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List of publications

Publication summary :
Publication summary :
- 3 non-peer reviewed publications (ArXiv)
- 25 submitted or written manuscripts
- 31 meeting reports (>2007).
- 198 peer reviewed : 155 research publications. 15 reviews. 29 chapters/comments/
- 3 books published by Springer.
- 2 Patents
- 2 books in preparation.

Field covered : Data modeling, Biophysics, Diffusion, Stochastic Processes, Simulations of Cellular Processes, Multiscale Modeling, Predictive Medicine.
- Passage time analysis, Narrow Escape Theory, Statistical Biophysics, Extreme Statistics, Computational Biology and Neurobiology, Electro-diffusion Theory, Phototransduction, Sub-cellular trafficking, trafficking in endoplasmic reticulum, diffusion on graphs
- statistics of single particle trajectories, potential well theory in cell biology
- Voltage dye deconvolution, Burst-synchronization, Up-Down state dynamics, neuronal networks, statistical medicine, EEG classification, anesthesia, predictive methods for coma, Integrative Cellular and Molecular Biology,
- Applied Mathematics, Asymptotic of Partial Differential Equations, Mathematical Neuroscience, conformal mapping. Nonlinear PDEs.
- Synaptic transmission, neuron-glia interaction, calcium signaling, organelle interaction.
- Physical biology, physical virology, modeling early step of influenza and AAV infection.
- Morphogenetic gradients, theory of neuron migration, triangulation of a source from diffusing fluxes,
- Nucleus organization, polymer models in genetics, chromatin reconstruction, HiC data analysis. Transcription factor search time, DNA breaks. Analysis of single trajectories, theory of remodelers.


1-. Floyrac, A. Doumergue, N. Kubis, D. Holcman, Outil prédictif de la sortie du coma des patients après arrêt cardio-respiratoire, 62/55/133PSL.
2-. J. Cartailler, P. Parutto, D. Holcman, Outil de prediction de Burst suppresion a partir des onde alpha de l’EEG, PSL.

List of publications

Published in ArXiv only.

3- D. Holcman N.Hoze, Z. Schuss, Analysis of single particle trajectories : when things go wrong, arXiv:1502.00286, 2015.
2- N.Hoze, D. Holcman, Potential wells for AMPA receptors organized in ring nanodomains, ArXiv q-bio > arXiv:1309.3436
1- D. Holcman, The Complexity of Synaptic Transmission Revealed by a Multiscale Analysis Approach From The Molecular to The Cellular Level, Correspondence, Quantitative Biology, arXiv:1202.2034v1, 2012

Books and Monographs
1- D. Holcman Z. Schuss Stochastic Narrow Escape in Molecular and Cellular Biology, Monographs, Springer 260 p 2015.

2- D. Holcman, Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology (Springer), 2017.

3- D. Holcman, Z. Schuss, Asymptotics of Elliptic and Parabolic PDEs and their Applications in Statistical Physics, Computational Neuroscience, and Biophysics, Applied mathematics Series, Springer, 2018.

Book chapters and Commentaries, View points, Opinions
28- I. Sokolov, D. Holcman, Editors of a special series about extreme statistics in biology, Euro. Phys B 2020.
27- J Cartailler, J Reingruber, D. Holcman, Théorie du petit trou et ses applications en biologie—>archives-ouverte
26- D. Holcman, Qu’est-ce qui définit les temps courts et longs en biologie : une histoire de forme, de mouvement et de petits trous Archives-ouvertes
25-DS Grebenkov, D Holcman, R Metzler, Preface : new trends in first-passage methods and applications in the life sciences and engineering - Journal of Physics A : Mathematical and Theoretical, 2020
24- D. Holcman, Paris - Optimiser le transport des hommes et des marchandises, un bien-être pour tous,, Mediapart 2019
23-J. Cartailler D. Holcman, Electro-diffusion approach to map the voltage distribution in dendritic spines at a nanometer scale Neuron, comment 2019.
22- D. Holcman, Et si une recherche justement financée permettait de payer moins d’impôts ? Mediapart 2019,
21-D. Holcman R.Yuste, Reply to ‘Only negligible deviations from electroneutrality are expected in dendritic spines’, Nature Review Neuroscience, 2019.
20-K. Basnayake D. Holcman, Fastest among equals : a novel paradigm in biology Reply to comments : Redundancy principle and the role of extreme statistics in molecular and cellular biology, Physics of Life Reviews 2019.
19- D. Holcman, Big data et cerveau : la neurobiologie computationnelle, De nouveaux outils de modélisation pour la neurobiologie, 2018
18-A. Amitai D. Holcman, Methods for analyzing single particle trajectories in the nucleus, 2018.
17- C. Guerrier, D. Holcman, Calcium dynamics in nanodomains to trigger vesicular release at neuronal synapses revealed by computational modeling, Frontiers in Neuroscience, 2018.
16-A. Amitai D. Holcman,Analysis of Chromatin Dynamics and Search Processes in the Nucleus, in Modeling the 3D Conformation of Genomes, 177, 2019.
15-D. Holcman, Comment l’économie High Tech peut émerger sans refondre le système universitaire, mediapart 2018
14- J. Reingruber, and D. Holcman. "Modeling and Stochastic Analysis of the Single Photon Response. Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology. Springer, Cham, 2017. 315-348.

PDF - 2 Mo

13- N. Hoze D. Holcman, Coagulation-fragmentation with a finite number of particles : models, stochastic analysis and applications to telomere clustering and viral capsid assembly, review chapter, Springer 2017.

PDF - 3.1 Mo

12- D. Holcman,La nouvelle physique mathématique en biologie, Gazette des Mathematiques(in French) n°147, Janvier 2016.
11- D. Holcman Z. Schuss, New mathematics and physics in life sciences and medicine, Physics Today 69 (1), 10 (2016).
10- N. Rouach, D Holcman, Modeling neuron-glia interactions (invited chapter) Springer.
9- K. Reynaud, Z Schuss, N Rouach, D Holcman, Why so many sperm cells ? Communicative & Integrative Biology:3, e1017156 ; 2015.
8- D. Holcman R. Yuste, The new nanophysiology : Towards nanophysiology : Regulation of ionic flow in neuronal subcompartments, Nature Reviews Neuroscience 16 (11), 685-692, 2015.

PDF - 3.4 Mo

7- D. Holcman, Multiscale modeling, stochastic and asymptotic approaches for analyzing neural networks based on synaptic dynamics, ESAIM : Proceedings and Surveys 47, 36-54 2015.
6- D. Holcman, Review on the book ”Nonlinear Filtering and Optimal phase tracking” by Zeev Schuss, SIAM Review 56 (2014), no. 2, 213–257.
5- D. Holcman, Unraveling novel features hidden in superresolution microscopy data, Perspective, Communicative & Integrative Biology, 1 ;6(3):e23893. 2013
4- C. Guerrier, E. Korkotian, D. Holcman Calcium dynamics in Microdomains : From mathematical modeling to data analysis, Encyclopedia Computational Neurobiology, Springer 2014, pp 1-37
3-D. Holcman I. Kupka, Some open questions in computational biology ; J. Fixed Point Theory Appl, contribution in the Honor of S. Smale (2010), 7 : 1 p.67-83.
2- D. Holcman, C’était mon patron, (in French) Gazette des Mathématiciens, 121, 2009
1-D. Holcman, Computational challenges in synaptic transmission, AMS Contemporary Mathematics (CONM) book series : Proceedings of the Conference on Imaging Microstructures : Mathematical and Computational Challenges, Contemporary Mathematics, 494, p:1-26 (2009).


16-U. Dobrasmyl, D. Holcman, Computational methods and emerging principles for triangulation sensing, Submitted 2020 ArXiv
15-M. Heine, D. Holcman, Nature and role of transient nanodomains in neurons underlying communication and network dynamics, Trends in Neuroscience, 2020.

PDF - 2.4 Mo

14-O. Shukron, A. Amitai, A Seeber, D. Holcman,Advances in SPTs of single locus for chromatin reconstruction, Trends in Genetics, 2019.

PDF - 5.5 Mo

13- Z. Schuss, K.Basnayake, D. Holcman,Redundancy principle for optimal random search in biology Physics of Live Science Review, 2019.
12- N Rouach, KD Duc, J Sibille, D. Holcman, ionic fluxes regulated neurons and astrocytes.Dynamics of ion fluxes between neurons, astrocytes and the extracellular space during neurotransmission, Opera Medica et Physiologica 4 (1), 1-18, 2018.PDF
11- D. Holcman Z. Schuss, 100 years after Smoluchowski : stochastic processes in cell biology, J. Phys. A (2016).

PDF - 3 Mo

10- D. Holcman N.Hoze, Statistical methods of short super-resolution stochastic single trajectories analysis, Annual Review of Statistics and Its Application, 4, 1-35 (2017).
9- D. Holcman N.Hoze, Z. Schuss, Analysis and Interpretation of Superresolution Single-Particle Trajectories, Biophysical Journal, 109 (9), 1761-1771 (2015).
8-J. Reingruber, D. Holcman G. Fain, Optimal interplay geometry-biochemistry in single photoresponse, Bioessays 37 (11), 1243-1252, (2015).
7-A. Amitai D. Holcman, Polymer physics of Single particle trajectories in the nucleus organization, Physics Report, 678, 1–83 (2017).
6-J. Reingruber D. Holcman, Computational and mathematical methods for morphogenetic gradient analysis, boundary formation and axonal targeting, Seminars in cell & developmental biology 35, 189-202 (2014).
5- D. Holcman Z. Schuss, the Narrow Escape Problem, SIAM Rev 56 no. 2, 213–257 2014.
4- Z. Schuss D. Holcman, Time scales of Diffusion for Molecular and Cellular processes, J.Phys A : Mathematical and Theoretical 47 (17), 173001 (2014).
3-D. Holcman Z. Schuss, Control of flux by narrow passages and hidden targets in cellular biology, Reports on Progress in Physics 76 (7):074601. (2013).
2- C. Giaume, A. Koulakoff, L. Roux, D. Holcman and N. Rouach, Astroglial connexin-mediated networks:a step further in neuroglial interactions, Nat Rev Neuroscience, 2010 ; 11(2):87-99.
1- T. Lagache, E. Dauty, D. Holcman, Physical principles and models describing intracellular virus particle dynamics, Current Opinion in Microbiology ;12(4):439-45 (2009).

Publications published or in press

155 L. Zonca D. Holcman, Noise-induced shift of the equilibrium and recurrent exit patterns in two-dimensional dynamical systems, (submitted) 2020.
154 L. Zonca D. Holcman, Modeling bursting in neuronal networks using facilitation-depression and afterhyperpolarization, (to appear) Communications in Nonlinear Science and Numerical Simulation 2020.
153-Basnayake, D. Mazaud N. Rouach, E. Korkotian D. Holcman. Nanometric organization and flux entries controls diffusing calcium safe replenishment in the endoplasmic reticulum of dendritic spines, submitted 2020.
152- J Reingruber, A Papale, D Holcman, Monitoring and predicting SARS-CoV-2 epidemic in France after deconfinement using a multiscale age-dependent rate model, medrxiv 2020,
151-A. Papale D. Holcman. Chromatin memory generated by cohesin-like interaction at looping sites, BioRxiv, 2020.
150- A Tricot, IM Sokolov, D Holcman, Voltage distribution in a non-locally but globally electroneutral confined electrolyte medium : applications for nanophysiology, arXiv preprint arXiv:2003.11147
149- L. Meng et al, The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes, Sc. Adv 2020 (to appear).
148-K Basnayake, D Holcman, Extreme escape from a cusp : When does geometry matter for the fastest Brownian particles moving in crowded cellular environments ?
The Journal of Chemical Physics 152 (13), 134104
147- L. Zonca D. Holcman, Analysis of bursting dynamics in a modified
facilitation-depression model accounting for

146-U. Dobramysl D. Holcman, Hybrid simulation in three simulation for the external narrow escape problem, ArXiv and submitted.
145-U. Dobramysl D. Holcman, Triangulation sensing, PRL 2020.
144- E. Crozat, C. Tardin, M. Salhi, P. Rousseau, A. Lablaine, T. Bertoni, D. Holcman, B. Sclavi, P. Cicuta, F. Cornet, Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP, Nat Comm, 2019. BioRxiv
143- A. Floryac, A. Doumergue N. Kubis, D. Holcman, Predictive analysis of exit from anoxic coma, . BioRxiv
142- A. Wondergem, F de Wit, T Reuvers, D Holcman, D. Heinrich,Controlling amoeboid migration by combining topotactic and chemotactic cues (submitted, BioRxiv).
141- A. Amitai, O. Shukron, A. Seeber, D. Holcman, Consequences of chromatin interaction removal and local reorganization during homologous search in the cell nucleus (submitted). BioRxiv
140-P. Parutto, M. Lu, c. Kaminski, M. Heine, E. Avezov. D. Holcman, Statistical methods to study organelle with super-resolution molecular trajectories (submitted).
139- M. Toulouze, A.Amitai, O. Shukron, D. Holcman*, K. Dubrana*, Heterogeneous organization of the chromatin revealed in the analysis of SPTs (submitted). *equal cont. BioRxiv
138- M. Dora, D. Holcman, Active unidirectional network flow generates molecular transport in packets, Roc Soc B, 2020. ArXiv

137- J. Cartailler, P. Parutto, C. Touchard, F. Vallee, D. Holcman, Predictive analysis of general anesthesia from Alpha rhythm during the phase of induction, 2:327.Comm Biology 2019.
136-P. Parutto,J. Hecke M. Heine D. Holcman, Reconstructing potential wells of high density regions from super-resolution single particle trajectories, Scientific Report 2019.
135-Basnayake, K., Mazaud, D., Bemelmans, A., Rouach, N., Korkotian, E., & Holcman, D. (2019).Fast calcium transients in dendritic spines driven by extreme statistics. PLoS biology, 17(6), e2006202.
134-P. J. Heck, P. Parutto, A. Ciuraszkiewicz, A. Bikbaev, R. Freund, M. Alonso, A.
Fejtova, D. Holcman*, M. Heine*, Dynamic calcium channel nanodomains contribute to variability of transmitter release, Neuron 2019 ;103(1):66-79.e12. doi : 10.1016/j.neuron.2019.04.030.
133- J. Cartailler and D. Holcman, Asymptotic of the Poisson-Nernst-Planck equations in three-dimensional microdomains with cusp-shaped funnels, J. Math Bio, 2019 ;79(1):155-185.2019
132-Shukron, O., Piras, V., Noordermeer, D., & Holcman, D. (2019). Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers. Nature communications, 10(1), 2626.

131-K.Basnayake, Z. Schuss D. Holcman, Extreme Narrow Escape : Shortest paths for the first particles among n to reach a target window. Physics Letters A 382 (48), 3449-3454 LINK-ARXIV
130-J. Cartailler D. Holcman, Electrical transient laws in neuronal microdomains based on electro-diffusion, Physical Chemistry Chemical Physics (revision) 2018. DOI : 10.1039/C8CP02593B
129-K.Basnayake, Z. Schuss D. Holcman, Asymptotic Formulas for Extreme Statistics of Escape Times in 1, 2 and 3-Dimensions. Journal of Nonlinear Science (2018) PDF or LINKARXIV
128-K. Tor, Z. Schuss D. Holcman, MFPT for the telomere length, J. The Biology. doi : 10.1016/j.jtbi.2018.05.001. Epub 2018 May 9. LINKARXIV
127- D. Holcman*c, P. Parutto*, J Chambers, L Young, S. Marciniak, C. Kaminski, D. Ron, E. Avezov* c, Single particle trajectories reveal active endoplasmic reticulum luminal flow, Nature Cell Biology 2018. c=corresponding
126-U. Dobramysl D. Holcman, Reconstructing the gradient source position from stochastic fluxes to small receptors, Scientific Report 355:22-36.
125- A. Amitai, D. Holcman, Encounter time of two chromatin loci is governed by polymer de-condensation and modification of local interactions, Phys. Rev.E ;97(3-1):032417. 2018. doi : 10.1103/PhysRevE.97.032417.
124-J. Cartailler T.Know, R. Yuste D. Holcman, Deconvolution of voltage sensor time series and electro-diffusion modeling of synaptic input in dendritic spines, Neuron, 2018 ;97(5):1126-1136 2018


123-U. Dobramysl D. Holcman, Exterior Narrow escape in two dimensions for reconstructing the source position from stochastic fluxes, J of Computational Physics, 2017
122-O. Shukron M. Hauer, D. Holcman, Two loci single particle trajectories analysis : constructing a first passage time statistics of local chromatin exploration, Scientific Reports, 2017
121- A. Amitai, A. Seeber, S. M. Gasser D. Holcman,Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories Cell Report 18(5):1200-1214 2017
120- M. Hauer A. Seeber R.Thierry A Amitai, J Eglinger D. Holcman T. Owen-Hughes S. Gasser, Histone degradation in response to DNA damage triggers general chromatin decompaction, Nat Struct. Bio, 24(2):99-107. 2017
119- O. Shukron D. Holcman, Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data, PLoS Comput Biol 13 (4), e1005469 2017
118-J. Cartailler, Z. Schuss and D. Holcman, Geometrical Effects on Nonlinear Electrodiffusion in Cell Physiology, 2017 Journal of Nonlinear Science, 1-30 2017
117- J. Cartailler, Z. Schuss and D. Holcman, Electrostatics of non-neutral biological microdomains, Scientific Report, 2017
116- C. Guerrier, D. Holcman, Multiscale models and stochastic simulation methods for computing rare but key binding events in cell biology, J. Computational Physics 340, 617-638 2017
115- N.Hoze, D. Holcman, Stochastic coagulation-fragmentation processes with a finite number of particles and applications, Ann. Applied Probability, 2017 doi:10.1214/17-AAP1334.
114-O. Shukron D. Holcman, Statistics of randomly cross-linked polymer models to interpret chromatin conformation capture data, Physical Review E 96, 012503 (2017)
113- T. Lagache C.Sieben. T Meyer, A. Herrmann D.Holcman,Stochastic Model of Acidification, Activation of Hemagglutinin and Escape of Influenza Viruses from an Endosome, Frontiers in Physics, 5, 25,2017

112- Lagache, T. D. Holcman, Narrow Escape to a composed target and application to viral entry in the nucleus, J.Stat. Physics, 166, 2, pp 244–266 2016.
111- G Tiana, A Amitai, T Pollex, T Piolot, D Holcman, E Heard, L Giorgetti, Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains, Biophys. Journal 110 (6), 1234-1245.
110- C. Guerrier, D. Holcman, Hybrid Markov-Poissonian model and simulations. Application to calcium dynamics for vesicular release at neuronal synapses, Sci Rep. 2016 ; 6 : 35506. 201
109-K. Dao duc, Z. Schuss D. Holcman, Oscillatory peaks for the escape of a stochastic process across a characteristic boundary, Multiscale Model. Simul., 14(2), 772–798. 201
108-J. Cartailler Z. Schuss D. Holcman, Electrical properties of dendritic spines, Physica D : Nonlinear Phenomena 2016. PDF


107-J. Yang I. Kupka. Z. Schuss D. Holcman, Spermatozoa motion and search for a small egg target in uterus, J. Math Bio. 2015 PDF
106- N.Hoze D. Holcman, Stochastic analysis and extracting features from superresolution data, Physical Review E 92 (5), 052109. 2015 PDF
105- A. Amitai, M Toulouze K. Dubrana D. Holcman, Analysis of single locus trajectories for extracting in vivo chromatin tethering interactions, PLoS Comput Biol 11 (8), e1004433 2015.
104- K. Dao Duc, P. Parutto, X. Chen, J. Epzstein, A Konnerth D. Holcman, Synaptic dynamics and neuronal network connectivity are reflected in the distribution of times in Up states, Frontiers Comp. Neuroscience doi : 10.3389/fncom.2015.00096. eCollection 2015.
103- C. Guerrier D. Holcman, Search time for a small ribbon and application to vesicular release at neuronal synapses, SIAM Multiscale Modeling and Simulations 2015.
102- C. Guerrier, J. Hayes, G. Fortin, D. Holcman, Robust network oscillations during mammalian respiratory rhythm generation driven by synaptic dynamics, PNAS, 112(31):9728-33, 2015.
101- K. Dao Duc, D. Cohen M. Segal, N. Rouach D. Holcman, Facilitation-depression synapses underlie neuronal network reverberation, PLoS One ; 10(5):e0124694. 2015 PDF
100- K. Dao Duc*, J Sibille*, D. Holcman*, N. Rouach*, Potassium regulation through the Kir4.1 channel in astrocyte, consequence for the neural activity PloS Computational Biology ;11(3):e1004137. 2015 * : equally.


99- C Guerrier, D Holcman, Brownian search for targets hidden in cusp-like pockets : Progress and Applications, The European Physical Journal, Special Topics 223 (14), 3273-3285 2014. PDF
98- N.Hoze, D. Holcman, Numerical simulations in empirical domains and residence time of receptors in dendritic spines, Biophysical Journal 107 (12), 2999-3008 2014.
97- N.Hoze, D. Holcman, Kinetics of aggregation with a finite number of particles and application to viral capsid assembly, J. Math Bio., 2014.
96-K. Dao duc, Z. Schuss D. Holcman, Oscillatory decay of the survival probability of activated diffusion across a limit cycle, Phys. Rev E ;89(3):030101. 2014
95- Z. Schuss D. Holcman, Oscillatory survival probability and eigenvalues of non-self adjoint elliptic operators, Multiscale Modeling and Simulations. 12(3), 1294–1308. (2014). PDF
94-U Pannasch, D Fresche, G Knott, P Ezan, K Benchenane, C Escartin, V Abudara, D Holcman, N Rouach, Connexin 30 controls synaptic strength through astroglial synapse invasion, Nat Neuroscience ;17(4):549-58. 2014.
93- D. Holcman K. Dao Duc, E. Byrne A. Jones K. Burrage, Successful delivery of PTEN in the cytoplasm escaping from micro RNA degradation. J. Math Bio., 2014 10.1007/s00285-014-0782-y


92- N.Hoze, D. Holcman, Aggregation with a finite number of particles for viral capsid assembly. Phys. Let. A 2013
91-A. Amitai, D. Holcman, Polymer model with long-range interactions : Analysis and applications to the chromatin structure, Phys. Rev E. 2013
90- A. Amitai, I. Kupka D. Holcman, Kinetics of diffusing polymer encounter in confined cellular microdomains, J. Stat. Phys. 2013
89- Dao Duc, D. Holcman, Computing the length of the shortest telomere across cell division, Phys. Rev Lett. 2013
88-J. Reingruber J. Pahlberg M. Woodroof A. Sampath G. Fain D. Holcman, Detection of of a single photon response in mouse and toad rods, PNAS 110(48):19378-83 doi:10.1073/pnas.1314030110 2013
87- N. Hoze Z. Schuss D. Holcman, Reconstruction of surface and stochastic dynamics from a planar projection of trajectories, SIAM Journal on Imaging Sciences 2013
86-Bouchoucha*, Y Reingruber*, J. Le Men, J Gilardi-Hebenstreit*, P, D. Holcman* Charnay*, P Dissection of a Krox20 positive feedback loop driving cell fate choices in hindbrain patterning. Mol Syst Biol. 2013 ;9:690 * : equally. 2013
85- Z. Xu, K. Dao Duc, D. Holcman, T. Teixeira, The length of the shortest telomere as the major determinant of the onset of replicative senescence (2013) Genetics
84-A. Amitai, D. Holcman, Diffusing polymers in confined microdomains and estimation of chromosomal territory sizes from chromosome capture data, Phys. Rev. Lett. 110, 248105 (2013)
83-N.Hoze, C. Amuroso, M. Ruault, A Taddei, D. Holcman, Dynamics of telomere clustering in the nucleus, Molecular Biology of the Cell, 24(11):1791-800 (2013)


83-A. Amitai, C. Amuroso, A. Ziskind, D. Holcman, Encounter dynamics of a small target by a polymer diffusing in a confined domain, J.Chem. Phys. 137, 244906 (2012)
82- N.Hoze, N. Deepak, E. Hosy, C. Sieben, S. Manley, A. Herrmann, JB Sibarita, D. Choquet, D. Holcman, Stochastic analysis of receptor trajectories from superresolution data, PNAS 2012
81- A. Amitai, I. Kupka D. Holcman, Computation of the Mean First-Encounter Time Between the Ends of a Polymer Chain, PRL 109, 108302, 2012
80-D. Fresche, C.Y. Lee N. Rouach, D. Holcman, Synaptic transmission in neurological disorders dissected by a quantitative approach, 5:5, 1-5 ; Communicative & Integrative Biology (2012)
79-D. Holcman Z. Schuss, Control of flux by narrow passages and hidden targets in cellular biology, Reports on Progress in Physics 76 (7) : 074601
78-Z. Schuss D. Holcman, Brownian Motion in Dire Straits, SIAM Multicale Modeling and simulations 10(4), 1204–1231, 2012
77-N. Hoze A., D. Holcman, Coagulation–fragmentation for a finite number of particles and application to telomere clustering in the yeast nucleus, Physics Letters A,376, 6–7, 845–849, 2012
76- K. Dao Duc, D. Holcman, Using default constraints of the spindle assembly checkpoint to estimate the associated chemical rates, BMC Biophysics ;5(1):1. 2012
75- T. Lagache, O. Danos , D. Holcman, Modeling the Step of Endosomal Escape during Cell Infection by a Nonenveloped Virus Biophysical J. 102(5):980-9. 2012
74- D. Holcman Z. Schuss, A Brownian needle in dire straits, Phys. Rev. E-Short Comm 85, 010103 (2012) .
73-O Stettler, RL. Joshi, A.Wizenmann, J. Reingruber, D. Holcman, C.Bouillot, F. Castagner, A. Prochiantz, and KL. Moya, Engrailed homeoprotein recruits the adenosine A1 receptor to potentiate Ephrin A5 function in retinal growth cones, Development ;139(1):215-24. (2012)
72- A. Amitai I. Kupka D. Holcman, Analysis of the Mean First Looping Time of a Rod-Polymer. Multiscale Model. Simul. 10-2, pp. 612-632 (2012)


71-D. Holcman Z. Schuss, Diffusion laws in dendritic spines, J. Math. Neuroscience 1:10 2011, doi:10.1186/2190-8567-1-10
70-C. Ribrault, J. Reingruber, N. E. Ziv, D. Holcman, A.Triller, Syntaxin1A diffusion
reveals transient and local SNARE interactions, J. Neuroscience 31(48):17590-17602. 2011
69-A. Biess, E.Korkotian D. Holcman, Barriers to diffusion in dendrites and estimation of calcium spread following synaptic inputs PloS Computational Biology 7(10), e1002182 2011
68- D. Holcman N. Hoze Z. Schuss, Narrow escape through a funnel and effective diffusion on a crowded neuronal membrane, Physical Review E, 84, 021906 (2011).
67- J. Reingruber D. Holcman, Transcription factor search for a DNA promoter in a three-state model Physical Review E, 84, 2, 020901 (2011). Selected in FACULTY OF 1000
66- C. Amoruso, T. Lagache D. Holcman, Modeling the early steps of cytoplasmic trafficking in viral infection and gene delivery, SIAM Appl. Math. 71, pp. 2334-2358
65- U. Pannasch, L.Vargova, J. Reingruber, P. Ezan, C. Giaume, D. Holcman, E. Sykova Nathalie Rouach, Astroglial networks scale synaptic activity and plasticity, PNAS 2011 A108 : 8467-8472
64 –S. Vakeroudis M. Yor D. Holcman, The Mean First Rotation Time of a planar
Polymer J. Stat. Phys. DOI : 10.1007/s10955-011-0227-6 (2011)
63- D. Fresche, U. Panache N. Rouach D Holcman, Synapse geometry and receptor dynamics modulate synaptic strength PloS One ;6(10):e25122, (2011) .
62- A. Taflia, D. Holcman, Estimating the synaptic current in a multi-conductance AMPA receptor model, Biophysical Journal. 101(4):781-92, (2011)
61- J. Reingruber D. Holcman, The Narrow Escape Time in a cylindrical domain,
application to the synaptic cleft, SIAM Multiscale analysis. 9, pp. 793-816 (2011)
60- D. Holcman I. Kupka, Semi-classical limit of the first eigenfunction and concentration on the recurrent sets of a dynamical system, Forum Math. 23, No. 1, 1-74 (2011) .


59-Bouzigues C, Holcman D, Dahan M., A Mechanism for the Polarity Formation of Chemoreceptors at the Growth Cone Membrane for Gradient Amplification during Directional Sensing, PLoS One. 2010, 22 ;5(2):e9243
58- Duc, K. D., & Holcman, D. (2010). Threshold activation for stochastic chemical reactions in microdomains. Physical Review E, 81(4), 041107.
57- Reingruber D. Holcman, Gated Narrow Escape Time for Molecular Signaling, J. of Cond. Matter. 22 (2010) 065103
56- G. Malherbe D. Holcman, Stochastic modeling of gene activation and application to cell regulation, J. Th.Bio 271, 1 p51-63 (2010)


55-G. Malherbe, D. Holcman, Search for a DNA target in the nucleus Phys. Lett. A (2009).
54- Reingruber D. Holcman, The Gated Narrow Escape Time for Molecular Signaling, Phys. Rev. Letter 103, 148102 (2009) .
53- D. Holcman I. Kupka, The probability of an encounter of two Brownian particles before escape, J.Phys A, 42, 31 : 315210 (2009)
52- J. Reingruber D. Holcman Narrow escape in a narrow domain, Phys Rev E Stat Nonlin Soft Matter Phys.79:030904 (2009). pdf
51- J. Reingruber, E. Abad, D Holcman, Narrow escape time to a structured target located on the boundary of a microdomain. J Chem Phys. ;130(9):094909 (2009).
50- T. Lagache, E. Dauty, D. Holcman, Toward a quantitative analysis of virus and plasmid trafficking in cells, Phys Rev E Stat Nonlin Soft Matter Phys. ;79:011921(2009)
49- K. Tsaneva, A.Burgo T. Galli, D. Holcman, Modeling neurite growth. Biophys J. ; 96(3):840-57(2009)


48- A. Singer, Z. Schuss, D. Holcman, Narrow escape and leakage of Brownian particles, 78,1 PRE 2008
47- J. Reingruber D. Holcman, Estimating the rate constant of cyclic GMP hydrolysis by activated phosphodiesterase in photoreceptors, J. Chem. Physics. 129,14.145102 2008
46- D. Holcman, Z. Schuss, The first eigenvalue of Laplace operator with small holes, J. Phys. A : Math. Theor. 41 155001 doi:10.1088/1751-8113/41/15/155001.
45- D. Holcman Z, Schuss, Diffusion through a cluster of small windows and flux regulation in microdomains, Phys Lett. A. 372, 21, 3768-3772, 2008
44- T. Lagache D. Holcman, Quantifying the intermittent transport in the cell cytoplasm, Phys. Rev. E 77, 030901(R) Short Com PRE 2008 .
43- T. Lagache D. Holcman, Effective motion of a virus trafficking inside a biological cell, SIAM of Applied Math.68 ,4,p1146-1167 2008 .
42-J. Reingruber D. Holcman, The dynamics of phosphodiesterase activation in rods and cones, 15 ;94(6):1954-70 Biophys. J. 2008 .
41- A. Singer, Z. Schuss, A. Osipov, D. Holcman, Partially Reflected Diffusion, SIAM J. Appl. Math., 68 (3):844-868, 2008 PDF .


40-Z. Schuss, A. Singer, D. Holcman, Narrow Escape : Theory and Applications to Cellular Microdomains, Proc. Nat. Acad. Sci. ;104(41):16098-103. 2007
39-A. Biess, E.Korkotian D. Holcman, Diffusion through a dendritic spine 76, 1, Phys.Rev E 2007
38- D. Holcman V. Kasatkin A. Prochiantz Modeling homeoprotein intercellular transfer unveils a parsimonious mechanism for gradient and boundary formation in early brain J. Theor. Biology 249(3):503-17, 2007
37-V. Kasatkin, A. Prochiantz, D. Holcman, Morphogenetic gradients and the stability of boundaries between neighboring morphogenetic regions ;70(1):156-78. Bull. Math Biology 2007
36-A. Taflia, D. Holcman, Dwell time of a molecule in a microdomain, J. chem. Phys. 126, (23):234107, (2007)
35- D. Holcman, Modeling viral and DNA trafficking in the cytoplasm of a cell J. of Statistical Physics. 127, 3, 471-494, 2007
34- D. Holcman, C. Pugh, The Boundary between Compact and Noncompact Complete Riemann Manifolds, Indiana Journal of Math. 56 No. 1, 437—458, 2007


33- D. Holcman A.Triller. Modeling synaptic dynamics and receptor trafficking, Biophysical Journal ;91(7):2405-15. 2006
32- D. Holcman M.Tsodyks. Emergence of the Up and Down States in cortical networks, PloS Comput Biol. 2(3):p23. 2006
31- D. Holcman, I. Kupka. Singular perturbation for the first eigenfunction and blow up analysis, Forum Math : 18, 3 p 445-518. 2006
30-A. Singer Z, Schuss, D. Holcman, B. Eisenberg. Narrow Escape I, J. of Statistical Physics. Vol. 122, 3 p437 – 463. 2006
29-A. Singer Z, Schuss, D. Holcman. Narrow Escape II J. of Statistical Physics. Vol. 122, 3 p465-89. 2006
28-A. Singer Z, Schuss, D. Holcman. Narrow Escape III J. of Statistical Physics. Vol. 122, 3 p491-509. 2006


27- D. Holcman, E. Korkotian, M. Segal. 2005. Dendritic spines : models and experiments, Review, Cell Calcium 2005 ;37(5):467-75
26-D. Holcman A. Marchevska Z. Schuss, The survival probability of diffusion with killing Phys. Rev. E. 72, 031910, 2005
25-E Bart, S. Bao, D. Holcman. Modeling the spontaneous activity in the auditory cortex, Journal of Computational Neuroscience ;19(3):357-78, 2005
24- D. Holcman, I. Kupka. Concentration of the first eigenfunction for a second order elliptic operator, C.R.A.S, 341 no. 4, 243-246, 2005
23- D. Holcman J. Korenbrot, The limit of photoreceptor sensitivity ; molecular mechanisms of dark current noise in retinal, J Gen Physiol.,125(6):641-60, 2005
22- D. Holcman, Z. Schuss. Stochastic chemical reactions in microdomains, Journal of Chemical Physics 122, 114710, 2005
21 - D. Holcman, Z. Schuss. Modeling Calcium Dynamics in Dendritic Spines SIAM of Applied Math 65, 3 pp. 1006-1026, 2005
20- D. Holcman, I. Kupka. Perturbation methods and first-order partial differential equations on Riemannian manifolds, Q.J. Math. 56, 1, 65-93


19- E. Korkotian, D. Holcman, M. Segal. Dynamic Regulation of Spine-Dendrite Coupling in Cultured Hippocampal Neurons, European Journal of Neuroscience, 20:2649-2663, 2004 PDF.
18- D. Holcman, Schuss Z : Escape through a small opening : receptor trafficking in a synaptic membrane. J. Statist. Phys. 117 (2004), 5-6, 975—1014 PDF.
17- D. Holcman, Z. Schuss, E. Korkotian. Calcium dynamic in dendritic spines and spine motility, Biophysical Journal, 87:81-91, 2004 PDF.
16- D. Holcman, J. Korenbrot. Longitudinal diffusion in retinal rod and cone outer segment cytoplasm : the consequence of cell structure, Biophysical Journal, 86:2566-2582, 2004. PDF


15- D.Holcman M.Margaliot, Stability Analysis of Switched Homogeneous Systems in the plane, SIAM J. of Control, 41 (2002), no. 5, 1609—1625. PDF


14-P. Greiner, D. Holcman, Y. Kannai. Wave Kernel related to second order operators, Duke Mathematical Journal. 114 (2002), no. 2, 329–386

13- D. Holcman. Prescribed Scalar Curvature problem on Complete manifolds, J. Math. Pures Appl. (9) 80, no. 2, 223-244
12- D. Holcman I. Kupka. Singular Perturbation and first order PDE on manifolds. C. R. Acad. Sci. Paris Sér. I Math. 333, no. 5:465-470 PDF.
11- D. Holcman, E. Humbert. Poincare-Sobolev inequality on manifolds with boundary, Math. Z. 237, no. 4, 669-695 .
10- D. Holcman. Solutions nodales d’EDP non linéaires sur les variétés non localement conformément plates. Comment. Math. Helv. 76, no. 3, 373-387

9- D. Holcman Nonlinear PDE with vector fields, J. Anal. Math. 81, 111-137.
8- D. Holcman. Influence de la masse sur les solutions nodales d’EDP non linéaires, Bull. Sci. Math. 124, no. 5, 385-414.

7- Barrie J.M., D. Holcman, Freeman W.J. Statistical evaluation of clusters derived by nonlinear mapping of EEG spatial patterns, Journal of Neuroscience Methods, 90:87-95.
6- D. Holcman. On the mass of manifolds with boundary, C. R. Acad. Sci. Paris Sér. I Math. 328, no. 12, 1191-1196.
5- D. Holcman. EDP non linéaires avec champ de vecteurs, Compt. Rend. Acad. Sci. Paris. Sér. I Math 329 n° 10, 871-879.
4- D. Holcman. Prescribed Scalar Curvature problem on Complete manifolds, Compt. Acad. Sci Série I,t 328, 321-326.
3- D. Holcman. Solutions nodales sur les variétés Riemanniennes, J. of Funct. Analys., 26, 219-245.

2- D. Holcman. Solutions nodales sur les variétés riemanniennes à bord, Compt. Rend. Acad. Sci. Paris, t.326, Série I, p1321-1324.
1- D. Holcman. Solutions nodales sur les variétés Riemanniennes compactes, Compt. Rend. Acad. Sci. Paris, t.326, Série I, 1205-1208.

Meeting reports in applied sciences (after 2007)

30- J Heck, P Parutto, R Freund, A Ciuraszkiewicz, A Bikbaev, M Andres-Alonso, A Fejtova, D Holcman, M Heine , Calcium channel surface dynamic influences synaptic transmission, JOURNAL OF NEUROCHEMISTRY 142, 122-1232017.
29- D Holcman, A Amitai, Dynamics of dsDNA Break, Organization of the Nucleus Based on Polymer Dynamics, Biophysical Journal 106 (2), 272a, 2014.
28- A. Amitai, M. Toulouze K. Dubrana, D. Holcman, DNA dynamics, nucleus organization, analysis of dsDNA break, based on a novel polymer model approach and analysis, EMBO 2013.
27- C. Sieben, N. Hoze, K. Horst, C. Wolff, MJ. Lehmann, D. Holcman, A. Herrmann. Single Influenza Virus Tracking Reveals Cell Specific Modes of Movement - a Key to Understand Cellular Tropism Biophysical Journal 104(2) pp. 415a - 416a
26- T. Lagache, O. Danos, D. Holcman Modeling the Step of Endosomal Escape during Cell Infection by a Nonenveloped Virus Biophysical Journal 102(5) pp. 980 - 989
25- D. Holcman, analyzing superresolution data, EMBO, ENS 2012
24- D. Holcman modeling potassium dynamics, FENS, Spain July 212
23- D. Holcman, Modeling the Synaptic Current in Neurobiology, 2011 Vancouver.
22- K. Tsaneva-Atanasova D. Holcman Modeling the Dynamics of Neurite Growth, ICIAM 2011 Vancouver.
21-D. Holcman Modeling Cellular Biology : What Have Learnt from Viral Infection
ICIAM 2011 Vancouver.
20- D. Holcman, unravealing chemical interaction at the molecular level for AMPAR trafficking, "Single Cell Physiology", EMBO 2012.
19-D. Holcman, modeling superresolution data, Jacques Monod Conference "Imaging neuronal functions : from molecules to circuits"2012.
18- J. Reingruber D. Holcman The Biophysics Of The Single Photon-response In Rods Accounting For The Molecular Background Noise749/A626 – Arvo 2012
17-. D.Holcman, G. Lejay, J. Reingrube, B. Minke Single Photonresponse In The Fly Photoreceptor, 4134 ARVO 2012
16- Bouchoucha, Y Reingruber, J Le Men, J Gilardi-Hebenstreit, P, D. Holcman Charnay, P Patterning of the vertebrate hindbrain : A computational approach, : 70th Annual Meeting of the Society-for-Developmental-Biology Location : Chicago, IL Jul, 2011, 356 Issue : 1 Pages : 237-237 DOI : 10.1016/j.ydbio.2011.05.411 Meeting Abstract : 449
15- A. Amitai I. Kupka D. Holcman, The Mean Looping Time of DNA, Biophys J., Volume 100, Issue 3, Supp, 2011, Page 76a
14-A de Meyer, N. Hoze, M. Ruault, D. Holcman, A. Taddei, Telomere clustering in budding yeast reveals principles for protein-mediated interactions between chromosomes
EMBO Workshop Advanced Light Microscopy Techniques, 10th International ELMI Meeting 2010.
13-Lagache, T. D. Holcman, Mean Time and Probability to Reach a Structured Target
Biophys J., vol. 98, issue 3, pp. 722a-722a 2010.
12-Hoze, N. Taddei, A. D. Holcman, Dynamics of Telomere Clustering in the Nucleus :
Biophys J., vol. 98, issue 3, pp. 58a-58a 2010.
11-Reingruber, J. ; Bosanac, L. ; Darzacq, X. D. Holcman. Transcription Factor Switching Dynamics Regulates Gene Activation, Biophys J., vol. 98, issue 3, pp. 70a-70a, 2010.
10- J. Reingruber D. Holcman, Estimating The Rate Constant Of Cyclic GMP Hydrolysis By Activated Phosphodiesterase In Photoreceptors Biophys J. Volume 96, Issue 3, Pages 269a-269a Page 525a (2009).
9- D. Fresche D. Holcman, Should a synapse be reliable ? Biophys J., Volume 96, Issue 3, Pages 269a-269a (2009).
8-Lagache.,T ; Danos, O. D. Holcman., Modeling The Endosomal Stage of Viral Infection : Biophys J., vol. 96, issue 3, pp. 307a-307a. (2009).
7-D. Holcman, Modeling neurite outgrowth, EMBO short-report, Spatial Conference (2009).
5-Biess, A ; Korkotian, E ; Holcman, D, Calcium diffusion in inhomogeneous dendrites, Biophys J. 185A-186A (2007).
4-Lagache, T ; Holcman, D, Effective motion of a virus trafficking inside a biological cell. : Biophys J. 154A-154A (2007).
3-Malherbe, G ; Holcman, D, Average search time for a transcription factor in the DNA : the case of one or more transcription factors : Biophys J. Pages : 411A-411A (2007)
2-Taflia, A ; Holcman, D Dwell time of a Brownian interacting molecule in a cellular microdomain. 51st Annual Meeting of the Biophysical-Society Biophys J.:185A-185A (2007)
1-Tsaneva-Atanasova, K ; Azzopardi, N ; Galli, T Holcman, D, Modeling vesicle trafficking and neurite growth, 51st Annual Meeting of the Biophysical-Society, Biophys J. : 115A-115A (2007)