David Holcman
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View article: Assessing One-Dimensional Cluster Stability by Extreme-Point Trimming
Assessing One-Dimensional Cluster Stability by Extreme-Point Trimming Open
We develop a probabilistic method for assessing the tail behavior and geometric stability of one-dimensional n i.i.d. samples by tracking how their span contracts when the most extreme points are trimmed. Central to our approach is the dia…
View article: Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms
Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms Open
Topologically associating domains (TADs) are sub-Megabase regions in vertebrate genomes with enriched intradomain interactions that restrict enhancer–promoter contacts across their boundaries. However, the mechanisms that separate TADs rem…
View article: A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation
A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation Open
The chromatin regulator MLL2 (KMT2B) is the primary histone 3 lysine 4 (H3K4) trimethyltransferase acting at bivalent promoters in embryonic stem cells (ESCs) and is required for differentiation toward neuroectoderm. Here, we demonstrate t…
View article: Unveiling the functional connectivity of astrocytic networks with AstroNet, a graph reconstruction algorithm coupled to image processing
Unveiling the functional connectivity of astrocytic networks with AstroNet, a graph reconstruction algorithm coupled to image processing Open
Astrocytes form extensive networks with diverse calcium activity, yet the organization and connectivity of these networks across brain regions remain largely unknown. To address this, we developed AstroNet, a data-driven algorithm that use…
View article: Voltage laws in nanodomains revealed by asymptotics and simulations of electro-diffusion equations
Voltage laws in nanodomains revealed by asymptotics and simulations of electro-diffusion equations Open
Characterizing the local voltage distribution within nanophysiological domains, driven by ionic currents through membrane channels, is crucial for studying cellular activity in modern biophysics, yet it presents significant experimental an…
View article: Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms
Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms Open
Topologically Associating Domains (TADs) are sub-Megabase regions in vertebrate genomes with enriched intra-domain interactions that restrict enhancer-promoter contacts across their boundaries. However, the mechanisms that separate TADs re…
View article: Unraveling Microglial Spatial Organization in the Developing Human Brain with DeepCellMap, a Deep Learning Approach Coupled to Spatial Statistics
Unraveling Microglial Spatial Organization in the Developing Human Brain with DeepCellMap, a Deep Learning Approach Coupled to Spatial Statistics Open
Mapping cellular organization in the developing brain presents significant challenges due to the multidimensional nature of the data, characterized by complex spatial patterns that are difficult to interpret without high-throughput tools. …
View article: Segmentation algorithms and modeling of recurrent bursting events in neuronal and glial time series
Segmentation algorithms and modeling of recurrent bursting events in neuronal and glial time series Open
Long-time series of neuronal recordings are resulting from the activity of connected neuronal networks. Yet how neuronal properties can be extracted remains empirical. We review here the data analysis based on network models to recover phy…
View article: Unveiling the Functional Connectivity of Astrocytic Networks with AstroNet, a Graph Reconstruction Algorithm Coupled to Image Processing
Unveiling the Functional Connectivity of Astrocytic Networks with AstroNet, a Graph Reconstruction Algorithm Coupled to Image Processing Open
Astrocytes form extended intercellular networks, displaying complex calcium activity. However, the specific organization of these astrocytic networks and the precise extent of their functional connectivity in different brain areas remain u…
View article: Voltage mapping in subcellular nanodomains using electro-diffusion modeling
Voltage mapping in subcellular nanodomains using electro-diffusion modeling Open
Voltage distribution in sub-cellular micro-domains such as neuronal synapses, small protrusions, or dendritic spines regulates the opening and closing of ionic channels, energy production, and thus, cellular homeostasis and excitability. Y…
View article: Astroglial gap junctions strengthen hippocampal network activity by sustaining afterhyperpolarization via KCNQ channels
Astroglial gap junctions strengthen hippocampal network activity by sustaining afterhyperpolarization via KCNQ channels Open
Throughout the brain, astrocytes form networks mediated by gap junction channels that promote the activity of neuronal ensembles. Although their inputs on neuronal information processing are well established, how molecular gap junction cha…
View article: EEG signatures at different propofol vs sevoflurane concentrations
EEG signatures at different propofol vs sevoflurane concentrations Open
The depth of anesthesia is contingent upon the concentration of administered hypnotics, but establishing an exact relationship proves challenging, given its variability among individual patients. To elucidate the connection between the dep…
View article: Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories Open
Phase separated domains (PSDs) are ubiquitous in cell biology, representing nanoregions of high molecular concentration. PSDs appear at diverse cellular domains, such as neuronal synapses but also in eukaryotic cell nucleus, limiting the a…
View article: Mean time to infection by small diffusing droplets containing SARS-CoV-2 during close social contacts
Mean time to infection by small diffusing droplets containing SARS-CoV-2 during close social contacts Open
Airborne viruses such as SARS-CoV-2 are partly spread through aerosols containing viral particles. Inhalation of infectious airborne particles can lead to infection, a route that can be even more predominant than droplet or contact transmi…
View article: Single particle algorithms to reveal cellular nanodomain organization
Single particle algorithms to reveal cellular nanodomain organization Open
Formation, maintenance and physiology of high-density protein-enriched organized nanodomains, first observed in electron microscopy images, remains challenging to investigate due to their small sizes. However, these regions regulate molecu…
View article: Mapping general anesthesia states based on electro-encephalogram transition phases
Mapping general anesthesia states based on electro-encephalogram transition phases Open
Cortical electro-encephalography (EEG) served as the clinical reference for monitoring unconsciousness during general anesthesia. The existing EEG-based monitors classified general anesthesia states as underdosed, adequate, or overdosed, l…
View article: Experiments in micro-patterned model membranes support the narrow escape theory
Experiments in micro-patterned model membranes support the narrow escape theory Open
The narrow escape theory (NET) predicts the escape time distribution of Brownian particles confined to a domain with reflecting borders except for one small window. Applications include molecular activation events in cell biology and bioph…
View article: Analyzing photoactivation with diffusion models to study transport in the Endoplasmic Reticulum network
Analyzing photoactivation with diffusion models to study transport in the Endoplasmic Reticulum network Open
Photoactivation is a paradigm consisting in local molecular fluorescent activation by laser illumination in a chosen region (source) while measuring the concentration at a target region. Data-driven modeling is concern with the following q…
View article: Modeling ionic flow between small targets: insights from diffusion and electro-diffusion theory
Modeling ionic flow between small targets: insights from diffusion and electro-diffusion theory Open
The flow of ions through permeable channels causes voltage drop in physiological nanodomains such as synapses, dendrites and dendritic spines, and other protrusions. How the voltage changes around channels in these nanodomains has remained…
View article: Mapping general anesthesia states based on electro-encephalogram transition phases
Mapping general anesthesia states based on electro-encephalogram transition phases Open
Background: Cortical electro-encephalography (EEG) has become the clinical reference for monitoring unconsciousness during general anesthesia. The current EEG-based monitors classify general anesthesia states simply as underdosed, adequate…
View article: Mapping general anesthesia states based on electro-encephalogram transition phases
Mapping general anesthesia states based on electro-encephalogram transition phases Open
Background: Cortical electro-encephalography (EEG) has become the clinical reference for monitoring unconsciousness during general anesthesia. The current EEG-based monitors classify general anesthesia states simply as underdosed, adequate…
View article: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD
Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD Open
To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer–promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensi…
View article: Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries
Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries Open
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of…
View article: The WQN algorithm for EEG artifact removal in the absence of scale invariance
The WQN algorithm for EEG artifact removal in the absence of scale invariance Open
Electroencephalogram (EEG) signals reflect brain activity across different brain states, characterized by distinct frequency distributions. Through multifractal analysis tools, we investigate the scaling behaviour of different classes of E…
View article: Mapping general anesthesia states based on electro-encephalogram transition phases
Mapping general anesthesia states based on electro-encephalogram transition phases Open
Cortical electro-encephalography (EEG) has become the clinical reference for monitoring unconsciousness during general anesthesia. The current EEG-based monitors classify general anesthesia states simply as underdosed, adequate, or overdos…
View article: Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" Open
3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03…
View article: Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" Open
3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03…