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Publications

Journal Articles

International (peer-reviewed)

  1. Mochizuki, H., Minamikawa, M. F., Hamazaki, K., Kunihisa, M., Moriya, S., Noshita, K., Hayashi, T., Katayose, Y., Yamamoto, T., Iwata, H. (2026) Haplotype bias detection using pedigree-based transmission simulation: traces of selection that occurred in apple breeding Horticulture Research 13(3), uhaf349. https://doi.org/10.1093/hr/uhaf349
  2. Nakao, H.*, Kaneda, A., Tamura, K., Noshita, K., Yoshida, M., Nakagawa, T. (2025) Population interaction in the Jōmon society via 3D data of human crania: geometric morphometric study JMIRx Bio 3, e72432-e72432. https://doi.org/10.2196/72432
  3. Noshita, K., Nakagawa, T., Kaneda, A., Tamura, K., Nakao, H.* (2025) The cultural transmission of Ongagawa style pottery in the prehistoric Japan: quantitative analysis on three-dimensional data of archaeological pottery in the early Yayoi period Journal of the Royal Society, Interface 22(223), 20240889. https://doi.org/10.1098/rsif.2024.0889
  4. Ohta, S.*, Noshita, K., Kimoto, K., Ishikawa, A., Sato, H., Shimizu, K., Endo, K.* (2025) Wnt activation causes shell malformation in lymnaeoidean gastropods Journal of Molluscan Studies 91(1), eyaf001. https://doi.org/10.1093/mollus/eyaf001
  5. Murata, H., Noshita, K.* (2024) Three-dimensional leaf edge reconstruction combining two- and three-dimensional approaches Plant Phenomics 6, 0181. https://doi.org/10.34133/plantphenomics.0181
  6. Nakao, H.*, Kaneda, A., Tamura, K., Noshita, K., Nakagawa, T. (2024) Macro-scale population patterns in the Kofun period of the Japanese archipelago: quantitative analysis of a larger sample of three-dimensional data from ancient human crania Humans 4(2), 131–147. https://doi.org/10.3390/humans4020008
  7. Ohta, S.*, Noshita, K., Kimoto, K., Ishikawa, A., Sato, H., Shimizu, K., Endo, K.* (2024) Possible roles of Wnt in the shell growth of the pond snail Lymnaea stagnalis Scientific Reports 14(1), 26488. https://doi.org/10.1038/s41598-024-74794-7
  8. Araki, A., Noshita, K.* (2023) Theoretical morphological analysis of differential morphospace occupation patterns for terrestrial and aquatic gastropods Evolution 77(8), 1864–1873. https://doi.org/10.1093/evolut/qpad110
  9. Iwamasa, K., Noshita, K.* (2023) Network feature-based phenotyping of leaf venation robustly reconstructs the latent space PLOS Computational Biology 19(7), e1010581. https://doi.org/10.1371/journal.pcbi.1010581
  10. Nakao, H.*, Nakagawa, T., Kaneda, A., Tamura, K., Noshita, K. (2023) Demic diffusion of the Yayoi people in the Japanese archipelago Letters on Evolutionary Behavioral Science 14(2), 1–7. https://doi.org/10.5178/lebs.2023.111
  11. Suzuki, R.†, Ono, Y.†, Noshita, K.†, Kim, K. S., Ito, H., Morioka, Y., Tamura, T., Okuzaki, D., Tagawa, T., Takenaka, T., Yoshizumi, T., Shimamura, T., Iwami, S., Fukuhara, T.* (2023) Smoking enhances the expression of angiotensin-converting enzyme 2 involved in the efficiency of severe acute respiratory syndrome coronavirus 2 infection Microbiology and Immunology 67(1), 22–31. https://doi.org/10.1111/1348-0421.13034
  12. Kaneda, A., Nakagawa, T., Tamura, K., Noshita, K., Nakao, H.* (2022) A proposal of a new automated method for SfM/MVS 3D reconstruction through comparisons of 3D data by SfM/MVS and handheld laser scanners PLOS One 17(7), e0270660. https://doi.org/10.1371/journal.pone.0270660
  13. Noshita, K.*, Murata, H., Kirie, S. (2022) Model-based plant phenomics on morphological traits using morphometric descriptors Breeding Science 72(1), 19–30. https://doi.org/10.1270/jsbbs.21078 Review
  14. Tsugawa, S.*, Teratsuji, K., Okura, F., Noshita, K., Tateno, M., Zhang, J., Demura, T. (2022) Exploring the mechanical and morphological rationality of tree branch structure based on 3D point cloud analysis and the finite element method Scientific Reports 12(1), 4054. https://doi.org/10.1038/s41598-022-08030-5
  15. Fukano, Y.*, Guo, W.†, Aoki, N., Ootsuka, S., Noshita, K., Uchida, K., Kato, Y., Sasaki, K., Kamikawa, S., Kubota, H. (2021) GIS-based analysis for UAV-supported field experiments reveals soybean traits associated with rotational benefit Frontiers in Plant Science 12, 637694. https://doi.org/10.3389/fpls.2021.637694
  16. Iwanami, S.†, Ejima, K.†, Kim, K. S., Noshita, K., Fujita, Y., Miyazaki, T., Kohno, S., Miyazaki, Y., Morimoto, S., Nakaoka, S., Koizumi, Y., Asai, Y., Aihara, K., Watashi, K., Thompson, R. N., Shibuya, K., Fujiu, K., Perelson, A. S., Iwami, S., Wakita, T. (2021) Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: a modeling study PLoS Medicine 18(7), e1003660. https://doi.org/10.1371/journal.pmed.1003660
  17. Minamikawa, M. F., Kunihisa, M., Noshita, K., Moriya, S., Abe, K., Hayashi, T., Katayose, Y., Matsumoto, T., Nishitani, C., Terakami, S., Yamamoto, T., Iwata, H.* (2021) Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study Horticulture Research 8(1), 49. https://doi.org/10.1038/s41438-021-00485-3
  18. Shimizu, K.*, Noshita, K., Kimoto, K., Sasaki, T. (2021) Phylogeography and shell morphology of the pelagic snail Limacina helicina in the Okhotsk Sea and western North Pacific Marine Biodiversity 51(2), 22. https://doi.org/10.1007/s12526-021-01166-z
  19. Yamauchi, T.*, Noshita, K., Tsutsumi, N. (2021) Climate-smart crops: key root anatomical traits that confer flooding tolerance Breeding Science 71(1), 51–61. https://doi.org/10.1270/jsbbs.20119 Review
  20. Guo, W.*, Fukano, Y., Noshita, K., Ninomiya, S. (2020) Field-based individual plant phenotyping of herbaceous species by unmanned aerial vehicle Ecology and Evolution 10(21), 12318–12326. https://doi.org/10.1002/ece3.6861
  21. Kirie, S., Iwasaki, H., Noshita, K., Iwata, H.* (2020) A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea) PLOS One 15(10), e0239781. https://doi.org/10.1371/journal.pone.0239781
  22. Fukano, Y.*, Guo, W., Noshita, K., Hashida, S., Kamikawa, S. (2019) Genotype-aggregated planting improves yield in Jerusalem artichoke (Helianthus tuberosus) due to self/non-self-discrimination Evolutionary Applications 12(3), 508–518. https://doi.org/10.1111/eva.12735
  23. Reynolds, D., Baret, F., Welcker, C., Bostrom, A., Ball, J., Cellini, F., Lorence, A., Chawade, A., Khafif, M., Noshita, K., Mueller-Linow, M., Zhou, J., Tardieu, F. (2019) What is cost-efficient phenotyping? Optimizing costs for different scenarios Plant Science 282, 14–22. https://doi.org/10.1016/j.plantsci.2018.06.015
  24. Sakamoto, L., Kajiya-Kanegae, H., Noshita, K., Takanashi, H., Kobayashi, M., Kudo, T., Yano, K., Tokunaga, T., Tsutsumi, N., Iwata, H.* (2019) Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology PLOS One 14(11), e0224695. https://doi.org/10.1371/journal.pone.0224695
  25. Guo, W.*, Zheng, B., Potgieter, A. B., Diot, J., Watanabe, K., Noshita, K., Jordan, D. R., Wang, X., Watson, J., Ninomiya, S., Chapman, S. C. (2018) Aerial imagery analysis – quantifying appearance and number of sorghum heads for applications in breeding and agronomy Frontiers in Plant Science 9, 1544. https://doi.org/10.3389/fpls.2018.01544
  26. Mu, Y., Fujii, Y., Takata, D., Zheng, B., Noshita, K., Honda, K., Ninomiya, S., Guo, W. (2018) Characterization of peach tree crown by using high-resolution images from an unmanned aerial vehicle Horticulture Research 5(1), 74. https://doi.org/10.1038/s41438-018-0097-z
  27. Shimizu, K.*, Kimoto, K., Noshita, K., Wakita, M., Fujiki, T., Sasaki, T. (2018) Phylogeography of the pelagic snail Limacina helicina (Gastropoda: Thecosomata) in the subarctic western North Pacific Journal of Molluscan Studies 84(1), 30–37. https://doi.org/10.1093/mollus/eyx040
  28. Fujiu, K., Shibata, M., Nakayama, Y., Ogata, F., Matsumoto, S., Noshita, K., Iwami, S., Nakae, S., Komuro, I., Nagai, R.*, Manabe, I.* (2017) A heart–brain–kidney network controls adaptation to cardiac stress through tissue macrophage activation Nature Medicine 23(5), 611–622. https://doi.org/10.1038/nm.4326
  29. Noshita, K.*, Shimizu, K., Sasaki, T. (2016) Geometric analysis and estimation of the growth rate gradient on gastropod shells Journal of Theoretical Biology 389, 11–19. https://doi.org/10.1016/j.jtbi.2015.10.011
  30. Noshita, K. (2014) Quantification and geometric analysis of coiling patterns in gastropod shells based on 3D and 2D image data Journal of Theoretical Biology 363, 93–104. https://doi.org/10.1016/j.jtbi.2014.08.010
  31. Noshita, K.*, Asami, T., Ubukata, T. (2012) Functional constraints on coiling geometry and aperture inclination in gastropods Paleobiology 38(2), 322–334. https://doi.org/10.1666/10060.1

Other Articles (Japanese)

  1. Hamazaki, K., Minamikawa, M., Ishimori, M., Kajiya-Kanegae, H., Noshita, K., Onogi, A. (2026) Pitfalls in data analysis: is your analysis really sound? Breeding Research 28(1), 81–86. https://doi.org/10.1270/jsbbr.28.W04
  2. Noshita, K. (2025) The cultural transmission of early Yayoi pottery: a view from three-dimensional morphology Science journal kagaku 95(8), 683–687. https://cir.nii.ac.jp/crid/1520023627019934848
  3. Noshita, K. (2025) A lifelong wandering in search of ways to measure form Newsletter of the Japanese Society for Mathematical Biology(105), 10–15.
  4. Noshita, K. (2023) An approach using general-purpose morphological descriptors toward morphological phenomics Medical science 74(2), 123–128. https://doi.org/10.11477/mf.2425201656
  5. Noshita, K., Nakagawa, T., Kaneda, A., Tamura, K., Nakao, H.* (2022) A Comparative Analysis of Two- and Three-dimensional Data Using Ongagawa Pottery as an Example Journal of Computer Archaeology 27(1・2), 1–10. https://cir.nii.ac.jp/crid/1520010842636081152
  6. Noshita, K., Kaneda, A., Tamura, K., Nakagawa, T., Nakao, H.* (2022) A Mathematical Study on Outline Morphologies of Yayoi Pottery: A Case Study Focusing on the Ongagawa-style Pottery from the Tamura, Yano, and Ayaragi-go Sites Nabunken ronso: papers of Nara National Research Institute for Cultural Properties 3, 65–82. https://cir.nii.ac.jp/crid/1010025255267924227
  7. Okura, F., Mizutani, M., Noshita, K., Toda, Y.* (2020) Past and Future of Plant Science with Artificial Intelligence BSJ-Review 11(C), 185–206. https://doi.org/10.24480/bsj-review.11c2.00191
  8. Okura, F., Noshita, K., Kinoshita, T., Toda, Y.* (2019) Perspectives of Plant Phenotypic Analysis Utilizing Deep Learning BSJ-Review 10(B), 99–107. https://doi.org/10.24480/bsj-review.10b7.00160
  9. Uchida, M.*, Noshita, K., Koyama, H. (2019) Application of deep learning for the occupational health of VDT workers SANGYO EISEIGAKU ZASSHI 61(6), 256–260. https://doi.org/10.1539/sangyoeisei.2018-040-C
  10. Uchida, M.*, Noshita, K., Tsutsui, Y., Koyama, H. (2018) Application of a deep learning for occupational health and safety recognition: a pilot study in a logistics industry SANGYO EISEIGAKU ZASSHI 60(6), 191–195. https://doi.org/10.1539/sangyoeisei.2018-022-C
  11. Noshita, K. (2018) 3D reconstruction of crop architecture under field environment Agricultural Biotechnology 2(3), 14–19. https://cir.nii.ac.jp/crid/1522543656033929216
  12. Noshita, K. (2017) Theoretical morphological models of coiling: the case of shelled molluscs Newsletter of the Japanese Society for Mathematical Biology(83), 19–23.
  13. Noshita, K. (2016) Notes from a stay in Philadelphia Newsletter of the Japanese Society for Mathematical Biology(78), 4–6.
  14. Yabe, S.*, Uehara, K., Yoshitsu, Y., Watanabe, K., Noshita, K. (2016) How far have phenotyping systems been evolving? Breeding Research 18(2), 67–71. https://doi.org/10.1270/jsbbr.18.67
  15. Noshita, K. (2012) A theoretical morphological approach to gastropod shells Newsletter of the Japanese Society for Mathematical Biology(67), 18–19.
  16. Noshita, K. (2010) Spiral Shell Form: A computer software package for theoretical morphological analysis of spiral shell form Geoscience reports of Shizuoka University 37, 57–73. https://doi.org/10.51053/shizuoka.37.0_57

Books (Contributed Chapters)

  1. Noshita, K. (2025) Phenotyping 理論生物学事典, 46–47. 朝倉書店. ISBN: 978-4-254-17203-4.
  2. Noshita, K. (2025) Shell morphology 理論生物学事典, 219–221. 朝倉書店. ISBN: 978-4-254-17203-4.
  3. Nakao, H., Noshita, K., Nakagawa, T., Tamura, K., Kaneda, A. (2024) Research with three-dimensional data: case studies カタチの由来、データの未来：三次元計測の人類史学, 89–123. 勁草書房. ISBN: 978-4-326-24854-4.
  4. Noshita, K., Tamura, K., Nakao, H. (2024) Research with three-dimensional data: methods カタチの由来、データの未来：三次元計測の人類史学, 71–88. 勁草書房. ISBN: 978-4-326-24854-4.
  5. Noshita, K. (2023) Digitization, quantification, and modeling of three-dimensional plant morphology 植物の超階層生物学：ゲノミクス×フェノミクス×生態学でひもとく多様性, 285–307. 文一総合出版. ISBN: 978-4-8299-6210-7.
  6. Kano, Y.*, Hon, J., Sulaiman, M. K., Aizu, M., Noshita, K., Samejima, H. (2020) Stream fish biodiversity and the effects of plantations in the Bintulu Region, Sarawak Anthropogenic tropical forests: human–nature interfaces on the plantation frontier, 235–274. Springer Singapore. ISBN: 978-981-13-7513-2. https://doi.org/10.1007/978-981-13-7513-2_13
  7. Noshita, K. (2019) Three-dimensional reconstruction of crop plants and canopies in the field 新スマート農業：進化する農業情報利用, 348–349. 農林統計出版. ISBN: 978-4-89732-407-4.
  8. Sasaki, T.*, Maekawa, Y., Takeda, Y., Atsushiba, M., Chen, C., Noshita, K., Uesugi, K., Hoshino, M. (2018) 3D visualization of calcified and non-calcified molluscan tissues using computed tomography Biomineralization, 83–93. Springer Singapore. ISBN: 978-981-13-1002-7. https://doi.org/10.1007/978-981-13-1002-7_9
  9. Noshita, K., Tamura, K. (2017) Geometric morphometrics: an analysis example using R Cultural evolution and archaeology, 179–218. 勁草書房. ISBN: 978-4-326-24845-2.

Presentations

28 of 128 shown; 7 of 40 invited. The rest were given in Japanese.

International Conferences

Oral

  1. Noshita, K., Iwamasa, K. (2025) Global morphospace occupation patterns of leaf vein network structures. ACMB-JSMB2025. Kyoto, Japan. 2025/07/11
  2. Iwamasa, K., Noshita, K. (2024) Network feature-based phenotyping of leaf venation robustly reconstructs the latent space. IPPS2024. University of Nebraska-Lincoln, Nebraska, USA. 2024/10/10
  3. Noshita, K. (2020) Quantitative Representation of Plant Style as Spacial Pattern of Foliage for Morphometrics on ill-defined Homology. Phenome2020. Tucson, AZ, USA. 2020/2/27
  4. Noshita, K., Guo, W. (2018) Model-based morphometrics for plant phenotyping. SMB-JSMB 2018. University of Sydney, Sydney, Australia. 2018/07/09
  5. Noshita, K., Guo, W., Kaga, A., Iwata, H. (2017) An image processing pipeline for acquiring 3D morphological information from "noisy" point cloud data. 2017 CIGR World Workshop in Matsuyama: OS 1 Precision measurement and modeling of dynamical plant information (Organizer: Fukuda, H.). Ehime Univ. 2017/9/3 Invited
  6. Noshita, K., Guo, W. (2017) 3D outline-based morphometrics for leaf shape with photogrammetry and image processing. The 5th International Symposium on Biological Shape Analysis. UTokyo, Tokyo, Japan. 2017/6/23
  7. Noshita, K., Guo, W., Kaga, A., Iwata, H. (2016) Monitoring of soybean growth in early stage based on 3D plant analysis. 1st Asia-Pacific Plant Phenotyping Conference. 北京蟹岛度假村 三点钟会议中心, Beijing, China. 2016/10/20
  8. Noshita, K. (2016) Leaf surface reconstruction from "noisy" point cloud data for geometric analysis. The 2016 (26th) annual meeting of the Japanese Society for Mathematical Biology. Kyushu University, Fukuoka, Japan. 2016/9/8
  9. Noshita, K., Shimizu, K., Sasaki, T. (2015) Estimation of the growth rate gradient on molluscan shells: From shape to growth. 2015 Joint Meeting of The 5th China-Japan-Korea Colloquium on Mathematical Biology and The Japanese Society for Mathematical Biology. Doshisha University, Kyoto, Japan. 2015/8/28
  10. Noshita, K. (2014) The difference of morphological diversity between land and marine gastropod shells. 2014 ESA Annual Meeting. Sacramento Convention Center, CA, USA. 2014/8/14
  11. Noshita, K. (2014) Quantification of coiling patterns in gastropod shells and evaluation of functional traits. Evolution2014. Raleigh Convention Center, NC, USA. 2014/6/21

Poster

  1. Noshita, K. (2022) Characterization of foliage structures using persistent homology analysis. IPPS2022. Wageningen, Nederland. 2022/9/27
  2. Noshita, K., Guo, W. (2019) Outline-based morphometrics and geometric analysis for leaf shapes in a three- dimensional space. IPPS2019. Nanjing, China. 2019/10/24
  3. Noshita, K., Guo, W. (2018) Model-based phenotyping of soybean canopies in early stage under a field condition with a photogrammetry studio. IPPS2018. National Wine Centre of Australia, Adelaide, Australia. 2018/10/04
  4. Noshita, K., Guo, W., Kaga, A., Iwata, H. (2017) 3D Point Cloud Phenotyping of Soybean Growth in Early Stage. PAG XXV. Town & Country Hotel, San Diego, CA, USA. 2017/1/16
  5. Noshita, K., Guo, W., Kaga, A., Iwata, H. (2016) 3D point cloud based monitoring of soybean growth in early stage. 4th. International Plant Phenotyping Symposium. 2016/12/13
  6. Noshita, K. (2012) "Theoretical morphological approach to the diversity of gastropod shells" 1st. Joint Congress on Evolutionary Biology（Ottawa, Canada） 2012/7/7
  7. Noshita, K. (2012) Morphological adaptation to fluid environments in gastropods. ESJ59/EAFES5（滋賀） 2012/3/19

Workshops and Seminars

  1. Noshita, K. (2023) Three-dimensional leaf edge reconstruction using a combination of two- and three-dimensional phenotyping approaches. Summit on the Frontiers of Plant Phenomics. Nanjing Agricultural University. 2023.12.09 Invited
  2. Noshita, K. (2023) Plant phenotyping methods using image analysis, machine learning, mathematics, and morphometrics. ICIAM WIS2023 Kyushu University. 2023.09.15 Invited
  3. Noshita, K. (2022) Phenotyping studies using morphometric descriptors for multi-omics analysis. 1st International Symposium on Aihara Moonshot Project. 2022.06.06
  4. Noshita, K. (2021) Morphometrics and its applications. RIMS Workshop Mathematical methods for the studies of flow, shape, and dynamics. Organizers: Masanobu Inubushi (Tokyo U. of Sci.), Kenta Ishimoto (Kyoto U.). 2021/08/31 Invited
  5. Noshita, K. (2019) 3D high through-put phenotyping for Smart agriculture. International Smart Agriculture Symposium (Organizer: Wei Guo). UTokyo. 2019/09/25
  6. Noshita, K. (2018) 3D field phenotyping of canopy development in soybean. PBIO Seminar (Host: Alexander Bucksch), UGA. 2018/11/12 Invited
  7. Noshita, K., Guo, W., Kaga, A., Iwata, H. (2017) Monitoring of soybean growth in early stage based on 3D plant analysis. Plant Phenotyping Symposium (Organizer: Ding, Y.) Nanjing Agricultural University, Nanjin, China. 2017/10/23 Invited
  8. Noshita, K. (2016) Monitoring of soybean growth in early stage based on point cloud data. JSMB 2016 satellite workshop: Mathematical modeling on Ecology & Evolution (Organizers: Tachiki Y. and Iritani R.) Kyushu Univ. 2016/9/11 Invited
  9. Noshita, K. (2016) Leaf surface reconstruction from point cloud data: a post-process of field phenotyping. Field Phenomics with Big Data. The University of Tokyo, Japan. 2016/2/10
  10. Noshita, K. (2014) University of Pennsylvania Plotkin Lab. Seminar 2014 年 4 月

Organized Meetings

4 of 22 shown; the rest were given in Japanese

  1. Iida, K., Noshita, K., Iwami, S. (2022) 1st International Symposium on Aihara Moonshot Project. Zoom Webinar. 2022/06/06-08
  2. Iwata, H., Ninomiya, S., Tatsuta, H., Guo, W., Noshita, K., Lestrel, P. E., Moon, W. (2017) The Fifth International Symposium of Biological Shape Analysis (ISBSA). UTokyo, June, 2017
  3. Noshita, K. (2016) Plant phenotyping with morphometrics. JSMB2016 8E1-S11 Kyushu Univ. 2016/9/8
  4. Guo, W., Watanabe, K., Noshita, K., Iwata, H., Ninomiya, S. (2016) Field Phenomics with Big Data. Feb. 10, 2016
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