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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen Ø
Mail:  cmolnbi.dk

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Namiko Mitarai

Namiko Mitarai
Position: Associate Professor
Email: mitarainbi.dk
www: http://www.nbi.dk/~mitarai/
Phone: +45 353 25402

Publications:
Cilie W. Feldager, Namiko Mitarai, Hiroki Ohta
Deterministic extinction by mixing in cyclically competing species
Phys. Rev. E 95:032318 (2017)
1609.08297

Florian Uekermann, Joachim Mathiesen, Namiko Mitarai
Characterization of phase transitions in a model ecosystem of sessile species
Phys. Rev. E 95:032409 (2017)
1611.00171

Jan O Haerter, Namiko Mitarai, Kim Sneppen
Existence and construction of large stable food webs
BioarXiv (preprint) 0: (2017)

Mette Eriksen, Kim Sneppen, Steen Pedersen, and Namiko Mitarai
Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination
Front. Microbiol. 8:362 (2017)

Jan O. Haerter, Namiko Mitarai, and Kim Sneppen
Food Web Assembly Rules for Generalized Lotka-Volterra Equations
Plos Computational Biology 12: e1004727 (2016)
1501.04497

Namiko Mitarai, Ivar Gunnarson, Buster Niels Pedersen, Christian Anker Rosiek, and Kim Sneppen
Three is much more than two in coarsening dynamics of cyclic competitions
Phys. Rev. E 93:042408 (2016)
1512.00769

Namiko Mitarai, Stanley Brown and Kim Sneppen
Population dynamics of phage and bacteria in spatially structured habitats using Phage λ and Escherichia coli
Journal of Bacteriology 198:1783 (2016)

Chengzhe Tian, Mohammad Roghanian, Mikkel Girke Jørgensen, Kim Sneppen, Michael Askvad Sørensen, Kenn Gerdes and Namiko Mitarai
Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases
Journal of Bacteriology 198:1918 (2016)

Chengzhe Tian and Namiko Mitarai
Bifurcation of transition paths induced by coupled bistable systems
The Journal of Chemical Physics 144:215102 (2016)
1603.04477

Namiko Mitarai, Mogens Høgh Jensen, Szabolcs Semsey
Coupled Positive and Negative Feedbacks Produce Diverse Gene Expression Patterns in Colonies
mBio 6:e00059-15 (2015)

Namiko Mitarai, Szabolcs Semsey, Kim Sneppen
Dynamic competition between transcription initiation and repression: Role of non-equilibrium steps in cell-to-cell heterogeneity
Phys. Rev. E 92:022710 (2015)
1502.03011

Bartłomiej Dybiec, Namiko Mitarai, and Kim Sneppen
Modeling rises and falls in money addicted social hierarchies
Physica Scripta 89:085002 (2014)

Filippo Botta and Namiko Mitarai
Disturbance accelerates the transition from low- to high-diversity state in a model ecosystem
Phys. Rev. E 89:022704 (2014)

Namiko Mitarai, Els Heinsalu, Kim Sneppen
Speciation, Diversification, and Coexistence of Sessile Species That Compete for Space
Plos One 9:e96665 (2014)

Jan O Haerter, Namiko Mitarai, and Kim Sneppen
Phage and bacteria support mutual diversity in a narrowing staircase of coexistence
The ISME Journal 8:2317 (2014)

Namiko Mitarai, Uri Alon, Mogens H. Jensen
Entrainment of noise-induced and limit cycle oscillators under weak noise
Chaos 23:023125 (2013)
1301.2440

Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, Namiko Mitarai
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
PLoS Comput Biol 9:e1003174 (2013)

Shin-ichiro Nagahiro, Hiizu Nakanishi, Namiko Mitarai
Experimental observation of shear thickening oscillation
EPL 104:28002 (2013)
1211.2886

Namiko Mitarai and Steen Pedersen
Control of ribosome traffic by position-dependent choice of synonymous codons
Phys. Biol. 10:056011 (2013)
arXiv:1309.0936

Sebastian Bernhardsson, Namiko Mitarai, Kim Sneppen
Protein Localization with Flexible DNA or RNA
Plos One 7:e29218 (2012)

Hiizu Nakanishi, Shin-ichiro Nagahiro, and Namiko Mitarai.
Fluid dynamics of dilatant fluid
Phys. Rev. E 85:011401 (2012)
1112.4593

Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery
Nuc. Acids Res. 40:6424 (2012)

Namiko Mitarai and Hiizu Nakanishi
Granular flow: Dry and wet
Eur. Phys. J. Special Topics 204:5 (2012)

Weihan Li, Sandeep Krishna, Simone Pigolotti, Namiko Mitarai, and Mogens H. Jensen.
Switching between oscillations and homeostasis in competing negative and positive feedback motifs
J. Theor. Biol. 307:205 (2012)
1204.3760

Bartlomiej Dybiec, Namiko Mitarai, Kim Sneppen
Information spreading and development of cultural centers
Phys. Rev. E 85:056116 (2012)

Namiko Mitarai, Joachim Mathiesen, Kim Sneppen
Emergence of diversity in a model ecosystem
Phys. Rev. E 86:011929 (2012)
1204.3398

Kim Sneppen and Namiko Mitarai
Multistability with a Metastable Mixed State
Phys. Rev. Lett. 109:100602 (2012)

Masayo Inoue, Namiko Mitarai, and Ala Trusina.
Circuit architecture explains functional similarity of bacterial heat shock responses
Phys. Biol. 9:066003 (2012)
1209.2504

Margit Pedersen, Søren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen, and Steen Pedersen
The Functional Half-Life of an mRNA Depends on the Ribosome Spacing in an Early Coding Region
J. Mol. Biol. 407:35 (2011)

L. Lizana, N. Mitarai, H. Nakanishi, and K. Sneppen
Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds
Phys. Rev. E 83:066116 (2011)
1101.3998

Joachim Mathiesen, Namiko Mitarai, Kim Sneppen, and Ala Trusina
Ecosystems with mutually exclusive interactions self-organize to a state of high diversity
Phys. Rev. Lett. 107 107:188101 (2011)
1108.2011

Hiizu Nakanishi and Namiko Mitarai
Shear Thickening Oscillation in a Dilatant Fluid
J. Phys. Soc. Jpn. 80:033801 (2011)
1010.5063

Mille A. Micheelsen, Namiko Mitarai, Kim Sneppen, Ian. B. Dodd
Theory for stability and regulation of epigenetic landscapes
Phys. Biol. 7:026010 (2010)
1002.1600

Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, Szabolcs Semsey, Zsolt Csiszovszki, Eric Massé, and Kim Sneppen
Dynamic features of gene expression control by small regulatory RNAs
Proc. Natl. Acad. Sci. USA 106:10655 (2009)

Szabolcs Semsey, Julie-Anna M. Benjamin, Namiko Mitarai, Sandeep Krishna, Zsolt Csiszovszki, Kim Sneppen and Eric Massé
Dynamics of the recovery from sRNA-mediated gene silencing
Cell Cycle 8:2863 (2009)

Namiko Mitarai and Hiizu Nakanishi
Simple Model for Wet Granular Materials with Liquid Clusters
Europhys. Lett. 88:64001 (2009)
0908.1477v2

Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen
The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
PLoS Comput. Biol. 4:e1000109 (2008)

Namiko Mitarai, Kim Sneppen, Steen Pedersen
Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization
J. Mol. Biol. 382:236 (2008)

Hiizu Nakanishi, Namiko Mitarai, Kim Sneppen
Dynamical Analysis on Gene Activity in the Presence of Repressors and an Interfering Promoter
Biophysical Journal 95:4228 (2008)

Namiko Mitarai, Anna M. C. Andersson, Sandeep Krishna, Szabolcs Semsey, and Kim Sneppen
Efficient degradation and expression prioritization with small RNAs
Phys. biol. 4:164 (2007)
q-bio.MN/0611069