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Items: 36

1.

Long-term hindlimb unloading causes a preferential reduction of medullary thymic epithelial cells expressing autoimmune regulator (Aire).

Horie K, Kudo T, Yoshinaga R, Akiyama N, Sasanuma H, Kobayashi TJ, Shimbo M, Jeon H, Miyao T, Miyauchi M, Shirakawa M, Shiba D, Yoshida N, Muratani M, Takahashi S, Akiyama T.

Biochem Biophys Res Commun. 2018 Jun 27;501(3):745-750. doi: 10.1016/j.bbrc.2018.05.060.

PMID:
29753741
2.

Stochastic and information-thermodynamic structures of population dynamics in a fluctuating environment.

Kobayashi TJ, Sughiyama Y.

Phys Rev E. 2017 Jul;96(1-1):012402. doi: 10.1103/PhysRevE.96.012402. Epub 2017 Jul 5.

PMID:
29347239
3.

Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity.

Kajita MK, Aihara K, Kobayashi TJ.

Phys Rev E. 2017 Jul;96(1-1):012405. doi: 10.1103/PhysRevE.96.012405. Epub 2017 Jul 14.

PMID:
29347185
4.

Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information.

Yokota R, Kaminaga Y, Kobayashi TJ.

Front Immunol. 2017 Nov 15;8:1500. doi: 10.3389/fimmu.2017.01500. eCollection 2017.

5.

Steady-state thermodynamics for population growth in fluctuating environments.

Sughiyama Y, Kobayashi TJ.

Phys Rev E. 2017 Jan;95(1-1):012131. doi: 10.1103/PhysRevE.95.012131. Epub 2017 Jan 19.

PMID:
28208406
6.

Systematic time-dependent visualization and quantitation of the neurogenic rate in brain organoids.

Kosodo Y, Suetsugu T, Kobayashi TJ, Matsuzaki F.

Biochem Biophys Res Commun. 2017 Jan 29;483(1):94-100. doi: 10.1016/j.bbrc.2016.12.187. Epub 2017 Jan 4.

PMID:
28063930
7.

Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary.

Arata Y, Hiroshima M, Pack CG, Ramanujam R, Motegi F, Nakazato K, Shindo Y, Wiseman PW, Sawa H, Kobayashi TJ, Brandão HB, Shibata T, Sako Y.

Cell Rep. 2016 Sep 27;17(1):316. doi: 10.1016/j.celrep.2016.09.044. Epub 2016 Sep 27. No abstract available.

8.

Discreteness-induced transitions in multibody reaction systems.

Saito Y, Sughiyama Y, Kaneko K, Kobayashi TJ.

Phys Rev E. 2016 Aug;94(2-1):022140. doi: 10.1103/PhysRevE.94.022140. Epub 2016 Aug 29.

PMID:
27627279
9.

Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary.

Arata Y, Hiroshima M, Pack CG, Ramanujam R, Motegi F, Nakazato K, Shindo Y, Wiseman PW, Sawa H, Kobayashi TJ, Brandão HB, Shibata T, Sako Y.

Cell Rep. 2016 Aug 23;16(8):2156-2168. doi: 10.1016/j.celrep.2016.07.047. Epub 2016 Aug 11. Erratum in: Cell Rep. 2016 Sep 27;17 (1):316.

10.

Fluctuation Relations of Fitness and Information in Population Dynamics.

Kobayashi TJ, Sughiyama Y.

Phys Rev Lett. 2015 Dec 4;115(23):238102. doi: 10.1103/PhysRevLett.115.238102. Epub 2015 Dec 2.

PMID:
26684143
11.

Positive and Negative Regulatory Mechanisms for Fine-Tuning Cellularity and Functions of Medullary Thymic Epithelial Cells.

Akiyama T, Tateishi R, Akiyama N, Yoshinaga R, Kobayashi TJ.

Front Immunol. 2015 Sep 8;6:461. doi: 10.3389/fimmu.2015.00461. eCollection 2015. Review.

12.

Pathwise thermodynamic structure in population dynamics.

Sughiyama Y, Kobayashi TJ, Tsumura K, Aihara K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Mar;91(3):032120. Epub 2015 Mar 12.

PMID:
25871067
13.

Balancing acts of two HEAT subunits of condensin I support dynamic assembly of chromosome axes.

Kinoshita K, Kobayashi TJ, Hirano T.

Dev Cell. 2015 Apr 6;33(1):94-106. doi: 10.1016/j.devcel.2015.01.034.

14.

Experimental and theoretical bases for mechanisms of antigen discrimination by T cells.

Kajita MK, Yokota R, Aihara K, Kobayashi TJ.

Biophysics (Nagoya-shi). 2015 Mar 26;11:85-92. doi: 10.2142/biophysics.11.85. eCollection 2015. Review.

15.

Improved and robust detection of cell nuclei from four dimensional fluorescence images.

Bashar MK, Yamagata K, Kobayashi TJ.

PLoS One. 2014 Jul 14;9(7):e101891. doi: 10.1371/journal.pone.0101891. eCollection 2014.

16.

In vivo oriented modeling with consideration of intracellular crowding.

Hiroi N, Iba K, Tabira A, Okuhara T, Kubojima T, Hiraiwa T, Kobayashi TJ, Oka K, Funahashi A.

Conf Proc IEEE Eng Med Biol Soc. 2013;2013:2716-9. doi: 10.1109/EMBC.2013.6610101.

PMID:
24110288
17.

Information decoding in microscopic biological processes.

Kobayashi TJ.

Conf Proc IEEE Eng Med Biol Soc. 2013;2013:2704-7. doi: 10.1109/EMBC.2013.6610098.

PMID:
24110285
18.

Single cell visualization of yeast gene expression shows correlation of epigenetic switching between multiple heterochromatic regions through multiple generations.

Mano Y, Kobayashi TJ, Nakayama J, Uchida H, Oki M.

PLoS Biol. 2013 Jul;11(7):e1001601. doi: 10.1371/journal.pbio.1001601. Epub 2013 Jul 2.

19.

Meeting report of the International Workshop on Quantitative Biology 2012: mesoscopic and microscopic worlds meet.

Draviam VM, Funahashi A, Hiroi N, Kimura A, Kobayashi TJ.

Front Physiol. 2013 Jan 11;3:479. doi: 10.3389/fphys.2012.00479. eCollection 2012. No abstract available.

20.

Physiological Intracellular Crowdedness is Defined by the Perimeter-to-Area Ratio of Sub-Cellular Compartments.

Hiroi N, Okuhara T, Kubojima T, Iba K, Tabira A, Yamashita S, Okada Y, Kobayashi TJ, Funahashi A.

Front Physiol. 2012 Jul 23;3:293. doi: 10.3389/fphys.2012.00293. eCollection 2012.

21.

Information processing and integration with intracellular dynamics near critical point.

Kamimura A, Kobayashi TJ.

Front Physiol. 2012 Jun 13;3:203. doi: 10.3389/fphys.2012.00203. eCollection 2012.

22.

Automatic extraction of nuclei centroids of mouse embryonic cells from fluorescence microscopy images.

Bashar MK, Komatsu K, Fujimori T, Kobayashi TJ.

PLoS One. 2012;7(5):e35550. doi: 10.1371/journal.pone.0035550. Epub 2012 May 8.

23.

Theoretical aspects of cellular decision-making and information-processing.

Kobayashi TJ, Kamimura A.

Adv Exp Med Biol. 2012;736:275-91. doi: 10.1007/978-1-4419-7210-1_16. Review.

PMID:
22161335
24.

Perturbation analyses of intermolecular interactions.

Koyama YM, Kobayashi TJ, Ueda HR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Aug;84(2 Pt 2):026704. Epub 2011 Aug 12.

PMID:
21929141
25.

Dynamics of intracellular information decoding.

Kobayashi TJ, Kamimura A.

Phys Biol. 2011 Oct;8(5):055007. doi: 10.1088/1478-3975/8/5/055007. Epub 2011 Aug 10.

PMID:
21832798
26.
27.

Implementation of dynamic Bayesian decision making by intracellular kinetics.

Kobayashi TJ.

Phys Rev Lett. 2010 Jun 4;104(22):228104. Epub 2010 Jun 3.

PMID:
20867209
28.

Atypical cadherins Dachsous and Fat control dynamics of noncentrosomal microtubules in planar cell polarity.

Harumoto T, Ito M, Shimada Y, Kobayashi TJ, Ueda HR, Lu B, Uemura T.

Dev Cell. 2010 Sep 14;19(3):389-401. doi: 10.1016/j.devcel.2010.08.004.

29.

Perturbational formulation of principal component analysis in molecular dynamics simulation.

Koyama YM, Kobayashi TJ, Tomoda S, Ueda HR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Oct;78(4 Pt 2):046702. Epub 2008 Oct 7.

PMID:
18999556
30.

Estimation of the source-by-source effect of autorepression on genetic noise.

Okano H, Kobayashi TJ, Tozaki H, Kimura H.

Biophys J. 2008 Aug;95(3):1063-74. doi: 10.1529/biophysj.107.124677. Epub 2008 Apr 4.

31.

Reconstructing the single-cell-level behavior of a toggle switch from population-level measurements.

Tozaki H, Kobayashi TJ, Okano H, Yamamoto R, Aihara K, Kimura H.

FEBS Lett. 2008 Apr 2;582(7):1067-72. doi: 10.1016/j.febslet.2008.02.057. Epub 2008 Mar 4.

32.

Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks.

Ukai H, Kobayashi TJ, Nagano M, Masumoto KH, Sujino M, Kondo T, Yagita K, Shigeyoshi Y, Ueda HR.

Nat Cell Biol. 2007 Nov;9(11):1327-34. Epub 2007 Oct 21.

PMID:
17952058
33.

An optimal number of molecules for signal amplification and discrimination in a chemical cascade.

Morishita Y, Kobayashi TJ, Aihara K.

Biophys J. 2006 Sep 15;91(6):2072-81. Epub 2006 Jun 23.

34.

Feedback repression is required for mammalian circadian clock function.

Sato TK, Yamada RG, Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA, Ueda HR, Hogenesch JB.

Nat Genet. 2006 Mar;38(3):312-9. Epub 2006 Feb 12.

35.

Evaluation of the performance of mechanisms for noise attenuation in a single-gene expression.

Morishita Y, Kobayashi TJ, Aihara K.

J Theor Biol. 2005 Jul 21;235(2):241-64. Epub 2005 Feb 25.

PMID:
15862593
36.

Dynamics of gene regulatory networks with cell division cycle.

Chen L, Wang R, Kobayashi TJ, Aihara K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jul;70(1 Pt 1):011909. Epub 2004 Jul 15.

PMID:
15324090

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