My Google Scholar website. A list of Japanease publication is summarized in another page.

Selected papers

[14] Chie Katsuyama, Shinji Nakaoka, Yasuhiro Takeuchi, Kanako Tago, Masahito Hayatsu and Kenji Kato, Complementary cooperation between two syntrophic bacteria in pesticide degradation, Journal of Theoretical Biology 256 (2009) 644--654.

[16] Odo Diekmann, Mats Gyllenberg, J.A.J. Metz, Shinji Nakaoka and André de Roos, Daphnia revisited: local stability and bifurcation theory for physiologically structured population models explained by way of an example, Journal of Mathematical Biology 61 (2010) 277--318.

[18] Shinji Nakaoka and Kazuyuki Aihara, Stochastic simulation of structured skin cell population dynamics, Journal of Mathematical Biology 66 (2013) 807--35.

[19] Shinji Nakaoka and Hisashi Inaba, Demographic modeling of transient amplifying cell population growth, Mathematical Biosciences and Engineering 11 (2014) 363--384.

[29] Shinji Nakaoka, Shingo Iwami, and Kei Sato, Dynamics of HIV infection in lymphoid tissue network, Journal of Mathematical Biology, 72:909--938 (2016) (DOI:10.1007/s00285-015-0940-x).

[36] Alexey Martyushev*, Shinji Nakaoka*, Kei Sato, Takeshi Noda, Shingo Iwami, Modelling Ebola Virus Dynamics: Implications for Therapy, Antiviral Research (2016) 135 62--73 [*equally contributed as a first author].

2004 -- 2009

[1] Shinji Nakaoka and Yasuhiro Takeuchi, How can three species coexist in a periodic chemostat? : Mathematical and Numerical Study, Difference equations and discrete dynamical systems World Sci. Publ., Hackensack, NJ, (2005) 121--133.

[2] Shinji Nakaoka and Yasuhiro Takeuchi, Competition in chemostat-type equations with two habitats, Mathematical Biosciences 201 (2006) 157--171.

[3] Shinji Nakaoka, Yasuhisa Saito and Yasuhiro Takeuchi, Stability, delay and chaotic behavior in a Lotka-Volterra predator-prey system, Mathematical Biosciences and Engineering 3 (2006) 173--187.

[4] Wendi Wang, Yasuhiro Takeuchi, Yasuhisa Saito and Shinji Nakaoka, Prey-predator system with parental care for predators, Journal of Theoretical Biology 241 (2006) 451--458.

[5] Shingo Iwami, Shinji Nakaoka and Yasuhiro Takeuchi, Frequency dependence and viral diversity imply chaos in HIV model, Physica D Nonlinear phenomena 223 (2006) 222--228.

[6] Shinji Nakaoka and Yasuhiro Takeuchi, Mathematical study on sharing metabolism, RIMS Kokyuroku Bessatsu B3 (2007) 193--205.

[7] Wendi Wang, Shinji Nakaoka and Yasuhiro Takeuchi, Invest Conflicts of Adult Predators, Journal of Theoretical Biology, 253 (2008) 12--23.

[8] Shingo Iwami, Shinji Nakaoka and Yasuhiro Takeuchi, Viral diversity limits immune diversity in asymptomatic phase of HIV infection, Theoretical Population Biology, 73 (2008) 332--41.

[9] Shingo Iwami, Shinji Nakaoka and Yasuhiro Takeuchi, Mathematical analysis of HIV model with frequency dependence and viral diversity, Mathematical Biosciences and Engineering, 5 (2008) 457--476.

[10] Yasuhiro Takeuchi, Wendi Wang, Shinji Nakaoka and Shingo Iwami, Dynamical Adaptation of Parental Care, Bulletin of Mathematical Biology 71 (2009) 931--951.

[11] Shingo Iwami, Shinji Nakaoka, Yasuhiro Takeuchi, Yoshiharu Miura, Tomoyuki Miura, Immune impairment thresholds in HIV infection, Immunology Letters 123 (2009) 149--154.

[12] Shingo Iwami, Yasuhiro Takeuchi, Xianning Liu and Shinji Nakaoka, A geographical spread of vaccine-resistance in avian influenza epidemics, Journal of Theoretical Biology 259 (2009) 219--228.

[13] Shingo Iwami, Tomoyuki Miura, Shinji Nakaoka and Yasuhiro Takeuchi, Immune impairment effect in HIV infection: Existence of risky and immunodeficiency thresholds, Journal of Theoretical Biology 260 (2009) 490--501.

[14] Chie Katsuyama, Shinji Nakaoka, Yasuhiro Takeuchi, Kanako Tago, Masahito Hayatsu and Kenji Kato, Complementary cooperation between two syntrophic bacteria in pesticide degradation, Journal of Theoretical Biology 256 (2009) 644--654.

[15] Shinji Nakaoka, Wendi Wang and Yasuhiro Takeuchi, Effect of parental care and aggregation on population dynamics, Journal of Theoretical Biology 260 (2009) 161--171.

2010 -- 2014

[16] Odo Diekmann, Mats Gyllenberg, J.A.J. Metz, Shinji Nakaoka and André de Roos, Daphnia revisited: local stability and bifurcation theory for physiologically structured population models explained by way of an example, Journal of Mathematical Biology 61 (2010) 277--318.

[17] Shinji Nakaoka and Kazuyuki Aihara, Mathematical study on kinetics of hematopoietic stem cells -- theoretical conditions for successful transplantation --, Journal of Biological Dynamics 6 (2012) 836--54.

[18] Shinji Nakaoka and Kazuyuki Aihara, Stochastic simulation of structured skin cell population dynamics, Journal of Mathematical Biology 66 (2013) 807--35.

[19] Shinji Nakaoka and Hisashi Inaba, Demographic modeling of transient amplifying cell population growth, Mathematical Biosciences and Engineering 11 (2014) 363--384.

[20] Hiroshi Nishiura, Keisuke Ejima, Kenji Mizumoto, Shinji Nakaoka, Hisashi Inaba, Seiya Imoto, Rui Yamaguchi, Masaya Saito. Cost-effective length and timing of school closure during an influenza pandemic depend on the severity, Theor Biol Med Model. 11(1) (2014) 5.

[21] Shinji Nakaoka, “Multi-scale mathematical modeling and simulation of cellular dynamical process”, Chapter 21 in “Epidermal cells” Volume III, Methods and Protocols, (2014) 269--283.

2015

[22] Shinji Nakaoka, Mathematical analysis and classification of tumor immune dynamics in T cell transfer treatment, Nonlinear Theory and Its Applications, IEICE. 6(1) (2015) 54--70.

[23] Hiroki Ikeda, Shinji Nakaoka, Naoko Misawa, Kei Sato, Yoshio Koyanagi and Shingo Iwami, Effect of eclipse phase on quantifying viral dynamics of acute HIV-1 infection in humanized mouse model, Nonlinear Theory and Its Applications, IEICE. 6(1) (2015) 47--53.

[24] Yusuke Kakizoe, Satoru Morita, Shinji Nakaoka, Yasuhiro Takeuchi, Kei Sato, Tomoyuki Miura, Catherine AA Beauchemin, Shingo Iwami, A conservation law for virus infection kinetics in vitro, Journal of Theoretical Biology, 376(7) (2015) 39--47.

[25] Yusuke Kakizoe, Shinji Nakaoka*, Catherine A.A. Beauchemin*, Satoru Morita, Hiromi Mori, Tatsuhiko Igarashi, Kazuyuki Aihara, Tomoyuki Miura and Shingo Iwami,.A method to determine the duration of the eclipse phase for in vitro infection with a highly pathogenic SHIV strain, Scientific reports 5 (2015) 10371. [* equally contributed as a second author]

[26] Kanako Tago, Yoshitomo Kikuchi, Sinji Nakaoka, Chie Katsuyama and Masahito Hayatsu, Insecticide applications to soil contribute to development of Burkholderia mediating insecticide resistance in stinkbugs, Molecular Ecology 24(14) (2015) 3766--3778.

[27] Shingo Iwami, Junko S. Takeuch, Shinji Nakaoka, Fabrizio Mammano, François Clavel, Hisashi Inaba, Tomoko Kobayashi, Naoko Misawa, Kazuyuki Aihara, Yoshio Koyanagi, and Kei Sato, Cell-to-cell infection by HIV contributes over half of virus infection, eLIFE 4 (2015) e08150.

[28] Mizuho Nagata, Yutaro Furuta, Yasuhiro Takeuchi, and Shinji Nakaoka, Dynamical behavior of combinational immune boost against tumor, Japan Journal of Industrial and Applied Mathematics 32 (2015) 759—770.

20016

[29] Shinji Nakaoka, Shingo Iwami, and Kei Sato, Dynamics of HIV infection in lymphoid tissue network, Journal of Mathematical Biology, 72:909--938 (2016) (DOI:10.1007/s00285-015-0940-x).

[30] Hiroshi Nishiura, Akira Endo, Masaya Saitoh, Ryo Kinoshita, Ryo Ueno, Shinji Nakaoka, Yuichiro Miyamatsu, Yueping Dong, Gerardo Chowell, Kenji Mizumoto, 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, 6 (2016) e009936.

[31] Takuwa Yasuda, Toshiyuki Fukada, Keigo nishida, Manabu Nakayama, Masashi Matsuda, Ikuo Miura, Teruki Dainichi, Shinji Fukuda, Kenji Kabashima, Shinji Nakaoka, Bum-Ho Bin, Masato Kubo, Hiroshi Ohno, Takanori Hasegawa, Osamu Ohara, Haruhiko Kosaki, Shigeharu Wakana, and Hisahiro Yoshida, Hyperactivation of JAK1 tyrosine kinase induces stepwise, progressive pruritic dermatitis, Journal of Clinical Investigation 126 (2016) 1--28 (doi:10.1172/JCI82887).

[32] Hiroki Ikeda*, Shinji Nakaoka*, Rob J. de Boer, Satoru Morita, Naoko Misawa, Yoshio Koyanagi, Kazuyuki Aihara, Kei Sato, and Shingo Iwami, Quantifying the effect of Vpu on the promotion of HIV-1 replication in the humanized mouse model, Retrovirology (2016) 13:26 [*equally contributed as a first author].

[33] Eiryo Kawakami, Shinji Nakaoka, Tazro Ohta and Hiroaki Kitano, Weighted Enrichment Method for Prediction of Transcription Regulators from Transcriptome and Global Chromatin Immunoprecipitation data, Nucleic Acids Research (2016) (doi: 10.1093/nar/gkw355).

[34] Daisuke Yoneoka, Eiko Saito, Shinji Nakaoka, New algorithm for constructing area-based index with geographical heterogeneities and variable selection: An application to gastric cancer screening, Scientific Report (2016) 6, 26582; doi: 10.1038/srep26582.

[35] Shinji Nakaoka, Sota Kuwahara, Chang Hyeong Lee, Hyejin Jeon, Junho Lee, Yasuhiro Takeuchi, Yangjin Kim, Dynamics of epidermis: A mathematical model, Applied Scence. (2016), 6(9), 252; doi: 10.3390/app6090252.

[36] Alexey Martyushev*, Shinji Nakaoka*, Kei Sato, Takeshi Noda, Shingo Iwami, Modelling Ebola Virus Dynamics: Implications for Therapy, Antiviral Research (2016) 135 62--73 [*equally contributed as a first author].

Conference papers

[1] Shinji Nakaoka and Yasuhiro Takeuchi, Two types of coexistence in cross-feeding microbial consortia, BIOCOMP 2007, AIP Conference Proceedings, 1028, (2008) 233--260.

[2] Shinji Nakaoka, Mathematical modeling and simulation for a coupled communication system of immune cells, IFAC-PapersOnLine Volume 48, Issue 18, 2015, Pages 41–46.

[3] Naoki Nakada, Mizuho Nagata, Yasuhiro Takeuchi and Shinji Nakaoka, Mathematical modeling and analysis of combinational immune boost for tumor elimination, AIP Conference Proceedings 1723 (2016) 020002.