Shinji Nakaoka and Keita Matsuyama, Information and statistical analysis pipeline for high-throughput RNA sequencing data, Springer protocol Epidermis, pp.1-10 (2019) https://doi.org/10.1007/7651_2019_245.
Sourav Kumar Sasmal, Yasuhiro Takeuchi, Shinji Nakaoka, T-cell mediated adaptive immunity and antibody-dependent enhancement in secondary dengue infection, Journal of Theoretical Biology, 470(7), 50-63 (2019), doi.org/10.1016/j.jtbi.2019.03.010.
Akane Hara, Shoya Iwanami, Yusuke Ito, Tomoyuki Miura, Shinji Nakaoka, Shingo Iwami, Revealing uninfected and infected target cell dynamics from peripheral blood data in highly and less pathogenic simian/human immunodeficiency virus infected Rhesus macaque, Journal of Theoretical Biology, 479, 29-36 (2019).
Yu Tsubouchi, Yasuhiro Takeuchi, Shinji Nakaoka, Calculation of final size for vector-transmitted epidemic model, Mathematical Biosciences and Engineering, 16(4) 2219-2232 (2019). doi: 10.3934/mbe.2019109..
Kosaku Kitagawa, Toshikazu Kuniya, Shinji Nakaoka, Yusuke Asai, Koichi Watashi, Shingo Iwami, Mathematical analysis of a transformed ODE from a PDE multiscale model of hepatitis C virus infection, Bulletin of Mathematical Biology, accepted.
Yueping Dong, Moitri Sen, Malay Banerjee, Yasuhiro Takeuchi and Shinji Nakaoka, Delayed feedback induced complex dynamics in an Escherichia coli and Tetrahymena system, Nonlinear Dynamics, 94(2), 1447-1466 (2018), 10.1007/s11071-018-4434-4.
Shinji Nakaoka, Data-driven mathematical modeling of microbial community dynamics, Handbook of Statistics Vol.39 Part A, pp.93--130.
Naoki Nakada, Mizuho Nagata, Yueping Dong, Yasuhiro Takeuchi, and Shinji Nakaoka, Dynamics of tumor immune escape via adaptive change, NOLTA, Vol.E9-N, No.2, Apr. 2018.
Hirokazu Toju, Kabir G. Peay, Masato Yamamichi, Kazuhiko Narisawa, Kei Hiruma, Ken Naito, Shinji Fukuda, Masayuki Ushio, Shinji Nakaoka, Yusuke Onoda, Kentaro Yoshida, Klaus Schlaeppi, Yang Bai, Ryo Sugiura, Yasunori Ichihashi, Kiwamu Minamisawa, E. Toby Kiers, Core microbiomes for sustainable agroecosystems, Nature plant, Volume 4, 247–257 (2018).
Kosaku Kitagawa, Shinji Nakaoka, Yusuke Asai, Koichi Watashi, Shingo Iwami, A multiscale model of hepatitis C virus infection described by PDE can be transformed to ODE, Journal of Theoretical Biology, Volume 448, 80-85 (2018).
Yueping Dong, Yasuhiro Takeuchi, Shinji Nakaoka, Multiple delayed feedback regulation system of the gut microbiota – antibiotics injection controlled by measured metagenomics data, Nonlinear Analysis RWA., Volume 43, 1-17 (2018).
Mohamed Mahgoub, Jun-ichirou Yasunaga, Shingo Iwami, Shinji Nakaoka, Yoshiki Koizumi, Kazuya Shimura, and Masao Matsuoka, Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells, PNAS, 2018 (doi:10.1073/pnas.1715724115).
Eri Yamada, Naoko Misawa, Shinji Nakaoka, Lukas Klein, Elisabeth Reith, Simon Langer, Shingo Iwami, Gideon Schreiber, Frank Kirchhoff, Yoshio Koyanagi, Daniel Sauter and Kei Sato, Human-specific adaptations in Vpu conferring anti-tetherin activity are critical for efficient early HIV-1 replication in vivo, Cell Host and Microbe, accepted.
Yusuke Ito, Azaria Remion, Alexandra Tauzin, Keisuke Ejima, Shinji Nakaoka, Yoh Iwasa, Shingo Iwami and Fabrizio Mammano, Number of infection events per cell during HIV-1 cell-free infection, Scientific Reports, (2017) 7, 6559; doi:10.1038/s41598-017-03954-9.
Yusuke Nakano, Naoko Misawa, Guillermo Juarez-Fernandez, Miyu Moriwaki, Shinji Nakaoka, Takaaki Funo, Eri Yamada, Andrew Soper, Rokusuke Yoshikawa, Diako Ebrahimi, Yuuya Tachiki, Shingo Iwami, Reuben S Harris, Yoshio Koyanagi, and Kei Sato, HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation, PLoS Pathogen, 13(5): e1006348. https://doi.org/10.1371/journal.ppat.1006348.
Shoya Iwanami, Yusuke Kakizoe, Satoru Morita, Tomoyuki Miura, Shinji Nakaoka, Shingo Iwami, A highly pathogenic simian/human immunodeficiency virus effectively produces infectious virions compared with a less pathogenic virus in cell culture, Theor Biol Med Model., (2017) 14(1):9 (doi: 10.1186/s12976-017-0055-8).
Shinji Nakaoka, Sota Kuwahara, Chang Hyeong Lee, Hyejin Jeon, Junho Lee, Yasuhiro Takeuchi, Yangjin Kim, Dynamics of epidermis: A mathematical model, Applied Science. (2016), 6(9), 252; doi: 10.3390/app6090252
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.
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) 44 (11): 5010-5021, (doi: 10.1093/nar/gkw355).
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).
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.
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.
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).
Mizuho Nagata, Yutaro Furuta, Yasuhiro Takeuchi, and Shinji Nakaoka, Dynamical behavior of combinational immune boost against tumor, Japan Journal of Industrial and Applied Mathematics32 (2015) 759–770.
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, eLIFE4 (2015) e08150.
Kanako Tago, Yoshitomo Kikuchi, Shinji Nakaoka, Chie Katsuyama and Masahito Hayatsu, Insecticide applications to soil contribute to development of Burkholderia mediating insecticide resistance in stinkbugs, Molecular Ecology24(14) (2015) 3766-–3778.
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 reports5 (2015) 10371. [* equally contributed]
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.
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.
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.
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.
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.
Shinji Nakaoka and Hisashi Inaba, Demographic modeling of transient amplifying cell population growth, Mathematical Biosciences and Engineering11 (2014) 363—384.
Shinji Nakaoka and Kazuyuki Aihara, Stochastic simulation of structured skin cell population dynamics, Journal of Mathematical Biology66 (2013) 807—35.
Shinji Nakaoka and Kazuyuki Aihara, Mathematical study on kinetics of hematopoietic stem cells -- theoretical conditions for successful transplantation --, Journal of Biological Dynamics6 (2012) 836--54.
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 Biology61 (2010) 277--318.
Shinji Nakaoka, Wendi Wang and Yasuhiro Takeuchi, Effect of parental care and aggregation on population dynamics, Journal of Theoretical Biology260 (2009) 161--171.
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 Biology256 (2009) 644--654.
Shingo Iwami, Tomoyuki Miura, Shinji Nakaoka and Yasuhiro Takeuchi, Immune impairment effect in HIV infection: Existence of risky and immunodeficiency thresholds, Journal of Theoretical Biology260 (2009) 490--501.
Shingo Iwami, Yasuhiro Takeuchi, Xianning Liu and Shinji Nakaoka, A geographical spread of vaccine-resistance in avian influenza epidemics, Journal of Theoretical Biology259 (2009) 219--228.
Shingo Iwami, Shinji Nakaoka, Yasuhiro Takeuchi, Yoshiharu Miura, Tomoyuki Miura, Immune impairment thresholds in HIV infection, Immunology Letters123 (2009) 149--154.
Yasuhiro Takeuchi, Wendi Wang, Shinji Nakaoka and Shingo Iwami, Dynamical Adaptation of Parental Care, Bulletin of Mathematical Biology71 (2009) 931--951.
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.
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.
Wendi Wang, Shinji Nakaoka and Yasuhiro Takeuchi, Invest Conflicts of Adult Predators, Journal of Theoretical Biology, 253 (2008) 12--23.
Shinji Nakaoka and Yasuhiro Takeuchi, Two types of coexistence in cross-feeding microbial consortia, BIOCOMP 2007, AIP Proceedings, Vol. 1028, A. Buonocore, E. Pirozzi, L.M. Ricciardi, eds. (2008) 233--260.
Shinji Nakaoka and Yasuhiro Takeuchi, Mathematical study on sharing metabolism, RIMS Kokyuroku BessatsuB3 (2007) 193--205.
Shingo Iwami, Shinji Nakaoka and Yasuhiro Takeuchi, Frequency dependence and viral diversity imply chaos in HIV model, Physica D Nonlinear phenomena223 (2006) 222--228.
Wendi Wang, Yasuhiro Takeuchi, Yasuhisa Saito and Shinji Nakaoka, Prey-predator system with parental care for predators, Journal of Theoretical Biology241 (2006) 451--458.
Shinji Nakaoka, Yasuhisa Saito and Yasuhiro Takeuchi, Stability, delay and chaotic behavior in a Lotka-Volterra predator-prey system, Mathematical Biosciences and Engineering3 (2006) 173--187.
Shinji Nakaoka and Yasuhiro Takeuchi, Competition in chemostat-type equations with two habitats, Mathematical Biosciences201 (2006) 157--171.
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.
Conference papers/proceedings
Shinji Nakaoka, Mathematical description for invasibility threshold and persistence of pathogenic bacterial species, NOLTA2018 (conference paper), accepted.
Shinji Nakaoka, Mathematical modeling and simulation for a coupled communication system of immune cells, IFAC-PapersOnLine Volume 48, Issue 18, 2015, Pages 41–46.
Invited talks
"Trajectory inference of disease onset from non-time series microbiome datasets", South Lake Workshop in Bioinformatics and System Biology Nov.17th-19th, 2018, Wuhan, China, November 2018.
"Invasibility threshold and persistence of bacterial species", Korean Society for Industrial and Applied Mathematics, Daejeon, May 2018.
"Meta-analysis of gut microbiome from HIV infected individuals", Workshop Infectious disease epidemiology, Institute of Mathematics of Polish Academy of Sciences in Warsaw Banach Center, Warsaw, February, 2018.
"Mathematical and information analysis of community composition change of the gut microbiota", International Workshop of Mathematical Biology, Cebu, Philippine, January, 2018.
"Investigation for population kinetics of reservoir cells in HIV infection", A3 Workshop on Interdisciplinary Research Connecting Mathematics and Biology, Beijing, China, April, 2016.
"Mathematical strategy for detection of reservoir cells in HIV infection", Annual Meeting of Korean Society for Mathematical Biology, Jeju, South Korea, June 17, 2016.
"Mathematical modeling and simulation of HIV infection in a lymph node network", 10th Colloquium on the Qualitative Theory of Differential Equations, Szeged, Hungary, July 2015.
"Mathematical Modeling and Simulation of Tumor immune therapy" Application of ecological and mathematical theory to cancer: new challenges, Daejeon, South Korea, May, 2014.
"Mathematical study on hematopoiesis", The Third China-Japan Colloquium of Mathematical Biology, Beijing, China, October 18--21, 2010.
