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Kimihito Ito (伊藤公人)

Professor

Ph.D. in Engineering
itok@czc.hokudai.ac.jp

Background

I received my Ph. D. degree in Engineering from Hokkaido University in 1999 for the study of algorithms that find the most specific general logical rule that satisfies a set of facts given as examples (Discovberey Science, 2003).

By applying this technique to real-world data, I developed software that enabled end-users to integrate databases and tools on the World Wide Web without programming (HyperText, 2003).

After working as an instructor at the Division of Computer Science at the Graduate School of Information Science and Technology, Hokkaido University, I was appointed as an associate professor in the Research Center for Zoonosis Control, Hokkaido University in 2005, and became a professor in the Division of Bioinformatics in 2014.

Since 2005, I’ve been working on the prediction of the evolution of viruses, especially influenza A viruses and SARS-CoV-2. From 2009 to 2013, I was selected as a PRESTO Researcher by the Japan Science and Technology Agency, which supports young researchers promoting unique and challenging, internationally high-level basic research. I am studying the relationship between the population genetics of a pathogen and the dynamics of infectious diseases caused by the pathogen.

Using a statistical modeling approach, I have developed a method to estimate the elevated reproduction number of SARS-CoV-2 variants using temporal changes in frequencies of detected variants (Euro Surveill, 2021). Since then, the method has been used in data from various countries ( Microbiol Spectr, 2025, Microbiol Spectr, 2024, Viruses, 2022, Math Biosci Eng, 2022, J Med Virol, 2022, J Clin Med, 2021). The developed model allows us to accurately predict the timing and trajectory of variant replacement in the future.

Research Interest

I’m currently interested in the relationship between the population genetics of a pathogen and the dynamics of infectious diseases caused by the pathogen. This new research field includes phylodynamics, of which theory is deeply associated with phylogenetics and coalescent theory.

Scientific Contribution

SARS-CoV-2 has undergone adaptive evolution since its emergence in the human population in 2019. Combining the renewal equation in mathematical epidemiology with theories in population genetics, we developed a novel epidemiological concept called relative instantaneous reproduction number (Euro Surveill, 2021). Applying this model to the adaptive evolution among multiple variants circulated in Japan, we have reported the prediction of variant replacement in the Advisory Board meeting for the control of COVID-19 at the Ministry of Health, Labour and Welfare, Japan 20 times since 2021. Using 58,669 sequences submitted to the GISAID Database from Denmark from November 1 to December 9, 2021, we estimated that Omicron is 3.19 times more transmissible than Delta (J Med Virol, 2022). The results were used by a public health alert in the CDC of the United States of America and reported to the world through CNN on January 4, 2022. The program to predict the future trajectory of variant replacement is an open-source program and is available at my repository on GitHub. In our paper (Virus Evol, 2021), we modeled the selective advantage of H1N1 influenza viruses using differences in patient age distribution. We found that the model could predict amino acid substitutions on hemagglutinin of H1N1 viruses with a sensitivity of 0.79, specificity of 0.87, and precision of 0.84. The results suggested that the influenza viruses were selected mainly in the adult population, and patient age is useful information to predict amino acid substitutions of H1N1 influenza viruses.

Personal Meeting Room

You can meet me fia Webex at my Personal Room in Zoom or Personal Room in Webex.

Teaching

I’m supervising Ph.D. students at the Graduate School of Infectious Diseases. In this graduate school, I teach

  • Advanced Topics in Information Science
  • Mathematical Biology of Infectious Diseases

You can attend to my classes at Hokkaido Summer Institute:

  • Computational Biology and Bioinformatics

Peer-reviewed Journal Articles and Peer-reviewed Conference Papars

  1. Arantes I, Ito K, Gomes M, Carvalho FCd, Ferreira de Almeida WA, Khouri R, Miyajima F, Wallau GL, Naveca FG, Pereira EC; COVID-19 Fiocruz Genomic Surveillance Network; Mendon?a Siqueira M, Resende PC, Bello G: Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived fromrecombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023, Microbiol Spectr, 13(1):e0119324 (2025) doi: 10.1128/spectrum.01193-24
  2. Samana K, Ito K, Suthienkul O, Ketsakorn A: The impact of respirable dust exposure on lung function parameters of motorcycle taxi drivers in Bangkok and adjacent provinces, Thailand, Air Qual Atmos Health, 1-13 (2024) doi: 10.1007/s11869-024-01599-y
  3. Samana K, Ito K, Suthienkul O, Ketsakorn A: Assessment of Health Risk from Exposure to Respirable Particulate Matter (RPM) among Motorcycle Taxi Drivers in Bangkok and Adjacent Provinces, Thailand, Environ Nat Rsour J, 22(4):1-8 (2024) doi: ?10.32526/ennrj/22/20230335
  4. Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H: Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire, J Virol, e0199523 (2024) doi: 10.1128/jvi.01995-23
  5. Arantes I, Gomes M, Ito K, Sarafim S, Graf T, Miyajima F, Khouri R, de Carvalho FC, de Almeida WAF, Siqueira MM, Resende PC, Naveca FG, Bello G; COVID-19 Fiocruz Genomic Surveillance Network: Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023, Microbiol Spectr, 12(3):e0383123 (2024) doi: 10.1128/spectrum.03831-23
  6. Peng S, Yamamoto A, Ito K: Link prediction on bipartite networks using matrix factorization with negative sample selection, PLoS One, 18(8):e0289568 (2023) doi: 10.1371/journal.pone.0289568
  7. Arantes I, Bello G, Nascimento V, Souza V, da Silva A, Silva D, Nascimento F, Mejia M, Brandao MJ, Goncalves L, Silva G, da Costa CF, Abdalla L, Santos JH, Ramos TCA, Piantham C, Ito K, Siqueira MM, Resende PC, Wallau GL, Delatorre E, Graf T, Naveca FG: Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas, Nature Commun, 14(1):2048 (2023) doi: 10.1038/s41467-023-37541-6
  8. Piantham C, Ito K. : Predicting the Trajectory of Replacements of SARS-CoV-2 Variants Using Relative Reproduction Numbers, Viruses, 14(11):2556 (2022) doi: 10.3390/v14112556
  9. Kim K, Ito K: Targeted sampling reduces the uncertainty in force of infection estimates from serological surveillance, Front Vet Sci, 9:754255 (2022) doi: 10.3389/fvets.2022.754255
  10. Ito K, Piantham C, Nishiura H: Estimating relative generation times and relative reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta in Denmark, Math Biosci Eng, 19(9): 9005-9017 (2022) doi: 10.3934/mbe.2022418
  11. Mohamed WMA, Moustafa MAM, Thu MJ, Kakisaka K, Chatanga E, Ogata S, Hayashi N, Taya Y, Ohari Y, Naguib D, Qiu Y, Matsuno K, Bawm S, Htun LL, Barker SC, Katakura K, Ito K, Nonaka N, Nakao R: Comparative mitogenomics elucidates the population genetic structure of Amblyomma testudinarium in Japan and a closely related Amblyomma species in Myanmar, Evol Appl, 00, 1–17 (2022) doi: 10.1111/eva.13426
  12. Shiohara M, Suzuki S, Shichinohe S, Ishigaki H, Nakayama M, Nomura N, Shingai M, Sekiya T, Ohno M, Iida S, Kawai N, Kawahara M, Yamagishi J, Ito K, Mitsumata R, Ikeda T, Motokawa K, Sobue T, Kida H, Ogasawara K, Itoh Y: Inactivated whole influenza virus particle vaccines induce neutralizing antibodies with an increase in immunoglobulin gene subclones of B-lymphocytes in cynomolgus macaques, Vaccine, 26;40(30):4026-4037 (2022) doi: 10.1016/j.vaccine.2022.05.045
  13. Ito K, Piantham C, Nishiura H: Relative Instantaneous Reproduction Number of Omicron SARS-CoV-2 variant with respect to the Delta variant in Denmark, J Med Virol, 27560 (2021) doi: 10.1002/jmv.27560
  14. Nishiura H, Ito K, Anzai A, Kobayashi T, Piantham C, Rodríguez-Morales AJ : Relative Reproduction Number of SARS-CoV-2 Omicron (B.1.1.529) Compared with Delta Variant in South Africa, J Clin Med., 11(1):30 (2021) doi: 10.3390/jcm11010030
  15. Ito K, Piantham C, Nishiura H: Predicted dominance of variant Delta of SARS-CoV-2 before Tokyo Olympic Games, Japan, July 2021, Eurosurveillance, 26(27):2100570 (2021) doi: 10.2807/1560-7917.ES.2021.26.27.2100570
  16. Piantham C, Ito K: Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions, Virus Evol, 7(1):veab049 (2021) doi: 10.1093/ve/veab049
  17. Moustafa MAM, Chel HM, Thu MJ, Bawm S, Htun LL, Win MM, Oo ZM, Ohsawa N, Lahdenperä M, Mohamed WMA, Ito K, Nonaka N, Nakao R, Katakura K: Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments, Sci Rep, 11(1):741 (2021) doi: 10.1038/s41598-020-80537-1
  18. Meade P, Kuan G, Strohmeier S, Maier HE, Amanat F, Balmaseda A, Ito K, Kirkpatrick E, Javier A, Gresh L, Nachbagauer R, Gordon A, Krammer F: Influenza virus infection induces a narrow antibody response in children but a broad recall response in adults, mBio, 11(1). pii: e03243-19 (2020) doi: 10.1128/mBio.03243-19
  19. Schachner A, Gonzalez G, Endler L, Ito K, Hess M: Fowl Adenovirus (FAdV) Recombination with Intertypic Crossovers in Genomes of FAdV-D and FAdV-E, Displaying Hybrid Serological Phenotypes, Viruses, 11(12). pii: E1094 (2019) doi: 10.3390/v11121094
  20. Mohamed W, Ito K, Omori R: Estimating Transmission Potential of H5N1 Viruses among Humans in Egypt Using Phylogeny, Genetic Distance and Sampling Time Interval, Front Microbiol, 10:2765 (2019) doi: 10.3389/fmicb.2019.02765
  21. Carr M, Gonzalez G, Martinelli A, Wastika CE, Ito K, Orba Y, Sasaki M, Hall WW, Sawa H: Upregulated expression of the antioxidant sestrin 2 identified by transcriptomic analysis of Japanese encephalitis virus-infected SH-SY5Y neuroblastoma cells, Virus Genes, Epub ahead of print (2019) doi: 10.1007/s11262-019-01683-x
  22. Sasaki Y, Shibuya T, Ito K, Arimura H: Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score, IEICE T Fund Electr, E102.A(9):1159-1170 (2019) doi: 10.1587/transfun.E102.A.1159
  23. Anindita PD, Sasaki M, Gonzalez G, Phongphaew W, Carr M, Hang’ombe BM, Mweene AS, Ito K, Orba Y, Sawa H: Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates, Sci Rep, 8;9(1):5045 (2019) doi: 10.1038/s41598-019-41358-z
  24. Salim B, Amin M, Igarashi M, Ito K, Jongejan F, Katakura K, Sugimoto C, Nakao R: Recombination and purifying and balancing selection determine the evolution of major antigenic protein 1 (map 1) family genes in Ehrlichia ruminantium, Gene, 683 216-224 (2019) doi: 10.1016/j.gene.2018.10.028
  25. Borthong J, Omori R, Sugimoto C, Suthienkul O, Nakao R, Ito K: Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis, Front Microbiol, 9:1272 (2018) doi: 10.3389/fmicb.2018.01272
  26. Tessmer HL, Ito K, Omori R: Can Machines Learn Respiratory Virus Epidemiology?: A Comparative Study of Likelihood-Free Methods for the Estimation of Epidemiological Dynamics, Front Microbiol, 9:343 (2018) doi: 10.3389/fmicb.2018.00343
  27. Donovan PD, Gonzalez G, Higgins DG, Butler G, Ito K: Identification of fungi in shotgun metagenomics datasets, PLoS One, 13(2):e0192898 (2018) doi: 10.1371/journal.pone.0192898
  28. Kim K, Omori R, Ito K: Inferring epidemiological dynamics of infectious diseases using Tajima’s D statistic on nucleotide sequences of pathogens, Epidemics, 21:21-29 (2017) doi: 10.1016/j.epidem.2017.04.004
  29. Carr M, Gonzalez G, Sasaki M, Dool SE, Ito K, Ishii A, Hang’ombe BM, Mweene AS, Teeling EC, Hall WW, Orba Y, Sawa H: Identification of the same polyomavirus species in different African horseshoe bat species is indicative of short range host-switching events, J Gen Virol, 98(11):2771-2785 (2017) doi: 10.1099/jgv.0.000935
  30. Carr M, Gonzalez G, Sasaki M, Ito K, Ishii A, Hang’ombe BM, Mweene AS, Orba Y, Sawa H: Discovery of African bat polyomaviruses and infrequent recombination in the large T antigen in the Polyomaviridae, J Gen Virol, 98(4):726-738 (2017) doi: 10.1099/jgv.0.000737
  31. Yokoyama M, Fujisaki S, Shirakura M, Watanabe S, Odagiri T, Ito K, Sato H: Molecular dynamics simulation of the influenza A(H3N2) hemagglutinin trimer reveals the structural basis for adaptive evolution of the recent epidemic clade 3C.2a, Front Microbiol, 8:584 (2017) doi: 10.3389/fmicb.2017.00584
  32. Nachbagauer R, Choi A, Hirsh A, Margine I, Iida S, Barrera A, Ferres M, Albrecht RA, García-Sastre A, Bouvier NM, Ito K, Medina RA, Palese P, Krammer F: Defining the antibody cross-reactome against the influenza virus surface glycoproteins, Nature Immunol, 18(4):464-473 (2017) doi: 10.1038/ni.3684
  33. Carr M, Kawaguchi A, Sasaki M, Gonzalez G, Ito K, Thomas Y, Hang’ombe BM, Mweene AS, Zhao G, Wang D, Orba Y, Ishii A, Sawa H: Isolation of a simian immunodeficiency virus from a malbrouck (Chlorocebus cynosuros), Arch Virol, 162(2):543-548 (2017) doi: 10.1007/s00705-016-3129-8
  34. Gonzalez G, Sasaki M, Burkitt-Gray L, Kamiya T, Tsuji NM, Sawa H, Ito K: An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus, Sci Rep, 7:40447 (2017) doi: 10.1038/srep40447
  35. Karnbunchob N, Omori R, Tessmer H, Ito K: Tracking the evolution of polymerase genes of influenza A viruses during interspecies transmission between avian and swine hosts, Front Microbiol, 7:2118 (2016) doi: 10.3389/fmicb.2016.02118
  36. Nyirenda M, Omori R, Tessmer HL, Arimura H, Ito K: Estimating the Lineage Dynamics of Human Influenza B Viruses, PLoS One, 11(11):e0166107 (2016) doi: 10.1371/journal.pone.0166107
  37. Sasaki M, Orba Y, Sasaki S, Gonzalez G, Ishii A, Hang’ombe BM, Mweene AS, Ito K, Sawa H: Multi-reassortant G3P[3] group A rotavirus in a horseshoe bat in Zambia, J Gen Virol, 97(10):2488-2493 (2016) doi: 10.1099/jgv.0.000591
  38. Nyirenda M, Arimura H, Ito K: Relaxing the Data Access Bottleneck of Geographic Big-data Analytics Applications using Distributed Quad trees, Proceedings of 2016 5th International Conference on Multimedia Computing and Systems (ICMCS), 189-194 (2016) doi: 10.1109/ICMCS.2016.7905524
  39. Sasaki M, Gonzalez G, Wada Y, Setiyono A, Handharyani E, Rahmadani I, Taha S, Adiani S, Latief M, Kholilullah ZA, Subangkit M, Kobayashi S, Nakamura I, Kimura T, Orba Y, Ito K, Sawa H: Divergent bufavirus harboured in megabats represents a new lineage of parvoviruses, Sci Rep, 6:24257 (2016) doi: 10.1038/srep24257
  40. Kim K, Omori R, Ueno K, Iida S, Ito K: Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review, PLoS One, 11(1):e0147021 (2016) doi: 10.1371/journal.pone.0147021
  41. Sasaki M, Orba Y, Anindita PD, Ishii A, Ueno K, Hang’ombe BM, Mweene AS, Ito K, Sawa H: Distinct Lineages of Bufavirus in Wild Shrews and Nonhuman Primates, Emerg Infect Dis, 21(7):1230-3 (2015) doi: 10.3201/eid2107.141969
  42. Sasaki Y, Shibuya T, Ito K, Arimura H: Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score, Proceedings of 3th International Conference on Similarity Search And Applications, SISAP 2015, 191-203 (2015) doi: 10.1007/978-3-319-25087-8_18
  43. Ogawa H, Miyamoto H, Nakayama E, Yoshida R, Nakamura I, Sawa H, Ishii A, Thomas Y, Nakagawa E, Matsuno K, Kajihara M, Maruyama J, Nao N, Muramatsu M, Kuroda M, Simulundu E, Changula K, Hang’ombe B, Namangala B, Nambota A, Katampi J, Igarashi M, Ito K, Feldmann H, Sugimoto C, Moonga L, Mweene A, Takada A: Seroepidemiological Prevalence of Multiple Species of Filoviruses in Fruit Bats (Eidolon helvum) Migrating in Africa, J Infect Dis, 212 Suppl 2:S101-8 (2015) doi: 10.1093/infdis/jiv063
  44. Ozawa M, Matsuu A, Yonezawa K, Igarashi M, Okuya K, Kawabata T, Ito K, Tsukiyama-Kohara K, Taneno A, Deguchi E.: Efficient isolation of Swine influenza viruses by age-targeted specimen collection, J Clin Microbio, 53(4):1331-8 (2015) doi: 10.1128/JCM.02941-14
  45. Sasaki M, Orba Y, Ueno K, Ishii A, Moonga L, Hang’ombe BM, Mweene AS, Ito K, Sawa H: Metagenomic analysis of shrew enteric virome reveals novel viruses related to human stool-associated viruses, J Gen Virol, 96(Pt 2):440-52 (2015) doi: 10.1099/vir.0.071209-0
  46. Ishii A, Ueno K, Orba Y, Sasaki M, Moonga L, Hang’ombe BM, Mweene AS, Umemura T, Ito K, Hall WW, Sawa H: A nairovirus isolated from African bats causes haemorrhagic gastroenteritis and severe hepatic disease in mice, Nat Commun, 5:5651 (2014) doi: 10.1038/ncomms6651
  47. Ueno K, Ishii A, Ito K: ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset, BMC Bioinform, 28(15):254 (2014) doi: 10.1186/1471-2105-15-254
  48. Nakao R, Qiu Y, Igarashi M, Magona JW, Zhou L, Ito K, Sugimoto C: High prevalence of spotted fever group rickettsiae in Amblyomma variegatum from Uganda and their identification using sizes of intergenic spacers, Ticks Tick Borne Dis, 4(6):506-512 (2013) doi: 10.1016/j.ttbdis.2013.07.001
  49. Shimada T, Hamada I, Hirata K, Kuboyama T, Yonezawa K, Ito K: Clustering of positions in nucleotide sequences by trim distance, Proceedings 2013 Second IIAI International Conference on Advanced Applied Informatics (IIAI-AAI 2013), 129-134 (2013) doi: 10.1109/IIAI-AAI.2013.72
  50. Muramatsu M, Yoshida R, Miyamoto H, Tomabechi D, Kajihara M, Maruyama J, Kimura T, Manzoor R, Ito K, Takada A: Heterosubtypic antiviral activity of hemagglutinin-specific antibodies induced by intranasal immunization with inactivated influenza viruses in mice, PLoS One, 8(8):e71534 (2013) doi: 10.1371/journal.pone.0071534
  51. Hayashida K, Abe T, Weir W, Nakao R, Ito K, Kajino K, Suzuki Y, Jongejan F, Geysen D, Sugimoto C: Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent, DNA Res, 20(3):209-20 (2013) doi: 10.1093/dnares/dst003
  52. Motohashi Y, Igarashi M, Okamatsu M, Noshi T, Sakoda Y, Yamamoto N, Ito K, Yoshida R, Kida H: Antiviral activity of stachyflin on influenza A viruses of different hemagglutinin subtypes, Virol J, 10:118 (2013) doi: 10.1186/1743-422X-10-118
  53. Yonezawa K, Igarashi M, Ueno K, Takada A, Ito K: Resampling nucleotide sequences with closest-neighbor trimming and its comparison to other methods, PLoS ONE, 8(2):e57684 (2013) doi: 10.1371/journal.pone.0057684
  54. Takano R, Kiso M, Igarashi M, Le QM, Sekijima M, Ito K, Takada A, Kawaoka Y: Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses, J Infect Dis, 207(1):89-97 (2013) doi: 10.1093/infdis/jis633
  55. Makino S, Shimada T, Hirata K, Yonezawa K, Ito K: A trim distance between positions as packaging signals in H3N2 influenza viruses, Joint 6th International Conference on Soft Computing and Intelligent Systems (SCIS) and 13th International Symposium on Advanced Intelligent Systems (ISIS), 1702-1707 (2012) doi: 10.1109/SCIS-ISIS.2012.6505355
  56. Shimada T, Hazemoto T, Makino S, Hirata K, Ito K: Finding correlated mutations among RNA segments in H3N2 influenza viruses, Joint 6th International Conference on Soft Computing and Intelligent Systems (SCIS) and 13th International Symposium on Advanced Intelligent Systems (ISIS), 1696-1701 (2012) doi: 10.1109/SCIS-ISIS.2012.6505354
  57. Muleya W, Namangala B, Simuunza M, Nakao R, Inoue N, Kimura T, Ito K, Sugimoto C, Sawa H: Population genetic analysis and sub-structuring of Theileria parva in the northern and eastern parts of Zambia, Parasit Vectors, 5:255 (2012) doi: 10.1186/1756-3305-5-255
  58. Makino S, Shimada T, Hirata K, Yonezawa K, Ito K: A trim distance between positions in nucleotide sequences, Discovery Science, Lecture Notes in Computer Science, 7569: 81-94 (2012) doi: 10.1007/978-3-642-33492-4_9
  59. Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, Kosuge T, Suzuki Y, Sato Y, Kawashima S, Katayama T, Wakaguri H, Inoue N, Homma K, Tada-Umezaki M, Yagi Y, Fujii Y, Habara T, Kanehisa M, Watanabe H, Ito K, Gojobori T, Sugawara H, Imanishi T, Weir W, Gardner M, Pain A, Shiels B, Hattori M, Nene V, and Sugimoto C: Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of theileria-induced leukocyte transformation, mBio, 3(5):e00204-12 (2012) doi: 10.1128/mBio.00204-12
  60. Nakahara KS, Masuta C, Yamada S, Shimura H, Kashihara Y, Wada TS, Meguro A, Goto K, Tadamura K, Sueda K, Sekiguchi T, Shao J, Itchoda N, Matsumura T, Igarashi M, Ito K, Carthew RW, Uyeda I.: Tobacco calmodulin-like protein provides secondary defense by binding to and directing degradation of virus RNA silencing suppressors, Proc Natl Acad Sci U S A, 109(25):10113-8 (2012) doi: 10.1073/pnas.1201628109
  61. Ueno K, Mineta K, Ito K, Endo T: Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands, BMC Struct Biol, 12(5) (2012) doi: 10.1186/1472-6807-12-5
  62. Yoshii K, Igarashi M, Ichii O, Yokozawa K, Ito K, Kariwa H, Takashima I: A conserved region in the prM protein is a critical determinant in the assembly of flavivirus particles, J Gen Virol, 93(Pt 1):27-38 (2012) doi: 10.1099/vir.0.035964-0
  63. Sasaki M, Kim E, Igarashi M, Ito K, Hasebe R, Fukushi H, Sawa H, Kimura T : Single amino acid residue in the A2 domain of major histocompatibility complex class I is involved in the efficiency of equine herpesvirus-1 entry, J Biol Chem, 286(45): 39370-39378 (2011) doi: 10.1074/jbc.M111.251751
  64. Ito K, Igarashi M, Miyazaki Y, Murakami T, Iida S, Kida H, Takada A: Gnarled-Trunk Evolutionary Model of Influenza A Virus Hemagglutinin, PLoS ONE, 6(10): e25953 (2011) doi: 10.1371/journal.pone.0025953
  65. Kajihara M, Matsuno K, Simulundu E, Muramatsu M, Noyori O, Manzoor R, Nakayama E, Igarashi M, Tomabechi D, Yoshida R, Okamatsu M, Sakoda Y, Ito K, Kida H, Takada A : An H5N1 highly pathogenic avian influenza virus that invaded Japan through waterfowl migration, Jpn J Vet Res, 59(2-3): 89-100 (2011) doi: 10.14943/jjvr.59.2-3.89
  66. Simulundu E, Ishii A, Igarashi M, Mweene AS, Suzuki Y, Hang’ombe BM, Namangala B, Moonga L, Manzoor R, Ito K, Nakamura I, Sawa H, Sugimoto C, Kida H, Simukonda C, Chansa W, Chulu J, Takada A: Characterization of influenza A viruses isolated from wild waterfowl in Zambia, J Gen Virol, 92(Pt 6): 1416-1427. (2011) doi: 10.1099/vir.0.030403-0
  67. Samad RAA, Sakoda Y, Tsuda Y, Simulundu E, Manzoor R, Okamatsu M, Ito K, Kida H: Virological surveillance and phylogenetic analysis of the PB2 genes of influenza viruses isolated from wild water birds flying from their nesting lakes in Siberia to Hokkaido, Japan in autumn, Jpn J Vet Res, 59(1): 15-22 (2011) doi: 10.14943/jjvr.59.1.15
  68. Yoshii K, Igarashi M, Ito K, Kariwa H, Holbrook MR, Takashima I: Construction of an infectious cDNA clone for Omsk hemorrhagic fever virus, and characterization of mutations in NS2A and NS5, Virus Research, 155(1): 61-68 (2011) doi: 10.1016/j.virusres.2010.08.023
  69. Ogawa H, Miyamoto H, Ebihara H, Ito K, Morikawa S, Feldmann H, Takada A: Detection of all known filovirus species by reverse transcription-polymerase chain reaction using a primer set specific for the viral nucleoprotein gene, J Virol Methods, 171(1): 310-313 (2011) doi: 10.1016/j.jviromet.2010.11.010
  70. Uchida Y, Kanehira K, Mase M, Takemae N, Watanabe C, Usui T, Fujimoto Y, Ito T, Igarashi M, Ito K, Takada A, Sakoda Y, Okamatsu M, Yamamoto Y, Nakamura K, Kida H, Hiromoto Y, Tsuda T, Saito T: Genetic characterization and susceptibility on poultry and mammal of H7N6 subtype avian influenza virus isolated in Japan in 2009, Vet Microbiol, 147(1-2): 1-10 (2011) doi: 10.1016/j.vetmic.2010.05.037
  71. Nakayama E, Yokoyama A, Miyamoto H, Igarashi M, Kishida N, Matsuno K, Marzi A, Feldmann H, Ito K, Saijo M, Takada A: Enzyme-linked immunosorbent assay for the detection of filovirus species-specific antibodies, Clin Vaccine Immunol., 17(11): 1723-1728 (2010) doi: 10.1128/CVI.00170-10
  72. Ito K, Zeugmann T, Zhu Y: Recent Experiences in Parameter-Free Data Mining, Lect Notes Electr Eng, 62:365–371 (2010) doi: 10.1007/978-90-481-9794-1_68
  73. Ito K, Zeugmann T, Zhu Y: Clustering the normalized compression distance for influenza virus data, Lect Notes Comput Sc, 6060: 130-146 (2010) doi: 10.1007/978-3-642-12476-1_9
  74. Watanabe Y, Hiraoka W, Igarashi M, Ito K, Shimoyama Y, Horiuchi M, Yamamori T, Yasui H, Kuwabara M, Inagaki F, Inanami O: A novel copper(II) coordination at His186 in full-length murine prion protein, Biochem Biophys Res Commun, 394(3):522-528 (2010) doi: 10.1016/j.bbrc.2010.03.003
  75. Igarashi M, Ito K, Yoshida R, Tomabechi D, Kida H, Takada A: Predicting the antigenic structure of the pandemic (H1N1) 2009 influenza virus hemagglutinin, PLoS ONE, 5(1): e8553 (2010) doi: 10.1371/journal.pone.0008553
  76. Yanagihashi F, Ito K, Arimura H: Inference of geographic transmission probability of influenza viruses from a large phylogenetic tree, Proceedings of the 20th International Conference on Genome Informatics (GIW2009), Poster Tracks 25 (2009) doi:
  77. Sata K, Hirata K, Ito K, Kuboyama T: Discovering networks for global propagation of influenza A (H3N2) viruses by clustering, Lect Notes Comput Sc, 5712: 490-497 (2009) doi: 10.1007/978-3-642-04592-9_61
  78. Simulundu E, Mweene AS, Tomabechi D, Hang’ombe BM, Ishii A, Suzuki Y, Nakamura I, Sawa H, Sugimoto C, Ito K, Kida H, Saiwana L, Takada A: Characterization of H3N6 avian influenza virus isolated from a wild white pelican in Zambia, Arch Virol, 54(9):1517-1522 (2009) doi: 10.1007/s00705-009-0467-9
  79. Ito K, Zeugmann T, Zhu Y: Clustering the normalized compression distance for virus data, Proceedings of the 6th Workshop on Learning with Logics and Logics for Learning (LLLL 2009), 56-67 (2009)
  80. Yoshida R, Igarashi M, Ozaki H, Kishida N, Tomabechi D, Kida H, Ito K, Takada A: Cross-protective potential of a novel monoclonal antibody directed against antigenic site B of the hemagglutinin of influenza A viruses, PLoS Pathog, 5(3) e1000350. (2009) doi: 10.1371/journal.ppat.1000350
  81. Igarashi M, Ito K, Kida H, Takada A: Genetically destined potentials for N-linked glycosylation of influenza virus hemagglutinin, Virology, 376(2):323-329 (2008) doi: 10.1016/j.virol.2008.03.036
  82. Minato S, Ito K: Symmetric item set mining method using zero-suppressed BDDs and application to biological data, Trans JSAI, 22:156-164 (2007) doi: 10.11185/imt.2.300
  83. Lamonova N, Ito K and Tanaka Y: From planning tools to intelligent assistants: meme media and logic programming technologies, Intelligent Assistant Systems: Concepts, Techniques and Technologies, Kaschek, R. eds., Idea Group, Inc., Hershey, PA:170-182 (2007)
  84. Ito K: Building intelligent multimodal assistants based on logic programming in the meme media architecture, Intelligent Assistant Systems: Concepts, Techniques and Technologies, Kaschek, R. eds., Idea Group, Inc., Hershey, PA: 146-169 (2007)
  85. Ito K, Igarashi M and Takada A: Data mining in amino acid sequences of H3N2 influenza viruses isolated during 1968 to 2006, Knowledge Media Technologies, pp. 154-158, Jantke, P.K. and Kreuzberger, G. eds., TU Ilmenau: 154-158 (2006)
  86. Ito K: A meme media framework for introducing multimodal user interface to existing web applications, Frontiers in Artificial Intelligence and Applications, 136: 83-93 (2006)
  87. Tanaka Y, Ito K, Fujima J: Meme media for clipping and combining web resources, World Wide Web, 9:117-142 (2006) doi: 10.1007/s11280-005-3043-6
  88. Ito K: Introducing multimodal character agents into existing web applications, Proceedings of the 14th International World Wide Web Conference (WWW2005), Poster Tracks 182 (2005) doi: 10.1145/1062745.1062821
  89. Ito K: Meme media and logic programming approach for intelligent media systems, Proceedings of the 2005 International Conference on Active Media Technology (AMT2005), 611-616 (2005) doi: 10.1109/AMT.2005.1505433
  90. Doetsch V, Ito K, Jantke KP: Human-agent co-operation in accessing and communicating knowledge media- A case in medical therapy planning, Lect Notes Comput Sc, 3359: 68-87 (2005) doi: 10.1007/978-3-540-32279-5_5
  91. Tanaka Y, Ito K: Meme media architecture for the reediting and redistribution of Web resources, Lect Notes Comput Sc, 3055: 1-12 (Invited Paper) (2004) doi: 10.1007/978-3-540-25957-2_1
  92. Tanaka Y, Ito K, Kurosaki D: Meme media architectures for re-editing and redistributing intellectual assets over the Web, Int J Hum Comput Stud, 60(4): 489-526 (2004) doi: 10.1016/j.ijhcs.2003.12.015
  93. Ito K, Tanaka Y: Web application wrapping by demonstration, Frontiers in Artificial Intelligence and Applications, 105:284-299 (2003)
  94. Ito K, Tanaka Y: A visual environment for web application composition, Proceedings of the 14th ACM Conference on Hypertext and Hypermedia (HyperText 03), 184-193 (2003) doi: 10.1145/900051.900092 Movies: [google_wrap.mpg, lycos-yahoo.mpg]
  95. Ito K, Sugibuchi T, Fujita Y, Oda T, Ohigashi M, Tanaka Y: Integrated visualization and reification of database and web contents, Proceedings of the 12th International World Wide Web Conference (WWW2003), Poster Tracks 182 (2003) http://www2003.org/cdrom/papers/poster/p129/p129-ito/p129-ito.html
  96. Ito K, Tanaka Y: Visual wrapping and functional linkage of web applications, Proceedings of Emerging Applications for Wireless and Mobile Access, (2003)
  97. Tanaka Y, Kurosaki D, Ito K: Live document framework for reediting and redistributing contents in WWW, Frontiers in Artificial Intelligence and Applications, 94:247-262 (2002)
  98. Ito K, Tanaka Y: Visual wrapping and composition of web applications for their interoperations, Proceedings of the 11th International World Wide Web Conference (WWW2002), Poster Tracks 64 (2002) http://wwwconference.org/proceedings/www2002/poster/64/index.html
  99. Yamamoto A, Ito K, Ishino A, Arimura H: Modelling semi-structured documents with hedges for deduction and induction, Lect Notes Artif Int, 2157: 240-247 (2001) doi: 10.1007/3-540-44797-0_20
  100. 伊藤公人, 田中譲: GUI部品とWebサービスの統合による分散アプリケーションの構築手法, インタラクティブシステムとソフトウェアIX, 137-142. 近代科学社 (2001) doi: https://www.kindaikagaku.co.jp/information/kd0299.htm
  101. 伊藤公人, 山本章博: スキーマと質問を用いた述語発見による論理プログラムの構成的学習アルゴリズム, 人工知能学会誌, 14(4): 679-688 (1999) http://id.nii.ac.jp/1004/00004701/
  102. 伊藤公人, 山本章博: 底節の最小汎化に基づく仮説の発見手法, 人工知能学会誌, 14(4): 709-716 (1999) http://id.nii.ac.jp/1004/00004704/
  103. Ito K, Yamamoto A: Finding hypotheses from examples by computing the least generalization of bottom clauses, Lect Notes Comput Sc, 1532: 303-314 (1998) doi: 10.1007/3-540-49292-5_27
  104. Ito K, Yamamoto A: Polynomial-time MAT learning of multilinear logic programs, Lect Notes Artif Int, 743: 63-74 (1993) doi: 10.1007/3-540-57369-0_28

Reviews and Book Chapters

  1. 渡邉真治，伊藤公人，佐藤裕徳: 季節性インフルエンザの流行予測, インフルエンザ, 20(4)，205-210 (2019)
  2. 渡邉真治，伊藤公人: インフルエンザの流行予測はどこまで可能か？, 感染症, 46巻1号，13-23 (2016)
  3. 伊藤公人: 計算機科学によるインフルエンザウイルスの抗原変異予測, 化学療法の領域, 30巻12号，68-74 (2014)
  4. 伊藤公人: 自然界から見る人獣共通感染症, みんぱく, 38巻11号，4-5 (2014)
  5. 伊藤公人: インフルエンザウイルスの変異予測, 感染・炎症・免疫, 42巻4号， 54-56 (2013)
  6. 伊藤公人: 数理科学はインフルエンザウイルスの変異を予測できるか？, 応用数理, 22巻3号: 15-17 (2012)
  7. 伊藤公人, 高田礼人: ウイルスはどうやって生き延びているのか？—インフルエンザウイルスの存続様式と進化, 遺伝, 66巻4号 (2012)
  8. 伊藤公人: バイオインフォマティクスによるインフルエンザウイルスの変異予測, 最新医学, 66(12): 2632-2640 (2011)
  9. 伊藤公人: インフルエンザウイルスの抗原変異とバイオインフォマティクス, ウイルス, 61(1): 3-13 (2011)
  10. Igarashi M, Ito K, Yoshida R, Tomabechi D, Kida H and Takada A: Prediction of the antigenic changes of the pandemic (H1N1) 2009 influenza virus hemagglutinin, Influenza and other respiratory viruses, 5 (supple. 1), 402-404. (2011)
  11. 伊藤公人, 高田礼人: インフルエンザウイルスの抗原変異予測とワクチン, VIRUS REPORT, 6(2): 60-68 (2009)
  12. 五十嵐学, 伊藤公人, 高田礼人: バイオインフォマティクスを用いたインフルエンザウイルスヘマグルチニンの糖鎖付加ポテンシャルの予測, Glycomicrobiology Now, http://www.glycoforum.gr.jp/science/glycomicrobiology/glycoinfeJ.html (2009)
  13. Igarashi M, Ito K, Takada A: Prediction of N-glycosylation potential of influenza virus hemagglutinin by a bioinformatic approach, Glycomicrobiology Now, http://www.glycoforum.gr.jp/science/glycomicrobiology/glycoinfeE.html (2009)
  14. Ito K and Tanaka Y: A visual environment for DOM-based wrapping and client-side linkage of web application, Intellectual Property Protection for Multimedia Information Technology, Sasaki, H. eds., Information Science Reference, IGI Global, Hershey, PA : 219-240 (2008)
  15. 伊藤公人: ウェブに公開されているサービスをキャラクタのガイドで気軽に活用する, 感じる・楽しむ・創りだす 感性情報学, 176. 工学舎 (2004)

Preprint

  1. Piantham C, Linton NM, Nishiura H, Ito K: Estimating the elevated transmissibility of the B.1.1.7 strain over previously circulating strains in England using GISAID sequence frequencies, medRxiv, (2021) doi: 10.1101/2021.03.17.21253775