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Items: 1 to 50 of 90

1.

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

Schuss Z, Basnayake K, Holcman D.

Phys Life Rev. 2019 Jan 11. pii: S1571-0645(19)30009-0. doi: 10.1016/j.plrev.2019.01.001. [Epub ahead of print] Review.

PMID:
30691960
2.

Single particle trajectories reveal active endoplasmic reticulum luminal flow.

Holcman D, Parutto P, Chambers JE, Fantham M, Young LJ, Marciniak SJ, Kaminski CF, Ron D, Avezov E.

Nat Cell Biol. 2018 Oct;20(10):1118-1125. doi: 10.1038/s41556-018-0192-2. Epub 2018 Sep 17.

PMID:
30224760
3.

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

Guerrier C, Holcman D.

Front Synaptic Neurosci. 2018 Jul 23;10:23. doi: 10.3389/fnsyn.2018.00023. eCollection 2018. Review.

4.

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

Cartailler J, Holcman D.

Phys Chem Chem Phys. 2018 Aug 15;20(32):21062-21067. doi: 10.1039/c8cp02593b.

PMID:
30074044
5.

Encounter times of chromatin loci influenced by polymer decondensation.

Amitai A, Holcman D.

Phys Rev E. 2018 Mar;97(3-1):032417. doi: 10.1103/PhysRevE.97.032417.

PMID:
29776075
6.

Do cells sense time by number of divisions?

Schuss Z, Tor K, Holcman D.

J Theor Biol. 2018 Sep 7;452:10-16. doi: 10.1016/j.jtbi.2018.05.001. Epub 2018 May 9.

PMID:
29752953
7.
8.

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

Cartailler J, Kwon T, Yuste R, Holcman D.

Neuron. 2018 Mar 7;97(5):1126-1136.e10. doi: 10.1016/j.neuron.2018.01.034. Epub 2018 Feb 8.

PMID:
29429935
9.

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

Shukron O, Holcman D.

Phys Rev E. 2017 Jul;96(1-1):012503. doi: 10.1103/PhysRevE.96.012503. Epub 2017 Jul 27.

PMID:
29347098
10.

Reconstructing the gradient source position from steady-state fluxes to small receptors.

Dobramysl U, Holcman D.

Sci Rep. 2018 Jan 17;8(1):941. doi: 10.1038/s41598-018-19355-5.

11.

Electrostatics of non-neutral biological microdomains.

Cartailler J, Schuss Z, Holcman D.

Sci Rep. 2017 Sep 12;7(1):11269. doi: 10.1038/s41598-017-11590-6.

12.

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

Shukron O, Hauer M, Holcman D.

Sci Rep. 2017 Sep 4;7(1):10346. doi: 10.1038/s41598-017-10842-9.

13.

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

Shukron O, Holcman D.

PLoS Comput Biol. 2017 Apr 3;13(4):e1005469. doi: 10.1371/journal.pcbi.1005469. eCollection 2017 Apr.

14.

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

Amitai A, Seeber A, Gasser SM, Holcman D.

Cell Rep. 2017 Jan 31;18(5):1200-1214. doi: 10.1016/j.celrep.2017.01.018.

15.

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

Hauer MH, Seeber A, Singh V, Thierry R, Sack R, Amitai A, Kryzhanovska M, Eglinger J, Holcman D, Owen-Hughes T, Gasser SM.

Nat Struct Mol Biol. 2017 Feb;24(2):99-107. doi: 10.1038/nsmb.3347. Epub 2017 Jan 9.

PMID:
28067915
17.

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.

Tiana G, Amitai A, Pollex T, Piolot T, Holcman D, Heard E, Giorgetti L.

Biophys J. 2016 Mar 29;110(6):1234-45. doi: 10.1016/j.bpj.2016.02.003.

18.

Search for a small egg by spermatozoa in restricted geometries.

Yang J, Kupka I, Schuss Z, Holcman D.

J Math Biol. 2016 Aug;73(2):423-46. doi: 10.1007/s00285-015-0955-3. Epub 2015 Dec 26.

19.

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

Hoze N, Holcman D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Nov;92(5):052109. doi: 10.1103/PhysRevE.92.052109. Epub 2015 Nov 9.

PMID:
26651649
20.

Analysis and Interpretation of Superresolution Single-Particle Trajectories.

Holcman D, Hoze N, Schuss Z.

Biophys J. 2015 Nov 3;109(9):1761-71. doi: 10.1016/j.bpj.2015.09.003. Review.

21.

Why so many sperm cells?

Reynaud K, Schuss Z, Rouach N, Holcman D.

Commun Integr Biol. 2015 Jul 6;8(3):e1017156. doi: 10.1080/19420889.2015.1017156. eCollection 2015 May-Jun.

22.

The new nanophysiology: regulation of ionic flow in neuronal subcompartments.

Holcman D, Yuste R.

Nat Rev Neurosci. 2015 Nov;16(11):685-92. doi: 10.1038/nrn4022. Epub 2015 Oct 14. Review.

PMID:
26462753
23.

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

Reingruber J, Holcman D, Fain GL.

Bioessays. 2015 Nov;37(11):1243-52. doi: 10.1002/bies.201500081. Epub 2015 Sep 10.

24.

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

Amitai A, Toulouze M, Dubrana K, Holcman D.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004433. doi: 10.1371/journal.pcbi.1004433. eCollection 2015 Aug.

25.

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

Dao Duc K, Parutto P, Chen X, Epsztein J, Konnerth A, Holcman D.

Front Comput Neurosci. 2015 Jul 29;9:96. doi: 10.3389/fncom.2015.00096. eCollection 2015.

26.

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

Guerrier C, Hayes JA, Fortin G, Holcman D.

Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):9728-33. doi: 10.1073/pnas.1421997112. Epub 2015 Jul 20.

27.

Bursting reverberation as a multiscale neuronal network process driven by synaptic depression-facilitation.

Dao Duc K, Lee CY, Parutto P, Cohen D, Segal M, Rouach N, Holcman D.

PLoS One. 2015 May 27;10(5):e0124694. doi: 10.1371/journal.pone.0124694. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0137884. Dao Duc, K [corrected to Dao Duc, Khanh]; Lee, C Y [corrected to Lee, Chun-Yao].

28.

The neuroglial potassium cycle during neurotransmission: role of Kir4.1 channels.

Sibille J, Dao Duc K, Holcman D, Rouach N.

PLoS Comput Biol. 2015 Mar 31;11(3):e1004137. doi: 10.1371/journal.pcbi.1004137. eCollection 2015 Mar.

29.

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

Hoze N, Holcman D.

Biophys J. 2014 Dec 16;107(12):3008-3017. doi: 10.1016/j.bpj.2014.10.018.

30.

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

Reingruber J, Holcman D.

Semin Cell Dev Biol. 2014 Nov;35:189-202. doi: 10.1016/j.semcdb.2014.08.015. Epub 2014 Sep 4. Review.

PMID:
25194659
31.

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

Hoze N, Holcman D.

J Math Biol. 2015 Jun;70(7):1685-705. doi: 10.1007/s00285-014-0819-2. Epub 2014 Aug 8.

PMID:
25103220
32.

Oscillatory decay of the survival probability of activated diffusion across a limit cycle.

Dao Duc K, Schuss Z, Holcman D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Mar;89(3):030101. Epub 2014 Mar 7.

PMID:
24730773
33.

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

Holcman D, Dao Duc K, Jones A, Byrne H, Burrage K.

J Math Biol. 2015 Mar;70(4):805-28. doi: 10.1007/s00285-014-0782-y. Epub 2014 Apr 8.

PMID:
24710662
34.

Connexin 30 sets synaptic strength by controlling astroglial synapse invasion.

Pannasch U, Freche D, Dallérac G, Ghézali G, Escartin C, Ezan P, Cohen-Salmon M, Benchenane K, Abudara V, Dufour A, Lübke JH, Déglon N, Knott G, Holcman D, Rouach N.

Nat Neurosci. 2014 Apr;17(4):549-58. doi: 10.1038/nn.3662. Epub 2014 Mar 2.

PMID:
24584052
35.

Computing the length of the shortest telomere in the nucleus.

Duc KD, Holcman D.

Phys Rev Lett. 2013 Nov 27;111(22):228104. Epub 2013 Nov 27.

PMID:
24329474
36.

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

Amitai A, Holcman D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052604. Epub 2013 Nov 27.

PMID:
24329289
37.

Detection of single photons by toad and mouse rods.

Reingruber J, Pahlberg J, Woodruff ML, Sampath AP, Fain GL, Holcman D.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19378-83. doi: 10.1073/pnas.1314030110. Epub 2013 Nov 8.

38.

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

Bouchoucha YX, Reingruber J, Labalette C, Wassef MA, Thierion E, Desmarquet-Trin Dinh C, Holcman D, Gilardi-Hebenstreit P, Charnay P.

Mol Syst Biol. 2013;9:690. doi: 10.1038/msb.2013.46.

39.

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

Holcman D, Schuss Z.

Rep Prog Phys. 2013 Jul;76(7):074601. doi: 10.1088/0034-4885/76/7/074601. Epub 2013 Jun 20. Review.

PMID:
23787818
40.

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

Amitai A, Holcman D.

Phys Rev Lett. 2013 Jun 14;110(24):248105. Epub 2013 Jun 14.

PMID:
25165966
41.

The length of the shortest telomere as the major determinant of the onset of replicative senescence.

Xu Z, Duc KD, Holcman D, Teixeira MT.

Genetics. 2013 Aug;194(4):847-57. doi: 10.1534/genetics.113.152322. Epub 2013 Jun 3.

42.

Unraveling novel features hidden in superresolution microscopy data.

Holcman D.

Commun Integr Biol. 2013 May 1;6(3):e23893. doi: 10.4161/cib.23893.

43.

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

Hozé N, Ruault M, Amoruso C, Taddei A, Holcman D.

Mol Biol Cell. 2013 Jun;24(11):1791-800, S1-10. doi: 10.1091/mbc.E13-01-0031. Epub 2013 Apr 10.

44.

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

Amitai A, Amoruso C, Ziskind A, Holcman D.

J Chem Phys. 2012 Dec 28;137(24):244906. doi: 10.1063/1.4772403.

PMID:
23277955
45.

Synaptic transmission in neurological disorders dissected by a quantitative approach.

Freche D, Lee CY, Rouach N, Holcman D.

Commun Integr Biol. 2012 Sep 1;5(5):448-52. doi: 10.4161/cib.20818.

46.

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

Hoze N, Nair D, Hosy E, Sieben C, Manley S, Herrmann A, Sibarita JB, Choquet D, Holcman D.

Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):17052-7. doi: 10.1073/pnas.1204589109. Epub 2012 Oct 3.

47.

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

Amitai A, Kupka I, Holcman D.

Phys Rev Lett. 2012 Sep 7;109(10):108302. Epub 2012 Sep 5.

PMID:
23005335
48.

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

Lagache T, Danos O, Holcman D.

Biophys J. 2012 Mar 7;102(5):980-9. doi: 10.1016/j.bpj.2011.12.037. Epub 2012 Mar 6.

49.

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

Holcman D, Schuss Z.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jan;85(1 Pt 1):010103. Epub 2012 Jan 5.

PMID:
22400499
50.

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

Dao Duc K, Holcman D.

BMC Biophys. 2012 Jan 19;5:1. doi: 10.1186/2046-1682-5-1.

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