Publication summary:
- 3 non-peer reviewed publications (ArXiv)
- 23 submitted or written manuscripts
- 29 meeting reports (>2007).
- 153 peer reviewed: 129 research publications. 11 reviews. 13 chapters/comments/ review.
- 3 books published by Springer.
- 1 book in production.

Field covered: Fields covered: Applied Mathematics, Biophysical Modeling, Stochastic Processes, Asymptotic of Partial Differential Equations, Statistical Physics, Computational Biology and Neurobiology, Integrative Cellular and Molecular Biology, Theoretical Biophysics, Stochastic Simulations of Cellular Processes, Multiscale Modeling in Neuroscience, Physical biology, Physical virology, Polymer models, Statistics of single particle trajectories, chromatin reconstruction, Phototransduction, Electro-diffusion, neuronal network, neuron-glia interaction, statistical medecine, EEG analysis.

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 (in production) 2015. http://www.springer.com/us/book/978…

Book chapters and Commentaries, View points, Opinions

16- C. Guerrier, D. Holcman, Calcium dynamics in nanodomains to trigger vesicular release at neuronal synapses revealed by computational modeling, Frontiers in Neuroscience (in preparation).

15- Z. Schuss, K.Basnayake, D. Holcman, Redundancy principle for optimal random search in biology 2017.

14-A. Amitai D. Holcman, Methods for analyzing single particle trajectories in the nucleus, (in preparation) 2018.

13-D. Holcman J. Reingruber, Modeling and stochastic analysis of the single photon response, review chapter, Springer 2017.

12- 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.

11- D. Holcman, La nouvelle physique mathématique en biologie, Gazette des Mathematiques (in French) n°147, Janvier 2016.

10- D. Holcman Z. Schuss, New mathematics and physics in life sciences and medicine, Physics Today 69 (1), 10 (2016).

9- N. Rouach, D Holcman, Modeling neuron-glia interactions (invited chapter) Springer.

8- K. Reynaud, Z Schuss, N Rouach, D Holcman, Why so many sperm cells? Communicative & Integrative Biology:3, e1017156; 2015.

7- D. Holcman R. Yuste, The new nanophysiology: Towards nanophysiology: Regulation of ionic flow in neuronal subcompartments, 16, Nat. Rev. Neuroscience 2015.

6- D. Holcman, Multiscale modeling, stochastic and asymptotic approaches for analyzing neural networks based on synaptic dynamics, ESAIM: Proceedings and Surveys 47, 36-54 2015.

5- D. Holcman, Review on the book ”Nonlinear Filtering and Optimal phase tracking” by Zeev Schuss, SIAM Review 2014.

4- D. Holcman, Unraveling novel features hidden in superresolution microscopy data, Perspective, Communicative & Integrative Biology, 1;6(3):e23893. 2013

3- C. Guerrier, E. Korkotian, D. Holcman Calcium dynamics in Microdomains: From mathematical modeling to data analysis, Encyclopedia Computational Neurobiology, Springer 2014, pp 1-37

2-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.

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

16-O. Shukron D. Holcman, Principle of chromatin reconstruction from hi-C using polymer models.

15-O. Shukron D. Holcman, Statistics of SPTs .

14-J. Cartailler D. Holcman, Understanding Electrodiffusion in cellular nano and microdomains to predict voltage distribution and synaptic transmission.

13-J. Cartailler D. Holcman, The physics of Electrodiffusion in microdomains

12-D. Herrmann, R. Metzler,…D. Holcman, Polymer modeling for nucleus organization, 2017 (submitted).

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 of Single Particle Trajectories, Biophysical Journal (in revision) 2015.

8-J. Reingruber, D. Holcman G. Fain, Optimal interplay geometry-biochemistry in single photoresponse.

7-A. Amitai D. Holcman, Polymer physics of the nucleus organization, 2015.

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), 1730012014.

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

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-J. Cartailler D. Holcman, Transient PNP.

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- A. Amitai, D. Holcman, Consequence of chromatin interaction removal and local reorganization during homologous search in the cell nucleus (pre-print) 2016.

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

137-J. Cartailler D. Holcman, PNP in Elliptic domains.

136- N.Hoze, J.C Poncer S. Levi D. Holcman, Organization of the perisynaptic space for KCC1 trafficking.

135- A.Amitai, Kupka D. Holcman, Asymptotic computation of the mean looping time for a Rouse polymer.

134-P. Parutto, N. Hoze. D. Holcman, Novel features hidden in superesolution data.

Publications published or in press

2018

133- J. Cartailler and D. Holcman, Asymptotic of the Poisson-Nernst-Planck equations in three-dimensional microdomains with cusp-shaped funnels, (revision) Mutiscale Modeling Simulation, 2018

132-O. Shukron D. Holcman, Statistics of cross-linked chromatin organization during cell differentiation reconstructed by heterogeneous polymer models

131-K.Basnayake, Z. Schuss D. Holcman, Fastest narrow escape: short-time asymptotics for the fastest Brownian particles to escape through a small window.

130-K. Tor, Z. Schuss D. Holcman, MFPT for the telomere length (revision).

129-K.Basnayake, E. Korkotian D. Holcman, Role of the ER in regulating unidirectional calcium flux in the dendritic spines (submitted).

128- A. Wondergem, F de Wit, T Reuvers, D Holcman, D. Heinrich, Controlling amoeboid migration by combining topotactic and chemotactic cues (submitted).

127- E. Avezov*, P. Parutto*, J Chambers, L Young, S. Marciniak, C. Kaminski, D. Ron, D. Holcman, Statistical analysis of super-resolution single particle trajectories reveals the functional topology of the Endoplasmic Reticulum controlling molecular flows (revision) 2017.

126-U. Dobramysl D. Holcman, Reconstructing the gradient source position from stochastic fluxes to small receptors, Scientific Report 2018.

125- A.Amitai, D. Holcman, Encounter time of two chromatin loci is governed by polymer de-condensation and modification of local interactions, submitted Phys. Rev.E (revision), 2017

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 (in press).

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.

122-O. Shukron M. Hauer, D. Holcman, First passage time statistics in two locus chromatin single trajectories, Scientific Report, 2017.

121- A. Amitai, A. Seeber, S. M. Gasser D. Holcman, Statistical polymer simulation distinguishes DNA double-strand break movement due to chromatin expansion and nuclear oscillation, 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, Polymer model reconstruction from chromosomal capture data and stochastic simulations of transient encounters, PLoS Comput Biol 13 (4), e1005469 2017.

118-J. Cartailler, Z. Schuss and D. Holcman, Effect of the domain geometry on Poisson-Nernst-Planck, 2017 Journal of Nonlinear Science, 1-30 2017.

117- J. Cartailler, Z. Schuss and D. Holcman, Geometrical effects on nonlinear electrodiffusion in cell physiology, Scientific Report, 2017.

116- C. Guerrier, D. Holcman, Analysis of hybrid model and simulations for ions and particle dynamics in synaptic micro-domains of neuronal cells, J. Computational Physics 340, 617-638 2017.

115- N.Hoze, D. Holcman, Stochastic aggregation-dissociation with a finite number of particles, Ann. Applied Probability, 2017.

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, Endosomal journey of the influenza virus, Frontiers in Physics, 5, 25,2017.

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.2…

2015

107-J. Yang I. Kupka. Z. Schuss D. Holcman, Spermatozoa motion and search for a small egg target in uterus, (revision), J. Math Bio.

106- N.Hoze D. Holcman, Stochastic analysis and extracting features from superresolution data (accepted), Phys. Rev. E.

105- A. Amitai, M Toulouze K. Dubrana D. Holcman, Analysis of single locus trajectories for extracting in vivo chromatin tethering interactions PloS Computational Biology (revision) 2015.

104- K. Dao Duc, P. Parutto, X. Chen ,J. Epzstein, A Konnerth D. Holcman, Peak-Oscillation of the sojourn times in the Up-state of neuronal network, Frontieres Comp. Neuroscience 2015.

103- C. Guerrier D. Holcman, MFPT to a cusp, Multiscale Modeling and Simulations (revision MMS) 2015.

102- C. Guerrier, J. Hayes, G. Fortin, D. Holcman, Modeling the PreBotzniger complex, PNAS 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.

91-A. Amitai, D. Holcman, beta-model application to DNA modeling in the nucleus, 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 Stochastic switching in a feedback loop controls vertebrate hindbrain patterning revision () Mol. Sys. Biol. *: 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)

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)

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 doi:10.1073/pnas.1204589109 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.

78-Z. Schuss D. Holcman, The dire strait time, SIAM Multicale Modeling and simulations, 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 endosomal escape of non enveloped viruses, case of the AAV 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, mean time for a polymer to loop. Multiscale Model. Simul. 10-2, pp. 612-632 (2012).

2011

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 http://f1000.com/13294037

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).

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

58-K. Dao Duc, D. Holcman, Mean time to threshold activation PRE 81,1 2010

57- Reingruber D. Holcman, Modeling with 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).

2009

55-G. Malherbe, D. Holcman, Search for a DNA target in the nucleus Phys. Lett. A doi:10.1016/j.physleta.2009.11.027 (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).

51- J. Reingruber, E. Abad, D Holcman, Narrow escape time to a three-dimensional protrusion 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).

2008

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® 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.

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

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.

2006

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.

2005

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. A theory of stochastic chemical reactions in confined microstructures, 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.

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.

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.

17- D. Holcman, Z. Schuss, E. Korkotian. Calcium dynamic in dendritic spines and spine motility, Biophysical Journal, 87:81-91, 2004.

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.

2003

15- D. Holcman, M. Margaliot. Stability Analysis of Switched Homogeneous Systems in the plane, SIAM J. of Control. 41: 1609-1625. 2002

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

2001

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.

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.

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)

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 Synpatic 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)

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