Researcher basic information

• PhD, Hokkaido University

• https://researchmap.jp/itok?lang=en

• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=200901097689198149
• http://www.czc.hokudai.ac.jp/bioinform/members/kimihito-ito/

• 200901097689198149

• Infectious Disease Modelling
• Population Genetics
• Evolutionary Biology
• Bioinformatics
• Influenza Viruses
• Computer Science
• Computational Biology
• Knowledge Discovery and Data Mining

• Life Science, Virology
• Life Science, Evolutionary biology
• Informatics, Intelligent informatics
• Informatics, Life, health and medical informatics

• Doctoral (PhD) degree program, Graduate School of Infectious Diseases

Research activity information

• Analysis of PM-bound polycyclic aromatic hydrocarbons exposure among motorcycle taxi drivers in six central provinces in Thailand in winter
  Kamonwan Samana; Kimihito Ito; Orasa Suthienkul; Arroon Ketsakorn
  PLOS One, 20, 12, e0336587, e0336587, Public Library of Science (PLoS), 01 Dec. 2025, [Peer-reviewed]
  English, Scientific journal, Motorcycle taxis are popular transportation in areas with heavy traffic in Thailand. In this study, we recruited motorcycle taxi drivers in six central provinces in Thailand between January and March 2023 and measured their particulate matter (PM) and PM-bound polycyclic aromatic hydrocarbon (PAH) exposures using personal air sampling. We found that the PM ₁₀ and PM _2.5 concentrations measured by personal air sampling were independent of those monitored at air quality monitoring stations or by area air sampling devices. Among the six provinces, motorcycle taxi drivers in Pathum Thani were exposed to the highest mean concentration of PM ₁₀ (224.9 µg/m ³ ), PM _2.5 (410.9 µg/m ³ ), PM ₁₀₋ bound total PAH (38.4 ng/m ³ ), and PM _2.5 -bound total PAH (36.9 ng/m ³ ). Four workstations (PTT-1 to PTT-4) using 22 samples of PM₁₀ and 25 samples of PM₂.₅ personal air samplers showed unexpectedly higher PM₂.₅ than PM₁₀, likely due to route-specific environmental factors, as drivers follow variable routes determined by passenger destinations and daily demand. The incremental lifetime cancer risk of PM ₁₀₋ bound PAH and PM _2.5 -bound PAH in Pathum Thani were 4.5 × 10 ⁻⁸ and 7.8 × 10 ⁻⁸ , respectively, which were acceptable levels. None of the individuals’ lung function parameters was significantly correlated with the individuals’ concentrations of PM ₁₀ , PM _2.5 , PM ₁₀₋ bound total PAH, or PM _2.5 -bound total PAH. However, province averages of PM ₁₀ -bound total PAH exposure of motorcycle taxi drivers were positively correlated with the proportions of participants who answered symptoms of chronic bronchitis in the province. The causal relationship between motorcycle taxi drivers’ PM and PM-bound PAH exposure in Pathum Thani and their respiratory symptoms needs to be further investigated.
• RelRe: A command-line tool to predict the trajectory of variant replacement in an epidemic using relative instantaneous reproduction numbers
  Kimihito Ito; Michael A. Zeller; Chayada Piantham; Richard Musonda
  SoftwareX, 32, 102440, 102440, Elsevier BV, Dec. 2025, [Peer-reviewed], [Lead author, Corresponding author]
  English, Scientific journal
• Forecasting influenza A pandemic lineage dominance in the United States using relative reproduction rates
  Michael A Zeller; Rong Zhang; Yvonne C F Su; Kimihitio Ito
  Virus Evolution, 11, 1, Oxford University Press (OUP), 09 Jan. 2025
  Scientific journal, Abstract
  
  The 2009 H1N1 pandemic (pdm09) lineage is a major component of the H1 influenza A virus (IAV) that causes seasonal outbreaks annually. Since its introduction in the 2009–10 season, this lineage has evolved into distinct, successive clades in humans. Predicting the fitness of influenza clades is essential to forecasting future prevalence, providing a critical opportunity to develop a response to mitigate infection. The relative fitness of pdm09 lineages was retrospectively inferred via relative reproduction rate (RRe) through RelRe, a programme that implements a renewal equation to estimate the relative difference in reproduction number between cocirculating clades. For this analysis, pdm09 lineage sequences from the USA, collected from 2017 to 2023 in both human and swine hosts, were downloaded from public databases. Clade designations were assigned using Nextclade. Human case count data were divided by each influenza season, and the RRe was estimated at 3-month intervals. The RRe was then used to forecast clade frequency 90 days into the future, and the predictions were compared to the historical data. The highest predicted frequency at 90 days corresponded to the most frequently detected lineage in 9 out of 13 predictions (69%). The pdm09 lineage plays an important role at the human–swine influenza interface. Bayesian inference using both human and swine data indicated unequal transmission rates of the pdm09 lineage, with 53–79 noted transmissions from human to swine and 0–2 in reverse using the available genetic data. Metadata analysis revealed that new clades of pdm09 in humans were typically detected in swine as early as ~8–20 months after clade emergence in humans. Understanding RRe and the fitness of contemporary IAV strains enables the identification of high-risk reverse-zoonotic strains and provides critical time for responding to emergent human clades.
• Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023
  Ighor Arantes; Kimihito Ito; Marcelo Gomes; Felipe Cotrim de Carvalho; Walquiria Aparecida Ferreira de Almeida; Ricardo Khouri; Fabio Miyajima; Gabriel Luz Wallau; Felipe Gomes Naveca; Elisa Cavalcante Pereira; Marilda Mendonça Siqueira; Paola Cristina Resende; Gonzalo Bello
  Microbiology Spectrum, 13, 1, American Society for Microbiology, 07 Jan. 2025
  Scientific journal, ABSTRACT
  
  Recombination plays a crucial role in the evolution of SARS-CoV-2. The Omicron XBB* recombinant lineages are a noteworthy example, as they have been the dominant SARS-CoV-2 variant worldwide in the first half of 2023. Since November 2023, a new recombinant lineage between Omicron subvariants XBB and BA.2.86, designated XDR, has been detected mainly in Brazil. In this study, we reconstructed the spatiotemporal dynamics and estimated the absolute and relative transmissibility of the XDR lineage. The XDR lineage displayed a recombination breakpoint in the ORF1a-coding region, and the most closely related sequences to the 5′ and 3′ ends of the recombinant correspond to JD.1.1 and JN.1.1 lineages, respectively. The first XDR sequences were detected in November 2023 in the Northeastern Brazilian region, and their prevalence rapidly surged from <1% to 25% by February 2024. The Bayesian phylogeographic analysis supports that the XDR lineage likely emerged in the Northeastern Brazilian region around late October 2023 and rapidly disseminated within and outside Brazilian borders from mid-November onward. The median effective reproductive number of the XDR lineage in Brazil during the initial expansion phase was estimated to be around 1.5, and the average relative instantaneous reproduction numbers of XDR and JN* lineages were estimated to be 1.37 and 1.29 higher than that of co-circulating XBB* lineages. In summary, these findings support that the recombinant lineage XDR arose in the Northeastern Brazilian region in October 2023, shortly after the first detection of JN.1 sequences in the country. In Brazil, the XDR lineage exhibited a higher transmissibility level than its parental XBB.* lineages and is spreading at a rate similar to or slightly faster than the JN.1* lineages.
  
  IMPORTANCE
  
  This study highlights the emergence and rapid dissemination of the recombinant SARS-CoV-2 XDR lineage, derived from the Omicron lineages JD.1.1 and JN.1.1. The XDR lineage exhibited equivalent transmissibility to its JN.1* parental lineages and quickly spread across Brazil in late 2023. The findings underscore the critical role of real-time genomic surveillance in detecting novel variants with higher transmission potential. By utilizing phylogenetic and epidemiological methods, this research provides important insights into the molecular dynamics of XDR, which could inform public health responses and vaccine composition updates. The study’s significance lies in its ability to document the impact of recombination on viral evolution, offering valuable information to the field of virology and pandemic preparedness.
• Assessment of Health Risk from Exposure to Respirable Particulate Matter (RPM) among Motorcycle Taxi Drivers in Bangkok and Adjacent Provinces, Thailand
  Kamonwan Samana; Kimihito Ito; Orasa Suthienkul; Arroon Ketsakorn
  Environment and Natural Resources Journal, 22, 4, 1, 8, Faculty of Environment and Resource Studies - Mahidol University, 01 Jul. 2024
  Scientific journal, Exposure to outdoor air pollutants, particularly respirable particulate matter (RPM), can cause adverse health outcomes. The cross-sectional study aimed to assess motorcycle taxi driver’s health risk from exposure to RPM. A total of 153 motorcycle taxi drivers were recruited in Bangkok and five adjacent provinces during May and June 2022. The standardized questionnaire for data collection contained exposure time (hour/day), frequency of exposure (days/years), duration of exposure (year), body weight (kg), and averaging time (days). The average RPM concentration from six provinces were assessed personal air sampling pumps and ranged from 0.006-0.031 mg/m3. Bangkok showed the highest average RPM concentration (0.031 mg/m3), followed by Pathumthani (0.028 mg/m3), Samut Prakan (0.009 mg/m3), Nakhon Pathom (0.008 mg/m3), Nonthaburi (0.007 mg/m3), and Samut Sakhon (0.006 mg/m3), respectively. The Hazard Quotient (HQ) values for a non-carcinogenic risk to human health caused by RPM exposure in each province indicated a negligible risk (HQ=0.005-0.028). HQ averages (HQ=0.013) from all provinces were also at an acceptable level (≤1). Not all motorcycle taxi drivers are safe from RPM exposure, although their exposure is within acceptable limits depending on their individual susceptibility. Therefore, this is the first report on quantifying exposure to RPM from personal air sampling and health risk assessment among motorcycle taxi drivers. These findings would be useful information for further preventing and controlling ambient air pollution including policies and strategies to mitigate the risks for motorcycle-taxi drivers and the other exposed populations.
• The impact of respirable dust exposure on lung function parameters of motorcycle taxi drivers in Bangkok and adjacent provinces, Thailand
  Kamonwan Samana; Kimihito Ito; Orasa Suthienkul; Arroon Ketsakorn
  Air Quality, Atmosphere & Health, 17, 11, 2739, 2751, Springer Science and Business Media LLC, 29 Jun. 2024
  Scientific journal, Abstract
  
  The motorcycle taxi drivers of Bangkok and adjacent provinces in Thailand may have been heavily exposed to ambient air pollution and the impact of this on their lungs has been neither documented nor studied. In this study, we recruited a total of 343 motorcycle taxi drivers in Bangkok and adjacent provinces in Thailand and their lung function parameters were analyzed using spirometry in May and June 2022. Of these, 153 participants were selected and their exposure to respirable dust during working was measured by personal air sampling. Respirable dust concentrations collected with personal air sampling suggested that motorcycle taxi drivers working at workstations where they were exposed to respirable dust at high concentrations tended to have a low percent predicted FEV₁. Twelve% and 7.3% of motorcycle taxi drivers recruited in this study had the symptoms of chronic bronchitis and acute bronchitis, respectively. These results suggested that some motorcycle taxi drivers around Bangkok and adjacent provinces had a high risk of occupational exposure to ambient air pollution. The government needs to establish a medical check-up system for motorcycle taxi drivers to monitor their health status.
• Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023.
  Ighor Arantes; Marcelo Gomes; Kimihito Ito; Sharbilla Sarafim; Tiago Gräf; Fabio Miyajima; Ricardo Khouri; Felipe Cotrim de Carvalho; Walquiria Aparecida Ferreira de Almeida; Marilda Mendonça Siqueira; Paola Cristina Resende; Felipe Gomes Naveca; Gonzalo Bello
  Microbiology spectrum, 12, 3, e0383123, 05 Mar. 2024, [International Magazine]
  English, Scientific journal, UNLABELLED: The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n = 11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil's epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead. IMPORTANCE: Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.
• Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire
  Masashi Shingai; Sayaka Iida; Naoko Kawai; Mamiko Kawahara; Toshiki Sekiya; Marumi Ohno; Naoki Nomura; Chimuka Handabile; Tomomi Kawakita; Ryosuke Omori; Junya Yamagishi; Kaori Sano; Akira Ainai; Tadaki Suzuki; Kazuo Ohnishi; Kimihito Ito; Hiroshi Kida
  Journal of Virology, American Society for Microbiology, 07 Feb. 2024, [Corresponding author]
  Scientific journal, As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
• Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas
  Ighor Arantes; Gonzalo Bello; Valdinete Nascimento; Victor Souza; Arlesson da Silva; Dejanane Silva; Fernanda Nascimento; Matilde Mejía; Maria Júlia Brandão; Luciana Gonçalves; George Silva; Cristiano Fernandes da Costa; Ligia Abdalla; João Hugo Santos; Tatyana Costa Amorim Ramos; Chayada Piantham; Kimihito Ito; Marilda Mendonça Siqueira; Paola Cristina Resende; Gabriel Luz Wallau; Edson Delatorre; Tiago Gräf; Felipe Gomes Naveca
  Nature Communications, 14, 1, Springer Science and Business Media LLC, 11 Apr. 2023
  Scientific journal, Abstract
  
  The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil’s most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.
• Link prediction on bipartite networks using matrix factorization with negative sample selection.
  Siqi Peng; Akihiro Yamamoto; Kimihito Ito
  PloS one, 18, 8, e0289568, 2023, [Last author], [International Magazine]
  English, Scientific journal, We propose a new method for bipartite link prediction using matrix factorization with negative sample selection. Bipartite link prediction is a problem that aims to predict the missing links or relations in a bipartite network. One of the most popular solutions to the problem is via matrix factorization (MF), which performs well but requires reliable information on both absent and present network links as training samples. This, however, is sometimes unavailable since there is no ground truth for absent links. To solve the problem, we propose a technique called negative sample selection, which selects reliable negative training samples using formal concept analysis (FCA) of a given bipartite network in advance of the preceding MF process. We conduct experiments on two hypothetical application scenarios to prove that our joint method outperforms the raw MF-based link prediction method as well as all other previously-proposed unsupervised link prediction methods.
• Predicting the Trajectory of Replacements of SARS-CoV-2 Variants Using Relative Reproduction Numbers.
  Chayada Piantham; Kimihito Ito
  Viruses, 14, 11, 18 Nov. 2022, [Corresponding author], [International Magazine]
  English, Scientific journal, New variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high effective reproduction numbers are continuously being selected by natural selection. To establish effective control measures for new variants, it is crucial to know their transmissibility and replacement trajectory in advance. In this paper, we conduct retrospective prediction tests for the variant replacement from Alpha to Delta in England, using the relative reproduction numbers of Delta with respect to Alpha estimated from partial observations. We found that once Delta's relative frequency reached 0.15, the date when the relative frequency of Delta would reach 0.90 was predicted with maximum absolute prediction errors of three days. This means that the time course of the variant replacement could be accurately predicted from early observations. Together with the estimated relative reproduction number of a new variant with respect to old variants, the predicted replacement timing will be crucial information for planning control strategies against the new variant.
• Inactivated whole influenza virus particle vaccines induce neutralizing antibodies with an increase in immunoglobulin gene subclones of B-lymphocytes in cynomolgus macaques.
  Masanori Shiohara; Saori Suzuki; Shintaro Shichinohe; Hirohito Ishigaki; Misako Nakayama; Naoki Nomura; Masashi Shingai; Toshiki Sekiya; Marumi Ohno; Sayaka Iida; Naoko Kawai; Mamiko Kawahara; Junya Yamagishi; Kimihito Ito; Ryotarou Mitsumata; Tomio Ikeda; Kenji Motokawa; Tomoyoshi Sobue; Hiroshi Kida; Kazumasa Ogasawara; Yasushi Itoh
  Vaccine, 40, 30, 4026, 4037, 26 Jun. 2022, [Peer-reviewed], [International Magazine]
  English, Scientific journal, The All-Japan Influenza Vaccine Study Group has been developing a more effective vaccine than the current split vaccines for seasonal influenza virus infection. In the present study, the efficacy of formalin- and/or β-propiolactone-inactivated whole virus particle vaccines for seasonal influenza was compared to that of the current ether-treated split vaccines in a nonhuman primate model. The monovalent whole virus particle vaccines or split vaccines of influenza A virus (H1N1) and influenza B virus (Victoria lineage) were injected subcutaneously into naïve cynomolgus macaques twice. The whole virus particle vaccines induced higher titers of neutralizing antibodies against H1N1 influenza A virus and influenza B virus in the plasma of macaques than did the split vaccines. At challenge with H1N1 influenza A virus or influenza B virus, the virus titers in nasal swabs and the increases in body temperatures were lower in the macaques immunized with the whole virus particle vaccine than in those immunized with the split vaccine. Repertoire analyses of immunoglobulin heavy chain genes demonstrated that the number of B-lymphocyte subclones was increased in macaques after the 1st vaccination with the whole virus particle vaccine, but not with the split vaccine, indicating that the whole virus particle vaccine induced the activation of vaccine antigen-specific B-lymphocytes more vigorously than did the split vaccine at priming. Thus, the present findings suggest that the superior antibody induction ability of the whole virus particle vaccine as compared to the split vaccine is attributable to its stimulatory properties on the subclonal differentiation of antigen-specific B-lymphocytes.
• Comparative mitogenomics elucidates the population genetic structure of Amblyomma testudinarium in Japan and a closely related Amblyomma species in Myanmar
  Wessam Mohamed Ahmed Mohamed; Mohamed Abdallah Mohamed Moustafa; May June Thu; Keita Kakisaka; Elisha Chatanga; Shohei Ogata; Naoki Hayashi; Yurie Taya; Yuma Ohari; Doaa Naguib; Yongjin Qiu; Keita Matsuno; Saw Bawm; Lat Lat Htun; Stephen C. Barker; Ken Katakura; Kimihito Ito; Nariaki Nonaka; Ryo Nakao
  Evolutionary Applications, 15, 7, 1062, 1078, Wiley, 23 Jun. 2022, [Peer-reviewed]
  Scientific journal
• Estimating relative generation times and relative reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta in Denmark
  Kimihito Ito; Chayada Piantham; Hiroshi Nishiura
  Math Biosci Eng, 19, 9, 9005, 9017, Cold Spring Harbor Laboratory, 21 Jun. 2022, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal, Abstract
  
  The Omicron variant is the most transmissible variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) we had so far. The BA.1 and BA.2 sublineages of Omicron are circulating in Europe and it is urgent to evaluate the transmissibility of these sub-lineages. Using a mathematical model describing trajectories of variant frequencies that assumes a constant ratio in generation times and a constant ratio in effective reproduction numbers among variants, trajectories of variant frequencies in Denmark from November 22, 2021 to February 26, 2022 were analyzed. We found that the generation times of Omicron BA.1 and BA.2 are 0.60 (95%CI: 0.59–0.62) and 0.51 (95%CI: 0.50–0.52) of the length of that of Delta, respectively. We also found that the effective reproduction number of Omicron BA.1 is 1.99 (95% CI: 1.98–2.02) times and that of Omicron BA.2 is 2.51 (95% CI: 2.48– 2.55) times larger than the effective reproduction number of Delta. The generation times of Omicron BA.2 is 0.85 (95% CI:0.84–0.86) the length of that of BA.1 and that the effective reproduction number of Omicron BA.2 is 1.26 (95% CI:1.25–1.26) times larger than that of Omicron BA.1. These estimates on the ratio of generation times and the ratio of effective reproduction numbers has epidemiologically important implications. The duration of quarantine for people who contacted with an Omicron BA.1 and BA.2 patient can be reduced to 60% and 51% of that for Delta, respectively. The control measures against Omicron BA.1 and BA.2 need to reduce contacts between infectious and susceptible people respectively by 50% (95% CI: 49–50%) and 60% (95% CI: 60–61%) compared to that against Delta to achieve the same effect on their control.
• Targeted sampling reduces the uncertainty in force of infection estimates from serological surveillance.
  Kiyeon Kim; Kimihito Ito
  Frontiers in veterinary science, 9, 754255, 754255, 2022, [International Magazine]
  English, Scientific journal, Age bins are frequently used in serological studies of infectious diseases in wildlife to deal with uncertainty in the age of sampled animals. This study analyzed how age binning and targeted sampling in serological surveillance affect the width of the 95% confidence interval (CI) of the estimated force of infection (FOI) of infectious diseases. We indicate that the optimal target population with the narrowest 95% CI differs depending on the expected FOI using computer simulations and mathematical models. In addition, our findings show that we can substantially reduce the number of animals required to infer transmission risk by tailoring targeted, age-based sampling to specific epidemiological situations.
• Relative Instantaneous Reproduction Number of Omicron SARS-CoV-2 variant with respect to the Delta variant in Denmark.
  Kimihito Ito; Chayada Piantham; Hiroshi Nishiura
  Journal of medical virology, 94, 5, 2265, 2268, 30 Dec. 2021, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal, The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become widespread across the world in a flashing manner. As of December 7, 2021, a total of 758 Omicron cases were confirmed in Denmark. Using the nucleotide sequences of the Delta and Omicron variants registered from Denmark in the GISAID database, we found that the effective (instantaneous) reproduction number of Omicron is 3.19 (95%CI 2.82-3.61) times greater than that of Delta under the same epidemiological conditions. Proportion of Omicron infections among all SARS-CoV-2 infections in Denmark was expected exceed the 95% on December 28, 2021 with a 95% CI from December 25 to December 31, 2021. Given that the Delta variant or variants less transmissible than Delta are dominant in most countries, the rapid increase in Omicron in the virus population may be observed as soon as the Omicron is introduced. Preparing proactive control measures is vital, assuming the substantial advantage of the transmission by Omicron. This article is protected by copyright. All rights reserved.
• Relative Reproduction Number of SARS-CoV-2 Omicron (B.1.1.529) Compared with Delta Variant in South Africa
  Hiroshi Nishiura; Kimihito Ito; Asami Anzai; Tetsuro Kobayashi; Chayada Piantham; Rodriguez-Morales AJ
  Journal of Clinical Medicine, 11, 1, Dec. 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, The world identified the rapidly increasing incidence of the causative variant of SARS-CoV-2 Pangolin B [...].
• Predicted dominance of variant Delta of SARS-CoV-2 before Tokyo Olympic Games, Japan, July 2021
  Kimihito Ito; Chayada Piantham; Hiroshi Nishiura
  Eurosurveillance, 27, 08 Jul. 2021, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• Estimating the increased transmissibility of the B.1.1.7 strain over previously circulating strains in England using frequencies of GISAID sequences and the distribution of serial intervals
  Piantham C; Ito K
  Cold Spring Harbor Laboratory, 17 Mar. 2021, [Last author, Corresponding author]
  English, The B.1.1.7 strain, a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is thought to have higher transmissibility than previously circulating strains in England. This paper proposes a method to estimate the selective advantage of a mutant strain over previously circulating strains using the time course of B.1.1.7 strain frequencies and the distribution of serial intervals. The method allows instantaneous reproduction numbers of infections to change during the target period of analysis. The proposed method, instead, assumes that the selective advantage of a mutant strain over previously circulating strains is constant over time. Applying this method to the sequence data of SARS-CoV-2 in England, the instantaneous reproduction number of the B.1.1.7 strain is estimated to be 33.7% (with a 95% confidence interval (CI) from 33.6% to 33.9%) higher than previously circulating strains in England, assuming that serial intervals of COVID-19 follow a lognormal distribution with a mean of 4.7 days and a standard deviation of 2.9 days. The result indicated that the control measure against B.1.1.7 strain needs to be strengthened by 33.7% from that against previously circulating strains. To get the same control effect as before, contact rates between individuals needed to be restricted to 0.748 of the contact rates that had been achieved by the control measure taken for previously circulating strains.
• Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions
  Chayada Piantham; Kimihito Ito
  Virus Evolution, 7, 1, 01 Jan. 2021, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal
• Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments
  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
  Scientific Reports, 11, 1, 741, Springer Science and Business Media LLC, Jan. 2021, [Peer-reviewed]
  English, Scientific journal
• Influenza Virus Infection Induces a Narrow Antibody Response in Children but a Broad Recall Response in Adults.
  Philip Meade; Guillermina Kuan; Shirin Strohmeier; Hannah E Maier; Fatima Amanat; Angel Balmaseda; Kimihito Ito; Ericka Kirkpatrick; Andres Javier; Lionel Gresh; Raffael Nachbagauer; Aubree Gordon; Florian Krammer
  mBio, 11, 1, 21 Jan. 2020, [Peer-reviewed], [International Magazine]
  English, Scientific journal, In contrast to influenza virus vaccination, natural infection induces long-lived and relatively broad immune responses. However, many aspects of the antibody response to natural infection are not well understood. Here, we assessed the immune response after H1N1 influenza virus infection in children and adults in a Nicaraguan household transmission study using an influenza virus protein microarray (IVPM). This technology allows us to simultaneously measure IgG and IgA antibody responses to hemagglutinins of many different virus strains and subtypes quantitatively with a high throughput. We found that children under 6 years of age responded to natural infection with a relatively narrow response that targeted mostly the hemagglutinin of the strain that caused the infection. Adults, however, have a much broader response, including a boost in antibodies to many group 1 subtype hemagglutinins. Also, a strong recall response against historic H1 hemagglutinins that share the K133 epitope with the pandemic H1N1 virus was observed. Of note, some children, while responding narrowly within H1 and group 1 hemagglutinins, induced a boost to H3 and other group 2 hemagglutinins when infected with H1N1 when they had experienced an H3N2 infection earlier in life. This is an interesting phenomenon providing evidence for immune imprinting and a significant new insight which might be leveraged in future universal influenza virus vaccine strategies. Finally, preexisting immunity to pandemic H1 hemagglutinins was significantly associated with protection from infection in both children and adults. In adults, preexisting immunity to non-H1 group 1 hemagglutinins was also significantly associated with protection from infection.IMPORTANCE It is known since Thomas Francis, Jr. published his first paper on original antigenic sin in 1960 that the first infection(s) with influenza virus leaves a special immunological imprint which shapes immune responses to future infections with antigenically related influenza virus strains. Imprinting has been implicated in both protective effects as well as blunting of the immune response to vaccines. Despite the fact that this phenomenon was already described almost 60 years ago, we have very little detailed knowledge of the characteristics and breadth of the immune response to the first exposure(s) to influenza virus in life and how this compares to later exposure as adults. Here, we investigate these immune responses in detail using an influenza virus protein microarray. While our findings are mostly descriptive in nature and based on a small sample size, they provide a strong basis for future large-scale studies to better understand imprinting effects.
• Publisher Correction: Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates (Scientific Reports, (2019), 9, 1, (5045), 10.1038/s41598-019-41358-z)
  Anindita, P.D.; Sasaki, M.; Gonzalez, G.; Phongphaew, W.; Carr, M.; Hang’ombe, B.M.; Mweene, A.S.; Ito, K.; Orba, Y.; Sawa, H.
  Scientific Reports, 9, 1, 8502, 8502, 2019, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Efficient approximate 3-dimensional point set matching using root-mean-square deviation score
  Sasaki, Y.; Shibuya, T.; Ito, K.; Arimura, H.
  IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E102A, 9, 1159, 1170, 2019, [Peer-reviewed]
  English, Scientific journal
• Recombination and purifying and balancing selection determine the evolution of major antigenic protein 1 (map 1) family genes in Ehrlichia ruminantium
  Salim, B.; Amin, M.; Igarashi, M.; Ito, K.; Jongejan, F.; Katakura, K.; Sugimoto, C.; Nakao, R.
  Gene, 683, 216, 224, Elsevier BV, 2019, [Peer-reviewed]
  Scientific journal
• Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates
  Anindita, P.D.; Sasaki, M.; Gonzalez, G.; Phongphaew, W.; Carr, M.; Hang’ombe, B.M.; Mweene, A.S.; Ito, K.; Orba, Y.; Sawa, H.
  Scientific Reports, 9, 1, 5045, 5045, 2019, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Upregulated expression of the antioxidant sestrin 2 identified by transcriptomic analysis of Japanese encephalitis virus-infected SH-SY5Y neuroblastoma cells
  Carr, M.; Gonzalez, G.; Martinelli, A.; Wastika, C.E.; Ito, K.; Orba, Y.; Sasaki, M.; Hall, W.W.; Sawa, H.
  Virus Genes, 55, 5, 630, 642, 2019, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Fowl Adenovirus (FAdV) recombination with intertypic crossovers in genomes of FAdV-D and FAdV-E, displaying hybrid serological phenotypes
  Schachner, A.; Gonzalez, G.; Endler, L.; Ito, K.; Hess, M.
  Viruses, 11, 12, 2019, [Peer-reviewed]
  Scientific journal
• Estimating Transmission Potential of H5N1 Viruses Among Humans in Egypt Using Phylogeny, Genetic Distance and Sampling Time Interval
  Mohamed, W.; Ito, K.; Omori, R.
  Frontiers in Microbiology, 10, 2765, 2019, [Peer-reviewed]
  Scientific journal
• Identification of fungi in shotgun metagenomics datasets
  Donovan, P.D.; Gonzalez, G.; Higgins, D.G.; Butler, G.; Ito, K.
  PLoS ONE, 13, 2, 2018, [Peer-reviewed]
  English, Scientific journal
• Comparison of database search methods for the detection of Legionella pneumophila in water samples using metagenomic analysis
  Borthong, J.; Omori, R.; Sugimoto, C.; Suthienkul, O.; Nakao, R.; Ito, K.
  Frontiers in Microbiology, 9, JUN, 2018, [Peer-reviewed]
  English, Scientific journal
• Can machines learn respiratory virus epidemiology?: A comparative study of likelihood-free methods for the estimation of epidemiological dynamics
  Tessmer, H.L.; Ito, K.; Omori, R.
  Frontiers in Microbiology, 9, MAR, 2018, [Peer-reviewed]
  English, Scientific journal
• Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens
  Kiyeon Kim; Ryosuke Omori; Kimihito Ito
  EPIDEMICS, 21, 21, 29, Dec. 2017, [Peer-reviewed]
  English, Scientific journal
• Molecular Dynamics Simulation of the Influenza A(H3N2) Hemagglutinin Trimer Reveals the Structural Basis for Adaptive Evolution of the Recent Epidemic Clade 3C. 2a
  Masaru Yokoyama; Seiichiro Fujisaki; Masayuki Shirakura; Shinji Watanabe; Takato Odagiri; Kimito Ito; Hironori Sato
  FRONTIERS IN MICROBIOLOGY, 8, Apr. 2017, [Peer-reviewed]
  English, Scientific journal
• Isolation of a simian immunodeficiency virus from a malbrouck (Chlorocebus cynosuros)
  Michael Carr; Akira Kawaguchi; Michihito Sasaki; Gabriel Gonzalez; Kimihito Ito; Yuka Thomas; Bernard M. Hang'ombe; Aaron S. Mweene; Guoyan Zhao; David Wang; Yasuko Orba; Akihiro Ishii; Hirofumi Sawa
  ARCHIVES OF VIROLOGY, 162, 2, 543, 548, Feb. 2017, [Peer-reviewed]
  English, Scientific journal
• Identification of the same polyomavirus species in different African horseshoe bat species is indicative of short-range host-switching events
  Carr, Michael; Gonzalez, Gabriel; Sasaki, Michihito; Dool, Serena E.; Ito, Kimihito; Ishii, Akihiro; Hang'ombe, Bernard M.; Mweene, Aaron S.; Teeling, Emma C.; Hall, William W.; Orba, Yasuko; Sawa, Hirofumi
  Journal of General Virology, 98, 11, 2771, 2785, 2017, [Peer-reviewed]
  English, Scientific journal
• Discovery of African bat polyomaviruses and infrequent recombination in the large T antigen in the Polyomaviridae
  Carr, M.; Gonzalez, G.; Sasaki, M.; Ito, K.; Ishii, A.; Hang’Ombe, B.M.; Mweene, A.S.; Orba, Y.; Sawa, H.
  Journal of General Virology, 98, 4, 726, 738, 2017, [Peer-reviewed]
  English, Scientific journal
• An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus
  Gonzalez, G.; Sasaki, M.; Burkitt-Gray, L.; Kamiya, T.; Tsuji, N.M.; Sawa, H.; Ito, K.
  Scientific Reports, 7, 40447, 2017, [Peer-reviewed]
  English, Scientific journal
• Defining the antibody cross-reactome directed against the influenza virus surface glycoproteins
  Nachbagauer, R.; Choi, A.; Hirsh, A.; Margine, I.; Iida, S.; Barrera, A.; Ferres, M.; Albrecht, R.A.; García-Sastre, A.; Bouvier, N.M.; Ito, K.; Medina, R.A.; Palese, P.; Krammer, F.
  Nature Immunology, 18, 4, 464, +, 2017, [Peer-reviewed]
  English, Scientific journal
• Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts
  Nipawit Karnbunchob; Ryosuke Omori; Heidi L. Tessmer; Kimihito Ito
  FRONTIERS IN MICROBIOLOGY, 7, 2118, Dec. 2016, [Peer-reviewed]
  English, Scientific journal
• Estimating the Lineage Dynamics of Human Influenza B Viruses
  Mayumbo Nyirenda; Ryosuke Omori; Heidi L. Tessmer; Hiroki Arimura; Kimihito Ito
  PLOS ONE, 11, 11, e0166107, Nov. 2016, [Peer-reviewed]
  English, Scientific journal
• Multi-reassortant G3P[3] group A rotavirus in a horseshoe bat in Zambia
  Michihito Sasaki; Yasuko Orba; Satoko Sasaki; Gabriel Gonzalez; Akihiro Ishii; Bernard M. Hang'ombe; Aaron S. Mweene; Kimihito Ito; Hirofumi Sawa
  JOURNAL OF GENERAL VIROLOGY, 97, 10, 2488, 2493, Oct. 2016, [Peer-reviewed]
  English, Scientific journal
• Divergent bufavirus harboured in megabats represents a new lineage of parvoviruses
  Michihito Sasaki; Gabriel Gonzalez; Yuji Wada; Agus Setiyono; Ekowati Handharyani; Ibenu Rahmadani; Siswatiana Taha; Sri Adiani; Munira Latief; Zainal Abidin Kholilullah; Mawar Subangkit; Shintaro Kobayashi; Ichiro Nakamura; Takashi Kimura; Yasuko Orba; Kimihito Ito; Hirofumi Sawa
  SCIENTIFIC REPORTS, 6, 24257, Apr. 2016, [Peer-reviewed]
  English, Scientific journal
• Relaxing the Data Access Bottleneck of Geographic Big-data Analytics Applications using Distributed Quad trees
  Mayumbo Nyirenda; Hiroki Arimura; Kimihito Ito
  PROCEEDINGS OF 2016 5TH INTERNATIONAL CONFERENCE ON MULTIMEDIA COMPUTING AND SYSTEMS (ICMCS), 189, 194, 2016, [Peer-reviewed]
  English, International conference proceedings
• Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review
  Kiyeon Kim; Ryosuke Omori; Keisuke Ueno; Sayaka Iida; Kimihito Ito
  PLOS ONE, 11, 1, e0147021, Jan. 2016, [Peer-reviewed]
  English, Scientific journal
• Seroepidemiological Prevalence of Multiple Species of Filoviruses in Fruit Bats (Eidolon helvum) Migrating in Africa
  Hirohito Ogawa; Hiroko Miyamoto; Eri Nakayama; Reiko Yoshida; Ichiro Nakamura; Hirofumi Sawa; Akihiro Ishii; Yuka Thomas; Emiko Nakagawa; Keita Matsuno; Masahiro Kajihara; Junki Maruyama; Naganori Nao; Mieko Muramatsu; Makoto Kuroda; Edgar Simulundu; Katendi Changula; Bernard Hang'ombe; Boniface Namangala; Andrew Nambota; Jackson Katampi; Manabu Igarashi; Kimihito Ito; Heinz Feldmann; Chihiro Sugimoto; Ladslav Moonga; Aaron Mweene; Ayato Takada
  JOURNAL OF INFECTIOUS DISEASES, 212, S101, S108, Oct. 2015, [Peer-reviewed]
  English, Scientific journal
• Distinct Lineages of Bufavirus in Wild Shrews and Nonhuman Primates
  Michihito Sasaki; Yasuko Orba; Paulina D. Anindita; Akihiro Ishii; Keisuke Ueno; Bernard M. Hang'ombe; Aaron S. Mweeile; Kimihito Ito; Hirofumi Sawa
  EMERGING INFECTIOUS DISEASES, 21, 7, 1230, 1233, Jul. 2015, [Peer-reviewed]
  English, Scientific journal
• Efficient Isolation of Swine Influenza Viruses by Age-Targeted Specimen Collection
  Makoto Ozawa; Aya Matsuu; Kouki Yonezawa; Manabu Igarashi; Kosuke Okuya; Toshiko Kawabata; Kimihito Ito; Kyoko Tsukiyama-Kohara; Akira Taneno; Eisaburo Deguchi
  JOURNAL OF CLINICAL MICROBIOLOGY, 53, 4, 1331, 1338, Apr. 2015, [Peer-reviewed]
  English, Scientific journal
• Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses
  Michihito Sasaki; Yasuko Orba; Keisuke Ueno; Akihiro Ishii; Ladslav Moonga; Bernard M. Hang'ombe; Aaron S. Mweene; Kimihito Ito; Hirofumi Sawa
  JOURNAL OF GENERAL VIROLOGY, 96, Pt 2, 440, 452, Feb. 2015, [Peer-reviewed]
  English, Scientific journal
• Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score
  Yoichi Sasaki; Tetsuo Shibuya; Kimihito Ito; Hiroki Arimura
  SIMILARITY SEARCH AND APPLICATIONS, SISAP 2015, 9371, 191, 203, 2015, [Peer-reviewed]
  English, International conference proceedings
• Closest-Neighbor Resampling for Huge Biological Sequence Datasets
  Kouki Yonezawa; Manabu Igarashi; Yasuo Ohara; Kimihito Ito
  GENES & GENETIC SYSTEMS, 89, 6, 313, 313, Dec. 2014, [Peer-reviewed]
  English
• A nairovirus isolated from African bats causes haemorrhagic gastroenteritis and severe hepatic disease in mice
  Akihiro Ishii; Keisuke Ueno; Yasuko Orba; Michihito Sasaki; Ladslav Moonga; Bernard M. Hang'ombe; Aaron S. Mweene; Takashi Umemura; Kimihito Ito; William W. Hall; Hirofumi Sawa
  NATURE COMMUNICATIONS, 5, 5651, Dec. 2014, [Peer-reviewed]
  English, Scientific journal
• ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset
  Keisuke Ueno; Akihiro Ishii; Kimihito Ito
  BMC BIOINFORMATICS, 15, 254, Jul. 2014, [Peer-reviewed]
  English, Scientific journal
• High prevalence of spotted fever group rickettsiae in Amblyomma variegatum from Uganda and their identification using sizes of intergenic spacers.
  Ryo Nakao; Yongjin Qiu; Manabu Igarashi; Joseph W Magona; Lijia Zhou; Kimihito Ito; Chihiro Sugimoto
  Ticks and tick-borne diseases, 4, 6, 506, 12, Dec. 2013, [Peer-reviewed], [International Magazine]
  English, Scientific journal, The spotted fever group (SFG) rickettsiae are obligate intracellular bacteria transmitted by ticks that cause several tick-borne rickettsioses in humans worldwide. This study was intended to determine the prevalence of SFG rickettsiae in Amblyomma variegatum from 7 districts across Uganda. In addition to sequencing of gltA and ompA genes, identification of Rickettsia species based on the sizes of highly variable intergenic spacers, namely, dksA-xerC, mppA-purC, and rpmE-tRNA(fMet) was carried out. Application of multiplex PCR for simultaneous amplification of 3 spacers combined with capillary electrophoresis separation allowed simple, accurate, and high-throughput fragment sizing with considerable time and cost savings. Rickettsia genus-specific real-time PCR detected 136 positives out of 140 samples, giving an overall prevalence of 97.1%. Most samples (n=113) had a size combination of 225, 195, and 341 bp for dksA-xerC, mppA-purC, and rpmE-tRNA(fMet), respectively, which was identical to that of R. africae, a causative agent of African tick bite fever. In addition, several samples had size variants in either dksA-xerC or rpmE-tRNA(fMet). Nonetheless, the partial sequences of gltA and ompA genes of samples of all size combinations showed the greatest similarity to R. africae (99.3-100% for gltA and 98.1-100% for ompA). Given these results, it is highly possible that the tested ticks were infected with R. africae or closely related species. This is a first report on molecular genetic detection of R. africae and its high endemicity in Uganda. Clinicians in this country should be aware of this pathogen as a cause of non-malarial febrile illness. This study provided a starting point for the development of Rickettsia species identification based on the sizes of intergenic spacers. The procedure is simple, rapid, and cost-effective to perform; hence it might be particularly well suited for preliminary species identification in epidemiological investigations. The results may be more detailed and reliable when simultaneous sequencing analysis is performed.
• Heterosubtypic Antiviral Activity of Hemagglutinin-Specific Antibodies Induced by Intranasal Immunization with Inactivated Influenza Viruses in Mice
  Mieko Muramatsu; Reiko Yoshida; Hiroko Miyamoto; Daisuke Tomabechi; Masahiro Kajihara; Junki Maruyama; Takashi Kimura; Rashid Manzoor; Kimihito Ito; Ayato Takada
  PLOS ONE, 8, 8, e71534, Aug. 2013, [Peer-reviewed]
  English, Scientific journal
• Whole-genome sequencing of theileria parva strains provides insight into parasite migration and diversification in the african continent
  Kyoko Hayashida; Takashi Abe; William Weir; Ryo Nakao; Kimihito Ito; Kiichi Kajino; Yutaka Suzuki; Frans Jongejan; Dirk Geysen; Chihiro Sugimoto
  DNA Research, 20, 3, 209, 220, Jun. 2013, [Peer-reviewed]
  English, Scientific journal
• Antiviral activity of stachyflin on influenza A viruses of different hemagglutinin subtypes
  Yurie Motohashi; Manabu Igarashi; Masatoshi Okamatsu; Takeshi Noshi; Yoshihiro Sakoda; Naoki Yamamoto; Kimihito Ito; Ryu Yoshida; Hiroshi Kida
  VIROLOGY JOURNAL, 10, 118, Apr. 2013, [Peer-reviewed]
  English, Scientific journal
• Resampling Nucleotide Sequences with Closest-Neighbor Trimming and Its Comparison to Other Methods
  Kouki Yonezawa; Manabu Igarashi; Keisuke Ueno; Ayato Takada; Kimihito Ito
  PLoS ONE, 8, 2, e57684, 27 Feb. 2013, [Peer-reviewed]
  English, Scientific journal
• Clustering of Positions in Nucleotide Sequences by Trim Distance
  Takaharu Shimada; Issei Hamada; Kouichi Hirata; Tetsuji Kuboyama; Kouki Yonezawa; Kimihito Ito
  2013 SECOND IIAI INTERNATIONAL CONFERENCE ON ADVANCED APPLIED INFORMATICS (IIAI-AAI 2013), 129, 134, 2013, [Peer-reviewed]
  English, International conference proceedings
• Molecular Mechanisms Underlying Oseltamivir Resistance Mediated by an I117V Substitution in the Neuraminidase of Subtype H5N1 Avian Influenza A Viruses
  Ryo Takano; Maki Kiso; Manabu Igarashi; Quynh Mai Le; Masakazu Sekijima; Kimihito Ito; Ayato Takada; Yoshihiro Kawaoka
  JOURNAL OF INFECTIOUS DISEASES, 207, 1, 89, 97, Jan. 2013, [Peer-reviewed]
  English, Scientific journal
• Population genetic analysis and sub-structuring of Theileria parva in the northern and eastern parts of Zambia
  Walter Muleya; Boniface Namangala; Martin Simuunza; Ryo Nakao; Noboru Inoue; Takashi Kimura; Kimihito Ito; Chihiro Sugimoto; Hirofumi Sawa
  PARASITES & VECTORS, 5, 255, Nov. 2012, [Peer-reviewed]
  English, Scientific journal
• Comparative Genome Analysis of Three Eukaryotic Parasites with Differing Abilities To Transform Leukocytes Reveals Key Mediators of Theileria-Induced Leukocyte Transformation
  Kyoko Hayashida; Yuichiro Hara; Takashi Abe; Chisato Yamasaki; Atsushi Toyoda; Takehide Kosuge; Yutaka Suzuki; Yoshiharu Sato; Shuichi Kawashima; Toshiaki Katayama; Hiroyuki Wakaguri; Noboru Inoue; Keiichi Homma; Masahito Tada-Umezaki; Yukio Yagi; Yasuyuki Fujii; Takuya Habara; Minoru Kanehisa; Hidemi Watanabe; Kimihito Ito; Takashi Gojobori; Hideaki Sugawara; Tadashi Imanishi; William Weir; Malcolm Gardner; Arnab Pain; Brian Shiels; Masahira Hattori; Vishvanath Nene; Chihiro Sugimoto
  MBIO, 3, 5, e00204, 12, Sep. 2012, [Peer-reviewed]
  English, Scientific journal
• Tobacco calmodulin-like protein provides secondary defense by binding to and directing degradation of virus RNA silencing suppressors
  Kenji S. Nakahara; Chikara Masuta; Syouta Yamada; Hanako Shimura; Yukiko Kashihara; Tomoko S. Wada; Ayano Meguro; Kazunori Goto; Kazuki Tadamura; Kae Sueda; Toru Sekiguchi; Jun Shao; Noriko Itchoda; Takeshi Matsumura; Manabu Igarashi; Kimihito Ito; Richard W. Carthew; Ichiro Uyeda
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109, 25, 10113, 10118, Jun. 2012, [Peer-reviewed]
  English, Scientific journal
• Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands
  Keisuke Ueno; Katsuhiko Mineta; Kimihito Ito; Toshinori Endo
  BMC STRUCTURAL BIOLOGY, 12, 5, Apr. 2012, [Peer-reviewed]
  English, Scientific journal
• A Trim Distance between Positions as Packaging Signals in H3N2 Influenza Viruses
  Shunsuke Makino; Takaharu Shimada; Kouichi Hirata; Kouki Yonezawa; Kimihito Ito
  6TH INTERNATIONAL CONFERENCE ON SOFT COMPUTING AND INTELLIGENT SYSTEMS, AND THE 13TH INTERNATIONAL SYMPOSIUM ON ADVANCED INTELLIGENT SYSTEMS, 1702, 1707, 2012, [Peer-reviewed]
  English, International conference proceedings
• Finding Correlated Mutations among RNA Segments in H3N2 Influenza Viruses
  Takaharu Shimada; Tatsuya Hazemoto; Shunsuke makino; Kouichi Hirata; Kimihito Ito
  6TH INTERNATIONAL CONFERENCE ON SOFT COMPUTING AND INTELLIGENT SYSTEMS, AND THE 13TH INTERNATIONAL SYMPOSIUM ON ADVANCED INTELLIGENT SYSTEMS, 1696, 1701, 2012, [Peer-reviewed]
  English, International conference proceedings
• A conserved region in the prM protein is a critical determinant in the assembly of flavivirus particles
  Kentaro Yoshii; Manabu Igarashi; Osamu Ichii; Kana Yokozawa; Kimihito Ito; Hiroaki Kariwa; Ikuo Takashima
  JOURNAL OF GENERAL VIROLOGY, 93, Pt 1, 27, 38, Jan. 2012, [Peer-reviewed]
  English, Scientific journal
• A trim distance between positions in nucleotide sequences
  Shunsuke Makino; Takaharu Shimada; Kouichi Hirata; Kouki Yonezawa; Kimihito Ito
  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7569, 81, 94, Springer, 2012, [Peer-reviewed]
  English, International conference proceedings
• Single Amino Acid Residue in the A2 Domain of Major Histocompatibility Complex Class I Is Involved in the Efficiency of Equine Herpesvirus-1 Entry
  Michihito Sasaki; Eunmi Kim; Manabu Igarashi; Kimihito Ito; Rie Hasebe; Hideto Fukushi; Hirofumi Sawa; Takashi Kimura
  JOURNAL OF BIOLOGICAL CHEMISTRY, 286, 45, 39370, 39378, Nov. 2011, [Peer-reviewed]
  English, Scientific journal
• Gnarled-Trunk Evolutionary Model of Influenza A Virus Hemagglutinin
  Kimihito Ito; Manabu Igarashi; Yutaka Miyazaki; Teiji Murakami; Syaka Iida; Hiroshi Kida; Ayato Takada
  PLOS ONE, 6, 10, e25953, Oct. 2011, [Peer-reviewed]
  English, Scientific journal
• An H5N1 highly pathogenic avian influenza virus that invaded Japan through waterfowl migration
  Masahiro Kajihara; Keita Matsuno; Edgar Simulundu; Mieko Muramatsu; Osamu Noyori; Rashid Manzoor; Eri Nakayama; Manabu Igarashi; Daisuke Tomabechi; Reiko Yoshida; Masatoshi Okamatsu; Yoshihiro Sakoda; Kimihito Ito; Hiroshi Kida; Ayato Takada
  JAPANESE JOURNAL OF VETERINARY RESEARCH, 59, 2-3, 89, 100, Aug. 2011, [Peer-reviewed]
  English, Scientific journal
• Characterization of influenza A viruses isolated from wild waterfowl in Zambia
  Edgar Simulundu; Akihiro Ishii; Manabu Igarashi; Aaron S. Mweene; Yuka Suzuki; Bernard M. Hang'ombe; Boniface Namangala; Ladslav Moonga; Rashid Manzoor; Kimihito Ito; Ichiro Nakamura; Hirofumi Sawa; Chihiro Sugimoto; Hiroshi Kida; Chuma Simukonda; Wilbroad Chansa; Jack Chulu; Ayato Takada
  JOURNAL OF GENERAL VIROLOGY, 92, Pt 6, 1416, 1427, Jun. 2011, [Peer-reviewed]
  English, Scientific journal
• Prediction of the antigenic changes of the pandemic (H1N1) 2009 influenza virus hemagglutinin
  Manabu Igarashi; Kimihito Ito; Reiko Yoshida; Daisuke Tomabechi; Hiroshi Kida; Ayato Takada
  INFLUENZA AND OTHER RESPIRATORY VIRUSES, 5, 402, 404, May 2011, [Peer-reviewed]
  English, Scientific journal
• 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
  Rozanah Asmah Abdul Samad; Yoshihiro Sakoda; Yoshimi Tsuda; Edgar Simulundu; Rashid Manzoor; Masatoshi Okamatsu; Kimihito Ito; Hiroshi Kida
  JAPANESE JOURNAL OF VETERINARY RESEARCH, 59, 1, 15, 22, Feb. 2011, [Peer-reviewed]
  English, Scientific journal
• Predicting Mutation Trend of Influenza A Virus through Dimensionality Reduction in Hamming Metric on HA Amino Acid Sequences
  Tetsuji Kuboyama; Kimihito Ito; Kouichi Hirata; Hiroshi Sakamoto
  Annual International Conference on BioInformatics and Computational Biology (BICB 2011), 2011
• Construction of an infectious cDNA clone for Omsk hemorrhagic fever virus, and characterization of mutations in NS2A and NS5
  Kentaro Yoshii; Manabu Igarashi; Kimihito Ito; Hiroaki Kariwa; Michael R. Holbrook; Ikuo Takashima
  VIRUS RESEARCH, 155, 1, 61, 68, Jan. 2011, [Peer-reviewed]
  English, Scientific journal
• Detection of all known filovirus species by reverse transcription-polymerase chain reaction using a primer set specific for the viral nucleoprotein gene
  Hirohito Ogawa; Hiroko Miyamoto; Hideki Ebihara; Kimihito Ito; Shigeru Morikawa; Heinz Feldmann; Ayato Takada
  JOURNAL OF VIROLOGICAL METHODS, 171, 1, 310, 313, Jan. 2011, [Peer-reviewed]
  English, Scientific journal
• Genetic characterization and susceptibility on poultry and mammal of H7N6 subtype avian influenza virus isolated in Japan in 2009
  Yuko Uchida; Katsushi Kanehira; Masaji Mase; Nobuhiro Takemae; Chiaki Watanabe; Tatsufumi Usui; Yoshikazu Fujimoto; Toshihiro Ito; Manabu Igarashi; Kimihito Ito; Ayato Takada; Yoshihiro Sakoda; Masatoshi Okamatsu; Yu Yamamoto; Kikuyasu Nakamura; Hiroshi Kida; Yasuaki Hiromoto; Tomoyuki Tsuda; Takehiko Saito
  VETERINARY MICROBIOLOGY, 147, 1-2, 1, 10, Jan. 2011, [Peer-reviewed]
  English, Scientific journal
• Enzyme-Linked Immunosorbent Assay for Detection of Filovirus Species-Specific Antibodies
  Eri Nakayama; Ayaka Yokoyama; Hiroko Miyamoto; Manabu Igarashi; Noriko Kishida; Keita Matsuno; Andrea Marzi; Heinz Feldmann; Kimihito Ito; Masayuki Saijo; Ayato Takada
  CLINICAL AND VACCINE IMMUNOLOGY, 17, 11, 1723, 1728, Nov. 2010, [Peer-reviewed]
  English, Scientific journal
• Meningoencephalitis Associated with Sarcocystis spp. in a Free-Living Japanese Raccoon Dog (Nyctereutes procyonoides viverrinus)
  M. Kubo; T. Kawachi; M. Murakami; M. Kubo; S. Tokuhiro; T. Agatsuma; K. Ito; T. Okano; M. Asano; H. Fukushi; M. Nagataki; H. Sakai; T. Yanai
  JOURNAL OF COMPARATIVE PATHOLOGY, 143, 2-3, 185, 189, Aug. 2010, [Peer-reviewed]
  English, Scientific journal
• A novel copper(II) coordination at His186 in full-length murine prion protein
  Yasuko Watanabe; Wakako Hiraoka; Manabu Igarashi; Kimihito Ito; Yuhei Shimoyama; Motohiro Horiuchi; Tohru Yamamoria; Hironobu Yasui; Mikinori Kuwabara; Fuyuhiko Inagaki; Osamu Inanami
  BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 394, 3, 522, 528, Apr. 2010, [Peer-reviewed]
  English, Scientific journal
• Predicting the Antigenic Structure of the Pandemic (H1N1) 2009 Influenza Virus Hemagglutinin
  Manabu Igarashi; Kimihito Ito; Reiko Yoshida; Daisuke Tomabechi; Hiroshi Kida; Ayato Takada
  PLOS ONE, 5, 1, e8553, Jan. 2010, [Peer-reviewed]
  English, Scientific journal
• Recent experiences in parameter-free data mining
  Kimihito Ito; Thomas Zeugmann; Yu Zhu
  Lecture Notes in Electrical Engineering, 62, 365, 371, Springer, 2010, [Peer-reviewed]
  English, International conference proceedings
• Clustering the Normalized Compression Distance for Influenza Virus Data
  Kimihito Ito; Thomas Zeugmann; Yu Zhu
  ALGORITHMS AND APPLICATIONS, 6060, 130, +, 2010, [Peer-reviewed]
  English, International conference proceedings
• Characterization of H3N6 avian influenza virus isolated from a wild white pelican in Zambia
  Edgar Simulundu; Aaron S. Mweene; Daisuke Tomabechi; Bernard M. Hang'ombe; Akihiro Ishii; Yuka Suzuki; Ichiro Nakamura; Hirofumi Sawa; Chihiro Sugimoto; Kimihito Ito; Hiroshi Kida; Lewis Saiwana; Ayato Takada
  ARCHIVES OF VIROLOGY, 154, 9, 1517, 1522, Sep. 2009, [Peer-reviewed]
  English, Scientific journal
• Cross-Protective Potential of a Novel Monoclonal Antibody Directed against Antigenic Site B of the Hemagglutinin of Influenza A Viruses
  Reiko Yoshida; Manabu Igarashi; Hiroichi Ozaki; Noriko Kishida; Daisuke Tomabechi; Hiroshi Kida; Kimihito Ito; Ayato Takada
  PLOS PATHOGENS, 5, 3, e1000350, Mar. 2009, [Peer-reviewed]
  English, Scientific journal
• Discovering Networks for Global Propagation of Influenza A (H3N2) Viruses by Clustering
  Kazuya Sata; Kouichi Hirata; Kimihito Ito; Tetsuji Kuboyama
  KNOWLEDGE-BASED AND INTELLIGENT INFORMATION AND ENGINEERING SYSTEMS, PT II, PROCEEDINGS, 5712, 490, +, 2009, [Peer-reviewed]
  English, International conference proceedings
• Genetically destined potentials for N-linked glycosylation of influenza virus hemagglutinin
  Manabu Igarashi; Kimihito Ito; Hiroshi Kida; Ayato Takada
  VIROLOGY, 376, 2, 323, 329, Jul. 2008, [Peer-reviewed]
  English, Scientific journal
• Symmetric Item Set Mining Method Using Zero-suppressed BDDs and Application to Biological Data
  MINATO Shin-ichi; ITO Kimihito
  Transactions of the Japanese Society for Artificial Intelligence, 22, 2, 156, 164, 人工知能学会, Nov. 2007, [Peer-reviewed]
  English, Scientific journal, In this paper, we present a method of finding symmetric items in a combinatorial item set database. The techniques for finding symmetric variables in Boolean functions have been studied for long time in the area of VLSI logic design, and the BDD (Binary Decision Diagram) -based methods are presented to solve such a problem. Recently, we have developed an efficient method for handling databases using ZBDDs (Zero-suppressed BDDs), a particular type of BDDs. In our ZBDD-based data structure, the symmetric item sets can be found efficiently as well as for Boolean functions. We implemented the p...
• Symmetric item set mining method using zero-suppressed BDDs and application to biological data
  Minato Shin-ichi; Ito Kimihito
  Inform. Media Technol., 2, 1, 300, 308, Information and Media Technologies Editorial Board, 2007, [Peer-reviewed]
  English, In this paper, we present a method of finding symmetric items in a combinatorial item set database. The techniques for finding symmetric variables in Boolean functions have been studied for long time in the area of VLSI logic design, and the BDD (Binary Decision Diagram) -based methods are presented to solve such a problem. Recently, we have developed an efficient method for handling databases using ZBDDs (Zero-suppressed BDDs), a particular type of BDDs. In our ZBDD-based data structure, the symmetric item sets can be found efficiently as well as for Boolean functions. We implemented the program of symmetric item set mining, and applied it to actual biological data on the amino acid sequences of influenza viruses. We found a number of symmetric items from the database, some of which indicate interesting relationships in the amino acid mutation patterns. The result shows that our method is helpful for extracting hidden interesting information in real-life databases.
• Data Mining in Amino Acid Sequences of H3N2 Influenza Viruses Isolated during 1968 to 2006.
  Ito K; Igarashi M; Takada A
  Knowledge Media Technologies, 21, 154, 158, TU Ilmenau, Jul. 2006, [Peer-reviewed]
  English, The hemagglutinin (HA) of influenza viruses undergoes antigenic drift to escape from antibody-mediated immune pressure. In order to predict possible structural changes of the HA molecules in future, it is important to understand the patterns of amino acid mutations and structural changes in the past. We performed a retrospective and comprehensive analysis of structural changes in H3 hemagglutinins of human influenza viruses isolated during 1968 to 2006. Amino acid sequence data of more than 2000 strains have been collected from NCBI Influenza virus resources. Information theoretic analysis of the collected sequences revealed a number of simultaneous mutations of amino acids at two or more different positions (correlated mutations). We also calculated the net charge of the HA1 subunit, based on thenumber of charged amino acid residues, and found that the net charge increased linearly from 1968 to 1984 and, after then, has been saturated. This level of the net charge may be an upper limit for H3 HA to be functional. It is noted that "correlated mutations" with the conversion of acidic and basic amino acid residues between two different positions were frequently found after 1984, suggesting that these mutations contributed to counterbalancing effect to keep the net charge of the HA . These approaches may open the way to find the direction of future antigenic drift of influenza viruses.
• Meme media for clipping and combining Web Resources
  Y Tanaka; K Ito; J Fujima
  WORLD WIDE WEB-INTERNET AND WEB INFORMATION SYSTEMS, 9, 2, 117, 142, Jun. 2006, [Peer-reviewed]
  English, Scientific journal
• A meme media framework for introducing a multimodal user interface to existing web applications
  Ito, Kimihito
  Information Modelling and Knowledge Bases XVII, 83, 93, 2006, [Peer-reviewed]
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface
  Aberg, J.; Agier, M.; Angelis, L.; Appice, A.; Belhajjame, K.; Berardi, M.; Bose, P.; Bulskov, H.; Capello, F.; Caruso, C.; Ceci, M.; Chen, M.; Chisalita, I.; Cholvy, L.; Colazzo, D.; Comito, C.; Congiusta, A.; Cuppens, F.; Daemi, A.; De Marchi, F.; Diaz, E.; Dubhashi, D.; Gammie, P.; Giacometti, A.; Giese, M.; Goutam, P.; Greco, G.; Hammiche, S.; Herault, T.; Im, S.H.; Ito, K.; Jiline, M.; Johannisson, K.; Jouanot, F.; K{\"a},{\"a}ri{\"a}inen, M.; Kiritchenko, S.; Knappe, R.; Lakhal, L.; Lambrix, P.; Lassen, T.; Laurent, A.; Laurent, D.; Lefebvre, A.; Alcantara, J.F.L.; Lindemann, G.; Loyer, Y.; Lu, J.; Mar, P.; Mastroianni, C.; Minor, M.; Monett, D.; Mundluru, D.; Obst, O.; Perego, R.; Ranta, A.; Safar, B.; Saitta, L.; Juan, E.S.; Schr{\"o}ter, K.; Sebag, M.; Shah, B.; Simon, L.; Spezzano, G.; Urbig, D.; Terney, T.V.; Tsay, L.-S.; Viet, P.-L.; Waldinger, R.; Wernhard, C.; Xie, Y.; Yan, J.; Yin, K.; Martini, J.L.Z.; Zhao, N.; Zhou, X.; Hacid, M.-S.; Murray, N.V.; Ras, Z.W.; Tsumoto, S.
  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3488 LNAI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2005
  Scientific journal
• Meme media and logic programming approach for intelligent media systems
  K Ito
  Proceedings of the 2005 International Conference on Active Media Technology (AMT 2005), 611, 616, 2005, [Peer-reviewed]
  English, International conference proceedings
• Introducing multimodal character agents into existing web applications
  Kimihito Ito
  14th International World Wide Web Conference, WWW2005, 966, 967, ACM, 2005, [Peer-reviewed]
  English, International conference proceedings
• Meme media architectures for re-editing and redistributing intellectual assets over the Web
  Y Tanaka; K Ito; D Kurosaki
  INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES, 60, 4, 489, 526, Apr. 2004, [Peer-reviewed]
  English, Scientific journal
• Web application wrapping by demonstration
  K Ito; Y Tanaka
  INFORMATION MODELLING AND KNOWLEDGE BASES XV, 105, 266, 281, 2004, [Peer-reviewed]
  English, International conference proceedings
• Meme media architecture for the reediting and redistribution of Web resources
  Y Tanaka; K Ito
  FLEXIBLE QUERY ANSWERING SYSTEMS, PROCEEDINGS, 3055, 1, 12, 2004, [Peer-reviewed]
  English, Scientific journal
• Human-agent co-operation in accessing and communicating knowledge media - A case in medical therapy planning
  Dotsch, V; K Ito; KP Jantke
  INTUITIVE HUMAN INTERFACES FOR ORGANIZING AND ACCESSING INTELLECTUAL ASSETS, 3359, 68, 87, 2004, [Peer-reviewed]
  English, Scientific journal
• Live document framework for re-editing and redistributing contents in WWW
  Y Tanaka; D Kurosaki; K Ito
  INFORMATION MODELLING AND KNOWLEDGE BASES XIV, 94, 247, 262, 2003, [Peer-reviewed]
  English, International conference proceedings
• Integrated Visualization and Reification of Database and Web Contents.
  Kimihito Ito; Tsuyoshi Sugibuchi; Yohei Fujita; Takeshi Oda; Makoto Ohigashi; Yuzuru Tanaka
  Proceedings of the Twelfth International World Wide Web Conference - Posters, WWW 2003, Budapest, Hungary, May 20-24, 2003, 2003, [Peer-reviewed]
• A visual environment for dynamic web application composition.
  Kimihito Ito; Yuzuru Tanaka
  HYPERTEXT 2003, Proceedings of the 14th ACM Conference on Hypertext and Hypermedia, August 26-30, 2003, Nottingham, UK, 184, 193, ACM, 2003, [Peer-reviewed]
• Web Application Wrapping by Demonstration.
  Kimihito Ito; Yuzuru Tanaka
  Information Modelling and Knowledge Bases XV, 13th European-Japanese Conference on Information Modelling and Knowledge Bases (EJC 2003), Kitakyushu, Japan, June 3-6, 2003, 266, 281, IOS Press, 2003, [Peer-reviewed]
• Modelling Semi-structured Documents with Hedges for Deduction and Induction.
  Akihiro Yamamoto; Kimihito Ito; Akira Ishino; Hiroki Arimura
  Inductive Logic Programming, 11th International Conference, ILP 2001, Strasbourg, France, September 9-11, 2001, Proceedings, 2157, 240, 247, Springer, 2001, [Peer-reviewed]
  International conference proceedings
• Finding hypotheses from examples by computing the least generalization of bottom clauses
  K Ito; A Yamamoto
  DISCOVERY SCIENCE, 1532, 303, 314, 1998, [Peer-reviewed]
  English, Scientific journal
• Polynomial-Time MAT Learning of Multilinear Logic Programs.
  Kimihito Ito; Akihiro Yamamoto
  Algorithmic Learning Theory, Third Workshop, ALT '92, Tokyo, Japan, October 20-22, 1992, Proceedings, 743, 63, 74, Springer, 1992, [Peer-reviewed]
  International conference proceedings
• Influencing Factors and Prediction of Lung Function Impairment among Motorcycle Taxi Drivers in Bangkok and Adjacent Provinces, Thailand
  Kimihito Ito

• 宿主タンパク質YB-1は狂犬病ウイルスmRNAに結合し遺伝子発現を促進する
  佐々木道仁; 伊藤直人; 杉山誠; GONZALEZ Gabriel; 伊藤公人; 伊藤公人; 大場靖子; 澤洋文; 澤洋文, 日本ウイルス学会学術集会プログラム・予稿集(Web), 67th, 2019
• 狂犬病ウイルスの遺伝子発現に関与する宿主因子の同定と機能解析
  佐々木道仁; GONZALEZ Gabriel; 伊藤直人; 杉山誠; 伊藤公人; 伊藤公人; 大場靖子; 澤洋文; 澤洋文, 日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
• 豚インフルエンザウイルスの効率的なサーベイランス方法の検討
  小澤真; 松鵜彩; 米澤弘毅; 五十嵐学; 奥谷公亮; 川畑淑子; 伊藤公人; 小原恭子; 種子野章; 出口栄三郎, 日本ウイルス学会学術集会プログラム・抄録集, 62nd, 162, 31 Oct. 2014
  Japanese
• 遺伝子配列データをリサンプリングするウェブアプリケーションの構築
  米澤弘毅; 五十嵐学; 小原康夫; 伊藤公人, 日本ウイルス学会学術集会プログラム・抄録集, 62nd, 380, 31 Oct. 2014
  Japanese
• 遺伝子配列リサンプリングのための近隣剪定法の設計とウェブアプリケーション構築
  米澤弘毅; 五十嵐学; 小原康雄; 伊藤公人, 日本遺伝学会大会プログラム・予稿集, 86th, 100, 31 Aug. 2014
  Japanese
• 計算科学手法を用いたインフルエンザウイルスヘマグルチニンと亜型間交差反応性抗体との分子間相互作用の解析
  五十嵐学; 吉田玲子; 関嶋政和; 常盤広明; 喜田宏; 伊藤公人; 高田礼人, 日本ウイルス学会学術集会プログラム・抄録集, 61st, 239, 29 Oct. 2013
  Japanese
• 近隣結合法による塩基配列データセットのリサンプリングとその性能評価
  米澤弘毅; 五十嵐学; 伊藤公人, 人工知能学会人工知能基本問題研究会資料, 88th, 103, 108, 17 Jan. 2013
  Japanese
• 近隣剪定法によるウイルス遺伝子配列のリサンプリング
  米澤弘毅; 五十嵐学; 伊藤公人, 日本ゲノム微生物学会年会要旨集, 7th, 75, 2013
  Japanese
• 近隣剪定法によるウイルス遺伝子配列のリサンプリング
  米澤弘毅; 五十嵐学; 高田礼人; 伊藤公人, 日本ウイルス学会学術集会プログラム・抄録集, 60th, 321, 31 Oct. 2012
  Japanese
• H3N2インフルエンザウイルスHAへの糖鎖付加と周辺アミノ酸残基にかかる選択圧の経詩的変化
  五十嵐学; 中尾亮; 喜田宏; 喜田宏; 高田礼人; 伊藤公人, 日本ウイルス学会学術集会プログラム・抄録集, 60th, 318, 31 Oct. 2012
  Japanese
• 心水症に対する効果的予防戦略確立に向けたEhrlichia ruminantiumの分子遺伝学的研究
  中尾亮; 林田京子; MORRISON Liam; 周麗佳; MAGONA Joseph; MAGONA Joseph; 伊藤公人; 鈴木穣; JONGEJAN Frans; 杉本千尋, 日本獣医学会学術集会講演要旨集, 153rd, 78, 01 Mar. 2012
  Japanese
• 次世代ゲノム解析によるタイレリアパルバ原虫遺伝的多様性の解明
  林田京子; 阿部貴志; 中尾亮; 伊藤公人; 梶野喜一; 鈴木穣; JONGEJAN Frans; GEYSEN Dirk; WEIR William; 杉本千尋, 日本寄生虫学会大会プログラム・抄録集, 81st, 56, Feb. 2012
  Japanese
• ウマMHC class Iが示すウマヘルペスウイルス1型レセプター機能の解析
  佐々木道仁; 五十嵐学; 澤洋文; 伊藤公人; 福士秀人; 木村享史, 日本獣医学会学術集会講演要旨集, 152nd, 239, 239, 31 Aug. 2011
  (公社)日本獣医学会, Japanese
• [Bioinformatics technologies for the analysis of antigenic evolution of influenza viruses].
  Ito K, Uirusu, 61, 1, 3, 13, Jun. 2011, [Peer-reviewed]
  Human influenza viruses mutate from time to time, causing annual epidemics worldwide. The strong immune pressure in the human population selects a new variant every year, and the antigenic change is one of the primary reasons why vaccination is not a perfect measure to control seasonal influenza. Thus prediction of antigenic change of influenza A virus has been one of the major public health goals. In this review bioinformatics technologies that have been developed to achieve this goal were summarized., The Japanese Society for Virology, Japanese
• H3N2インフルエンザウイルスHAに付加された糖鎖は周辺エピトープを覆い隠していたか?〜糖鎖付加部位周辺アミノ酸残基の多様性変化の解析〜
  五十嵐学; 高田礼人; 喜田宏; 喜田宏; 喜田宏; 伊藤公人; 伊藤公人, 日本ウイルス学会学術集会プログラム・抄録集, 58th, 227, 15 Oct. 2010
  Japanese
• フィロウイルス種特異抗体検出ELISA法の開発
  中山絵里; 横山文香; 宮本洋子; 岸田典子; 松野啓太; 五十嵐学; MARZI Andrea; FELDMANN Heinz; 伊藤公人; 高田礼人, 日本ウイルス学会学術集会プログラム・抄録集, 58th, 286, 15 Oct. 2010
  Japanese
• Cys80 of JC Virus Capsid Protein, VP1 is Essential for Intrapentamer Disulfide Bond and Pentamer Formation
  Shintaro Kobayashi; Tadaki Suzuki; Manabu Igarashi; Noriko Ohtake; Keita Nagakawa; Kimihito Ito; Kenichi Niikura; Takashi Kimura; Harumi Kasamatsu; Hirofumi Sawa, JOURNAL OF NEUROVIROLOGY, 16, 45, 46, Oct. 2010
  English, Summary international conference
• インフルエンザウイルスの抗原変異予測と亜型間交差感染防制
  高田礼人; 吉田玲子; 五十嵐学; 伊藤公人, 日本薬学会年会要旨集, 130th, 1, 339, 05 Mar. 2010
  Japanese
• 次世代シークエンサーによるEhrlichia ruminantium弱毒ワクチン株の全長ゲノム解読と弱毒化機序の遺伝的背景の解析
  中尾亮; 林田京子; 伊藤公人; 鈴木穣; 渡辺純一; JONGEJAN Frans; 杉本千尋, 日本獣医学会学術集会講演要旨集, 149th, 248, 2010
  Japanese
• 愛知県でウズラから分離されたH7N6亜型鳥インフルエンザウイルスの遺伝子解析
  内田裕子; 真瀬昌司; 竹前喜洋; 廣本靖明; 五十嵐学; 伊藤公人; 高田礼人; 西藤岳彦; 津田知幸; 山口成夫, 日本ウイルス学会学術集会プログラム・抄録集, 57th, 346, 01 Oct. 2009
  Japanese
• ホモロジーモデリング法による新型H1N1インフルエンザウイルスのヘマグルチニンの抗原構造の解析
  五十嵐学; 伊藤公人; 吉田玲子; 喜田宏; 喜田宏; 喜田宏; 高田礼人, 日本ウイルス学会学術集会プログラム・抄録集, 57th, 180, 01 Oct. 2009
  Japanese
• インフルエンザウイルスのヘマグルチニンのMDS解析と変異予測への応用
  伊藤公人; 五十嵐学; 村上悌治; 喜田宏; 喜田宏; 高田礼人, 日本ウイルス学会学術集会プログラム・抄録集, 57th, 181, 01 Oct. 2009
  Japanese
• マウスプリオンタンパク質ヒスチジン186周辺の銅イオン結合部位に関する構造解析
  稲波修; 渡辺康子; 五十嵐学; 伊藤公人; 堀内基広; 桑原幹典; 平岡和佳子, 日本獣医学会学術集会講演要旨集, 148th, 199, 2009
  Japanese
• インフルエンザウイルスHA遺伝子の塩基配列上に潜在する糖鎖付加ポテンシャルの解析
  五十嵐学; 伊藤公人; 喜田宏; 喜田宏; 喜田宏; 高田礼人, 日本ウイルス学会学術集会プログラム・抄録集, 56th, 144, 01 Oct. 2008
  Japanese
• インフルエンザウイルスHA遺伝子の塩基配列上に潜在する糖鎖付加ポテンシャルの解析
  五十嵐学; 伊藤公人; 喜田宏; 喜田宏; 喜田宏; 高田礼人, 日本ウイルス学会北海道支部夏季シンポジウム講演抄録, 42nd, 12, 2008
  Japanese
• 動物インフルエンザのグローバルサーベイランスと全ての亜型ウイルスライブラリーの構築
  梶原将大; 梶原将大; 迫田義博; 迫田義博; 伊藤壽啓; 高田礼人; 伊藤公人; 岸田典子; 五十嵐学; 磯田典和; 磯田典和; 曽田公輔; 曽田公輔; WEBSTER R.G; 喜田宏; 喜田宏; 喜田宏, 日本獣医学会学術集会講演要旨集, 144th, 91, 27 Aug. 2007
  Japanese
• ペプチド‐水相互作用系の光イオン化ダイナミクス
  五十嵐学; 五十嵐学; 伊藤公人; 田池川浩人; 玉城英彦, 日本化学会北海道支部研究発表会講演要旨集, 2006, 116, 20 Jan. 2006
  Japanese
• Webサービスを提供するGUI部品を用いた分散アプリケーションの構築手法
  伊藤公人; 田中譲, 情報処理学会全国大会講演論文集, 63rd, 3, 3.373-3.374, 26 Sep. 2001
  Japanese
• 相対包摂のもとでの最小汎化が存在するための条件
  山本 章博; 伊藤 公人, 人工知能基礎論研究会, 37, 53, 56, 07 Jul. 1999
  人工知能学会, Japanese
• Finding Hypotheses from Examples by Computing the Least Generalization of Bottom Clauses
  ITO Kimihito; YAMAMOTO Akihiro, IPSJ SIG Notes. ICS, 1998, 90, 37, 42, 02 Oct. 1998
  In this paper we propose a new ILP method Bottom Reduction. It is an extension of Bottom Generalization for treating multiple examples. Using Bottom Reduction we can find all hypotheses which subsume all of given examples relative to a background theory in Plotkin's sense. We do not assume any restriction on the head predicates of the examples. Applying Bottom Reduction to examples which have a predicate different from those of other examples, we can reduce the search space of hypotheses. We have already implemented a simple learning system named BORDA based on Bottom Reduction on a Prolog system, and we present, in this paper, some techniques in its implementation., Information Processing Society of Japan (IPSJ), Japanese
• 底汎化法を用いた帰納推論システムの実装方式
  伊藤 公人; 山本 章博, 人工知能基礎論研究会, 32, 133, 138, Mar. 1998
  人工知能学会, Japanese

• 感染症学特別研究Ⅰ, 2024年, 博士後期課程, 国際感染症学院
• 大学院共通授業科目（一般科目）：自然科学・応用科学, 2024年, 修士課程, 大学院共通科目
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• 情報科学特論, 2024年, 博士後期課程, 獣医学院
• 感染症学特別研究ⅡA, 2024年, 博士後期課程, 国際感染症学院
• 情報科学特論, 2024年, 博士後期課程, 国際感染症学院
• 感染症学特別研究ⅡB, 2024年, 博士後期課程, 国際感染症学院
• 感染症数理生物学特論, 2024年, 博士後期課程, 国際感染症学院
• 保全医学演習, 2024年, 博士後期課程, 獣医学院
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• 人獣共通感染症対策専門特論, 2024年, 博士後期課程, 国際感染症学院
• 微生物学, 2024年, 学士課程, 医学部

• Transformerの演繹推論能力の解明と説明可能なAIへの応用
  科学研究費助成事業
  01 Apr. 2025 - 31 Mar. 2030
  山本 章博; 佐藤 健; 杉山 麿人; 大久保 好章; 伊藤 公人; 市瀬 夏洋; 明石 望洋
  日本学術振興会, 基盤研究(A), 京都大学, 25H01112
• Statistical Machine Learning in Population Genetics and Its Application to Infectious Disease Epidemiology
  Grants-in-Aid for Scientific Research
  01 Apr. 2021 - 31 Mar. 2026
  伊藤 公人
  本研究では，遺伝子の多様性を表す集団遺伝学モデルに感染者数を表す疫学モデルを組み込み，ウイルスの多様性から感染者数や変異ウイルスの割合の時間変動を推定する手法を開発し，実際に観測される遺伝子データと疫学データを統計的機械学習により解析し，データ同化の手法を用いて感染者数や変異株の割合がどのように変化するかをリアルタイムに予測するとともに，予測の精度を検証することを目的としている。
  2022年度までに変異株の従来株に対する相対実効再生産数を計算し，従来株から変異株への置き換わりを予測する手法を開発した。2023年度は，本手法をブラジルでのSARS-CoV-2変異株の置き換わりのデータに適用した。ブラジルでのガンマ株からデルタ株，デルタ株からオミクロンBA.1株への置き換わりを解析した結果，本手法により推定された相対実効再生産数は，Birth-Death-Skyline モデルで推定した実効再生産数の比とほぼ一致していることを明らかにした (Nat Comm, 2023)。また，同手法を用いて，ブラジルで流行するXBBの変異株を解析した結果， XBB＋F486P株，XBB＋F486P＋F456L株，XBB＋F486P＋F456L＋L455F株の他の流行株（主にBQ.1/BE株）に対する相対実効再生産数は，それぞれ1.24，1.33，1.48であることを明らかにした (Microbiol Spectr, 2024)。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 23K21692
• Statistical Machine Learning in Population Genetics and Its Application to Infectious Disease Epidemiology
  Grants-in-Aid for Scientific Research
  01 Apr. 2021 - 31 Mar. 2026
  伊藤 公人
  本研究では，遺伝子の多様性を表す集団遺伝学モデルに感染者数を表す疫学モデルを組み込み，ウイルスの多様性から感染者数や変異ウイルスの割合の時間変動を推定する手法を開発し，実際に観測される遺伝子データと疫学データを統計的機械学習により解析し，データ同化の手法を用いて感染者数や変異株の割合がどのように変化するかをリアルタイムに予測するとともに，予測の精度を検証することを目的としている。
  ２０２１年度は，下記の項目の研究を実施した。
  変異株の従来株に対する相対実効再生産数を計算し，従来株から変異株への置き換わりを予測する手法を開発した。開発手法を国内外のデータに適用し，アルファ株，デルタ株，オミクロン株の従来株に対する相対実効再生産数を計算した。デルタ株については，従来株に比べて実効再生産数が1.95倍高いことを明らかにし(Eurosurveillance, 2021)，オミクロン株については，デルタ株より実効再生産数が3.2倍高いことを明らかにした (J Med Virol, 2021)。これらの結果に基づき，国内における変異株の割合の推移をリアルタイムに予測し，厚生労働省アドバイザリーボードに計20回報告した。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 21H03490
• Next-generation semi-structured data mining technologies for real-world knowledge infrastructures
  Grants-in-Aid for Scientific Research
  01 Apr. 2016 - 31 Mar. 2020
  Arimura Hiroki
  The goal of this research is to establish base technologies for forming large-scale knowledge bases from massive data in real and cyber spaces. For this purpose, we study next-generation data mining technologies for efficiently extracting useful knowledge as patterns and rules from large semi-structured data, that is, huge and heterogeneous collections of weakly structured data. In more detail, we studied (1) efficient semi-structured data mining engines in the optimal pattern discovery framework, (2) semi-strcuture mining based on spatio-temporal information, (3) combination of search, compression, and indexing/storage technologies for massive semi-structured data, development of knowledge base creation systems based on semi-structured data mining.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 16H01743
• Prediction of antigenic evolution of influenza viruses through Bayesian estimation using statistics on strings
  Grants-in-Aid for Scientific Research
  01 Apr. 2016 - 31 Mar. 2019
  Ito Kimihito
  By integrating the quasi spices theory with infectious disease modelling, we developed a mathematical model of viral sequences, infection, and herd immunity. Actual observations of viral sequences and the number of reported cases of H1N1 2009 pandemic viruses were integrated into computer simulations, and parameters in the model were estimated by the data assimilation technique called the particle filter. For every 30 days 100,000 simulations were ran and filter distributions of parameters were calculated using amino acid sequences observed in the corresponding periods. Six-month period predictions were made using the estimated parameters. As a result, the developed method predicts the actual amino acid substitutions on the hemagglutinin molecule with a precision ratio of 79% and recall ratio of 53% .
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 16H02863
• Knowledge Discovery Methods based on Closed Set Construction for Data with Attributes Whose Values are from Ordered Sets
  Grants-in-Aid for Scientific Research
  01 Apr. 2014 - 31 Mar. 2017
  Yamamoto Akihiro; AVIS David; KOBAYASHI Yasuaki; IKEDA Madori; OTAKI Keisuke; KARIYAMA Kazuaki; YAMAZAKI Tomoya; NISHIMURA Shoichi
  The goal of this research is to develop methods for knowledge discovery that uses both orders for attribute values and closed sets of from mixed data. Since knowledge discovery by closed set is one kind of technique called bi-clustering of binary relational data, we obtained a method for bi-clustering for matrix factorization and search of matrices. Also we analyzed relationship between closed sets obtained by various bi-clustering method. Moreover, we developed methods for principal component analysis of the tree structure using the partial order of the substructure of tree data, the thesaurus expansion using the order relation of the vocabulary in the natural language thesaurus, and discovery methods of the similarity of the tree structure data with the integer programming.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Kyoto University, 26280085
• Cross-reactive antibodies to influenza virus hemagglutinins and their epitopes
  Grants-in-Aid for Scientific Research
  01 Apr. 2012 - 31 Mar. 2017
  Takada Ayato; ITO Kimihito; IGARASHI Manabu; YOSHIDA Reiko; MURAMATSU Mieko; MIYAMOTO Hiroko; Wilson Ian
  By focusing on a novel antiviral function (budding inhibition), we found potential roles of anti-hemagglutinin antibodies in cross-protective immunity against influenza A viruses with multiple HA subtypes. It was particularly noted that the comparison between IgG and IgA antibodies recognizing the same epitope on the HA molecule clearly demonstrated the greater potential of HA-specific IgA than IgG antibodies in antiviral activities. It was also attempted to modify antibody specificity by structure-based molecular simulation and production of recombinant antibodies.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 24390110
• Predicting antigenic changes of influenza viruses using text data assimilation.
  Grants-in-Aid for Scientific Research
  01 Apr. 2013 - 31 Mar. 2016
  Kimihito Ito; TAKADA Ayato; IGARASHI Manabu
  Human influenza viruses mutate from time to time, causing annual epidemics worldwide. Given the high mutation rate of the viral gene, influenza vaccine strains need to be updated every two to three years. In order to prepare an effective vaccine strain prior to each influenza season, we investigated text data assimilation methods that allow us to predict the evolution of viral amino acid sequences. As a result, we developed a mathematical model consisting of human herd immunity, the number of infections, and population of circulating vires. The model provides a mathematical basis of bioinformatics methods to prepare an effective vaccine strain prior to influenza seasons.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 25280080
• Development of Next-Generation Semi-structured Data Mining for Large-Scale Knowledge Base Formation
  Grants-in-Aid for Scientific Research
  01 Apr. 2012 - 31 Mar. 2016
  Arimura Hiroki; UNO TAKEAKI; MINATO S.; HIRATA KOUICHI; ITO K.; SHIMOZONO S.; KIDA T.
  The final goal of this research is to establish a strategy for forming large-scale knowledge bases from massive data and information on a wide range of human activities on social, scientific, and industrial aspects in the cyber space. For this purpose, we study next-generation data mining technologies for efficiently extracting useful knowledge as patterns and rules from semi-structured data, that is, huge and heterogeneous collections of weakly structured data in the cyber space. (1) Efficient semi-structured data mining engines based on optimal pattern discovery framework. (2) Semi-strcuture mining based on spatio-temporal information. (3) Combining semi-structured data mining with stochastic information processing schema. (4) Knowledge federation technologies for large-scale knowledge bases creation. (5) Knowledge indexing technologies for large-scale knowledge bases creation. (6) Development of knowledge base creation systems based on semi-structured data mining.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 24240021
• Analyzing Nucleotide Sequences of Influenza Viruses Based on Phylogenetic Distance between Positions
  Grants-in-Aid for Scientific Research
  01 Apr. 2013 - 31 Mar. 2015
  HIRATA Kouichi; ITO Kimihito
  In this research, we have analyzed nucleotide sequences of influenza A viruses based on the relabeled phylogenetic tree obtained by replacing labels of leaves in a reconstructed phylogenetic tree with nucleotides at a position and the trimmed phylogenetic tree obtained by trimming binary branches in a relabeled phylogenetic tree as possible. First, by introducing a trim distance between trimmed phylogenetic trees, we have applied the clustering to positions based on the trim distance as pandemic analysis for influenza A viruses. Next, by introducing an agreement subtree mapping kernel and a leaf-path kernel that are tractable and applicable to phylogenetic trees, we have classified relabeled and trimmed phylogenetic trees as pandemic analysis, regional analysis and analysis of positions in packaging signals for influenza A viruses.
  Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, Kyushu Institute of Technology, 25540137
• Antibody-mediated inhibition of filovirus budding
  Grants-in-Aid for Scientific Research
  01 Apr. 2012 - 31 Mar. 2014
  TAKADA Ayato; ITO Kimihito; IGARASHI Manabu
  Monoclonal antibodies (MAbs) specific to Marburg virus glycoprotein (GP) were produced to analyze their activity to suppress the virus budding. We found that some of the MAbs, which did not have a classical neutralizing activity, efficiently inhibited the budding and release of MARV particles from infected cells. A couple of escape variants selected by these MAbs had deletions of the mucin-like region in GP or single amino acid substitutions in the furin-recognition motif in GP. These results demonstrate a novel mechanism of antibody-mediated inhibition of MARV budding and the extraordinary structural flexibility and variability of MARV GP to escape from immunological pressure of antibodies.
  Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, Hokkaido University, 24658252
• Studies on cross-reactive antibodies to multiple subtypes of influenza virus henagglutinin induced by mucosal immunization
  Grants-in-Aid for Scientific Research
  2009 - 2011
  TAKADA Ayato; SUZUKI Yasuhiko; ITO Kimihito
  Currently used parenteral influenza vaccines induce serum IgG antibody response against hemagglutinin (HA), but do not protect primary infection in the respiratory tissues. In addition, vaccine-induced antibodies are not cross-reactive to viruses with different HA subtypes from that of vaccine strains. In this study, we found that intranasal immunization of mice with inactivated influenza viruses induced antibodies cross-reactive to multiple HA subtypes. Furthermore, it was suggested that IgA antibodies associated with mucosal immunity played an important role in heterosubtypic inhibition of virus replication.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 21390134
• Establishing the federation model of smart objects and the creation of its novel applications
  Grants-in-Aid for Scientific Research
  2009 - 2011
  TANAKA Yuzuru; YOSHIDA Tetsuya; LUNZER Aran; MIYAZAKI Yutaka; SJOBERGH Jonas; ITO Kimihito
  This research has focused on three different levels for modeling the proximity-based federation of smart objects. For each of these three levels, i.e., the modeling of the federation mechanism of each smart object, the modeling of the federation mechanism among more than one smart objects, and the modeling of application scenarios, it has proposed three formal models and clarified the mapping among them. They are respectively the port matching model, the graph rewriting model, and the catalytic reaction network model.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 21240003
• Next-Generation Semi-structured Data Mining for Large-Scale Knowledge Base Formation
  Grants-in-Aid for Scientific Research
  2008 - 2011
  ARIMURA Hiroki; KIDA Takuya; MINATO Shin-ichi; ITO Kimihito; UNO Takeaki; HIRATA Kouichi
  In this research, we study efficient semi-structured data mining technologies and related knowledge federation and indexing technologies, which enables knowledge extraction from massive semi-structured data in the real world. Finally, we made a number of knowledge extraction experiments.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 20240014
• インフルエンザウイルスのRNA分節間に形成される塩基対の検索
  科学研究費助成事業
  2009 - 2010
  伊藤 公人; 高田 礼人
  本研究では、公共データベースに蓄積された大量のウイルスゲノムを計算機を用いて解析することにより、RNA分節の選択的集合を説明し得る塩基対の構造を網羅的に探索することを目的とする。平成22年度は、下記項目に関して研究を行った。
  1.RNA分節において、塩基が極度に保存されている位置を明らかにする
  従来研究の成績からパッケージングシグナルは、各RNA分節のから5'末端および3'末端付近の領域に存在することが示唆されている。パンデミック2009インフルエンザウイルス(H1N1)の2285株分の塩基配列をNCBIから取得し、平均情報量を指標に各RNA分節において塩基が極度に保存されている領域を検索した。その結果、ほとんど全てのRNA分節において、3'末端付近の領域に塩基置換が見られた。
  2.二つのRNA分節で同時に変異する傾向にある塩基対があるか否かを確認する
  二つのRNA分節で同時に変異する傾向にある塩基対を高速に検索するために、同時エントロピーの比を用いる手法を開発した。同法を用いて、パンデミック2009インフルエンザウイルス(H1N1)のRNA分節間で同時に変異している塩基を探索した。その結果、PB2の95番目とNPの1530番目、PB2の573番目とNPの44番目、PB1の288番目とHAの1715番目、PAの64番目とNPの417番目、PAの64番目とNPの1419番目、NPの327番目とNAの347番目において、ワトソンクリック型塩基対を保持したまま同時に変異していることが判明した。
  3.RNA分節間の塩基対の連続性あるいは周期性が統計的に有意か否かを判定する
  PB2の95番目とNPの1530番目、PB1の288番目とHAの1715番目、NPの327番目とNAの347番目においては、連続した前後の塩基配列のアライメントを計算したところ、ワトソンクリック型塩基対が統計的に有意に多く見られること(p<0.03)を確認した。
  日本学術振興会, 挑戦的萌芽研究, 北海道大学, 21650067
• Predicting Antigenic Changes of Influenza Viruses by Discovering Patterns of Viral Evolution
  Grants-in-Aid for Scientific Research
  2007 - 2009
  ITO Kimihito; TAKADA Ayato; MINATO Shin-ichi
  Human influenza viruses mutate from time to time, causing annual epidemics worldwide. Given the high mutation rate of the viral gene, it is difficult to select an effective vaccine strain prior to each influenza season. In order to elucidate the pattern of viral evolution, we introduce a bioinformatics technology that analyzes a large number of epidemic strains in a multidimensional space. We found that the relative sequence distances among past epidemic strains could be predicted by a mathematical model. Retrospective tests for 12 years showed that the model could predict the direction of viral evolution with high accuracy.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 19300041
• Crossover Concept Mining Based on Conceptual Abstraction Hierarchies
  Grants-in-Aid for Scientific Research
  2007 - 2008
  MAKOTO Haraguchi; ETSUJI Tomita; KIMIHITO Ito; MASAHARU Yoshioka; YOSHIAKI Okubo
  潜在的なクラスタ間接続を, たとえ, 外延的な重なりが小さな場合でも, 内包的な繋がりが高い場合は有意義なクラスタ間接続関係を与える「情間」と捉える.こうした「情間」は, クラスタの外延と内包に対する評価関数を設定することにより, 制約条件下の最適化問題として捉えることができ, 具体的には, 形式概念束探索における分枝限定アルゴリズムとして設計・開発・実証を行った.形式概念束は, 概念の抽象階層と見なすことができ, 主要なクラスタを繋ぐ適切な概念を抽象階層から見出すことを意味している.実証実験において, カテゴリとしては離れた異種文書群から, それらを跨ぐ, 機能的な概念を情間(クロスオーバ概念)として抽出することに成功している.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 19300040
• Flexible aggregate extraction and aggregate federation of knowledgeresources over the Web and the integrated generic technologies for their reuse andvisualization
  Grants-in-Aid for Scientific Research
  2006 - 2007
  TANAKA Yuzuru; LUNZER ARAN EDWARD; ITO Kimihito; YOSHIDA Testuya
  群抽出・群連携の理論を確立し、これに基づくジェネリックな技術を開発し、さらには、これらの技術を用いたウェブ上の知的資源の統合再利用・可視化基盤技術を確立した。具体的には, (a)ウェブ上の知的資源の群抽出・群連携理論を確立し、(b)ウェブ上の知的資源の群抽出・群連携インタラクティブシステムを開発し、(c)ウェブ上の知的資源の統合再利用基盤技術を確立し、(d)ウェブ上の知的資源の統合可視化基盤技術を確立し、(e)統合再利用・可視化基盤技術の応用と評価を行った。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 19200007
• Efficient Pattern Discovery from Massive Semi-Structured Data for Knowledge Infrastructure Formation on the Web
  Grants-in-Aid for Scientific Research
  2005 - 2007
  ARIMURA Hiroki; KIDA Takuya; MINATO Shin-ichi; ITO Kimihito
  By rapid progress of network and storage technologies for the last decade, a huge amount of weakly structured electronic data of various types, called semi-structured data, become available over the Internet. In this research project, we study efficient semi-structured data mining technologies that supports human's discovery of useful knowledge from massive collections of semi-structured data. In particular, we develop high-speed semi-structured data mining engines as a core of large-scale knowledge Infrastructure formation from the Internet and establish their architecture and base technologies. In particular, we have studied the following research topics:
  1. High-speed semi-structured data mining technologies. We developed efficient depth-first mining algorithms for sequences and trees based on the rightmost expansion technique, proposed by Hiroki Arimura and other researchers. We also devised various optimization techniques in frequent and maximal pattern mining frameworks. We made theoretical analysis of their computational complexity, and show that they are actually polynomial delay and polynomial space complexity enumeration algorithms, which means that they can be used as light-weight and high-throughput mining engines. From theory point of view, they are the first maximal pattern mining algorithms for non-trivial subclasses of semi-structured data having theoretically guaranteed performance.
  2. Knowledge indexing technologies. The pre- and post-processing of the data and patterns are important issues for the next-generation data mining. We developed an efficient knowledge indexing data structure, called VSOP, based on Zero-suppressed BDD (ZBDD) proposed by Shin-ichi Minato. VSOP is a compressed indexing structure for discrete structure, equipped with a rich set of algebraic manipulation operators for compressed transactions and itemsets. On the top of VSOP, we devised efficient data mining algorithms that can extract interesting structures hidden in a huge input dataset in an highly interactive way.
  3. Knowledge federation technologies. We combine semi-structured data processing techniques with information retrieval and information extraction from the web and stream data. As results, we developed fast pattern matching algorithms for multi-dimensional numerical streams based on bit-parallel techniques and semi-automatic information extraction algorithms from the Web based on demonstration-by-example. We also implemented a set of knowledge discovery tools based on our algorithms and technologies devised in this project. We also made experiments to evaluate the prototype system on real world data on the Web and in Bioinformatics fields.
  Japan Society for the Promotion of Science, Grant-in-Aid for Specially Promoted Research, Hokkaido University, 17002008
• Webアプリケーション間の自動連携のための学習推論技術に関する研究
  科学研究費助成事業
  2005 - 2006
  伊藤 公人
  近年のWWWの急速な普及・発展により、様々な科学技術研究領域のデータベースや解析ツールがWeb上に公開されている。Web上のデータベースや解析ツールは今なお増え続けており、生命情報学分野においてはその数が5000以上にのぼると言われている。WWWの研究基盤としての浸透により、研究データや解析ツールの個々別々な利用に関しては、従来に比べ格段に簡便化された。しかし、逆に、利用可能なデータやツールの数・種類が膨大化・多様化したため、ユーザがこれらの有効な組み合わせ方を見つけ出すことが困難となっている。
  この問題を解決するために本研究では、計算機を用いてWeb上のデータやツールの組み合わせ方を自動的に見つける手法を開発することを目的とした。これまでに研究代表者らは、IntelligentPadシステムを用いることにより、エンドユーザがWebアプリケーションを自由に部品化し、さらにそれらを組み合わせて新しいツールを合成することが可能な基盤技術を開発した。そこで、部品化の際にユーザが指定した入出力関係を積極的に利用することにより、この技術を計算機によるWebアプリケーションの自動連携に発展させる手法を考案した。IntelligentPadのスロット値間の関係を一階述語論理により形式化した結果、Webアプリケーションの入出力値をProlog言語の単位節として、また、エンドユーザが定義したWebアプリケーション間の連携を確定節として、演繹データベース化することが可能となった。さらに、この演繹データベースに格納された入出力および連携のデータに対して、研究代表者らが開発した帰納論理プログラミング手法「底節交差汎化法」を適用することによって、計算機がWeb上のデータベースやツールの連携可能性を見つけてユーザに提示することが可能であることを明らかにした。
  日本学術振興会, 若手研究(B), 北海道大学, 17700088
• Federal Integration and Advanced Reusing Technologies for Scientific and Technological Knowledge Resources including Retrieval and Computation Services
  Grants-in-Aid for Scientific Research
  2005 - 2006
  TANAKA Yuzuru; LUNZER Aran; ITOH Kimihito; YOSHIDA Tetsuya
  Before this research project, there were no enabling technologies for the federal integration and reuse of knowledge resources to extract related knowledge fragments from knowledge resources over the Web, and to relate them for their federal integration into a new reusable knowledge resource. Users needed to manually make a copy of each output of a service and to put it into an input form of another service. Or otherwise, they needed to rely on Web Service technologies. In the latter case, API of the servers needs to be publicized and some programming effort is required, which may work for the definition of routine knowledge integration, but cannot work for ad hoc knowledge federation. Some services may graphically out put their results. There are increasing needs for the knowledge federation of services with 2D and 3D GUIs. This research aimed at the establishment of the generic technologies for the federal integration and advanced reuse of scientific and technological knowledge resources including the retrieval and computation services such as information retrieval, database, and simulation systems. In order to achieve this goal, we have developed the following 5 generic software technologies: (1) interactive extraction of related knowledge fragments over the Web into a tabular form, (2) federation and integration of extracted knowledge fragments, (3) federation and integration of extracted knowledge resources with legacy applications, (4) meta information description about the federation and integration capabilities, and automatic federation based on such descriptions, and (5) publication and distribution infrastructure for newly composed knowledge resources. The Web has mutually related knowledge resources embedded in Web pages as a list in a text or as inputs and outputs of the same web application. This project established a new technology to extract them as interoperable and mutually relatable resources. We proposed a new representation format named the knowledge media view to represent extracted knowledge resources and to federate them. For legacy applications with 2D and 3D GUIs, we have developed a new view integration technologies by extending the shadow copy technologies from those for the integration of 2D and 2D applications to those for the 2D and 3D applications integration and for the 3D and 3D application integration. We have related these technologies to the knowledge media view representation, and established the knowledge federation technologies between an arbitrary knowledge fragments extracted from the Web and an arbitrary legacy application.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 17200004