Javier Alegre-Cortés
@alegrecortes.bsky.social
Postdoc at @karalis-lab.bsky.social - @institutducerveau.bsky.social
Neuroscientist using computational methods to explain physiological mechanisms.
Philosophy of science aficionado
Neuroscientist using computational methods to explain physiological mechanisms.
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.
If you are interested in providing mechanistic explanations to how neuromodulators shape neuronal dynamics and communication among brain regions, don't miss this chance to join us!
We invite applications for postdoctoral researchers with strong expertise in in vivo electrophysiology and circuit neuroscience to join our team at the Paris Brain Institute (ICM).
December 17, 2025 at 2:50 PM
If you are interested in providing mechanistic explanations to how neuromodulators shape neuronal dynamics and communication among brain regions, don't miss this chance to join us!
Reposted by Javier Alegre-Cortés
Our newest research in @currentbiology.bsky.social:
www.cell.com/current-biol...
We find dominant baboons have more interrupted and less rest at night.
Author list and story in comments below :-)
www.cell.com/current-biol...
We find dominant baboons have more interrupted and less rest at night.
Author list and story in comments below :-)
December 14, 2025 at 6:53 PM
Our newest research in @currentbiology.bsky.social:
www.cell.com/current-biol...
We find dominant baboons have more interrupted and less rest at night.
Author list and story in comments below :-)
www.cell.com/current-biol...
We find dominant baboons have more interrupted and less rest at night.
Author list and story in comments below :-)
Reposted by Javier Alegre-Cortés
Dissecting GPCR Selectivity: A complex interplay of various intracellular motifs determines G-protein binding and activation https://www.biorxiv.org/content/10.64898/2025.12.12.693856v1
December 15, 2025 at 6:00 PM
Dissecting GPCR Selectivity: A complex interplay of various intracellular motifs determines G-protein binding and activation https://www.biorxiv.org/content/10.64898/2025.12.12.693856v1
Reposted by Javier Alegre-Cortés
🥳Excited to share our latest human multipatch paper, now out in @natneuro.nature.com
🧠 We studied the cellular and synaptic physiology of human L2–3 pyramidal neurons and identified subtype-specific local connectivity rules across individuals.
www.nature.com/articles/s41...
Join us: penglab.de
🧠 We studied the cellular and synaptic physiology of human L2–3 pyramidal neurons and identified subtype-specific local connectivity rules across individuals.
www.nature.com/articles/s41...
Join us: penglab.de
December 13, 2025 at 7:59 AM
🥳Excited to share our latest human multipatch paper, now out in @natneuro.nature.com
🧠 We studied the cellular and synaptic physiology of human L2–3 pyramidal neurons and identified subtype-specific local connectivity rules across individuals.
www.nature.com/articles/s41...
Join us: penglab.de
🧠 We studied the cellular and synaptic physiology of human L2–3 pyramidal neurons and identified subtype-specific local connectivity rules across individuals.
www.nature.com/articles/s41...
Join us: penglab.de
Reposted by Javier Alegre-Cortés
🧠📢 New preprint alert
Large-scale ephys is exploding but spike sorting remains the computational bottleneck. A 2-hr, 6-probe Neuropixels 2.0 Quad Base session can take over a week to sort on a single machine. Here's a better solution. 🧵
#neuroskyence #compneurosky
Large-scale ephys is exploding but spike sorting remains the computational bottleneck. A 2-hr, 6-probe Neuropixels 2.0 Quad Base session can take over a week to sort on a single machine. Here's a better solution. 🧵
#neuroskyence #compneurosky
December 5, 2025 at 8:42 PM
🧠📢 New preprint alert
Large-scale ephys is exploding but spike sorting remains the computational bottleneck. A 2-hr, 6-probe Neuropixels 2.0 Quad Base session can take over a week to sort on a single machine. Here's a better solution. 🧵
#neuroskyence #compneurosky
Large-scale ephys is exploding but spike sorting remains the computational bottleneck. A 2-hr, 6-probe Neuropixels 2.0 Quad Base session can take over a week to sort on a single machine. Here's a better solution. 🧵
#neuroskyence #compneurosky
Bassins des Lumières, Bordeaux
December 8, 2025 at 7:23 AM
Bassins des Lumières, Bordeaux
Reposted by Javier Alegre-Cortés
Finally got the job ad—looking for 2 PhD students to start spring next year:
www.gao-unit.com/join-us/
If comp neuro, ML, and AI4Neuro is your thing, or you just nerd out over brain recordings, apply!
I'm at neurips. DM me here / on the conference app or email if you want to meet 🏖️🌮
www.gao-unit.com/join-us/
If comp neuro, ML, and AI4Neuro is your thing, or you just nerd out over brain recordings, apply!
I'm at neurips. DM me here / on the conference app or email if you want to meet 🏖️🌮
December 3, 2025 at 9:37 AM
Finally got the job ad—looking for 2 PhD students to start spring next year:
www.gao-unit.com/join-us/
If comp neuro, ML, and AI4Neuro is your thing, or you just nerd out over brain recordings, apply!
I'm at neurips. DM me here / on the conference app or email if you want to meet 🏖️🌮
www.gao-unit.com/join-us/
If comp neuro, ML, and AI4Neuro is your thing, or you just nerd out over brain recordings, apply!
I'm at neurips. DM me here / on the conference app or email if you want to meet 🏖️🌮
Reposted by Javier Alegre-Cortés
Great read. Too many people assume that the role of theory papers in neuro is to "explain neural data". I'm not even sure we can explain anything yet. Data is more like a muse for theory.
How I contributed to rejecting one of my favorite papers of all times, Yes, I teach it to students daily, and refer to it in lots of papers. Sorry. open.substack.com/pub/kording/...
How I contributed to rejecting one of my favorite papers of all time
I believe we should talk about the mistakes we make.
open.substack.com
December 2, 2025 at 1:52 AM
Great read. Too many people assume that the role of theory papers in neuro is to "explain neural data". I'm not even sure we can explain anything yet. Data is more like a muse for theory.
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...