D. Holcman

发表

Over Astroglial Networks: a Step Further in Neuroglial and Gliovascular Interactions

L. Roux, N. Rouach, C. Giaume, 2022 .

Stability Analysis of Second-Order Switched Homogeneous Systems

Michael Margaliot, David Holcman, M. Margaliot, 2002, SIAM J. Control. Optim..

Polymer physics of nuclear organization and function

D. Holcman, A. Amitai, 2016, bioRxiv.

Polymer physics of nuclear organization and function

David Holcman, Assaf Amitai, D. Holcman, 2016, bioRxiv.

Modeling the Early Steps of Cytoplasmic Trafficking in Viral Infection and Gene Delivery

Thibault Lagache, David Holcman, C. Amoruso, 2011, SIAM J. Appl. Math..

Stochastic Model of Acidification, Activation of Hemagglutinin and Escape of Influenza Viruses from an Endosome

T. Lagache, T. Meyer, D. Holcman, 2017, Front. Phys..

Elementary Theory of Stochastic Narrow Escape

Z. Schuss, D. Holcman, 2015 .

Modeling the Early Steps of Viral Infection in Cells

Z. Schuss, D. Holcman, 2015 .

Time scale of diffusion in molecular and cellular biology

David Holcman, Zeev Schuss, Z. Schuss, 2014 .

The narrow escape problem for diffusion in cellular microdomains

Z. Schuss, D. Holcman, A. Singer, 2007, Proceedings of the National Academy of Sciences.

Modeling DNA and Virus Trafficking in the Cell Cytoplasm

D. Holcman, 2007 .

Diffusion escape through a cluster of small absorbing windows

Z. Schuss, D. Holcman, 2008 .

Quantifying intermittent transport in cell cytoplasm.

T. Lagache, D. Holcman, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Quantitative analysis of virus and plasmid trafficking in cells.

T. Lagache, D. Holcman, E. Dauty, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

Narrow escape time to a structured target located on the boundary of a microdomain.

E. Abad, D. Holcman, J. Reingruber, 2009, The Journal of chemical physics.

Extended Narrow Escape with Many Windows for Analyzing Viral Entry into the Cell Nucleus

T. Lagache, D. Holcman, 2016, Journal of Statistical Physics.

Narrow escape to small windows on a small ball modeling the viral entry into the cell nucleus

Thibault Lagache, David Holcman, T. Lagache, 2016 .

Narrow Escape to a structured target and application to viral entry in the nucleus

Thibault Lagache, David Holcman, T. Lagache, 2016 .

Modeling the step of endosomal escape during cell infection by a nonenveloped virus.

Thibault Lagache, David Holcman, Olivier Danos, 2012, Biophysical journal.

Physical principles and models describing intracellular virus particle dynamics.

T. Lagache, D. Holcman, E. Dauty, 2009, Current opinion in microbiology.

Escape Through a Small Opening: Receptor Trafficking in a Synaptic Membrane

Z. Schuss, D. Holcman, 2004 .

Narrow Escape, Part II: The Circular Disk

Z. Schuss, D. Holcman, A. Singer, 2004, math-ph/0412050.

Narrow Escape, Part I

R. Eisenberg, Z. Schuss, D. Holcman, 2004, math-ph/0412048.

Survival probability of diffusion with trapping in cellular neurobiology.

David Holcman, Zeev Schuss, Z. Schuss, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

Narrow Escape, Part III: Non-Smooth Domains and Riemann Surfaces

Z. Schuss, D. Holcman, A. Singer, 2006 .

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Wei Zhang, D. Klenerman, Xiaoyan Ma, 2020, bioRxiv.

Escape from an attractor generated by recurrent exit

D. Holcman, L. Zonca, 2020, 2009.06745.

Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium channels and phospholipids

D. Holcman, P. Parutto, J. Heck, 2019, Scientific Reports.

Transient Confinement of CaV2.1 Ca2+-Channel Splice Variants Shapes Synaptic Short-Term Plasticity

David Holcman, Pierre Parutto, Romy Freund, 2019, Neuron.

Fast calcium transients in dendritic spines driven by extreme statistics

E. Korkotian, N. Rouach, D. Holcman, 2019, PLoS biology.

Do cells sense time by number of divisions?

Z. Schuss, D. Holcman, K. Tor, 2017, Journal of theoretical biology.

Single particle trajectories reveal active Endoplasmic Reticulum luminal flow

Clemens F Kaminski, Marcus Fantham, David Holcman, 2018, Nature Cell Biology.

Poisson-Nernst-Planck equations in a ball

D. Holcman, Z. S. J. Cartailler, 2015, 1505.02173.

Deconvolution of Voltage Sensor Time Series and Electro-diffusion Modeling Reveal the Role of Spine Geometry in Controlling Synaptic Strength

Rafael Yuste, David Holcman, R. Yuste, 2018, Neuron.

Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration

D. Holcman, O. Shukron, M. Hauer, 2017, bioRxiv.

Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration

D. Holcman, Michael H. Hauer, O. Shukron, 2017, bioRxiv.

Statistics of randomly cross-linked polymer models to interpret chromatin conformation capture data.

D. Holcman, O. Shukron, 2017, Physical review. E.

100 years after Smoluchowski: stochastic processes in cell biology

Z. Schuss, D. Holcman, 2016, 1612.08381.

Search for a small egg by spermatozoa in restricted geometries

Z. Schuss, I. Kupka, D. Holcman, 2015, Journal of Mathematical Biology.

Brownian search for targets hidden in cusp-like pockets: Progress and Applications

D. Holcman, C. Guerrier, 2014 .

Oscillatory Survival Probability: Analytical, Numerical Study for oscillatory narrow escape and applications to neural network dynamics

Z. Schuss, D. Holcman, Z. Schuss, 2014 .

Analysis of the Poisson–Nernst–Planck equation in a ball for modeling the Voltage–Current relation in neurobiological microdomains

David Holcman, Zeev Schuss, Z. Schuss, 2017 .

Encounter dynamics of a small target by a polymer diffusing in a confined domain.

D. Holcman, A. Amitai, C. Amoruso, 2013, The Journal of chemical physics.

Hybrid Markov-mass action law model for cell activation by rare binding events: Application to calcium induced vesicular release at neuronal synapses

D. Holcman, C. Guerrier, 2016, Scientific Reports.

Random Search with Switching

Z. Schuss, D. Holcman, 2015 .

Applications to Cellular Biology and Simulations

Z. Schuss, D. Holcman, 2015 .

Markov Models for Stochastic Chemical Reactions

Z. Schuss, D. Holcman, 2015 .

Post-transcriptional regulation in the nucleus and cytoplasm: study of mean time to threshold (MTT) and narrow escape problem

K. Burrage, D. Holcman, H. Byrne, 2014, Journal of Mathematical Biology.

Table of Contents

D. Holcman, 2014, Biological Psychiatry.

Residence times of receptors in dendritic spines analyzed by stochastic simulations in empirical domains.

David Holcman, D. Holcman, N. Hozé, 2014, Biophysical journal.

Narrow Escape in $${\mathbb{R}}^{3}$$

Z. Schuss, D. Holcman, 2013 .

Control of flux by narrow passages and hidden targets in cellular biology

D Holcman, Z Schuss, Z. Schuss, 2013, Reports on progress in physics. Physical Society.

C 20xx Society for Industrial and Applied Mathematics Brownian Motion in Dire Straits *

Z. Schuss, D. Holcman, 2012 .

Stochastic modeling of gene activation and applications to cell regulation.

D. Holcman, G. Malherbe, 2010, Journal of theoretical biology.

Estimating the synaptic current in a multiconductance AMPA receptor model.

D. Holcman, A. Taflia, 2010, Biophysical journal.

Diffusion laws in dendritic spines

David Holcman, Zeev Schuss, Z. Schuss, 2011, Journal of mathematical neuroscience.

The Mean First Rotation Time of a Planar Polymer

David Holcman, Marc Yor, M. Yor, 2011, 1101.1737.

Some questions related to modeling in cellular biology

I. Kupka, D. Holcman, 2010 .

Narrow escape for a stochastically gated Brownian ligand

D. Holcman, J. Reingruber, 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

Quantifying neurite growth mediated by interactions among secretory vesicles, microtubules, and actin networks.

David Holcman, Krasimira Tsaneva-Atanasova, K. Tsaneva-Atanasova, 2009, Biophysical journal.

Diffusion in narrow domains and application to phototransduction.

D. Holcman, J. Reingruber, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Narrow escape and leakage of Brownian particles.

Z. Schuss, D. Holcman, A. Singer, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Estimating the rate constant of cyclic GMP hydrolysis by activated phosphodiesterase in photoreceptors.

D. Holcman, J. Reingruber, 2008, The Journal of chemical physics.

Diffusion through a cluster of small windows and flux regulation in microdomains

Z. Schuss, D. Holcman, 2008 .

Dynamic regulation of spine–dendrite coupling in cultured hippocampal neurons

David Holcman, Eduard Korkotian, Menahem Segal, 2004, The European journal of neuroscience.

0 41 20 89 v 1 2 5 D ec 2 00 4 Stochastic Chemical Reactions in Micro-domains

Z. Schuss, D. Holcman, 2008 .

Modeling synaptic dynamics driven by receptor lateral diffusion.

David Holcman, Antoine Triller, A. Triller, 2006, Biophysical journal.

Dwell time of a Brownian molecule in a microdomain with traps and a small hole on the boundary.

D. Holcman, A. Taflia, 2007, The Journal of chemical physics.

Modeling DNA and Virus Trafficking 1 in the Cell Cytoplasm 1 2

D. Holcman, 2007 .

Computational and mathematical methods for morphogenetic gradient analysis, boundary formation and axonal targeting.

David Holcman, Jürgen Reingruber, D. Holcman, 2014, Seminars in cell & developmental biology.

Narrow Escape: Theory and Applications to Cellular Microdomains

Z. Schuss, D. Holcman, A. Singer, 2006 .

Reconstruction of Surface and Stochastic Dynamics from a Planar Projection of Trajectories

David Holcman, Zeev Schuss, N. Hoze, 2013, SIAM J. Imaging Sci..

Statistical Methods for Large Ensembles of Super-Resolution Stochastic Single Particle Trajectories in Cell Biology

D. Holcman, N. Hozé, 2017 .

Synapse Geometry and Receptor Dynamics Modulate Synaptic Strength

N. Rouach, D. Holcman, U. Pannasch, 2011, PloS one.

Diffusion in a dendritic spine: the role of geometry.

D Holcman, E. Korkotian, A. Biess, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging

S. Manley, E. Hosy, J. Sibarita, 2012, Proceedings of the National Academy of Sciences.

Single Particle Trajectories Reveal Active Endoplasmic Reticulum Luminal Flow

Laurence J Young, C. Kaminski, D. Holcman, 2019, Biophysical Journal.

Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics.

D. Holcman, A. Amitai, O. Shukron, 2019, Trends in genetics : TIG.

The new nanophysiology: regulation of ionic flow in neuronal subcompartments

Rafael Yuste, David Holcman, R. Yuste, 2015, Nature Reviews Neuroscience.

The Narrow Escape Problem in a Flat Cylindrical Microdomain with Application to Diffusion in the Synaptic Cleft

David Holcman, Jürgen Reingruber, D. Holcman, 2011, Multiscale Model. Simul..

Fastest among equals: a novel paradigm in biology: Reply to comments: Redundancy principle and the role of extreme statistics in molecular and cellular biology.

D. Holcman, K. Basnayake, 2019, Physics of life reviews.

Modeling and Stochastic Analysis of the Single Photon Response

D. Holcman, J. Reingruber, 2017 .

The Complexity of Synaptic Transmission Revealed by a Multiscale Analysis Approach From The Molecular to The Cellular Level

D. Holcman, 2012, 1202.2034.

Longitudinal diffusion in retinal rod and cone outer segment cytoplasm: the consequence of cell structure.

D. Holcman, J. I. Korenbrot, 2004, Biophysical journal.

Redundancy principle and the role of extreme statistics in molecular and cellular biology.

Z. Schuss, D. Holcman, K. Basnayake, 2019, Physics of life reviews.

Redundancy principle for optimal random search in biology

Z. Schuss, D. Holcman, K. Basnayake, 2017, bioRxiv.

Calcium dynamics in dendritic spines, modeling and experiments.

D Holcman, M Segal, M. Segal, 2005, Cell calcium.

Detection of single photons by toad and mouse rods

Gordon L. Fain, David Holcman, Alapakkam P. Sampath, 2013, Proceedings of the National Academy of Sciences.

The Limit of Photoreceptor Sensitivity

David Holcman, D. Holcman, J. I. Korenbrot, 2005, The Journal of general physiology.

Connexin 30 sets synaptic strength by controlling astroglial synapse invasion

G. Knott, J. Lübke, Karim Benchenane, 2014, Nature Neuroscience.

Encounter times of chromatin loci influenced by polymer decondensation.

D. Holcman, A. Amitai, 2018, Physical review. E.

A Mechanism for the Polarity Formation of Chemoreceptors at the Growth Cone Membrane for Gradient Amplification during Directional Sensing

David Holcman, Maxime Dahan, Cedric Bouzigues, 2010, PloS one.

Reconstructing a point source from diffusion fluxes to narrow windows in three dimensions

D. Holcman, U. Dobramysl, 2019, Proceedings of the Royal Society A.

Triangulation Sensing to Determine the Gradient Source from Diffusing Particles to Small Cell Receptors.

D. Holcman, U. Dobramysl, 2020, Physical review letters.

SC ] 2 9 O ct 2 01 7 Asymptotics of extreme statistics of escape time in 1 , 2 and 3-dimensional diffusions

Z. Schuss, D. Holcman, K. Basnayake, 2017 .

The dynamics of phosphodiesterase activation in rods and cones.

David Holcman, Jürgen Reingruber, D. Holcman, 2008, Biophysical journal.

The First 100 nm Inside the Pre-synaptic Terminal Where Calcium Diffusion Triggers Vesicular Release

D. Holcman, C. Guerrier, 2018, Front. Synaptic Neurosci..

The first one hundred nanometers inside the pre-synaptic terminal where calcium diffusion triggers vesicular release

D. Holcman, C. Guerrier, David Holcman, 2018, bioRxiv.

The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes

Marcus J. Fantham, Charles N Christensen, C. Holt, 2020, bioRxiv.

The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes

Charles N Christensen, C. Holt, C. Kaminski, 2020, Science advances.

Astroglial networks scale synaptic activity and plasticity

E. Syková, L. Vargova, N. Rouach, 2011, Proceedings of the National Academy of Sciences.

Robust network oscillations during mammalian respiratory rhythm generation driven by synaptic dynamics

J. A. Hayes, G. Fortin, D. Holcman, 2015, Proceedings of the National Academy of Sciences.

Steady-state voltage distribution in three-dimensional cusp-shaped funnels modeled by PNP

D. Holcman, J. Cartailler, 2019, Journal of mathematical biology.

Voltage laws for three-dimensional microdomains with cusp-shaped funnels derived from Poisson-Nernst-Planck equations

D. Holcman, J. Cartailler, 2017, 1710.02423.

NET in Molecular and Cellular Biology

Z. Schuss, D. Holcman, 2015 .

Calcium dynamics in dendritic spines and spine motility.

D Holcman, Z Schuss, E. Korkotian, 2004, Biophysical journal.

Predictive analysis of patient recovery from cardiac-respiratory arrest

D. Holcman, N. Kubis, Aymeric Floyrac, 2019, bioRxiv.

Single particle trajectory statistic to reconstruct chromatin organization and dynamics

D. Holcman, A. Amitai, O. Shukron, 2019, bioRxiv.

Stochastic Narrow Escape in Molecular and Cellular Biology: Analysis and Applications

Z. Schuss, D. Holcman, 2015 .

Extreme Narrow Escape: shortest paths for the first particles to escape through a small window

Z. Schuss, D. Holcman, K. Basnayake, 2018, 1804.10808.

Fast calcium transients in neuronal spines driven by extreme statistics

E. Korkotian, D. Holcman, K. Basnayake, 2018, bioRxiv.

Dissection of a Krox20 positive feedback loop driving cell fate choices in hindbrain patterning

C. Labalette, D. Holcman, J. Reingruber, 2013, Molecular systems biology.

Stochastic coagulation-fragmentation processes with a finite number of particles and applications

D. Holcman, N. Hozé, 2016, The Annals of Applied Probability.

Kinetics of Diffusing Polymer Encounter in Confined Cellular Microdomains

I. Kupka, D. Holcman, A. Amitai, 2013 .

Local decondensation at double-stranded DNA breaks modifies chromatin at long distances and reduces encounter times during homology search

D. Holcman, A. Amitai, O. Shukron, 2018 .

Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories.

S. Gasser, D. Holcman, A. Amitai, 2017, Cell reports.

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

S. Gasser, Vijender Singh, T. Owen-Hughes, 2017, Nature Structural &Molecular Biology.

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

D. Holcman, V. Piras, O. Shukron, 2019, Nature Communications.

Heterogeneous cross-linked polymers to reconstruct chromatin reorganization during cell differentiation

D. Holcman, O. Shukron, 2017, bioRxiv.

Extreme Narrow Escape: Shortest paths for the first particles among n to reach a target window

Z. Schuss, D. Holcman, K. Basnayake, 2018, Physics Letters A.

Dynamics of ion fluxes between neurons, astrocytes and the extracellular space during neurotransmission

N. Rouach, D. Holcman, K. Dao Duc, 2018, bioRxiv.

Exit versus escape a basin of attraction in noisy dynamical systems

D. Holcman, L. Zonca, 2020, 2010.06699.

Alpha rhythm collapse predicts iso-electric suppressions during anesthesia

D. Holcman, P. Parutto, J. Cartailler, 2019, Communications Biology.

Engrailed homeoprotein recruits the adenosine A1 receptor to potentiate ephrin A5 function in retinal growth cones

A. Prochiantz, D. Holcman, R. Joshi, 2012, Development.

Statistical segmentation and correlation analysis of the EEG between the different phases of general anesthesia

D. Holcman, D. Longrois, C. Sun, 2022, medRxiv.

How large should be the redundant numbers of copy to make a rare event probable

D. Holcman, F. Paquin-Lefebvre, Suney Toste, 2022, 2206.12687.

Arrival time for the fastest among $N$ switching stochastic particles

D. Holcman, Suney Toste, 2021, 2112.12760.

Narrow Escape in Other Cellular Processes

Z. Schuss, D. Holcman, 2015 .

Partially Reflected Diffusion

Z. Schuss, D. Holcman, A. Singer, 2006, SIAM J. Appl. Math..

The Length of the Shortest Telomere as the Major Determinant of the Onset of Replicative Senescence

D. Holcman, K. D. Duc, Zhou Xu, 2013, Genetics.

Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP

P. Cicuta, Estelle Crozat, C. Tardin, 2019, Nature Communications.

The survival probability of diffusion with killing

Z. Schuss, D. Holcman, A. Marchewka, 2005, math-ph/0502035.

An active zone state switch concentrates and immobilizes voltage-gated Ca2+ channels to promote long-term plasticity

Alexander M. Walter, D. Holcman, P. Parutto, 2022 .

Mixed analytical-stochastic simulation method for the recovery of a Brownian gradient source from probability fluxes to small windows

David Holcman, Ulrich Dobramysl, D. Holcman, 2017, J. Comput. Phys..

Partially Reflected Diffusion

Z. Schuss, D. Holcman, A. Singer, 2006, SIAM J. Appl. Math..

D ec 2 00 4 NARROW ESCAPE , PART

R. Eisenberg, Z. Schuss, D. Holcman, 2022 .

The WQN algorithm to adaptively correct artifacts in the EEG signal

S. Jaffard, D. Holcman, M. Dora, 2022, Applied and Computational Harmonic Analysis.

Combining transient statistical markers from the EEG signal to predict brain sensitivity to general anesthesia

D. Holcman, Christopher Sun, 2022, Biomed. Signal Process. Control..

High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization

D. Holcman, E. Avezov, P. Parutto, 2022, Cell reports methods.

Brownian needle in dire straits: stochastic motion of a rod in very confined narrow domains.

Z. Schuss, D. Holcman, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

Narrow Escape, Part II: The Circular Disk

Z. Schuss, D. Holcman, A. Singer, 2004, math-ph/0412050.

How large should be the redundant numbers of copy to make a rare event probable

D. Holcman, F. Paquin-Lefebvre, Suney Toste, 2022, 2206.12687.

Nanoscale molecular architecture controls calcium diffusion and ER replenishment in dendritic spines

E. Korkotian, N. Rouach, D. Holcman, 2021, bioRxiv.

On the mass of manifolds with boundary

D. Holcman, 1999 .

Prescribed scalar curvature problem on complete manifolds

D. Holcman, 1999 .

Stochastic chemical reactions in microdomains.

Z. Schuss, D. Holcman, 2004, The Journal of chemical physics.

Dynamic Regulation of Mitochondrial [Ca2+] in Hippocampal Neurons

E. Korkotian, D. Holcman, K. Basnayake, 2022, International journal of molecular sciences.

Computational methods and diffusion theory in triangulation sensing to model neuronal navigation

D. Holcman, U. Dobramysl, 2022, Reports on progress in physics. Physical Society.

Two-dimensional maps to predict the neurological recovery after cardiac arrest

E. Vicaut, D. Holcman, P. Lozeron, 2022, medRxiv.

Concentration of the first eigenfunction for a second order elliptic operator

I. Kupka, D. Holcman, 2005, math-ph/0506059.

NARROW ESCAPE, part III: Riemann surfaces and non-smooth domains

Z. Schuss, D. Holcman, A. Singer, 2004, math-ph/0412051.

Geometrical Effects on Nonlinear Electrodiffusion in Cell Physiology

Z. Schuss, D. Holcman, J. Cartailler, 2017, Journal of Nonlinear Science.

The Limit of Photoreceptor Sensitivity: Molecular Mechanisms of Dark Noise in Retinal Cones

D. Holcman, J. I. Korenbrot, 2005 .

Search for a small egg by spermatozoa in restricted geometries

Z. Schuss, I. Kupka, D. Holcman, 2015, Journal of mathematical biology.

Bursting Reverberation as a Multiscale Neuronal Network Process Driven by Synaptic Depression-Facilitation

M. Segal, N. Rouach, D. Holcman, 2015, PloS one.

Arrival time for the fastest among N switching stochastic particles

D. Holcman, S. Toste, 2021, The European Physical Journal B.

Singular perturbations and first order PDE on manifolds

D. Holcman, I. K. W. I. O. Science, Paris VI University, 2000, math/0006053.

Steady-state voltage distribution in three-dimensional cusp-shaped funnels modeled by PNP

D. Holcman, J. Cartailler, 2019, Journal of Mathematical Biology.

Modeling vesicle trafficking and neurite growth

K. Tsaneva-Atanasova, T. Galli, D. Holcman, 2007 .

Chromatin phase separated nanoregions regulated by cross-linkers and explored by single particle trajectories

D. Holcman, A. Papale, 2022, bioRxiv.

Astroglial gap junctions strengthen hippocampal network activity by sustaining afterhyperpolarization via KCNQ channels

L. Vargova, O. Chever, N. Rouach, 2022, bioRxiv.

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.

Guido Tiana, David Holcman, Edith Heard, 2016, Biophysical journal.

Electro-diffusion modulation of synaptic input in dendritic spines using deconvolved voltage sensor time series

R. Yuste, D. Holcman, T. Kwon, 2016, bioRxiv.

Regulation of ionic flow in neuronal subcompartments : the new nanophysiology

R. Yuste, D. Holcman, 2015 .

Calcium Dynamics in Neuronal Microdomains: Modeling, Stochastic Simulations, and Data Analysis

David Holcman, Claire Guerrier, Eduard Korkotian, 2014, Encyclopedia of Computational Neuroscience.

Data-driven multiscale dynamical framework to control a pandemic evolution with non-pharmaceutical interventions

J. Timsit, D. Holcman, A. Papale, 2023, PloS one.

Monitoring and forecasting the SARS-Covid-19 pandemic in France

J. Timsit, D. Holcman, S. Ruckly, 2021, medRxiv.

Syntaxin1A Lateral Diffusion Reveals Transient and Local SNARE Interactions

N. Ziv, T. Galli, A. Triller, 2011, The Journal of Neuroscience.

The search for a DNA target in the nucleus

D. Holcman, Godefroy Malherbe, 2010 .

Spatial telomere organization and clustering in yeast Saccharomyces cerevisiae nucleus is generated by a random dynamics of aggregation–dissociation

D. Holcman, C. Amoruso, N. Hozé, 2013, Molecular biology of the cell.

A complex CTCF binding code defines TAD boundary structure and function

D. Holcman, A. Papale, A. Leforestier, 2021, bioRxiv.

Post-transcriptional regulation in the nucleus and cytoplasm: study of mean time to threshold (MTT) and narrow escape problem

D. Holcman, K. Dao Duc, K. Burrage, 2014, Journal of Mathematical Biology.

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

D. Holcman, V. Piras, O. Shukron, 2019, Nature Communications.

Adaptive Single-Channel EEG Artifact Removal With Applications to Clinical Monitoring

D. Holcman, M. Dora, 2021, IEEE Transactions on Neural Systems and Rehabilitation Engineering.

Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs

Armin Biess, David Holcman, Eduard Korkotian, 2011, PLoS Comput. Biol..

Using default constraints of the spindle assembly checkpoint to estimate the associated chemical rates

David Holcman, Khanh Dao Duc, D. Holcman, 2012, BMC biophysics.

Coagulation–fragmentation for a finite number of particles and application to telomere clustering in the yeast nucleus

D. Holcman, N. Hozé, 2012, 1201.2620.

Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging

S. Manley, E. Hosy, J. Sibarita, 2012, Proceedings of the National Academy of Sciences.

Telomeric chromosome ends are highly mobile and behave like free double-strand DNA breaks

K. Dubrana, D. Holcman, A. Amitai, 2019, bioRxiv.

Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions

David Holcman, Assaf Amitai, Mathias Toulouze, 2015, PLoS Comput. Biol..

The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels

Jérémie Sibille, Khanh Dao Duc, David Holcman, 2015, PLoS Comput. Biol..

Multiscale models and stochastic simulation methods for computing rare but key binding events in cell biology

David Holcman, Claire Guerrier, D. Holcman, 2017, J. Comput. Phys..

Analysis of bursting dynamics in a modified facilitation-depression model accounting for afterhyperpolarization

D. Holcman, L. Zonca, 2020, 2001.11432.

MULTISCALE MODELING, STOCHASTIC AND ASYMPTOTIC APPROACHES FOR ANALYZING NEURAL NETWORKS BASED ON SYNAPTIC DYNAMICS

David Holcman, D. Holcman, 2014 .

MULTISCALE MODELING AND ASYMPTOTICS APPROACHES FOR ANALYZING NEURAL NETWORK DYNAMICS

D. Holcman, 2014 .

Modeling the Spontaneous Activity of the Auditory Cortex

David Holcman, Evgeniy Bart, Shaowen Bao, 2005, Journal of Computational Neuroscience.

Multiple activities of the MatP protein are involved in post-replicative pairing of sister chromosomes in Escherichia coli

P. Cicuta, Estelle Crozat, C. Tardin, 2019, bioRxiv.

Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data

David Holcman, Ofir Shukron, D. Holcman, 2017, PLoS Comput. Biol..

Structure of Topologically Associating Domains and gene regulation embedded in the 5C data revealed by a polymer model and stochastic simulations

David Holcman, Ofir Shukron, D. Holcman, 2016, bioRxiv.

Kinetics of Diffusing Polymer Encounter in Confined Cellular Microdomains

D. Holcman, A. Amitai, I. Kupka, 2013, Journal of Statistical Physics.

Polymer model with long-range interactions: analysis and applications to the chromatin structure.

D Holcman, D. Holcman, A. Amitai, 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

Computation of the mean first-encounter time between the ends of a polymer chain.

D Holcman, I. Kupka, D. Holcman, 2012, Physical review letters.

Statistical methods for large ensemble of super-resolution stochastic single particle trajectories

David Holcman, Nathanael Hoze, D. Holcman, 2017, bioRxiv.

Diffusing polymers in confined microdomains and estimation of chromosomal territory sizes from chromosome capture data.

D Holcman, D. Holcman, A. Amitai, 2013, Physical review letters.

Analysis of the Mean First Looping Time of a Rod-Polymer

David Holcman, Assaf Amitai, Ivan Kupka, 2012, Multiscale Model. Simul..

Preface: new trends in first-passage methods and applications in the life sciences and engineering

Ralf Metzler, Denis S. Grebenkov, David Holcman, 2020, Journal of Physics A: Mathematical and Theoretical.

The probability of an encounter of two Brownian particles before escape

I. Kupka, D. Holcman, 2009, 0906.3631.

Extended Narrow Escape with Many Windows for Analyzing Viral Entry into the Cell Nucleus

T. Lagache, D. Holcman, David Holcman, 2017 .

The Emergence of Up and Down States in Cortical Networks

Misha Tsodyks, David Holcman, M. Tsodyks, 2006, PLoS Comput. Biol..

Electrostatics of non-neutral biological microdomains

Z. Schuss, D. Holcman, J. Cartailler, 2016, Scientific Reports.

Spectral EEG correlations from the different phases of general anesthesia

D. Holcman, D. Longrois, Christopher Sun, 2023, Frontiers in Medicine.

How rods respond to single photons: Key adaptations of a G‐protein cascade that enable vision at the physical limit of perception

G. Fain, D. Holcman, J. Reingruber, 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

Interactive nanocluster compaction of the ELKS scaffold and Cacophony Ca2+ channels drives sustained active zone potentiation

Alexander M. Walter, D. Holcman, P. Parutto, 2023, Science advances.

Stochastic model of endosomal escape of Influenza virus

T. Lagache, T. Meyer, D. Holcman, 2015, 1510.06382.

Experiments in micro-patterned model membranes support the narrow escape theory

D. Holcman, N. Vogel, S. Fenz, 2023, bioRxiv.

Synaptic dynamics and neuronal network connectivity are reflected in the distribution of times in Up states

Xiaowei Chen, Khanh Dao Duc, David Holcman, 2015, Front. Comput. Neurosci..

Active unidirectional network flow generates a packet molecular transport in cells

D. Holcman, M. Dora, 2018, 1810.07272.

Morphogenetic Gradients and the Stability of Boundaries Between Neighboring Morphogenetic Regions

A. Prochiantz, D. Holcman, V. Kasatkin, 2008, Bulletin of mathematical biology.

Modeling homeoprotein intercellular transfer unveils a parsimonious mechanism for gradient and boundary formation in early brain development.

A. Prochiantz, D. Holcman, V. Kasatkin, 2007, Journal of theoretical biology.

Singular perturbation for the first eigenfunction and blow-up analysis

I. Kupka, D. Holcman, 2004, math-ph/0412088.

SPtsAnalysis: a high-throughput super-resolution single particle trajectory analysis to reconstruct organelle dynamics and membrane re-organization

D. Holcman, E. Avezov, P. Parutto, 2021, bioRxiv.

Asymmetry Between Pre- and Postsynaptic Transient Nanodomains Shapes Neuronal Communication

D. Holcman, M. Heine, 2020, Trends in Neurosciences.

Reconstructing wells from high density regions extracted from super-resolution single particle trajectories

D. Holcman, P. Parutto, J. Heck, 2019, bioRxiv.

Coagulation-Fragmentation with a Finite Number of Particles: Models, Stochastic Analysis, and Applications to Telomere Clustering and Viral Capsid Assembly

D. Holcman, N. Hozé, 2017 .

Commentary: New mathematical physics needed for life sciences

David Holcman, Zeev Schuss, Z. Schuss, 2016 .

Analysis and Interpretation of Superresolution Single-Particle Trajectories.

N Hoze, D Holcman, Z Schuss, 2015, Biophysical journal.

Recovering a stochastic process from super-resolution noisy ensembles of single-particle trajectories.

N Hoze, D Holcman, D. Holcman, 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

Analysis of single particle trajectories: when things go wrong

Z. Schuss, D. Holcman, N. Hoze, 2015, 1502.00286.

Determination of Features from Super-Resolution Data

Z. Schuss, D. Holcman, 2015 .

Potential wells for AMPA receptors organized in ring nanodomains

D. Holcman, N. Hozé, 2013, 1309.3436.

Unraveling novel features hidden in superresolution microscopy data

David Holcman, D. Holcman, 2013, Communicative & integrative biology.

Simultaneous photoactivation and high-speed structural tracking reveal diffusion-dominated motion in the endoplasmic reticulum

Christopher J. Obara, D. Holcman, M. Dora, 2023, bioRxiv.

Active flow network generates molecular transport by packets: case of the endoplasmic reticulum

M. Dora, D. Holcman, D. Holcman, 2020, Proceedings of the Royal Society B.

Dissection of a Krox 20 feedback loop driving cell fate choices in hindbrain patterning

C. Labalette, D. Holcman, J. Reingruber, 2013 .

The Narrow Escape Problem

David Holcman, Zeev Schuss, Z. Schuss, 2014, SIAM Rev..

The boundary between compact and noncompact complete Riemann manifolds

C. Pugh, D. Holcman, D. Holcman, 2005, math/0501414.

Narrow Escape, Part I

R. Eisenberg, Z. Schuss, D. Holcman, 2004, math-ph/0412048.

Correction: Bursting Reverberation as a Multiscale Neuronal Network Process Driven by Synaptic Depression-Facilitation

M. Segal, N. Rouach, D. Holcman, 2015, PloS one.

Semi-classical limits of the first eigenfunction and concentration on the recurrent sets of a dynamical system

I. Kupka, D. Holcman, 2008, 0802.0858.

Emergence and fragmentation of the alpha-band driven by neuronal network dynamics

D. Holcman, L. Zonca, 2021, bioRxiv.

Exit Versus Escape for Stochastic Dynamical Systems and Application to the Computation of the Bursting Time Duration in Neuronal Networks

D. Holcman, L. Zonca, 2022, Journal of Nonlinear Science.

Exit versus escape in a stochastic dynamical system of neuronal networks explains heterogenous bursting intervals.

D. Holcman, L. Zonca, 2020 .

Chemotaxis and topotaxis add vectorially for amoeboid cell migration

D. Holcman, D. Heinrich, J. Wondergem, 2019, bioRxiv.

Dwell time of a Brownian interacting molecule in a cellular microdomain

D. Holcman, A. Taflia, 2006, physics/0609035.

0 41 20 50 v 1 1 5 D ec 2 00 4 NARROW ESCAPE , part II : The circular disk

Z. Schuss, D. Holcman, A. Singer, 2008 .

Narrow escape through a funnel and effective diffusion on a crowded membrane.

Z. Schuss, D. Holcman, N. Hozé, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Modeling bursting in neuronal networks using facilitation-depression and afterhyperpolarization

Lou Zonca, David Holcman, D. Holcman, 2020, Commun. Nonlinear Sci. Numer. Simul..

Predicting neurological outcome after cardiac arrest by combining computational parameters extracted from standard and deviant responses from auditory evoked potentials

E. Vicaut, D. Holcman, P. Lozeron, 2023, Frontiers in Neuroscience.

Narrow Escape in Composite Domains Forming Heterogeneous Networks

D. Holcman, K. Basnayake, F. Paquin-Lefebvre, 2022, SSRN Electronic Journal.

Asymptotics for the fastest among N stochastic particles: role of an extended initial distribution and an additional drift component

David Holcman, Suney Toste, D. Holcman, 2020, Journal of Physics A: Mathematical and Theoretical.

Alpha rhythm collapse predicts iso-electric suppressions during anesthesia

D. Holcman, P. Parutto, J. Cartailler, 2019, Communications Biology.

Synaptic transmission in neurological disorders dissected by a quantitative approach

N. Rouach, D. Holcman, D. Freche, 2012, Communicative & integrative biology.

Brownian Motion in Dire Straits

David Holcman, Zeev Schuss, Z. Schuss, 2012, Multiscale Model. Simul..

Effective Motion of a Virus Trafficking Inside a Biological Cell

Thibault Lagache, David Holcman, T. Lagache, 2007, SIAM J. Appl. Math..

The search kinetics of a target inside the cell nucleus

D. Holcman, G. Malherbe, 2007, 0712.3467.

Modeling Calcium Dynamics in Dendritic Spines

David Holcman, Zeev Schuss, Z. Schuss, 2005, SIAM J. Appl. Math..

Mean time to infection by small diffusing droplets containing SARS-CoV-2 during close social contacts

D. Holcman, C. Sieben, U. Dobramysl, 2021, medRxiv.

Single particle trajectories reveal active endoplasmic reticulum luminal flow

Laurence J Young, Marcus J. Fantham, C. Kaminski, 2018, Nature Cell Biology.

Kinetics of aggregation with a finite number of particles and application to viral capsid assembly

D. Holcman, N. Hozé, 2015, Journal of mathematical biology.

Kinetics of aggregation with a finite number of particles and application to viral capsid assembly

D. Holcman, N. Hozé, 2014, Journal of Mathematical Biology.

Active unidirectional network flow generates molecular transport in packets

D. Holcman, M. Dora, 2021 .

Electrical transient laws in neuronal microdomains based on electro-diffusion.

D. Holcman, J. Cartailler, 2018, Physical chemistry chemical physics : PCCP.

Search Time for a Small Ribbon and Application to Vesicular Release at Neuronal Synapses

David Holcman, Claire Guerrier, D. Holcman, 2015, Multiscale Model. Simul..

Threshold activation for stochastic chemical reactions in microdomains.

D Holcman, D. Holcman, K. Dao Duc, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

Asymptotic Formulas for Extreme Statistics of Escape Times in 1, 2 and 3-Dimensions

Z. Schuss, D. Holcman, K. Basnayake, 2018, Journal of nonlinear science.

Asymptotic Formulas for Extreme Statistics of Escape Times in 1, 2 and 3-Dimensions

David Holcman, Zeev Schuss, K. Basnayake, 2017, J. Nonlinear Sci..

Modeling the voltage distribution in a non-locally but globally electroneutral confined electrolyte medium: applications for nanophysiology

D Holcman, I M Sokolov, A Tricot, 2020, Journal of Mathematical Biology.

Reply to ‘Only negligible deviations from electroneutrality are expected in dendritic spines’

R. Yuste, D. Holcman, 2019, Nature Reviews Neuroscience.

Electrical transient laws in neuronal microdomains based on electro-diffusion

D. Holcman, J. Cartailler, 2018, bioRxiv.

Geometrical Effects on Nonlinear Electrodiffusion in Cell Physiology

David Holcman, Zeev Schuss, J. Cartailler, 2017, J. Nonlinear Sci..

Chromatin memory generated by cohesin-like interaction at looping sites

D. Holcman, A. Papale, 2020, bioRxiv.

High changing curvature regions detect chromatin enrichment in single cell data

D. Holcman, A. Papale, W. Boucher, 2023, bioRxiv.

Chromatin stability generated by stochastic binding and unbinding of cross-linkers at looping sites revealed by Markov models

D. Holcman, A. Papale, 2021, Physical biology.

Gated narrow escape time for molecular signaling.

David Holcman, Jürgen Reingruber, D. Holcman, 2009, Physical review letters.

Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data

D. Holcman, O. Shukron, 2017, PLoS Comput. Biol..

Astroglial networks: a step further in neuroglial and gliovascular interactions

L. Roux, N. Rouach, C. Giaume, 2010, Nature Reviews Neuroscience.

Estimating the rate constant of cyclic GMP hydrolysis by activated phosphodiesterase in photoreceptors.

D. Holcman, J. Reingruber, 2008, The Journal of chemical physics.

Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

D. Klenerman, D. Holcman, C. Schaffitzel, 2023, Nature Structural & Molecular Biology.

Modeling the step of endosomal escape during cell infection by a nonenveloped virus.

T. Lagache, D. Holcman, O. Danos, 2012, Biophysical journal.

David Holcman, Yakar Kannai, Peter Greiner, 2002 .

Nonlinear PDE with vector fields

D. Holcman, 2000 .