Shinji Nakaoka

Shinji Nakaoka

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Shinji Nakaoka

Shinji Nakaoka

Publications by authors named "Shinji Nakaoka"

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Revealing uninfected and infected target cell dynamics from peripheral blood data in highly and less pathogenic simian/human immunodeficiency virus infected Rhesus macaque.

J Theor Biol 2019 Oct 9;479:29-36. Epub 2019 Jul 9.

Department of Biology, Kyushu University, Nishi-ku, Fukuoka, Japan; MIRAI, JST, Kawaguchi, Saitama, Japan; CREST, JST, Kawaguchi, Saitama, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.07.005DOI Listing
October 2019

T-Cell mediated adaptive immunity and antibody-dependent enhancement in secondary dengue infection.

J Theor Biol 2019 Jun 13;470:50-63. Epub 2019 Mar 13.

Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan; PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.03.010DOI Listing
June 2019

Information and Statistical Analysis Pipeline for High-Throughput RNA Sequencing Data.

Methods Mol Biol 2019 Jun 22. Epub 2019 Jun 22.

Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.

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http://dx.doi.org/10.1007/7651_2019_245DOI Listing
June 2019

Mathematical Analysis of a Transformed ODE from a PDE Multiscale Model of Hepatitis C Virus Infection.

Bull Math Biol 2019 May 14;81(5):1427-1441. Epub 2019 Jan 14.

Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, 819-0395, Japan.

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http://dx.doi.org/10.1007/s11538-018-00564-yDOI Listing
May 2019

Calculation of final size for vector-transmitted epidemic model.

Math Biosci Eng 2019 03;16(4):2219-2232

Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.

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http://dx.doi.org/10.3934/mbe.2019109DOI Listing
March 2019

A PDE multiscale model of hepatitis C virus infection can be transformed to a system of ODEs.

J Theor Biol 2018 07 7;448:80-85. Epub 2018 Apr 7.

Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan; PRESTO, JST, Saitama 332-0012, Japan; CREST, JST, Saitama 332-0012, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2018.04.006DOI Listing
July 2018

Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells.

Proc Natl Acad Sci U S A 2018 02 22;115(6):E1269-E1278. Epub 2018 Jan 22.

Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;

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http://dx.doi.org/10.1073/pnas.1715724115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819419PMC
February 2018

Human-Specific Adaptations in Vpu Conferring Anti-tetherin Activity Are Critical for Efficient Early HIV-1 Replication In Vivo.

Cell Host Microbe 2018 Jan;23(1):110-120.e7

Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2017.12.009DOI Listing
January 2018

Erratum to: Daphnia revisited: local stability and bifurcation theory for physiologically structured population models explained by way of an example.

J Math Biol 2017 07;75(1):259-261

Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s00285-017-1148-zDOI Listing
July 2017

Modelling Ebola virus dynamics: Implications for therapy.

Antiviral Res 2016 11 12;135:62-73. Epub 2016 Oct 12.

Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, 8128581, Japan; PRESTO, JST, Kawaguchi, Saitama, 3320012, Japan; CREST, JST, Kawaguchi, Saitama, 3320012, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.antiviral.2016.10.004DOI Listing
November 2016

Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data.

Nucleic Acids Res 2016 06 30;44(11):5010-21. Epub 2016 Apr 30.

Laboratory for disease systems modeling, RIKEN Center for Integrated Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan The Systems Biology Institute, Minato-ku, Tokyo 108-0071, Japan Sony Computer Science Laboratories, Inc, Shinagawa-ku, Tokyo 141-0022, Japan Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa 904-0495, Japan.

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http://dx.doi.org/10.1093/nar/gkw355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914117PMC
June 2016

New algorithm for constructing area-based index with geographical heterogeneities and variable selection: An application to gastric cancer screening.

Sci Rep 2016 05 24;6:26582. Epub 2016 May 24.

Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1038/srep26582DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877577PMC
May 2016

Quantifying the effect of Vpu on the promotion of HIV-1 replication in the humanized mouse model.

Retrovirology 2016 Apr 18;13:23. Epub 2016 Apr 18.

Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka, 812-8581, Japan.

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http://dx.doi.org/10.1186/s12977-016-0252-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834825PMC
April 2016

Dynamics of HIV infection in lymphoid tissue network.

J Math Biol 2016 Mar 27;72(4):909-938. Epub 2015 Oct 27.

Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan.

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http://dx.doi.org/10.1007/s00285-015-0940-xDOI Listing
March 2016

Identifying determinants of heterogeneous transmission dynamics of the Middle East respiratory syndrome (MERS) outbreak in the Republic of Korea, 2015: a retrospective epidemiological analysis.

BMJ Open 2016 Feb 23;6(2):e009936. Epub 2016 Feb 23.

CREST, Japan Science and Technology Agency, Saitama, Japan Graduate School of Medicine, Hokkaido University, Sapporo-shi, Hokkaido, Japan Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1136/bmjopen-2015-009936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769415PMC
February 2016

A conservation law for virus infection kinetics in vitro.

J Theor Biol 2015 Jul 14;376:39-47. Epub 2015 Apr 14.

Department of Biology, Kyushu University, Fukuoka, Japan; CREST, JST, Saitama, Japan; PRESTO, JST, Saitama, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2015.03.034DOI Listing
July 2015

A method to determine the duration of the eclipse phase for in vitro infection with a highly pathogenic SHIV strain.

Sci Rep 2015 May 21;5:10371. Epub 2015 May 21.

1] Department of Biology, Kyushu University, Fukuoka 812-8581, Japan [2] PRESTO, JST, Kawaguchi, Saitama 3320012, Japan [3] CREST, JST, Kawaguchi, Saitama 3320012, Japan.

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http://www.nature.com/articles/srep10371
Publisher Site
http://dx.doi.org/10.1038/srep10371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440524PMC
May 2015

Multiscale mathematical modeling and simulation of cellular dynamical process.

Authors:
Shinji Nakaoka

Methods Mol Biol 2014 ;1195:269-83

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http://dx.doi.org/10.1007/7651_2014_78DOI Listing
February 2015

Demographic modeling of transient amplifying cell population growth.

Math Biosci Eng 2014 Apr;11(2):363-84

Laboratory for Mathematical Modeling of Immune System, RCAI, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, 230-0045, Japan.

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http://dx.doi.org/10.3934/mbe.2014.11.363DOI Listing
April 2014

Cost-effective length and timing of school closure during an influenza pandemic depend on the severity.

Theor Biol Med Model 2014 Jan 21;11. Epub 2014 Jan 21.

Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 1130033, Japan.

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http://dx.doi.org/10.1186/1742-4682-11-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901768PMC
January 2014

Stochastic simulation of structured skin cell population dynamics.

J Math Biol 2013 Mar 20;66(4-5):807-35. Epub 2012 Dec 20.

Laboratory for Mathematical Modeling of Immune System, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1007/s00285-012-0618-6DOI Listing
March 2013

Mathematical study on kinetics of hematopoietic stem cells--theoretical conditions for successful transplantation.

J Biol Dyn 2012 14;6:836-54. Epub 2011 Jun 14.

FIRST, Aihara Innovative Mathematical Modelling Project, Japan Science and Technology Agency, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.

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http://dx.doi.org/10.1080/17513758.2011.588343DOI Listing
December 2012

Daphnia revisited: local stability and bifurcation theory for physiologically structured population models explained by way of an example.

J Math Biol 2010 Aug 22;61(2):277-318. Epub 2009 Sep 22.

Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P. O. Box 94248, 1090 GE, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s00285-009-0299-yDOI Listing
August 2010

Immune impairment in HIV infection: existence of risky and immunodeficiency thresholds.

J Theor Biol 2009 Oct 3;260(4):490-501. Epub 2009 Jul 3.

Graduate School of Science and Technology, Shizuoka University, Japan.

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http://dx.doi.org/10.1016/j.jtbi.2009.06.023DOI Listing
October 2009

Effect of parental care and aggregation on population dynamics.

J Theor Biol 2009 Sep 17;260(1):161-71. Epub 2009 Jun 17.

The University of Tokyo, Komaba, Meguro, Japan.

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http://dx.doi.org/10.1016/j.jtbi.2009.06.012DOI Listing
September 2009

A geographical spread of vaccine-resistance in avian influenza epidemics.

J Theor Biol 2009 Jul 8;259(2):219-28. Epub 2009 Apr 8.

Graduate School of Science and Technology, Shizuoka University, Japan.

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http://dx.doi.org/10.1016/j.jtbi.2009.03.040DOI Listing
July 2009

Dynamical adaptation of parental care.

Bull Math Biol 2009 May 20;71(4):931-51. Epub 2009 Feb 20.

Graduate School of Science and Technology, Shizuoka University, Hamamatsu, 432-8561, Japan.

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http://dx.doi.org/10.1007/s11538-008-9388-0DOI Listing
May 2009

Immune impairment thresholds in HIV infection.

Immunol Lett 2009 Apr 24;123(2):149-54. Epub 2009 Mar 24.

Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku Naka-ku, Hamamatsu 432-8561, Japan.

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http://dx.doi.org/10.1016/j.imlet.2009.03.007DOI Listing
April 2009

Complementary cooperation between two syntrophic bacteria in pesticide degradation.

J Theor Biol 2009 Feb 11;256(4):644-54. Epub 2008 Nov 11.

Department of Environment and Energy System, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.

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http://dx.doi.org/10.1016/j.jtbi.2008.10.024DOI Listing
February 2009

Invest conflicts of adult predators.

J Theor Biol 2008 Jul 22;253(1):12-23. Epub 2007 Sep 22.

Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing 400715, PR China.

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http://dx.doi.org/10.1016/j.jtbi.2007.09.021DOI Listing
July 2008

Mathematical analysis of a HIV model with frequency dependence and viral diversity.

Math Biosci Eng 2008 Jul;5(3):457-76

Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan.

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July 2008

Viral diversity limits immune diversity in asymptomatic phase of HIV infection.

Theor Popul Biol 2008 May 7;73(3):332-41. Epub 2008 Feb 7.

Graduate School of Science and Technology, Shizuoka University, Japan.

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http://dx.doi.org/10.1016/j.tpb.2008.01.003DOI Listing
May 2008

Prey-predator system with parental care for predators.

J Theor Biol 2006 Aug 18;241(3):451-8. Epub 2006 Jan 18.

Department of Mathematics, Southwest Normal University, Chongqing 400715, PR China.

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http://dx.doi.org/10.1016/j.jtbi.2005.12.008DOI Listing
August 2006

Competition in chemostat-type equations with two habitats.

Math Biosci 2006 May 30;201(1-2):157-71. Epub 2006 Jan 30.

Graduate School of Science and Technology, Shizuoka University, Johoku 3-5-1, Hamamatsu, Shizuoka 432-8561, Japan.

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http://dx.doi.org/10.1016/j.mbs.2005.12.011DOI Listing
May 2006