Selected Papers

Division of Bioinformatics

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