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Items: 1 to 50 of 99

1.

Alpha rhythm collapse predicts iso-electric suppressions during anesthesia.

Cartailler J, Parutto P, Touchard C, Vallée F, Holcman D.

Commun Biol. 2019 Sep 2;2:327. doi: 10.1038/s42003-019-0575-3. eCollection 2019.

2.

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

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

Trends Genet. 2019 Sep;35(9):685-705. doi: 10.1016/j.tig.2019.06.007. Epub 2019 Jul 29. Review.

PMID:
31371030
3.

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

Shukron O, Piras V, Noordermeer D, Holcman D.

Nat Commun. 2019 Jun 14;10(1):2626. doi: 10.1038/s41467-019-10402-x.

4.

Fast calcium transients in dendritic spines driven by extreme statistics.

Basnayake K, Mazaud D, Bemelmans A, Rouach N, Korkotian E, Holcman D.

PLoS Biol. 2019 Jun 4;17(6):e2006202. doi: 10.1371/journal.pbio.2006202. eCollection 2019 Jun.

5.

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

Basnayake K, Holcman D.

Phys Life Rev. 2019 Mar;28:96-99. doi: 10.1016/j.plrev.2019.03.017. Epub 2019 May 22. No abstract available.

PMID:
31151792
6.

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

Holcman D, Yuste R.

Nat Rev Neurosci. 2019 Aug;20(8):509. doi: 10.1038/s41583-019-0182-9.

PMID:
31123354
7.

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

Holcman D, Yuste R.

Nat Rev Neurosci. 2019 Aug;20(8):510. doi: 10.1038/s41583-019-0181-x.

PMID:
31123353
8.

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

Heck J, Parutto P, Ciuraszkiewicz A, Bikbaev A, Freund R, Mitlöhner J, Andres-Alonso M, Fejtova A, Holcman D, Heine M.

Neuron. 2019 Jul 3;103(1):66-79.e12. doi: 10.1016/j.neuron.2019.04.030. Epub 2019 May 16.

PMID:
31104951
9.

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

Cartailler J, Holcman D.

J Math Biol. 2019 Jul;79(1):155-185. doi: 10.1007/s00285-019-01353-4. Epub 2019 Apr 9.

PMID:
30968199
10.

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

Schuss Z, Basnayake K, Holcman D.

Phys Life Rev. 2019 Mar;28:52-79. doi: 10.1016/j.plrev.2019.01.001. Epub 2019 Jan 11. Review.

PMID:
30691960
11.

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.

12.

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.

13.

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
14.

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
15.

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
16.
17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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
26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

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. Erratum in: Nat Rev Neurosci. 2019 Aug;20(8):510. Nat Rev Neurosci. 2019 Aug;20(8):509.

PMID:
26462753
32.

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.

33.

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.

34.

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.

35.

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.

36.

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].

37.

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.

38.

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.

39.

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
40.

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
41.

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
42.

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
43.

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
44.

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
45.

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
46.

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.

47.

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.

48.

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
49.

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
50.

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.

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