David Holcman

The paper develops a diffusion-reaction model to analyze how vesicular acidification modulates AMPA receptor function and synaptic current.

The paper shows synaptic input triggers on-demand mitochondrial ATP production and delivery in spines with a spine apparatus, optimized by geometry and calcium signaling.

The paper identifies specialized astrocyte subtypes in the VLPO, including long-projection astrocytes with hominid-like morphology, revealing enhanced glial network integration in a sleep-promoting nucleus.

This paper uses in vivo recordings and a neural mass model to show how thalamocortical excitatory-inhibitory dynamics generate α-wave patterns during anesthesia, linking EEG oscillations to network dynamics.

The paper tracks SOX2 and NANOG dynamics in live cells using advanced microscopy and analysis pipelines, revealing differences in their spatiotemporal behavior due to protein-protein interactions.

The paper reconstructs functional connectivity in the mouse motor cortex using 3D two-photon calcium imaging and identifies column-like subnetworks with specific connectivity patterns and information flow.

The paper investigates how TAD boundary width influences insulation between adjacent TADs, showing that wider boundaries reduce inter-TAD contacts and enhance insulation.

This study shows MLL2 stabilizes 3D chromatin loops during pluripotent cell differentiation without requiring its enzymatic activity.

The paper introduces DeepCellMap, a deep learning tool for analyzing spatial cellular organization in developing brains, revealing microglial phenotypes and spatial clustering patterns.

The paper introduces AstroNet, a graph reconstruction algorithm that maps functional connectivity in astrocytic networks using two-photon calcium imaging, revealing region-specific connectivity patterns in the hippocampus and motor cortex.

The paper shows astroglial gap junctions enhance hippocampal network activity by maintaining afterhyperpolarization through KCNQ channels, independent of glutamate or metabolic factors.

The paper develops an algorithm to predict general anesthesia overdose by analyzing EEG transition phases in mice, identifying key patterns that anticipate overdose several minutes in advance.

The paper reveals that CTCF binding at TAD boundaries is modular and clustered, challenging existing models of loop extrusion blocking and highlighting a complex code for TAD structure and function.

This study identifies high changing curvature (HCC) regions in Hi-C data that correlate with gene expression and CTCF density, showing cell-to-cell variability.

The paper studies how cross-linkers generate chromatin phase separated nanoregions and quantifies their impact on molecular access using single particle trajectories.

The paper models neuronal network dynamics to show how alpha-band oscillations emerge and fragment through interactions between excitatory and inhibitory networks with synaptic plasticity and noise.

The paper shows dendritic spines refill ER calcium stores through controlled calcium entry without depletion, using computational modeling and imaging.

The paper uses Markov models to analyze how chromatin loops remain stable through stochastic binding and unbinding of cross-linkers, showing that a positive feedback mechanism ensures loop stability.

The paper develops a polymer model to analyze chromatin organization changes during differentiation, finding synchronous compaction/decompaction of TADs and secondary structures in 5C data.

The paper predicts patient recovery from cardiac-respiratory arrest using EEG-based features from auditory responses to determine consciousness outcomes.

The paper discusses statistical methods to reconstruct chromatin organization and dynamics from single particle trajectories of loci under cellular stress.

The paper shows that local chromatin decondensation at DNA breaks reduces encounter times for homologous sequences during repair.

The paper reviews a tri-compartment model of potassium dynamics between neurons, astrocytes, and the extracellular space, showing how astrocytes buffer potassium and how channel disruptions affect neuronal activity.

The paper derives novel electro-diffusion laws for neuronal microdomains, showing deviations from Ohm's law and the impact of narrow passages on electrical conduction.

The paper models how dendritic spine geometry modulates voltage from synaptic current using electro-diffusion theory and deconvolved voltage sensor data.

The paper uses a polymer model and stochastic simulations to analyze 5C data and reveal how TAD structure influences gene regulation through encounter probabilities and chromatin dynamics.