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List of publications

Publication summary : Total (peer reviewed)=192.
3 non-peer reviewed publications.
26 submitted or written.
156 research publications.
17 reviews.
25 chapters/comments/review.
29 meeting reports (>2007).
3 books (Springer) .

Field covered : Computational Biology and Neurobiology, Integrative Cellular and Molecular Biology, Applied Mathematics, Stochastic processes, Asymptotic of Partial differential Equations, Statistical Physics, Biophysics, Stochastic simulations of cellular processes. Multiscale modeling in neuroscience.

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. http://www.springer.com/us/book/9781493931026

2- D. Holcman, Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology (Springer), 2017.
http://www.springer.com/it/book/9783319626260

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.
https://www.springer.com/fr/book/9783319768946

In preparation :
- D. Holcman, Modeling and statistical analysis of the cell nucleus, Springer.
- D. Holcman, Z. Schuss, Modern modeling, simulations and data analysis in cell biology and neuroscience.
- D. Holcman, Stochastic and Statistical Methods of Single Trajectories and their Applications in biophysics and cell biology

Book chapters and Commentaries, View points, Opinions

18-A. Amitai D. Holcman, Methods for analyzing single particle trajectories in the nucleus, (in press) 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- Z. Schuss, K.Basnayake, D. Holcman, Redundancy principle for optimal random search in biology (PLREV, submitted) 2018.
15-D. Holcman, Comment l’économie High Tech peut émerger sans refondre le système universitaire, mediapart 2018
https://blogs.mediapart.fr/edition/au-coeur-de-la-recherche/article/050418/comment-leconomie-high-tech-peut-emerger-sans-refondre-le-systeme-universit
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.
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.
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.
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).

Reviews (in preparation)

16-O. Shukron D. Holcman, Principle of chromatin reconstruction from Hi-C using polymer models (in prep).
15-O. Shukron D. Holcman, Statistics of SPTs (in prep).
14-J. Cartailler D. Holcman, Understanding Electrodiffusion in cellular nano and microdomains to predict voltage distribution and synaptic transmission (in prep).
13-J. Cartailler D. Holcman, The physics of Electrodiffusion in microdomains (in prep).

Reviews

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.
11- D. Holcman Z. Schuss, 100 years after Smoluchowski : stochastic processes in cell biology, J. Phys. A (2016).
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 : early pre-prints

160- N.Hoze, J.C Poncer S. Levi D. Holcman, Organization of the perisynaptic space for KCC1 trafficking.
159-P. Parutto, N. Hoze. D. Holcman, Novel features hidden in superesolution data.
158-K. Tor, Z. Schuss D. Holcman, Jump processes and MFPT, extreme event and application to telomere length dynamics.
157-J. Cartailler D. Holcman N. Rouach, Potassium dynamics at the Mossyfiber synapse.
156-J. Cartailler D. Holcman N. Rouach, Glutamate dynamics in the Mossyfiber synaptic cleft.
155- P. Parutto D. Holcman, Protein fluxes in the ER.
154- U. Dobramysl D. Holcman, Gradient combinatorix for neuronal patterning.
152-U. Dobramysl D. Holcman, Exterior Narrow escape in three dimensions and time dependent analysis of a source position reconstructing from fluxes.
151- C. Guerrier, D. Holcman, Short-term synaptic plasticity revealed by stochastic molecular events, 2017.
150- N.Hoze, D. Holcman, Three-dimensional SPTs analysis and reconstruction of cellular local geometry.
149-J. Cartailler D. Holcman, Epileptic oscillation in Cx30 KO.
148- A.Amitai, Kupka D. Holcman, Asymptotic computation of the mean looping time for a Rouse polymer.
147- Z. Schuss D. Holcman, escape on a square window.
146- Z. Schuss D. Holcman, spectrum of the FPE with critical points on a limit cycles.
145-O. Shukron D. Holcman, Analysis of looping and passage times in TADs
144-P. Parutto, N. Hoze. D. Holcman, Reconstructing the boundary of a potential well from SPTs.
143-J. Yang T. Lagache, D. Heinrich K. Reynaud D. Holcman, Sperm motion in uterus.
142- A.Amitai, M. Toulouze, K. Dubrana D. Holcman, Heterogeneous organization of the chromatin revealed in the analysis of SPTs.
141-J. Cartailler D. Holcman, PNP in Elliptic domains.
140-J. Cartailler D. Holcman, Stationary PNP with two charge population in a bounded domain.
139-C. Lespagnol, D. Holcman, NET for a needle
138- N. Despierre, D. Holcman, Theory of Escape time for correlated particles and applications


Publications published or in press

2019
138- Z.Schuss, K.Basnayake, D.Holcman. Redundancy principle and the role of extreme statistics in molecular and cellular biology. Physics of Life Reviews, 2019
https://doi.org/10.1016/j.plrev.2019.01.001
ARXIV-> https://doi.org/10.1101/210443

2018
137- A. Amitai, O. Shukron, D. Holcman, Consequence of chromatin interaction removal and local reorganization during homologous search in the cell nucleus (submitted) https://www.biorxiv.org/content/biorxiv/early/2018/12/31/508689.full.pdf.
136-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 https://doi.org/10.1016/j.physleta.2018.09.040
135-J. Cartailler D. Holcman, Electrical transient laws in neuronal microdomains based on electro-diffusion, Physical Chemistry Chemical Physics (revision) 2018. DOI : 10.1039/C8CP02593B https://arxiv.org/pdf/1803.03940.pdf
134-P. J. Heck, P. Parutto, A. Ciuraszkiewicz, A. Bikbaev, R. Freund, M. Alonso, A.
Fejtova, D. Holcman*, M. Heine*, Calcium channel surface dynamic influences synaptic transmission, JOURNAL OF NEUROCHEMISTRY .

133- J. Cartailler and D. Holcman, Asymptotic of the Poisson-Nernst-Planck equations in three-dimensional microdomains with cusp-shaped funnels, (revision) Multiscale Modeling Simulation, 2018 LINKARXIV
132-O. Shukron D. Holcman, Statistics of cross-linked chromatin organization during cell differentiation reconstructed by heterogeneous polymer models (revision).
131-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) LINKARXIV https://doi.org/10.1007/s00332-018-9493-7
130-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
129-K. Basnayake, E. Korkotian D. Holcman, Fast calcium transients in neuronal spines driven by extreme statistics. doi : https://doi.org/10.1101/290734
128- A. Wondergem, F de Wit, T Reuvers, D Holcman, D. Heinrich, Controlling amoeboid migration by combining topotactic and chemotactic cues (submitted).
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 https://doi.org/10.1038/s41556-018-0192-2
126-U. Dobramysl D. Holcman, Reconstructing the gradient source position from stochastic fluxes to small receptors, Scientific Report 355:22-36.
https://doi.org/10.1038/s41598-018-19355-5
2018. LINARKIV
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. doi : 10.1103/PhysRevE.97.032417. 2018.LINKARXIV
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 https://doi.org/10.1016/j.neuron.2018.01.034.

2017

123-U. Dobramysl D. Holcman, Exterior Narrow escape in two dimensions for reconstructing the source position from stochastic fluxes, J of Computational Physics, 2017 https://doi.org/10.1016/j.jcp.2017.10.058.
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 https://doi.org/10.1038/s41598-017-10842-9.
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 https://doi.org/10.1016/j.celrep.2017.01.018.
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 https://doi.org/10.1038/nsmb.3347.
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 https://doi.org/10.1371/journal.pcbi.1005469.
118-J. Cartailler, Z. Schuss and D. Holcman, Geometrical Effects on Nonlinear Electrodiffusion in Cell Physiology, 2017 Journal of Nonlinear Science, 1-30 2017 https://doi.org/10.1007/s00332-017-9393-2.
117- J. Cartailler, Z. Schuss and D. Holcman, Electrostatics of non-neutral biological microdomains, Scientific Report, 2017 https://doi.org/10.1038/s41598-017-11590-6.
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 https://doi.org/10.1016/j.jcp.2017.03.058.
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) https://doi.org/10.1103/PhysRevE.96.012503.
LINKARXIV
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 https://doi.org/10.3389/fphy.2017.00025.

2016
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. 2016.
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. 2016.
108-J. Cartailler Z. Schuss D. Holcman, Electrical properties of dendritic spines, Physica D : Nonlinear Phenomena 2016. http://dx.doi.org/10.1016/j.physd.2016.09.001

2015

107-J. Yang I. Kupka. Z. Schuss D. Holcman, Spermatozoa motion and search for a small egg target in uterus, J. Math Bio. 2015
106- N.Hoze D. Holcman, Stochastic analysis and extracting features from superresolution data, Physical Review E 92 (5), 052109. 2015
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. 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
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.

2014

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.
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).
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


2013

92- N.Hoze, D. Holcman, Aggregation with a finite number of particles for viral capsid assembly. Phys. Let. A 2013 https://link.springer.com/article/10.1007%2Fs00285-014-0819-2.
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 https://link.springer.com/article/10.1007/s10955-013-0876-8
89- Dao Duc, D. Holcman, Computing the length of the shortest telomere across cell division, Phys. Rev Lett. 2013 https://physics.aps.org/featured-article-pdf/10.1103/PhysRevLett.111.228104
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 https://www.pnas.org/content/110/48/19378.
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 https://epubs.siam.org/doi/pdf/10.1137/130907513
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 https://www.ncbi.nlm.nih.gov/pubmed/24061538
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 http://www.genetics.org/content/194/4/847.long.
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) https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.110.248105
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) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667730/

2012

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) https://aip.scitation.org/doi/10.1063/1.4772403
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 https://doi.org/10.1073/pnas.1204589109.
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 https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.109.108302.
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) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502205/.
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 https://iopscience.iop.org/article/10.1088/0034-4885/76/7/074601/meta.
78-Z. Schuss D. Holcman, Brownian Motion in Dire Straits, SIAM Multicale Modeling and simulations 10(4), 1204–1231, 2012 https://arxiv.org/pdf/1202.2775.pdf.
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 https://arxiv.org/pdf/1201.2620.pdf.
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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368725/
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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302482/
74- D. Holcman Z. Schuss, A Brownian needle in dire straits, Phys. Rev. E-Short Comm 85, 010103 (2012) https://journals.aps.org/pre/pdf/10.1103/PhysRevE.85.010103 .
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) http://dev.biologists.org/content/139/1/215.long.
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) https://epubs.siam.org/doi/pdf/10.1137/110842624.

2011

71-D. Holcman Z. Schuss, Diffusion laws in dendritic spines, J. Math. Neuroscience 1:10 2011, doi:10.1186/2190-8567-1-10 https://mathematical-neuroscience.springeropen.com/articles/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 http://www.jneurosci.org/content/31/48/17590.long.
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 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002182.
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). https://journals.aps.org/pre/pdf/10.1103/PhysRevE.84.021906
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 http://f1000.com/13294037 https://arxiv.org/pdf/1104.2204.pdf
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 https://arxiv.org/pdf/1109.1495.pdf
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 https://www.pnas.org/content/108/20/8467.long
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) https://arxiv.org/pdf/1101.1737.pdf.
63- D. Fresche, U. Panache N. Rouach D Holcman, Synapse geometry and receptor dynamics modulate synaptic strength PloS One ;6(10):e25122, (2011) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025122 .
62- A. Taflia, D. Holcman, Estimating the synaptic current in a multi-conductance AMPA receptor model, Biophysical Journal. 101(4):781-92, (2011) https://arxiv.org/pdf/1009.0867.pdf.
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) https://arxiv.org/pdf/1104.1090.pdf
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) https://arxiv.org/pdf/0802.0858.pdf .

2010

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 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009243
58- Duc, K. D., & Holcman, D. (2010). Threshold activation for stochastic chemical reactions in microdomains. Physical Review E, 81(4), 041107. https://journals.aps.org/pre/pdf/10.1103/PhysRevE.81.041107.
57- Reingruber D. Holcman, Gated Narrow Escape Time for Molecular Signaling, J. of Cond. Matter. 22 (2010) 065103 https://iopscience.iop.org/article/10.1088/0953-8984/22/6/065103/meta.
56- G. Malherbe D. Holcman, Stochastic modeling of gene activation and application to cell regulation, J. Th.Bio 271, 1 p51-63 (2010) https://arxiv.org/pdf/1010.3001.pdf.

2009

55-G. Malherbe, D. Holcman, Search for a DNA target in the nucleus Phys. Lett. A https://arxiv.org/pdf/0712.3467.pdf (2009).
54- Reingruber D. Holcman, The Gated Narrow Escape Time for Molecular Signaling, Phys. Rev. Letter 103, 148102 (2009) https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.103.148102 .
53- D. Holcman I. Kupka, The probability of an encounter of two Brownian particles before escape, J.Phys A, 42, 31 : 315210 (2009) https://iopscience.iop.org/article/10.1088/1751-8113/42/31/315210.
52- J. Reingruber D. Holcman Narrow escape in a narrow domain, Phys Rev E Stat Nonlin Soft Matter Phys.79:030904 (2009).
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) https://arxiv.org/pdf/0711.4262.pdf.
49- K. Tsaneva, A.Burgo T. Galli, D. Holcman, Modeling neurite growth. Biophys J. ; 96(3):840-57(2009) https://www.sciencedirect.com/science/article/pii/S0006349508001100.

2008

48- A. Singer, Z. Schuss, D. Holcman, Narrow escape and leakage of Brownian particles, 78,1 PRE 2008 https://web.math.princeton.edu/~amits/publications/PRE-leakage.pdf.
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 https://aip.scitation.org/doi/10.1063/1.2991174.
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 http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.446.4574&rep=rep1&type=pdf.
44- T. Lagache D. Holcman, Quantifying the intermittent transport in the cell cytoplasm, Phys. Rev. E 77, 030901(R) Short Com PRE 2008 https://journals.aps.org/pre/pdf/10.1103/PhysRevE.77.030901 .
43- T. Lagache D. Holcman, Effective motion of a virus trafficking inside a biological cell, SIAM of Applied Math.68 ,4,p1146-1167 2008 https://epubs.siam.org/doi/pdf/10.1137/060672820 .
42-J. Reingruber D. Holcman, The dynamics of phosphodiesterase activation in rods and cones, 15 ;94(6):1954-70 Biophys. J. 2008 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2257895/ .
41- A. Singer, Z. Schuss, A. Osipov, D. Holcman, Partially Reflected Diffusion, SIAM J. Appl. Math., 68 (3):844-868, 2008 https://www.jstor.org/stable/40233749?seq=1#metadata_info_tab_contents .

2007

40-Z. Schuss, A. Singer, D. Holcman, Narrow Escape : Theory and Applications to Cellular Microdomains, Proc. Nat. Acad. Sci. ;104(41):16098-103. 2007 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994903/
39-A. Biess, E.Korkotian D. Holcman, Diffusion through a dendritic spine 76, 1, Phys.Rev E 2007 https://pdfs.semanticscholar.org/1aa1/518264c90004c2cfef0a3a68afa259bc2886.pdf.
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 https://www.ncbi.nlm.nih.gov/pubmed/17904161.
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 https://www.ncbi.nlm.nih.gov/pubmed/17906901.
36-A. Taflia, D. Holcman, Dwell time of a molecule in a microdomain, J. chem. Phys. 126, (23):234107, (2007) https://aip.scitation.org/doi/10.1063/1.2746840.
35- D. Holcman, Modeling viral and DNA trafficking in the cytoplasm of a cell J. of Statistical Physics. 127, 3, 471-494, 2007 http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.186.3452&rep=rep1&type=pdf.
34- D. Holcman, C. Pugh, The Boundary between Compact and Noncompact Complete Riemann Manifolds, Indiana Journal of Math. 56 No. 1, 437—458, 2007 https://arxiv.org/pdf/math/0501414.pdf.

2006

33- D. Holcman A.Triller. Modeling synaptic dynamics and receptor trafficking, Biophysical Journal ;91(7):2405-15. 2006 https://www.sciencedirect.com/science/article/pii/S0006349506719567.
32- D. Holcman M.Tsodyks. Emergence of the Up and Down States in cortical networks, PloS Comput Biol. 2(3):p23. 2006 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1409813/.
31- D. Holcman, I. Kupka. Singular perturbation for the first eigenfunction and blow up analysis, Forum Math : 18, 3 p 445-518. 2006 https://arxiv.org/abs/math-ph/0412088.
30-A. Singer Z, Schuss, D. Holcman, B. Eisenberg. Narrow Escape I, J. of Statistical Physics. Vol. 122, 3 p437 – 463. 2006 https://link.springer.com/article/10.1007/s10955-005-8026-6.
29-A. Singer Z, Schuss, D. Holcman. Narrow Escape II J. of Statistical Physics. Vol. 122, 3 p465-89. 2006 https://link.springer.com/article/10.1007/s10955-005-8027-5.
28-A. Singer Z, Schuss, D. Holcman. Narrow Escape III J. of Statistical Physics. Vol. 122, 3 p491-509. 2006 https://link.springer.com/article/10.1007/s10955-005-8028-4.

2005

27- D. Holcman, E. Korkotian, M. Segal. 2005. Dendritic spines : models and experiments, Review, Cell Calcium 2005 ;37(5):467-75 https://www.sciencedirect.com/science/article/pii/S0143416005000321
26-D. Holcman A. Marchevska Z. Schuss, The survival probability of diffusion with killing Phys. Rev. E. 72, 031910, 2005 https://arxiv.org/pdf/math-ph/0502035.pdf.
25-E Bart, S. Bao, D. Holcman. Modeling the spontaneous activity in the auditory cortex, Journal of Computational Neuroscience ;19(3):357-78, 2005 https://link.springer.com/article/10.1007/s10827-005-3099-4.
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 https://arxiv.org/abs/math-ph/0506059.
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 https://www.ncbi.nlm.nih.gov/pubmed/15928405.
22- D. Holcman, Z. Schuss. Stochastic chemical reactions in microdomains, Journal of Chemical Physics 122, 114710, 2005 https://arxiv.org/abs/math-ph/0412089.
21 - D. Holcman, Z. Schuss. Modeling Calcium Dynamics in Dendritic Spines SIAM of Applied Math 65, 3 pp. 1006-1026, 2005 https://epubs.siam.org/doi/pdf/10.1137/S003613990342894X.
20- D. Holcman, I. Kupka. Perturbation methods and first-order partial differential equations on Riemannian manifolds, Q.J. Math. 56, 1, 65-93 https://ieeexplore.ieee.org/document/8158382.

2004

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

2003

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


2002

14-P. Greiner, D. Holcman, Y. Kannai. Wave Kernel related to second order operators, Duke Mathematical Journal. 114 (2002), no. 2, 329–386 https://pdfs.semanticscholar.org/f048/bfd7913171703c1e56ffb3ad7dd7f0e76a2a.pdf.

2001
13- D. Holcman. Prescribed Scalar Curvature problem on Complete manifolds, J. Math. Pures Appl. (9) 80, no. 2, 223-244 https://www.sciencedirect.com/science/article/pii/S0764444299802183.
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 https://link.springer.com/article/10.1007/PL00004886 .
10- D. Holcman. Solutions nodales d’EDP non linéaires sur les variétés non localement conformément plates. Comment. Math. Helv. 76, no. 3, 373-387
PDF

2000
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.

1999
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.

1998
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)