John Pearson
@jmxpearson.bsky.social
Computational neuroscience, neuroML, natural behavior. I charge more for miracles. PI @ pearsonlab.github.io. @dukemedschool.bsky.social.
Pinned
John Pearson
@jmxpearson.bsky.social
· Nov 11
Pearson Lab at Duke University
pearsonlab.github.io
Okay, long-overdue introduction. I’m a computational neuroscientist at Duke, where my lab (pearsonlab.github.io) does theory “bottom up”: we try to start by modeling data and build toward principles.
Reposted by John Pearson
Tom Waits talking to a puppet named TB who's a worm dressed like a newsie with tuberculosis. "WeLl if iT iSNt BeTtE mIdLeR" and she's dressed like a sexy 30s fallen woman. They sing White Christmas with a bunch of junkyard dogs roaming around. It writes itself
December 13, 2024 at 4:53 PM
Tom Waits talking to a puppet named TB who's a worm dressed like a newsie with tuberculosis. "WeLl if iT iSNt BeTtE mIdLeR" and she's dressed like a sexy 30s fallen woman. They sing White Christmas with a bunch of junkyard dogs roaming around. It writes itself
Reposted by John Pearson
For about ten years I've thought about what a Tom Waits TV Christmas special produced in the early 80s would have been like. It's almost real to me. The set is a Depression-era shack he built and a stream of celebrity hobos keep knocking on the door and Tom goes "I wOnDEr WHo tHaT cOuLd bE"
December 13, 2024 at 4:49 PM
For about ten years I've thought about what a Tom Waits TV Christmas special produced in the early 80s would have been like. It's almost real to me. The set is a Depression-era shack he built and a stream of celebrity hobos keep knocking on the door and Tom goes "I wOnDEr WHo tHaT cOuLd bE"
Reposted by John Pearson
If you really want to ‘put the Christ back into Christmas’ make refugees welcome.
December 24, 2025 at 12:15 PM
If you really want to ‘put the Christ back into Christmas’ make refugees welcome.
Reposted by John Pearson
Development of the primate projection-targeting opto methods was supported in part through a DIBS Germinator award to the incredibly talented Dr. Bohlen.
December 23, 2025 at 9:30 PM
Development of the primate projection-targeting opto methods was supported in part through a DIBS Germinator award to the incredibly talented Dr. Bohlen.
Reposted by John Pearson
Beautiful work on a frontal cortex to brainstem pathway in the primate brain, from NEI intramural investigators with help from Martin Bohlen and others in the Sommer Lab at Duke! Optogenetics for projection targeting and causal manipulation, to study visuomotor behavior.
I’m excited to share our new Current Biology paper! We use retrograde optogenetics in non-human primate and revealed a visuomotor convergence mechanism in the FEF-SC pathway.
www.cell.com/current-biol...
www.cell.com/current-biol...
Retrograde optogenetics reveals sensorimotor convergence within a corticotectal pathway of non-human primates
Yu et al. demonstrate that diverse frontal eye field signals converge on motor-selective
superior colliculus neurons to generate saccades, revealing visuomotor convergence
and establishing retrograde ...
www.cell.com
December 23, 2025 at 9:29 PM
Beautiful work on a frontal cortex to brainstem pathway in the primate brain, from NEI intramural investigators with help from Martin Bohlen and others in the Sommer Lab at Duke! Optogenetics for projection targeting and causal manipulation, to study visuomotor behavior.
Reposted by John Pearson
Do you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!
December 23, 2025 at 7:52 PM
Do you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!
Reposted by John Pearson
New Perspective from myself, Sarah Heilbronner and @myoo.bsky.social . “Rethinking the centrality of brain areas in understanding functional organization” in Nature Neuroscience. 🧵
rdcu.be/eVZ1A
rdcu.be/eVZ1A
Rethinking the centrality of brain areas in understanding functional organization
Nature Neuroscience - Parcellation of the cortex into functionally modular brain areas is foundational to neuroscience. Here, Hayden, Heilbronner and Yoo question the central status of brain areas...
rdcu.be
December 23, 2025 at 1:02 PM
New Perspective from myself, Sarah Heilbronner and @myoo.bsky.social . “Rethinking the centrality of brain areas in understanding functional organization” in Nature Neuroscience. 🧵
rdcu.be/eVZ1A
rdcu.be/eVZ1A
Reposted by John Pearson
Just in time for Xmas! Check out some new work from my lab looking at noise-invariant representations in excitatory cell-types! Congrats to Tommy Suarez-Omedas! www.biorxiv.org/content/10.6...
Canonical cortical architecture supports the emergence of noise-invariant auditory representations
Neurons in the auditory system must represent behaviorally relevant sounds in the presence of background noise (BN) to support noise-invariant perception and behavior. Although primary auditory cortex...
www.biorxiv.org
December 23, 2025 at 1:25 AM
Just in time for Xmas! Check out some new work from my lab looking at noise-invariant representations in excitatory cell-types! Congrats to Tommy Suarez-Omedas! www.biorxiv.org/content/10.6...
Reposted by John Pearson
Our python package for real-time targeting of birdsong syllables "Moove" is finally out!
Thanks to my co-authors Nils Riekers, @goebl.bsky.social and Lena Veit.
Our pre-print is online on biorxiv and our code is available on GitHub. Check it out!
doi.org/10.64898/202...
github.com/veitlab/moove
Thanks to my co-authors Nils Riekers, @goebl.bsky.social and Lena Veit.
Our pre-print is online on biorxiv and our code is available on GitHub. Check it out!
doi.org/10.64898/202...
github.com/veitlab/moove
Real-Time Segmentation and Classification of Birdsong Syllables for Learning Experiments
Songbirds are essential animal models for studying neuronal and behavioral mechanisms of learned vocalizations. Bengalese finch (Lonchura striata domestica) songs contain a limited number of acoustica...
www.biorxiv.org
December 22, 2025 at 11:06 AM
Our python package for real-time targeting of birdsong syllables "Moove" is finally out!
Thanks to my co-authors Nils Riekers, @goebl.bsky.social and Lena Veit.
Our pre-print is online on biorxiv and our code is available on GitHub. Check it out!
doi.org/10.64898/202...
github.com/veitlab/moove
Thanks to my co-authors Nils Riekers, @goebl.bsky.social and Lena Veit.
Our pre-print is online on biorxiv and our code is available on GitHub. Check it out!
doi.org/10.64898/202...
github.com/veitlab/moove
Reposted by John Pearson
Fellows-to-Faculty awardee Chen Ran maps the senses of internal organs. Receiving this award — which is currently open for apps — has been crucial in enabling his work: https://www.simonsfoundation.org/autism-and-neuroscience-innovators-awardees-share-their-research-at-the-annual-retreat/ #science
December 21, 2025 at 7:17 PM
Fellows-to-Faculty awardee Chen Ran maps the senses of internal organs. Receiving this award — which is currently open for apps — has been crucial in enabling his work: https://www.simonsfoundation.org/autism-and-neuroscience-innovators-awardees-share-their-research-at-the-annual-retreat/ #science
Reposted by John Pearson
Real-Time Segmentation and Classification of Birdsong Syllables for Learning Experiments https://www.biorxiv.org/content/10.64898/2025.12.19.695629v1
December 21, 2025 at 10:45 AM
Real-Time Segmentation and Classification of Birdsong Syllables for Learning Experiments https://www.biorxiv.org/content/10.64898/2025.12.19.695629v1
Reposted by John Pearson
The UNC system just released its final policy on mandatory syllabi disclosure, stating that syllabi are university (not faculty) IP and certain course info must be posted on new, publicly searchable databases before every semester.
A thread about what's changed from the draft I reported on earlier:
A thread about what's changed from the draft I reported on earlier:
NEW: Public universities in red states, from Texas to Florida, are increasingly required to make their syllabi public. The University of North Carolina may be next. Does "syllabi transparency" help combat distrust in higher ed, or feed ill-informed suspicions of it? www.chronicle.com/article/when...
When Everyone Can See Your Syllabus
More states are requiring public colleges to make class syllabi available to the masses. Proponents say these measures boost higher ed’s credibility, while faculty fear being targeted.
www.chronicle.com
December 19, 2025 at 8:46 PM
The UNC system just released its final policy on mandatory syllabi disclosure, stating that syllabi are university (not faculty) IP and certain course info must be posted on new, publicly searchable databases before every semester.
A thread about what's changed from the draft I reported on earlier:
A thread about what's changed from the draft I reported on earlier:
Reposted by John Pearson
Sweet postdoc in ML for budgie bioacoustics 🔊
www.oeaw.ac.at/en/oeaw-home...
www.oeaw.ac.at/en/oeaw-home...
Job vacancies at the Austrian Academy of Sciences
www.oeaw.ac.at
December 19, 2025 at 2:43 PM
Sweet postdoc in ML for budgie bioacoustics 🔊
www.oeaw.ac.at/en/oeaw-home...
www.oeaw.ac.at/en/oeaw-home...
Reposted by John Pearson
Last month, our new Simons Collaboration on Ecological Neuroscience (SCENE) held their first annual meeting at the foundation. Learn more about SCENE: https://www.simonsfoundation.org/neuroscience/simons-collaboration-on-ecological-neuroscience/ #science #neuroscience
December 19, 2025 at 8:05 PM
Last month, our new Simons Collaboration on Ecological Neuroscience (SCENE) held their first annual meeting at the foundation. Learn more about SCENE: https://www.simonsfoundation.org/neuroscience/simons-collaboration-on-ecological-neuroscience/ #science #neuroscience
Reposted by John Pearson
If you're (1) into nhp neurophysiology and/or biological motor control, (2) a foreign big shot and (3) interested in moving here, please reach out -- this new program looks extremely attractive (min. $8M over 8y)! www.uwo.ca/research/can...
Canada-Impact-Plus - Research - Western University
www.uwo.ca
December 18, 2025 at 9:15 PM
If you're (1) into nhp neurophysiology and/or biological motor control, (2) a foreign big shot and (3) interested in moving here, please reach out -- this new program looks extremely attractive (min. $8M over 8y)! www.uwo.ca/research/can...
Reposted by John Pearson
Grateful to @pewtrusts.org for funding our snow fly work, in collaboration with Sebastian Brauchi at Universidad Austral de Chile.
We are now looking for post-docs to work on the biophysical mechanisms that allow snow fly neurons and muscles to function below zero.
newsroom.uw.edu/news-release...
We are now looking for post-docs to work on the biophysical mechanisms that allow snow fly neurons and muscles to function below zero.
newsroom.uw.edu/news-release...
Most insects slow down in bitter cold. Not snow flies. - UW Medicine | Newsroom
newsroom.uw.edu
December 18, 2025 at 10:48 PM
Grateful to @pewtrusts.org for funding our snow fly work, in collaboration with Sebastian Brauchi at Universidad Austral de Chile.
We are now looking for post-docs to work on the biophysical mechanisms that allow snow fly neurons and muscles to function below zero.
newsroom.uw.edu/news-release...
We are now looking for post-docs to work on the biophysical mechanisms that allow snow fly neurons and muscles to function below zero.
newsroom.uw.edu/news-release...
Reposted by John Pearson
We took a stab at how to infer both the dynamics and control parameters of partially-observable systems.
It’s a nasty problem, but @vgeadah.bsky.social made tremendous progress, ending up with some really elegant formalisms.
It’s a nasty problem, but @vgeadah.bsky.social made tremendous progress, ending up with some really elegant formalisms.
In a system subject to unobserved control, can you infer both the underlying dynamics and the control objective? 🤔
A year ago, I was presenting our work at IEEE CDC on solving this problem for stochastic LQR.
arxiv.org/abs/2502.15014
Short 🧵 on the results, and how I think about them a year later.
A year ago, I was presenting our work at IEEE CDC on solving this problem for stochastic LQR.
arxiv.org/abs/2502.15014
Short 🧵 on the results, and how I think about them a year later.
December 18, 2025 at 6:51 PM
We took a stab at how to infer both the dynamics and control parameters of partially-observable systems.
It’s a nasty problem, but @vgeadah.bsky.social made tremendous progress, ending up with some really elegant formalisms.
It’s a nasty problem, but @vgeadah.bsky.social made tremendous progress, ending up with some really elegant formalisms.
Reposted by John Pearson
In a system subject to unobserved control, can you infer both the underlying dynamics and the control objective? 🤔
A year ago, I was presenting our work at IEEE CDC on solving this problem for stochastic LQR.
arxiv.org/abs/2502.15014
Short 🧵 on the results, and how I think about them a year later.
A year ago, I was presenting our work at IEEE CDC on solving this problem for stochastic LQR.
arxiv.org/abs/2502.15014
Short 🧵 on the results, and how I think about them a year later.
December 18, 2025 at 5:54 PM
In a system subject to unobserved control, can you infer both the underlying dynamics and the control objective? 🤔
A year ago, I was presenting our work at IEEE CDC on solving this problem for stochastic LQR.
arxiv.org/abs/2502.15014
Short 🧵 on the results, and how I think about them a year later.
A year ago, I was presenting our work at IEEE CDC on solving this problem for stochastic LQR.
arxiv.org/abs/2502.15014
Short 🧵 on the results, and how I think about them a year later.
Reposted by John Pearson
New preprint from the lab!
A frontal motor circuit for economic decisions and actions:
www.biorxiv.org/content/10.6...
We use a novel task in mice, cortex-wide imaging and optogenetics, NPX recording and modelling to reveal a circuit mechanism that transforms abstract decisions to spatial actions.
A frontal motor circuit for economic decisions and actions:
www.biorxiv.org/content/10.6...
We use a novel task in mice, cortex-wide imaging and optogenetics, NPX recording and modelling to reveal a circuit mechanism that transforms abstract decisions to spatial actions.
A frontal motor circuit for economic decisions and actions
Flexible behaviour requires transforming abstract cognitive representations, such as value preferences, into concrete motor actions. During economic decision-making, individuals evaluate options to gu...
www.biorxiv.org
December 14, 2025 at 10:59 AM
New preprint from the lab!
A frontal motor circuit for economic decisions and actions:
www.biorxiv.org/content/10.6...
We use a novel task in mice, cortex-wide imaging and optogenetics, NPX recording and modelling to reveal a circuit mechanism that transforms abstract decisions to spatial actions.
A frontal motor circuit for economic decisions and actions:
www.biorxiv.org/content/10.6...
We use a novel task in mice, cortex-wide imaging and optogenetics, NPX recording and modelling to reveal a circuit mechanism that transforms abstract decisions to spatial actions.
Reposted by John Pearson
human, macaque, marmoset!
Cross-species consensus atlas of the primate basal ganglia https://www.biorxiv.org/content/10.64898/2025.12.15.694496v1
December 16, 2025 at 2:28 PM
human, macaque, marmoset!
Reposted by John Pearson
Fully-funded International Neuroscience Doctoral Programme🧠 Champalimaud Foundation, Lisbon, Portugal 🇵🇹
Deadline: Jan 31, 2026
fchampalimaud.org/champalimaud...
Research program spans systems/computational/theoretical/clinical/sensory/motor neuroscience, neuroethology, intelligence, and more!!
Deadline: Jan 31, 2026
fchampalimaud.org/champalimaud...
Research program spans systems/computational/theoretical/clinical/sensory/motor neuroscience, neuroethology, intelligence, and more!!
December 16, 2025 at 7:20 PM
Fully-funded International Neuroscience Doctoral Programme🧠 Champalimaud Foundation, Lisbon, Portugal 🇵🇹
Deadline: Jan 31, 2026
fchampalimaud.org/champalimaud...
Research program spans systems/computational/theoretical/clinical/sensory/motor neuroscience, neuroethology, intelligence, and more!!
Deadline: Jan 31, 2026
fchampalimaud.org/champalimaud...
Research program spans systems/computational/theoretical/clinical/sensory/motor neuroscience, neuroethology, intelligence, and more!!
Reposted by John Pearson
Applications are due in one month for our Workshop on Canonical Cortical Computations: https://www.simonsfoundation.org/2025/11/13/simons-foundation-now-accepting-applications-for-workshop-on-canonical-cortical-computations/ #science #neuroscience
Simons Foundation Now Accepting Applications for Workshop on Canonical Cortical Computations
Simons Foundation Now Accepting Applications for Workshop on Canonical Cortical Computations on Simons Foundation
www.simonsfoundation.org
December 5, 2025 at 4:13 PM
Applications are due in one month for our Workshop on Canonical Cortical Computations: https://www.simonsfoundation.org/2025/11/13/simons-foundation-now-accepting-applications-for-workshop-on-canonical-cortical-computations/ #science #neuroscience
Reposted by John Pearson
Hopkins Cog Sci is hiring! We have two open faculty positions: one in vision, and one language. Please repost!
December 12, 2025 at 6:18 PM
Hopkins Cog Sci is hiring! We have two open faculty positions: one in vision, and one language. Please repost!
Reposted by John Pearson
Honestly, I couldn't say -- I'm hardly an expert in pre-whitening.
Luckily, Mandy Mejia is a co-author on the paper (and also wrote this awesome blogpost, like, 10 years ago).
We basically followed her approach as close as possible.
mandymejia.wordpress.com/2016/11/06/h...
Luckily, Mandy Mejia is a co-author on the paper (and also wrote this awesome blogpost, like, 10 years ago).
We basically followed her approach as close as possible.
mandymejia.wordpress.com/2016/11/06/h...
How to efficiently prewhiten fMRI timeseries the “right” way
I recently got around to reading the high-profile PNAS paper titled “Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates” (Eklund et al. 2016), wh…
mandymejia.wordpress.com
December 12, 2025 at 10:27 PM
Honestly, I couldn't say -- I'm hardly an expert in pre-whitening.
Luckily, Mandy Mejia is a co-author on the paper (and also wrote this awesome blogpost, like, 10 years ago).
We basically followed her approach as close as possible.
mandymejia.wordpress.com/2016/11/06/h...
Luckily, Mandy Mejia is a co-author on the paper (and also wrote this awesome blogpost, like, 10 years ago).
We basically followed her approach as close as possible.
mandymejia.wordpress.com/2016/11/06/h...
Reposted by John Pearson
Seven-parameter drift-diffusion pdfs and cdfs now in Stan
statmodeling.stat.columbia.edu/2025/12/11/s...
statmodeling.stat.columbia.edu/2025/12/11/s...
Seven-parameter drift-diffusion pdfs and cdfs now in Stan | Statistical Modeling, Causal Inference, and Social Science
statmodeling.stat.columbia.edu
December 11, 2025 at 9:00 PM
Seven-parameter drift-diffusion pdfs and cdfs now in Stan
statmodeling.stat.columbia.edu/2025/12/11/s...
statmodeling.stat.columbia.edu/2025/12/11/s...