Javier Alegre-Cortés
@alegrecortes.bsky.social
Postdoc at @karalis-lab.bsky.social - @institutducerveau.bsky.social
I create computational models to build hypothesis and make predictions.
Philosophy of science aficionado
I create computational models to build hypothesis and make predictions.
Philosophy of science aficionado
Pinned
Global and local nature of cortical slow waves
Explaining the macroscopic activity of a neuronal population from its microscopic
properties poses a great challenge, not just because of the many local agents that
play a role, but due to the impact ...
www.cell.com
I'm excited to share my latest publication! 🚨
Global and local nature of cortical slow waves:
www.cell.com/iscience/ful...
In brief, we explored in silico how cortical slow waves are shaped by both external inputs and intrinsic properties of neuronal populations.
Global and local nature of cortical slow waves:
www.cell.com/iscience/ful...
In brief, we explored in silico how cortical slow waves are shaped by both external inputs and intrinsic properties of neuronal populations.
Reposted by Javier Alegre-Cortés
🚨 Registration open for the 1st Systems-IN-Action neuroscience meeting on Circuits, Systems, Behaviour, and Computation at the @neuroalc.bsky.social in Alicante (Spain)
Deadline: Jan 15 or until 120 participants!
Orgs: @kardamakis.bsky.social, Ramón Reig & Isabel Pérez Otaño
systems-in-action.umh.es
Deadline: Jan 15 or until 120 participants!
Orgs: @kardamakis.bsky.social, Ramón Reig & Isabel Pérez Otaño
systems-in-action.umh.es
November 25, 2025 at 10:02 PM
🚨 Registration open for the 1st Systems-IN-Action neuroscience meeting on Circuits, Systems, Behaviour, and Computation at the @neuroalc.bsky.social in Alicante (Spain)
Deadline: Jan 15 or until 120 participants!
Orgs: @kardamakis.bsky.social, Ramón Reig & Isabel Pérez Otaño
systems-in-action.umh.es
Deadline: Jan 15 or until 120 participants!
Orgs: @kardamakis.bsky.social, Ramón Reig & Isabel Pérez Otaño
systems-in-action.umh.es
This is an amazing initiative
🗣️ With the support of the @danafoundation.bsky.social, we are very excited to announce the Philosophy & Neuroscience Collaborative Mentorship Program! 🧠
For more details & submission requirements, visit: philandneuro.com/mentorship
(This is 1/2 announcements we will make over the next 1-2 weeks.)
For more details & submission requirements, visit: philandneuro.com/mentorship
(This is 1/2 announcements we will make over the next 1-2 weeks.)
November 24, 2025 at 8:25 AM
This is an amazing initiative
Reposted by Javier Alegre-Cortés
My collaborator @aditijh.bsky.social has some cool work on cell-type LDS :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Disentangling the Roles of Distinct Cell Classes with Cell-Type Dynamical Systems
Latent dynamical systems have been widely used to characterize the dynamics of neural population activity in the brain. However, these models typically ignore the fact that the brain contains multiple...
www.biorxiv.org
November 23, 2025 at 6:30 PM
My collaborator @aditijh.bsky.social has some cool work on cell-type LDS :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Javier Alegre-Cortés
“Our findings challenge the conventional focus on low-dimensional coding subspaces as a sufficient framework for understanding neural computations, demonstrating that dimensions previously considered task-irrelevant and accounting for little variance can have a critical role in driving behavior.”
Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification
Most behaviors involve neural dynamics in high-dimensional activity spaces. A common approach is to extract dimensions that capture task-related variability, such as those separating stimuli or choice...
www.biorxiv.org
November 23, 2025 at 1:38 PM
“Our findings challenge the conventional focus on low-dimensional coding subspaces as a sufficient framework for understanding neural computations, demonstrating that dimensions previously considered task-irrelevant and accounting for little variance can have a critical role in driving behavior.”
Reposted by Javier Alegre-Cortés
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...
doi.org/10.1101/2025...
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...
doi.org
November 19, 2025 at 3:24 AM
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...
doi.org/10.1101/2025...
I will be in Bordeaux presenting my ongoing work in the @karalis-lab.bsky.social at the #NeuralNet2025 meeting.
If anyone is attending, come say hi!
If anyone is attending, come say hi!
November 18, 2025 at 10:27 AM
I will be in Bordeaux presenting my ongoing work in the @karalis-lab.bsky.social at the #NeuralNet2025 meeting.
If anyone is attending, come say hi!
If anyone is attending, come say hi!
Reposted by Javier Alegre-Cortés
I'm really happy to share our latest work:
“Cholinergic heterogeneity facilitates synchronization and information flow in a whole-brain model”
www.biorxiv.org/content/10.1...
“Cholinergic heterogeneity facilitates synchronization and information flow in a whole-brain model”
www.biorxiv.org/content/10.1...
Cholinergic heterogeneity facilitates synchronization and information flow in a whole-brain model
The human brain displays substantial regional variability in molecular, anatomical, and physiological organization. Yet, how this heterogeneity shapes large-scale neuronal dynamics remains poorly unde...
www.biorxiv.org
October 29, 2025 at 12:58 PM
I'm really happy to share our latest work:
“Cholinergic heterogeneity facilitates synchronization and information flow in a whole-brain model”
www.biorxiv.org/content/10.1...
“Cholinergic heterogeneity facilitates synchronization and information flow in a whole-brain model”
www.biorxiv.org/content/10.1...
Reposted by Javier Alegre-Cortés
Thrilled that our paper is out today in Nature!
www.nature.com/articles/s4...
www.nature.com/articles/s4...
Sensory expectations shape neural population dynamics in motor circuits
Nature - Experiments with human volunteers and macaques show that expectations produced by probabilistic cueing of future sensory inputs shape motor circuit dynamics in order to increase the...
www.nature.com
October 29, 2025 at 4:11 PM
Thrilled that our paper is out today in Nature!
www.nature.com/articles/s4...
www.nature.com/articles/s4...
Reposted by Javier Alegre-Cortés
My co-authors have yet to move to Bluesky, so I'm pleased to announce our latest work has just been published in @nature.com Neuroscience. Amazing work led by Junheng Li, revealing that falling asleep follows a predictable bifurcation pattern #neuroskyence #sleep
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Falling asleep follows a predictable bifurcation dynamic - Nature Neuroscience
Li et al. propose a conceptual framework to study the phenomenon of falling asleep based on electroencephalogram data. They show that a tipping point marks the brain’s nonlinear wake-to-sleep transiti...
www.nature.com
October 28, 2025 at 5:35 PM
My co-authors have yet to move to Bluesky, so I'm pleased to announce our latest work has just been published in @nature.com Neuroscience. Amazing work led by Junheng Li, revealing that falling asleep follows a predictable bifurcation pattern #neuroskyence #sleep
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Javier Alegre-Cortés
📰 "Un modelo computacional avanzado basado en datos reales sobre la anatomía y la fisiología del cerebro de mamíferos permite simular con realismo cómo se comportan las redes neuronales al conectarse".
🔬 @alegrecortes.bsky.social
🏛️ @neuroalc.bsky.social
🔗
🔬 @alegrecortes.bsky.social
🏛️ @neuroalc.bsky.social
🔗
Un estudio del Instituto de Neurociencias CSIC-UMH revela cómo el cerebro organiza y dirige su actividad más lenta | Consejo Superior de Investigaciones Científicas
El cerebro nunca descansa, incluso durante el sueño profundo o bajo anestesia mantiene una actividad eléctrica rítmica conocida como oscilaciones lentas.
buff.ly
October 27, 2025 at 9:02 AM
📰 "Un modelo computacional avanzado basado en datos reales sobre la anatomía y la fisiología del cerebro de mamíferos permite simular con realismo cómo se comportan las redes neuronales al conectarse".
🔬 @alegrecortes.bsky.social
🏛️ @neuroalc.bsky.social
🔗
🔬 @alegrecortes.bsky.social
🏛️ @neuroalc.bsky.social
🔗
Silent hills vibes at Izu peninsula
October 20, 2025 at 9:26 AM
Silent hills vibes at Izu peninsula
Here we go again
October 2, 2025 at 7:41 AM
Here we go again
Reposted by Javier Alegre-Cortés
🔥A new study led by @reiglab.bsky.social and @alegrecortes.bsky.social is now published on @cp-iscience.bsky.social 🙌
Researchers reveal how the brain organizes and directs its slowest activity: slow waves 🧠
More info 👇
in.umh-csic.es/en/articulos...
Researchers reveal how the brain organizes and directs its slowest activity: slow waves 🧠
More info 👇
in.umh-csic.es/en/articulos...
September 23, 2025 at 10:11 AM
🔥A new study led by @reiglab.bsky.social and @alegrecortes.bsky.social is now published on @cp-iscience.bsky.social 🙌
Researchers reveal how the brain organizes and directs its slowest activity: slow waves 🧠
More info 👇
in.umh-csic.es/en/articulos...
Researchers reveal how the brain organizes and directs its slowest activity: slow waves 🧠
More info 👇
in.umh-csic.es/en/articulos...
Reposted by Javier Alegre-Cortés
Stimulus-Dependent Dopamine Dynamics from LocusCoeruleus Axons https://www.biorxiv.org/content/10.1101/2025.09.15.676390v1
September 16, 2025 at 8:18 AM
Stimulus-Dependent Dopamine Dynamics from LocusCoeruleus Axons https://www.biorxiv.org/content/10.1101/2025.09.15.676390v1
Reposted by Javier Alegre-Cortés
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...
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...
September 8, 2025 at 4:25 PM
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...
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...
Reposted by Javier Alegre-Cortés
Finding correlates of the same signal in different brain areas is not evidence against specialisation, it is evidence for interconnection.
When I flush my toilet, the level in the tank and the flow rate in the supply pipe become perfectly correlated. Yet these toilet areas have distinct functions.
When I flush my toilet, the level in the tank and the flow rate in the supply pipe become perfectly correlated. Yet these toilet areas have distinct functions.
Sad day for peope who still believe brain areas are the primary organizational units of function in the brain.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A brain-wide map of neural activity during complex behaviour - Nature
The International Brain Laboratory presents a brain-wide electrophysiological map obtained from pooling data from 12 laboratories that performed the same standardized perceptual decision-making task i...
www.nature.com
September 4, 2025 at 11:52 AM
Finding correlates of the same signal in different brain areas is not evidence against specialisation, it is evidence for interconnection.
When I flush my toilet, the level in the tank and the flow rate in the supply pipe become perfectly correlated. Yet these toilet areas have distinct functions.
When I flush my toilet, the level in the tank and the flow rate in the supply pipe become perfectly correlated. Yet these toilet areas have distinct functions.
Reposted by Javier Alegre-Cortés
Scientists in training should be taught the creative scientific process, to gain confidence in their self-efficacy for research and identity as a scientist, & also for greater work satisfaction and a better chance of remaining in science long-term. Join our community at www.night-science.org
September 4, 2025 at 3:36 AM
Scientists in training should be taught the creative scientific process, to gain confidence in their self-efficacy for research and identity as a scientist, & also for greater work satisfaction and a better chance of remaining in science long-term. Join our community at www.night-science.org
Reposted by Javier Alegre-Cortés
I wrote a Comment on neurotheory, and now you can read it!
Some thoughts on where neurotheory has and has not taken root within the neuroscience community, how it has shaped those subfields, and where we theorists might look next for fresh adventures.
www.nature.com/articles/s41...
Some thoughts on where neurotheory has and has not taken root within the neuroscience community, how it has shaped those subfields, and where we theorists might look next for fresh adventures.
www.nature.com/articles/s41...
Theoretical neuroscience has room to grow
Nature Reviews Neuroscience - The goal of theoretical neuroscience is to uncover principles of neural computation through careful design and interpretation of mathematical models. Here, I examine...
www.nature.com
August 20, 2025 at 4:09 PM
I wrote a Comment on neurotheory, and now you can read it!
Some thoughts on where neurotheory has and has not taken root within the neuroscience community, how it has shaped those subfields, and where we theorists might look next for fresh adventures.
www.nature.com/articles/s41...
Some thoughts on where neurotheory has and has not taken root within the neuroscience community, how it has shaped those subfields, and where we theorists might look next for fresh adventures.
www.nature.com/articles/s41...
Reposted by Javier Alegre-Cortés
We should always take seriously where computational descriptions fail, as it tells us something about where the current boundaries of what we can describe in language lie
August 18, 2025 at 10:47 PM
We should always take seriously where computational descriptions fail, as it tells us something about where the current boundaries of what we can describe in language lie
Reposted by Javier Alegre-Cortés
1. The philosophy of science sometimes gets an unearned reputation as a purely academic exercise that offers little by way of concrete tools for advancing research.
This is wrong.
And today, as we grapple with how AI is changing the nature of scientific activity, it's desperately wrong.
This is wrong.
And today, as we grapple with how AI is changing the nature of scientific activity, it's desperately wrong.
August 19, 2025 at 4:59 AM
1. The philosophy of science sometimes gets an unearned reputation as a purely academic exercise that offers little by way of concrete tools for advancing research.
This is wrong.
And today, as we grapple with how AI is changing the nature of scientific activity, it's desperately wrong.
This is wrong.
And today, as we grapple with how AI is changing the nature of scientific activity, it's desperately wrong.
Reposted by Javier Alegre-Cortés
If you want to join us for a short stay and learn with us, that's a good opportunity. If you are interested, get in touch!
Want to develop your #neuroscience skills abroad?
Apply for the #FENS / #IBRO–PERC #ExchangeFellowships programme and conduct research at a lab in another European country! 🚀
🗓️ Deadline: 15 October 2025
👉 https://loom.ly/DhYSWlQ
@ibroorg.bsky.social
Apply for the #FENS / #IBRO–PERC #ExchangeFellowships programme and conduct research at a lab in another European country! 🚀
🗓️ Deadline: 15 October 2025
👉 https://loom.ly/DhYSWlQ
@ibroorg.bsky.social
August 8, 2025 at 8:10 AM
If you want to join us for a short stay and learn with us, that's a good opportunity. If you are interested, get in touch!
Reposted by Javier Alegre-Cortés
Lakatos on Popper isn't half bad
“Popper seems to cultivate rhetoric deliberately, partly to cover up the weaknesses of his argument and partly, I suppose, for moral reasons, to give the impression that he has an argument when he has none. This is characteristic of his whole life’s work. Most of his famous theses are slogans
August 7, 2025 at 3:41 AM
Lakatos on Popper isn't half bad
Reposted by Javier Alegre-Cortés
🚨 Upcoming postdoc openings 🚨
We will soon be hiring postdocs to work on neural data analysis & modelling in the context of a recently awarded ARIA grant aimed at "precision control" of neural population dynamics (w. collabs. across the UK)
Reach out if interested!
www.aria.org.uk/opportunity-...
We will soon be hiring postdocs to work on neural data analysis & modelling in the context of a recently awarded ARIA grant aimed at "precision control" of neural population dynamics (w. collabs. across the UK)
Reach out if interested!
www.aria.org.uk/opportunity-...
Precision Neurotechnologies
Backed by £69m, this programme aims to unlock new methods to interface with the human brain at the cellular level, with unprecedented precision.
www.aria.org.uk
August 4, 2025 at 10:32 AM
🚨 Upcoming postdoc openings 🚨
We will soon be hiring postdocs to work on neural data analysis & modelling in the context of a recently awarded ARIA grant aimed at "precision control" of neural population dynamics (w. collabs. across the UK)
Reach out if interested!
www.aria.org.uk/opportunity-...
We will soon be hiring postdocs to work on neural data analysis & modelling in the context of a recently awarded ARIA grant aimed at "precision control" of neural population dynamics (w. collabs. across the UK)
Reach out if interested!
www.aria.org.uk/opportunity-...