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Selected Papers

Division of Bioinformatics

February, 2024
Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire.
Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H
J Virol, , e0199523. doi: 10.1128/jvi.01995-23 , PMID: 38323813 , Abstract
August, 2023
Link prediction on bipartite networks using matrix factorization with negative sample selection.
Peng S, Yamamoto A, Ito K
PLoS One, 18 (8), e0289568. doi: 10.1371/journal.pone.0289568 , PMID: 37585433 , Abstract
November, 2022
Predicting the Trajectory of Replacements of SARS-CoV-2 Variants Using Relative Reproduction Numbers.
Piantham C, Ito K
Viruses, 14 (11). doi: 10.3390/v14112556 , PMID: 36423165 , Abstract
November, 2022
Future behaviours decision-making regarding travel avoidance during COVID-19 outbreaks.
Ito K, Kanemitsu S, Kimura R, Omori R
Sci Rep, 12 (1), 19780. doi: 10.1038/s41598-022-24323-1 , PMID: 36396687 , Abstract
October, 2022
Measuring impact of vaccination among wildlife: The case of bait vaccine campaigns for classical swine fever epidemic among wild boar in Japan.
Matsuyama R, Yamamoto T, Hayama Y, Omori R
PLoS Comput Biol, 18 (10), e1010510. doi: 10.1371/journal.pcbi.1010510 , PMID: 36201410 , Abstract
July, 2022
Targeted sampling reduces the uncertainty in force of infection estimates from serological surveillance.
Kim K, Ito K
Front Vet Sci, 9, 754255. doi: 10.3389/fvets.2022.754255 , PMID: 35968015 , Abstract
June, 2022
Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark
Ito K, Piantham C, Nishiura H
Math Biosci Eng, 9(19):9005-9017. doi: 10.3934/mbe.2022418 , Abstract
December, 2021
Relative Instantaneous Reproduction Number of Omicron SARS-CoV-2 variant with respect to the Delta variant in Denmark.
Ito K, Piantham C, Nishiura H
J Med Virol, . doi: 10.1002/jmv.27560 , PMID: 34967453 , Abstract
December, 2021
Estimation of the Lethality Rate, Recovery Rate, and Case Fatality Ratio of Classical Swine Fever in Japanese Wild Boar: An Analysis of the Epidemics From September 2018 to March 2019.
Matsuyama R, Yamamoto T, Hayama Y, Omori R
Front Vet Sci, 8, 772995. doi: 10.3389/fvets.2021.772995 , PMID: 34977211 , Abstract
June, 2021
Age-dependent association between SARS-CoV-2 cases reported by passive surveillance and viral load in wastewater.
Omori R, Miura F, Kitajima M
Sci Total Environ, 792, 148442. doi: 10.1016/j.scitotenv.2021.148442 , PMID: 34147797 , Abstract
May, 2021
Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions.
Piantham C, Ito K
Virus Evol, 7 (1), veab049. doi: 10.1093/ve/veab049 , PMID: 34285812 , Abstract
October, 2020
The age distribution of mortality from novel coronavirus disease (COVID-19) suggests no large difference of susceptibility by age.
Omori R, Matsuyama R, Nakata Y
Sci Rep, 10 (1), 16642. doi: 10.1038/s41598-020-73777-8 , PMID: 33024235 , Abstract
May, 2020
Ascertainment rate of novel coronavirus disease (COVID-19) in Japan.
Omori R, Mizumoto K, Nishiura H
Int. J. Infect. Dis., S1201-9712(20)30292-7. doi: 10.1016/j.ijid.2020.04.080 , PMID: 32389846 , Abstract
April, 2020
Changes in testing rates could mask the novel coronavirus disease (COVID-19) growth rate.
Omori R, Mizumoto K, Chowell G
Int. J. Infect. Dis., S1201-9712(20)30236-8. doi: 10.1016/j.ijid.2020.04.021 , PMID: 32320809 , Abstract
December, 2019
Estimating Transmission Potential of H5N1 Viruses Among Humans in Egypt Using Phylogeny, Genetic Distance and Sampling Time Interval.
Mohamed W, Ito K, Omori R
Front Microbiol, 10, 2765. doi: 10.3389/fmicb.2019.02765 , PMID: 31849902 , Abstract
January, 2019
The change of susceptibility following infection can induce failure to predict outbreak potential by R₀.
Nakata Y, Omori R
Math Biosci Eng, 16 (2), 813-830. doi: 10.3934/mbe.2019038 , PMID: 30861667 , Abstract
September, 2018
Does infection with Chlamydia trachomatis induce long-lasting partial immunity? Insights from mathematical modelling.
Omori R, Chemaitelly H, Althaus CL, Abu-Raddad LJ
Sex Transm Infect, 95 (2), 115-121. doi: 10.1136/sextrans-2018-053543 , PMID: 30181327 , Abstract
June, 2018
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
Front Microbiol, 9, 1272. doi: 10.3389/fmicb.2018.01272 , PMID: 29971047 , Abstract
March, 2018
Can Machines Learn Respiratory Virus Epidemiology?: A Comparative Study of Likelihood-Free Methods for the Estimation of Epidemiological Dynamics.
Tessmer HL, Ito K, Omori R
Front Microbiol, 9, 343. doi: 10.3389/fmicb.2018.00343 , PMID: 29552000 , Abstract
December, 2017
Tajima's D and Site-specific Nucleotide Frequency in a Population During an Infectious Disease Outbreak
Omori R, Wu J
SIAM J. Appl. Math, 77 (6) 2156-2171. doi: 10.1137/17M1114946 , Abstract
December, 2017
HIV and herpes simplex virus type 2 epidemiological synergy: misguided observational evidence? A modelling study.
Omori R, Nagelkerke N, Abu-Raddad LJ
Sex Transm Infect, 94 (5), 372-376. doi: 10.1136/sextrans-2017-053336 , PMID: 29203577 , Abstract
August, 2017
Nonpaternity and Half-Siblingships as Objective Measures of Extramarital Sex: Mathematical Modeling and Simulations.
Omori R, Nagelkerke N, Abu-Raddad LJ
Biomed Res Int, 2017, 3564861. doi: 10.1155/2017/3564861 , PMID: 28904953 , Abstract
July, 2017
Modelling infectious diseases with relapse: a case study of HSV-2.
Wang J, Yu X, Tessmer HL, Kuniya T, Omori R
Theor Biol Med Model, 14 (1), 13. doi: 10.1186/s12976-017-0059-4 , PMID: 28716140 , Abstract
May, 2017
Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens.
Kim K, Omori R, Ito K
Epidemics, 21, 21-29. doi: S1755-4365(17)30085-3 , PMID: 28552262 , Abstract
January, 2017
An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus.
Gonzalez G, Sasaki M, Burkitt-Gray L, Kamiya T, Tsuji NM, Sawa H, Ito K
Sci Rep, 7, 40447. doi: 10.1038/srep40447 , PMID: 28071766 , Abstract
December, 2016
Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts.
Karnbunchob N, Omori R, Tessmer HL, Ito K
Front Microbiol, 7, 2118. doi: 10.3389/fmicb.2016.02118 , PMID: 28082971 , Abstract
January, 2016
Population sexual behavior and HIV prevalence in Sub-Saharan Africa: missing links?
Omori R, Abu-Raddad LJ
Int. J. Infect. Dis., 44, 1-3. doi: 10.1016/j.ijid.2016.01.005 , PMID: 26780269 , Abstract
January, 2016
Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review.
Kim K, Omori R, Ueno K, Iida S, Ito K
PLoS ONE, 11 (1), e0147021. doi: 10.1371/journal.pone.0147021 , PMID: 26760775 , Abstract
September, 2015
The determinant of periodicity in Mycoplasma pneumoniae incidence: an insight from mathematical modelling.
Omori R, Nakata Y, Tessmer HL, Suzuki S, Shibayama K
Sci Rep, 5, 14473. doi: 10.1038/srep14473 , PMID: 26412506 , Abstract
March, 2015
Dynamics of non-cohabiting sex partnering in sub-Saharan Africa: a modelling study with implications for HIV transmission.
Omori R, Chemaitelly H, Abu-Raddad LJ
Sex Transm Infect, 91 (6), 451-7. doi: 10.1136/sextrans-2014-051925 , PMID: 25746040 , Abstract
July, 2014
ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset.
Ueno K, Ishii A, Ito K
BMC Bioinformatics, 15, 254. doi: 10.1186/1471-2105-15-254 , PMID: 25069839 , Abstract
February, 2013
Resampling nucleotide sequences with closest-neighbor trimming and its comparison to other methods.
Yonezawa K, Igarashi M, Ueno K, Takada A, Ito K
PLoS ONE, 8 (2), e57684. doi: 10.1371/journal.pone.0057684 , PMID: 23460894 , Abstract
October, 2011
Gnarled-trunk evolutionary model of influenza A virus hemagglutinin.
Ito K, Igarashi M, Miyazaki Y, Murakami T, Iida S, Kida H, Takada A
PLoS ONE, 6 (10), e25953. doi: 10.1371/journal.pone.0025953 , PMID: 22028800 , Abstract