa02 steering neuron matched between FAFB and the BANC
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
One adult female fly: dissected, cut into 7,010 slices, EM-imaged, aligned to 3D @mindyisminsu.bsky.social @jasper-tms.bsky.social. Neural nets (zetta.ai) segmented cells, synapses and transmitters; SixEleven and Aelysia (aelysia.eu) teams proofread over ~3.5 years. 3/18
dissection, sectioning, imaging and alignment pipeline
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Alexander Shakeel Bates @asbates.bsky.social · 09/06/2026
Connectomes are accelerating, from the ~300 neurons of C. elegans 40 years ago to the fly brain last year (FAFB, bbc.com/news/articles/c0lw0nxw71po). The BANC is the next big step, a full CNS, brain and nerve cord together, a powerful hypothesis-generation engine. 2/18
a timeline of connectomes from C. elegans to the BANC
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openworm.org @openworm.org · 01/05/2026
In 1986, John White published "The Mind of a Worm," the first complete wiring diagram of any animal's brain. 7,000+ synapses in C. elegans, mapped by hand. This year he won the Wiley Prize in Biomedical Sciences. And he's donating his share to OpenWorm.
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Bing Wen Brunton @bingbrunton.bsky.social · 24/03/2026
Some of you saw a preview of this result at my Cosyne talk last week. We may have had too much fun working on this worm-fly model 🤣🤓🤣 (The digital sphinx may be imagery, but the lessons are real.)
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John Tuthill @tuthill.bsky.social · 24/03/2026
🧵 New preprint led by @bingbrunton.bsky.social, @elliottabe.bsky.social, @lawrencehu.bsky.social We gave a worm brain control of a fly body and it walked What did we learn? Nothing, other than deep reinforcement learning is effective We call it the digital sphinx www.biorxiv.org/content/10.6...
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Robert Hart @theroberthart.bsky.social · 18/03/2026
Serious question… is this is a real fly? A startup thinks it's a "real uploaded animal". What do you think? for @theverge.com with @shahabbakht.bsky.social @asbates.bsky.social @anayebi.bsky.social @birchlse.bsky.social @tom-mcclelland.bsky.social www.theverge.com/ai-artificia...
theverge.com
This is not a fly uploaded to a computer
Ceci n’est pas une fly.
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Alexander Shakeel Bates @asbates.bsky.social · 03/11/2025
A small and interesting neural controller for object pursuit on the fly:
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Matt Collie @mottcallie.bsky.social · 03/11/2025
Delighted to share an updated pre-print on how adaptive control in visual pursuit is implemented at the circuit level. New behavior and neuronal data in females (!) shows how two AOTU pathways are key elements in both sexes. Check it out on @biorxiv-neursci.bsky.social : doi.org/10.1101/2025...
doi.org
Specialized parallel pathways for adaptive control of visual object pursuit
To pursue a moving visual object, the brain must generate motor commands that continuously steer the object to the center of the visual field via feedback. The gain of this control loop is flexible, y...
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Alexander Shakeel Bates @asbates.bsky.social · 28/08/2025
We have been answering redditors questions today on the #BANC fly connectome in a public AMA if anyone wants to take a look: www.reddit.com/r/askscience...
reddit.com
From the askscience community on Reddit
Explore this post and more from the askscience community
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Erika Dona @erikadona.bsky.social · 21/08/2025
We integrated our atlas with the connectome using shared features, such as lineage, segment, molecular info (i.e. neurotransmitter, Notch) and neurogenesis timing. We mapped 122 transcriptional pools, each one containing an average of 26 anatomically defined neuron types. 4/8
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sebastiancachero.bsky.social @sebastiancachero.bsky.social · 21/08/2025
With this atlas in place, we mapped sex differences in the atlas and adult connectomes, identifying female-specific apoptosis and transcriptional divergence as drivers of sexually dimorphic development. 7/8
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Erika Dona @erikadona.bsky.social · 21/08/2025
Thanks to all authors and support from #MRC_LMB, @neurohub-cnr.bsky.social , @camzoology.bsky.social , #flyconnectome, @wellcometrust.bsky.social , ‪@erc.europa.eu‬, @astra-zeneca.bsky.social and @cruk-ci.bsky.social. FIN
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Greg Jefferis @jefferis.bsky.social · 21/08/2025
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns? To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠 #preprint thread ⬇️1/8
ALT text: A UMAP representation of a single cell RNAseq dataset from the Drosophila ventral nerve cord as well as images of the Drosophila nerve cord connectome and different stages of fly development.
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Ben de Bivort @debivort.bsky.social · 20/08/2025
Fly labs — Now is the time to show some solidarity and chip in support for this vital resource!
clip art of Drosophila flies at different life stages
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Alexander Shakeel Bates @asbates.bsky.social · 17/08/2025
The #BANC connectome sample was the best dissection of ~150 by @mindyisminsu.bsky.social! Behaviourally characterised by @debivort.bsky.social lab, microCT used to assess integrity before continuing. Then Minsu and @jasper-tms.bsky.social imaged over ~7 months Details: github.com/jasper-tms/t...
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Minsu Kim @mindyisminsu.bsky.social · 05/08/2025
It’s surreal to think that every neuron and synapse in the fly brain + cord that was dissected almost five years ago (the photo’s still on the lab slack!) is now just a click away on Codex codex.flywire.ai?dataset=banc. This wouldn’t have been possible without the incredible team behind it!
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Alexander Shakeel Bates @asbates.bsky.social · 08/08/2025
The fly #BANC connectome benefits from specialists’ annotations. @ellenlesser.bsky.social‬ helped us annotate wing sensory neurons and ‪@tony-azevedo.bsky.social‬ wing + other motor neurons, see them here!: ng.banc.community/2025a/wing-n... In Codex: codex.flywire.ai/app/search?f...
ng.banc.community
neuroglancer
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Alexander Shakeel Bates @asbates.bsky.social · 07/08/2025
Explore neurons that enter/exit the fly central nervous system by body part with this clickable fly!: codex.flywire.ai/app/body_par... (graphics: @mottcallie.bsky.social‬, tool: Arie Matisliah) Vector graphics! github.com/wilson-lab/s... Effector cells in 3D! ng.banc.community/2025a/effere...
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Alexander Shakeel Bates @asbates.bsky.social · 06/08/2025
For the BANC, ‪@jasper-tms.bsky.social‬ and I have added layers for neurons in other datasets to our neuroglancer environment. Search by name and see your favourite neurons in the same space! See an example here: ng.banc.community/2025a/DNa01-...
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Alexander Shakeel Bates @asbates.bsky.social · 06/08/2025
Ah! Wei has already done a great job of this, credits at the end of this thread: bsky.app/profile/darb...
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
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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ellenlesser.bsky.social @ellenlesser.bsky.social · 03/06/2025
So happy to share this project detailing fly wing sensory neurons! I started this project just by asking what the axons of the wing chordotonal organ looked like, and I found many other cool structures along the way.
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Sophia Renauld @sophia-renauld.bsky.social · 04/08/2025
What a joy to work on such an incredibly collaborative project!! Congrats to all who poured time energy and effort into this new resource. (So excited about this that I had to make a bluesky account!)
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
The dataset includes ~160,000 cells, segmented nuclei and mitochondria, synapses and neurotransmitter predictions, and annotations linking the CNS to peripheral sensory, motor, and visceral systems. Info: banc.community Data: codex.flywire.ai?dataset=banc Viewer: ng.banc.community/view
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Alexander Shakeel Bates @asbates.bsky.social · 02/08/2025
It’s a big project and I’m taking a short holiday now after the preprint! So I’ll make another post later showing all the bits of it, and how we did this as a community !
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Alexander Shakeel Bates @asbates.bsky.social · 02/08/2025
Flywire collaborators @princetonneuro.bsky.social‬ were essential in building the connectome, and theory collaborators in interpreting it! @jdrugowitsch.bsky.social‬ Art by ‪@amysterling.bsky.social!
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