Scientist I/ Brain Health @AllenInstitute 🇺🇸 | Computational Neuroscientist 🧠 | Physicist 👩🔬 | she/her
Seattle, WA
- Tweets 48
- Following 297
- Followers 80
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📣 #NewPaper!
Circuit and cell-type mechanisms of the spectrolaminar motif of cortical oscillations 🧠 〰️
doi.org/10.64898/2026.11.04.…
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This work involved extensive simulations with and without perturbations and model modifications (21 conditions). The code, models, and all simulation results are freely shared, so anyone can build on our results.
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Many thanks to all the co-authors: Shinya Ito (@shixnya), Darrell Haufler, Kael Dai, Ahmed Abdaltawab, Yiti Li, Eli Z. Sennesh, Diego Mendoza-Halliday, Andre M. Bastos (@BastosLabNeuro), and especially @AntonSArkhipov.
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Beatriz Herrera retweeted
Day 2 of the @AllenInstitute Modeling Software workshop, with presentations by Laura Green and
@shixnya.
- Your models need inputs-and how to stimulate them.
- And, all about differentiable bio-realistic models of brain circuits (we can train them via backpropagation!).
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Beatriz Herrera retweeted
First day of the @AllenInstitute Modeling Software workshop - welcome to all the participants.
@beaherrera kicks us off with introduction to our Brain Modeling ToolKit (BMTK), SONATA data format, and VND. Darrell Haufler follows up with tutorials about biophysical modeling.
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Beatriz Herrera retweeted
ANNs can match neural activity.
But without biological constraints, they achieve it via the wrong mechanisms.
In our new V1 model, biologically constrained training achieves both.
Full story from our team leader, @AntonSArkhipov.
bioRxiv link: doi.org/10.64898/2026.03.13.…
New paper!
Deep-learning-assisted simulation of a cortical circuit:
integrating anatomy, physiology and function
biorxiv.org/cgi/content/shor…
It comes with a new major model release from @AllenInstitute.
Find models and code here: github.com/AllenInstitute/bi…
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Beatriz Herrera retweeted
New paper!
Deep-learning-assisted simulation of a cortical circuit:
integrating anatomy, physiology and function
biorxiv.org/cgi/content/shor…
It comes with a new major model release from @AllenInstitute.
Find models and code here: github.com/AllenInstitute/bi…
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Beatriz Herrera retweeted
A reminder that we will have a nice and fun Modeling Software Workshop @AllenInstitute on July 20–22.
It's free. We offer some travel support. And you get to learn about BMTK, SONATA, and VND.
Apply by March 15!
alleninstitute.org/events/20…
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Beatriz Herrera retweeted
Presenting today at SC’25: a full microscopic-level simulation of the entire mouse cortex on the Fugaku supercomputer.
Big day for the collaboration between our @AllenInstitute group and the lab of Prof. Tadashi Yamazaki.
See here: sc25.conference-program.com/…
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Beatriz Herrera retweeted
Check out our #Sfn2025 posters this afternoon: @shixnya and @beaherrera present simulations of cortical neurons and circuits and Paul Olsen talks about linking in vivo ophys with spatial transcriptions.
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Beatriz Herrera retweeted
Great work by Laura Green, @beaherrera, Kael Dai in collaboration with Tadashi Yamazaki's group.
What happens when you combine 10 years of brain data with one of the world’s fastest supercomputers?
A virtual mouse cortex simulation, thanks to a global collaboration.
Discover how it was made and how it could help researchers study brain diseases: alleninstitute.org/news/one-…
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Beatriz Herrera retweeted
Many thanks to all the attendees, team members, and @AllenInstitute staff for an exciting and productive Modeling Software Workshop!
Check out training materials at alleninstitute.github.io/bmt… and sign up for our newsletter if you'd like to receive updates:
signup.e2ma.net/signup/20108…
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Beatriz Herrera retweeted
Cool updates in our newsletter:
📺 3D neuronal visualization in VND linked to Python notebooks via zmq
🧠 Stabilized Supralinear Networks implemented in BMTK
📢 Upcoming presentations at CNS*2025 and JNS by @beaherrera and @shixnya
See more and subscribe:
t.e2ma.net/message/3njjhi/jw…
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Beatriz Herrera retweeted
Join us at the @AllenInstitute Modeling Software Workshop on July 28-30, 2025 in Seattle!
Apply here: alleninstitute.org/events/20…
And whether applying or not, please help us understand what the field needs by filling out this brief survey:
forms.office.com/pages/respo…
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