Antigenic Cartography

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Concept of Shape space

• Basic of antigenic cartography tracks back the concept of "shape space" first propound by Perelson and Oster back in 1979.
• In this concept, antigen and antibody are considered as 'points in an abstract shape space' with their own coordinates which consist of abstract parameters. Distances between those points denote affinity with each other.

Perelson, A. S., & Oster, G. F. (1979). Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination. Journal of Theoretical Biology, 81(4), 645–670. https://doi.org/10.1016/0022-5193(79)90275-3

Lapedes, A., & Farber, R. (2001). The geometry of shape space: Application to influenza. Journal of Theoretical Biology, 212(1), 57–69. https://doi.org/10.1006/jtbi.2001.2347

Klingenberg, C. P. (2020). Walking on Kendall’s Shape Space: Understanding Shape Spaces and Their Coordinate Systems. Evolutionary Biology, 47(4), 334–352. https://doi.org/10.1007/s11692-020-09513-x

生形貴男. (2011). 生物のかたちの測定と比較. 化石, 89, 39–54. https://doi.org/10.14825/kaseki.89.0_39

Multidimensional scaling (MDS)

• 多次元尺度構成法 in Japanese

• The follwings are comprehensive reviews of multidimensional scaling

Carroll, J. D., & Arabie, P. (1980). Multidimensional Scaling. Annual Review of Psychology, 31(1), 607–649. https://doi.org/10.1146/annurev.ps.31.020180.003135

Jaworska, N., & Chupetlovska-Anastasova, A. (2009). A Review of Multidimensional Scaling (MDS) and its Utility in Various Psychological Domains. Tutorials in Quantitative Methods for Psychology, 5(1), 1–10. https://doi.org/10.20982/tqmp.05.1.p001

倉林武. (1977). 多次元尺度構成法(MDS)の紹介. 人間工学, 13(4), 137–142. https://doi.org/10.5100/jje.13.137

奥喜正. (2012). 多次元尺度法概論とそのアルゴリズム. 流通経済大学流通情報学部紀要, 17(1), 257–274. https://rku.repo.nii.ac.jp/records/4942

小杉考司. (2019, August 6). 多次元尺度構成法　その基礎と広がり. 認知心理学会テクニカルレポート. https://cogpsy.jp/wp/wp-content/uploads/COGPSY-TR-002.pdf

• The followings are standard textbooks

Nesselroade, J. R., & Cattell, R. B. (1988). Handbook of Multivariate Experimental Psychology (J. R. Nesselroade & R. B. Cattell, Eds.; 2nd ed.). Springer US. https://doi.org/10.1007/978-1-4613-0893-5

Borg, I., Groenen, P. J. F., & Mair, P. (2018). Applied Multidimensional Scaling and Unfolding. Springer International Publishing. https://doi.org/10.1007/978-3-319-73471-2

k-Means clustering

k-means法とは？可視化してわかりやすく解説 https://hogetech.info/algorithm/kmeans

Antigenic distance

Cai, Z., Zhang, T., & Wan, X. F. (2012). Antigenic distance measurements for seasonal influenza vaccine selection. Vaccine, 30(2), 448–453. https://doi.org/10.1016/j.vaccine.2011.10.051

Antigenic cartography

• The first propounders of Antigenic Cartography were Smith DJ et al. in 2004 by using hemagluttinin inhibition (HI) assay of influenza AH3N2 viruses.

Smith, D. J., Lapedes, A. S., de Jong, J. C., Bestebroer, T. M., Rimmelzwaan, G. F., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2004). Mapping the Antigenic and Genetic Evolution of Influenza Virus. Science, 305(5682), 371–376. https://doi.org/10.1126/science.1097211

• The following is a well documented review of antigenic cartography.

Sitaras, I. (2020). Antigenic cartography: Overview and current developments. In Methods in Molecular Biology (Vol. 2123, pp. 61–68). Humana Press Inc. https://doi.org/10.1007/978-1-0716-0346-8_5