Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 48

1.

Dynamic Modeling of Indole Glucosinolate Hydrolysis and Its Impact on Auxin Signaling.

Vik D, Mitarai N, Wulff N, Halkier BA, Burow M.

Front Plant Sci. 2018 Apr 26;9:550. doi: 10.3389/fpls.2018.00550. eCollection 2018.

2.

Theory of invasion extinction dynamics in minimal food webs.

Haerter JO, Mitarai N, Sneppen K.

Phys Rev E. 2018 Feb;97(2-1):022404. doi: 10.1103/PhysRevE.97.022404.

PMID:
29548095
3.

Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology.

Harms A, Brodersen DE, Mitarai N, Gerdes K.

Mol Cell. 2018 Jun 7;70(5):768-784. doi: 10.1016/j.molcel.2018.01.003. Epub 2018 Feb 3. Review.

PMID:
29398446
4.

Existence and construction of large stable food webs.

Haerter JO, Mitarai N, Sneppen K.

Phys Rev E. 2017 Sep;96(3-1):032406. doi: 10.1103/PhysRevE.96.032406. Epub 2017 Sep 8.

PMID:
29346992
5.

A growing microcolony can survive and support persistent propagation of virulent phages.

Eriksen RS, Svenningsen SL, Sneppen K, Mitarai N.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):337-342. doi: 10.1073/pnas.1708954115. Epub 2017 Dec 19.

6.

Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation.

Tian C, Semsey S, Mitarai N.

Nucleic Acids Res. 2017 Aug 21;45(14):8180-8189. doi: 10.1093/nar/gkx552.

7.

Deterministic extinction by mixing in cyclically competing species.

Feldager CW, Mitarai N, Ohta H.

Phys Rev E. 2017 Mar;95(3-1):032318. doi: 10.1103/PhysRevE.95.032318. Epub 2017 Mar 20.

PMID:
28415345
8.

Characterization of phase transitions in a model ecosystem of sessile species.

Uekermann F, Mathiesen J, Mitarai N.

Phys Rev E. 2017 Mar;95(3-1):032409. doi: 10.1103/PhysRevE.95.032409. Epub 2017 Mar 13.

PMID:
28415313
9.

Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination.

Eriksen M, Sneppen K, Pedersen S, Mitarai N.

Front Microbiol. 2017 Mar 14;8:362. doi: 10.3389/fmicb.2017.00362. eCollection 2017.

10.

Bifurcation of transition paths induced by coupled bistable systems.

Tian C, Mitarai N.

J Chem Phys. 2016 Jun 7;144(21):215102. doi: 10.1063/1.4953242.

PMID:
27276971
11.

Three is much more than two in coarsening dynamics of cyclic competitions.

Mitarai N, Gunnarson I, Pedersen BN, Rosiek CA, Sneppen K.

Phys Rev E. 2016 Apr;93:042408. doi: 10.1103/PhysRevE.93.042408. Epub 2016 Apr 12.

PMID:
27176330
12.

Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Module-Encoded mRNases.

Tian C, Roghanian M, Jørgensen MG, Sneppen K, Sørensen MA, Gerdes K, Mitarai N.

J Bacteriol. 2016 Jun 27;198(14):1918-1926. doi: 10.1128/JB.00062-16. Print 2016 Jul 15.

13.

Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli.

Mitarai N, Brown S, Sneppen K.

J Bacteriol. 2016 May 27;198(12):1783-93. doi: 10.1128/JB.00965-15. Print 2016 Jun 15.

14.

Food Web Assembly Rules for Generalized Lotka-Volterra Equations.

Haerter JO, Mitarai N, Sneppen K.

PLoS Comput Biol. 2016 Feb 1;12(2):e1004727. doi: 10.1371/journal.pcbi.1004727. eCollection 2016 Feb.

15.

Dynamic competition between transcription initiation and repression: Role of nonequilibrium steps in cell-to-cell heterogeneity.

Mitarai N, Semsey S, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Aug;92(2):022710. Epub 2015 Aug 13.

PMID:
26382435
16.

Coupled positive and negative feedbacks produce diverse gene expression patterns in colonies.

Mitarai N, Jensen MH, Semsey S.

MBio. 2015 Apr 7;6(2). pii: e00059-15. doi: 10.1128/mBio.00059-15.

17.

Disturbance accelerates the transition from low- to high-diversity state in a model ecosystem.

Botta F, Mitarai N.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Feb;89(2):022704. Epub 2014 Feb 4.

PMID:
25353506
18.

Phage and bacteria support mutual diversity in a narrowing staircase of coexistence.

Haerter JO, Mitarai N, Sneppen K.

ISME J. 2014 Nov;8(11):2317-26. doi: 10.1038/ismej.2014.80. Epub 2014 May 23.

19.

Speciation, diversification, and coexistence of sessile species that compete for space.

Mitarai N, Heinsalu E, Sneppen K.

PLoS One. 2014 May 12;9(5):e96665. doi: 10.1371/journal.pone.0096665. eCollection 2014.

20.

Control of ribosome traffic by position-dependent choice of synonymous codons.

Mitarai N, Pedersen S.

Phys Biol. 2013 Oct;10(5):056011. doi: 10.1088/1478-3975/10/5/056011. Epub 2013 Oct 8.

PMID:
24104350
21.

Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy.

Cataudella I, Sneppen K, Gerdes K, Mitarai N.

PLoS Comput Biol. 2013;9(8):e1003174. doi: 10.1371/journal.pcbi.1003174. Epub 2013 Aug 29.

22.

Entrainment of noise-induced and limit cycle oscillators under weak noise.

Mitarai N, Alon U, Jensen MH.

Chaos. 2013 Jun;23(2):023125. doi: 10.1063/1.4808253.

PMID:
23822490
23.

Circuit architecture explains functional similarity of bacterial heat shock responses.

Inoue M, Mitarai N, Trusina A.

Phys Biol. 2012 Dec;9(6):066003. doi: 10.1088/1478-3975/9/6/066003. Epub 2012 Oct 31.

PMID:
23114274
24.

Emergence of diversity in a model ecosystem.

Mitarai N, Mathiesen J, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1 Pt 1):011929. Epub 2012 Jul 30.

PMID:
23005473
25.

Multistability with a metastable mixed state.

Sneppen K, Mitarai N.

Phys Rev Lett. 2012 Sep 7;109(10):100602. Epub 2012 Sep 5.

PMID:
23005273
26.

Information spreading and development of cultural centers.

Dybiec B, Mitarai N, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 May;85(5 Pt 2):056116. Epub 2012 May 18.

PMID:
23004830
27.

Switching between oscillations and homeostasis in competing negative and positive feedback motifs.

Li W, Krishna S, Pigolotti S, Mitarai N, Jensen MH.

J Theor Biol. 2012 Aug 21;307:205-10. doi: 10.1016/j.jtbi.2012.04.011. Epub 2012 Apr 21.

PMID:
22762992
28.

Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery.

Cataudella I, Trusina A, Sneppen K, Gerdes K, Mitarai N.

Nucleic Acids Res. 2012 Aug;40(14):6424-34. doi: 10.1093/nar/gks297. Epub 2012 Apr 11.

29.

Fluid dynamics of dilatant fluids.

Nakanishi H, Nagahiro S, Mitarai N.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jan;85(1 Pt 1):011401. Epub 2012 Jan 11.

PMID:
22400567
30.

Protein localization with flexible DNA or RNA.

Bernhardsson S, Mitarai N, Sneppen K.

PLoS One. 2012;7(2):e29218. doi: 10.1371/journal.pone.0029218. Epub 2012 Feb 10.

31.

Ecosystems with mutually exclusive interactions self-organize to a state of high diversity.

Mathiesen J, Mitarai N, Sneppen K, Trusina A.

Phys Rev Lett. 2011 Oct 28;107(18):188101. Epub 2011 Oct 25.

PMID:
22107676
32.

Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds.

Lizana L, Mitarai N, Sneppen K, Nakanishi H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jun;83(6 Pt 2):066116. Epub 2011 Jun 28.

PMID:
21797450
33.

The functional half-life of an mRNA depends on the ribosome spacing in an early coding region.

Pedersen M, Nissen S, Mitarai N, Lo Svenningsen S, Sneppen K, Pedersen S.

J Mol Biol. 2011 Mar 18;407(1):35-44. doi: 10.1016/j.jmb.2011.01.025. Epub 2011 Jan 19.

PMID:
21255584
34.

Theory for the stability and regulation of epigenetic landscapes.

Micheelsen MA, Mitarai N, Sneppen K, Dodd IB.

Phys Biol. 2010 Jun 4;7(2):026010. doi: 10.1088/1478-3975/7/2/026010.

PMID:
20526030
35.

Nonideal behavior of the intramolecular structure factor of dilute polymers in a theta solvent.

Shimomura K, Nakanishi H, Mitarai N.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Nov;80(5 Pt 1):051804. Epub 2009 Nov 30.

PMID:
20364998
36.

Loewner driving functions for off-critical percolation clusters.

Kondo Y, Mitarai N, Nakanishi H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Nov;80(5 Pt 1):050102. Epub 2009 Nov 4.

PMID:
20364936
37.

Dynamics of the recovery from sRNA-mediated gene silencing.

Semsey S, Benjamin JA, Mitarai N, Krishna S, Csiszovszki Z, Sneppen K, Massé E.

Cell Cycle. 2009 Sep 15;8(18):2863-4. Epub 2009 Sep 30. No abstract available.

PMID:
19729996
38.

Dynamic features of gene expression control by small regulatory RNAs.

Mitarai N, Benjamin JA, Krishna S, Semsey S, Csiszovszki Z, Massé E, Sneppen K.

Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10655-9. doi: 10.1073/pnas.0901466106. Epub 2009 Jun 16.

39.

Dynamical analysis on gene activity in the presence of repressors and an interfering promoter.

Nakanishi H, Mitarai N, Sneppen K.

Biophys J. 2008 Nov 1;95(9):4228-40. doi: 10.1529/biophysj.108.132894. Epub 2008 Jul 25.

40.

Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization.

Mitarai N, Sneppen K, Pedersen S.

J Mol Biol. 2008 Sep 26;382(1):236-45. doi: 10.1016/j.jmb.2008.06.068. Epub 2008 Jul 1.

PMID:
18619977
41.

The generation of promoter-mediated transcriptional noise in bacteria.

Mitarai N, Dodd IB, Crooks MT, Sneppen K.

PLoS Comput Biol. 2008 Jul 11;4(7):e1000109. doi: 10.1371/journal.pcbi.1000109.

42.

Anomalous fluctuations in sliding motion of cytoskeletal filaments driven by molecular motors: model simulations.

Imafuku Y, Mitarai N, Tawada K, Nakanishi H.

J Phys Chem B. 2008 Feb 7;112(5):1487-93. doi: 10.1021/jp074838l. Epub 2008 Jan 12.

PMID:
18189378
43.

Efficient degradation and expression prioritization with small RNAs.

Mitarai N, Andersson AM, Krishna S, Semsey S, Sneppen K.

Phys Biol. 2007 Oct 2;4(3):164-71.

PMID:
17928655
44.

Velocity correlations in dense granular shear flows: effects on energy dissipation and normal stress.

Mitarai N, Nakanishi H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Mar;75(3 Pt 1):031305. Epub 2007 Mar 26.

PMID:
17500691
45.

Bagnold scaling, density plateau, and kinetic theory analysis of dense granular flow.

Mitarai N, Nakanishi H.

Phys Rev Lett. 2005 Apr 1;94(12):128001. Epub 2005 Apr 1. Erratum in: Phys Rev Lett. 2006 Jul 7;97(1):019902.

PMID:
15903963
46.

Hard-sphere limit of soft-sphere model for granular materials: stiffness dependence of steady granular flow.

Mitarai N, Nakanishi H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Feb;67(2 Pt 1):021301. Epub 2003 Feb 19.

PMID:
12636665
47.

Collisional granular flow as a micropolar fluid.

Mitarai N, Hayakawa H, Nakanishi H.

Phys Rev Lett. 2002 Apr 29;88(17):174301. Epub 2002 Apr 12.

PMID:
12005760
48.

Spatiotemporal structure of traffic flow in a system with an open boundary

Mitarai N, Nakanishi H.

Phys Rev Lett. 2000 Aug 21;85(8):1766-9.

PMID:
10970609

Supplemental Content

Loading ...
Support Center