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Items: 50


Intrahost cytomegalovirus population genetics following antibody pretreatment in a monkey model of congenital transmission.

Vera Cruz D, Nelson CS, Tran D, Barry PA, Kaur A, Koelle K, Permar SR.

PLoS Pathog. 2020 Feb 14;16(2):e1007968. doi: 10.1371/journal.ppat.1007968. eCollection 2020 Feb.


Correction for Sobel Leonard et al., "Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus".

Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K.

J Virol. 2019 Aug 13;93(17). pii: e00936-19. doi: 10.1128/JVI.00936-19. Print 2019 Sep 1. No abstract available.


Within-host infectious disease models accommodating cellular coinfection, with an application to influenza.

Koelle K, Farrell AP, Brooke CB, Ke R.

Virus Evol. 2019 Jul 8;5(2):vez018. doi: 10.1093/ve/vez018. eCollection 2019 Jul. Erratum in: Virus Evol. 2019 Nov 19;5(2):vez052.


Asymptomatic Infection and Transmission of Pertussis in Households: A Systematic Review.

Craig R, Kunkel E, Crowcroft NS, Fitzpatrick MC, de Melker H, Althouse BM, Merkel T, Scarpino SV, Koelle K, Friedman L, Arnold C, Bolotin S.

Clin Infect Dis. 2020 Jan 1;70(1):152-161. doi: 10.1093/cid/ciz531.


Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?

Li ZT, Zarnitsyna VI, Lowen AC, Weissman D, Koelle K, Kohlmeier JE, Antia R.

J Virol. 2019 Mar 5;93(6). pii: e01534-18. doi: 10.1128/JVI.01534-18. Print 2019 Mar 15.


Intrahost Dynamics of Human Cytomegalovirus Variants Acquired by Seronegative Glycoprotein B Vaccinees.

Nelson CS, Vera Cruz D, Su M, Xie G, Vandergrift N, Pass RF, Forman M, Diener-West M, Koelle K, Arav-Boger R, Permar SR.

J Virol. 2019 Feb 19;93(5). pii: e01695-18. doi: 10.1128/JVI.01695-18. Print 2019 Mar 1.


Causes and Consequences of Spatial Within-Host Viral Spread.

Gallagher ME, Brooke CB, Ke R, Koelle K.

Viruses. 2018 Nov 13;10(11). pii: E627. doi: 10.3390/v10110627. Review.


Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context.

Ben-Shachar R, Koelle K.

Nat Commun. 2018 Jun 15;9(1):2355. doi: 10.1038/s41467-018-04595-w.


The ecosystem services of animal microbiomes.

McKenney EA, Koelle K, Dunn RR, Yoder AD.

Mol Ecol. 2018 Apr;27(8):2164-2172. doi: 10.1111/mec.14532. Epub 2018 Mar 12.


Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution.

Raghwani J, Thompson RN, Koelle K.

Virus Evol. 2017 Nov 9;3(2):vex034. doi: 10.1093/ve/vex034. eCollection 2017 Jul.


Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys.

Nelson CS, Cruz DV, Tran D, Bialas KM, Stamper L, Wu H, Gilbert M, Blair R, Alvarez X, Itell H, Chen M, Deshpande A, Chiuppesi F, Wussow F, Diamond DJ, Vandergrift N, Walter MR, Barry PA, Cohen-Wolkowiez M, Koelle K, Kaur A, Permar SR.

JCI Insight. 2017 Jul 6;2(13). pii: 94002. doi: 10.1172/jci.insight.94002. eCollection 2017 Jul 6.


Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.

Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K.

J Virol. 2017 Jun 26;91(14). pii: e00171-17. doi: 10.1128/JVI.00171-17. Print 2017 Jul 15. Erratum in: J Virol. 2019 Aug 13;93(17):.


The effective rate of influenza reassortment is limited during human infection.

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K, Illingworth CJ.

PLoS Pathog. 2017 Feb 7;13(2):e1006203. doi: 10.1371/journal.ppat.1006203. eCollection 2017 Feb.


The Long-Term Safety, Public Health Impact, and Cost-Effectiveness of Routine Vaccination with a Recombinant, Live-Attenuated Dengue Vaccine (Dengvaxia): A Model Comparison Study.

Flasche S, Jit M, Rodríguez-Barraquer I, Coudeville L, Recker M, Koelle K, Milne G, Hladish TJ, Perkins TA, Cummings DA, Dorigatti I, Laydon DJ, España G, Kelso J, Longini I, Lourenco J, Pearson CA, Reiner RC, Mier-Y-Terán-Romero L, Vannice K, Ferguson N.

PLoS Med. 2016 Nov 29;13(11):e1002181. doi: 10.1371/journal.pmed.1002181. eCollection 2016 Nov.


Drivers of Inter-individual Variation in Dengue Viral Load Dynamics.

Ben-Shachar R, Schmidler S, Koelle K.

PLoS Comput Biol. 2016 Nov 17;12(11):e1005194. doi: 10.1371/journal.pcbi.1005194. eCollection 2016 Nov.


Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification.

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K.

J Virol. 2016 Nov 28;90(24):11247-11258. Print 2016 Dec 15.


The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans.

Koelle K, Rasmussen DA.

Elife. 2015 Sep 15;4:e07361. doi: 10.7554/eLife.07361.


Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections.

Ben-Shachar R, Koelle K.

J R Soc Interface. 2015 Feb 6;12(103). pii: 20140886. doi: 10.1098/rsif.2014.0886.


Phylodynamic inference for structured epidemiological models.

Rasmussen DA, Volz EM, Koelle K.

PLoS Comput Biol. 2014 Apr 17;10(4):e1003570. doi: 10.1371/journal.pcbi.1003570. eCollection 2014 Apr.


Influenza: Prediction is worth a shot.

Koelle K, Rasmussen DA.

Nature. 2014 Mar 6;507(7490):47-8. doi: 10.1038/nature13054. Epub 2014 Feb 26. No abstract available.


Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam.

Rasmussen DA, Boni MF, Koelle K.

Mol Biol Evol. 2014 Feb;31(2):258-71. doi: 10.1093/molbev/mst203. Epub 2013 Oct 22.


Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics.

Scholle SO, Ypma RJ, Lloyd AL, Koelle K.

Am Nat. 2013 Oct;182(4):494-513. doi: 10.1086/672000. Epub 2013 Aug 20.


Navigating the devious course of evolution: the importance of mechanistic models for identifying eco-evolutionary dynamics in nature.

Luo S, Koelle K.

Am Nat. 2013 May;181 Suppl 1:S58-75. doi: 10.1086/669952. Epub 2013 Mar 15.


Viral phylodynamics.

Volz EM, Koelle K, Bedford T.

PLoS Comput Biol. 2013;9(3):e1002947. doi: 10.1371/journal.pcbi.1002947. Epub 2013 Mar 21. Review.


The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis.

Yuan HY, Koelle K.

Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120204. doi: 10.1098/rstb.2012.0204. Print 2013 Mar 19.


Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study.

Ratmann O, Donker G, Meijer A, Fraser C, Koelle K.

PLoS Comput Biol. 2012;8(12):e1002835. doi: 10.1371/journal.pcbi.1002835. Epub 2012 Dec 27.


Coalescent entanglement and the conditional dependence of the times to common ancestry of mutually exclusive pairs of individuals.

Wu S, Koelle K, Rodrigo A.

J Hered. 2013 Jan-Feb;104(1):86-91. doi: 10.1093/jhered/ess074. Epub 2012 Oct 16.


The impact of host immune status on the within-host and population dynamics of antigenic immune escape.

Luo S, Reed M, Mattingly JC, Koelle K.

J R Soc Interface. 2012 Oct 7;9(75):2603-13. doi: 10.1098/rsif.2012.0180. Epub 2012 May 9.


Assessing the potential of a candidate dengue vaccine with mathematical modeling.

WHO-VMI Dengue Vaccine Modeling Group, Beatty M, Boni MF, Brown S, Buathong R, Burke D, Coudeville L, Cummings DA, Edelman R, Farrar J, Focks DA, Gomes MG, Guignard A, Halstead S, Hombach J, Knerer G, Koelle K, Lam FC, Lang J, Longini I, Medlock J, Namgyal P, Powell M, Recker M, Rohani P, Standaert B, Struchiner C, Teyssou R, Wearing H.

PLoS Negl Trop Dis. 2012;6(3):e1450. doi: 10.1371/journal.pntd.0001450. Epub 2012 Mar 27. No abstract available.


Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza.

Arinaminpathy N, Ratmann O, Koelle K, Epstein SL, Price GE, Viboud C, Miller MA, Grenfell BT.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3173-7. doi: 10.1073/pnas.1113342109. Epub 2012 Feb 7.


Network perspectives on infectious disease dynamics.

Meyers LA, Kerr B, Koelle K.

Interdiscip Perspect Infect Dis. 2011;2011:146765. doi: 10.1155/2011/146765. Epub 2012 Jan 9. No abstract available.


Rates of coalescence for common epidemiological models at equilibrium.

Koelle K, Rasmussen DA.

J R Soc Interface. 2012 May 7;9(70):997-1007. doi: 10.1098/rsif.2011.0495. Epub 2011 Sep 15.


Inference for nonlinear epidemiological models using genealogies and time series.

Rasmussen DA, Ratmann O, Koelle K.

PLoS Comput Biol. 2011 Aug;7(8):e1002136. doi: 10.1371/journal.pcbi.1002136. Epub 2011 Aug 25.


A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses.

Koelle K, Ratmann O, Rasmussen DA, Pasour V, Mattingly J.

Proc Biol Sci. 2011 Dec 22;278(1725):3723-30. doi: 10.1098/rspb.2011.0435. Epub 2011 May 4.


A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza.

Koelle K, Khatri P, Kamradt M, Kepler TB.

J R Soc Interface. 2010 Sep 6;7(50):1257-74. doi: 10.1098/rsif.2010.0007. Epub 2010 Mar 24.


Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: influenza as a case study.

Koelle K, Kamradt M, Pascual M.

Epidemics. 2009 Jun;1(2):129-37. doi: 10.1016/j.epidem.2009.05.003. Epub 2009 Jun 2.


The impact of climate on the disease dynamics of cholera.

Koelle K.

Clin Microbiol Infect. 2009 Jan;15 Suppl 1:29-31. doi: 10.1111/j.1469-0691.2008.02686.x. Review.


Capturing escape in infectious disease dynamics.

Cobey S, Koelle K.

Trends Ecol Evol. 2008 Oct;23(10):572-7. doi: 10.1016/j.tree.2008.06.008. Epub 2008 Aug 19. Review.


Decreases in dengue transmission may act to increase the incidence of dengue hemorrhagic fever.

Nagao Y, Koelle K.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2238-43. doi: 10.1073/pnas.0709029105. Epub 2008 Feb 4.


Global patterns in seasonal activity of influenza A/H3N2, A/H1N1, and B from 1997 to 2005: viral coexistence and latitudinal gradients.

Finkelman BS, Viboud C, Koelle K, Ferrari MJ, Bharti N, Grenfell BT.

PLoS One. 2007 Dec 12;2(12):e1296.


Shifting patterns: malaria dynamics and rainfall variability in an African highland.

Pascual M, Cazelles B, Bouma MJ, Chaves LF, Koelle K.

Proc Biol Sci. 2008 Jan 22;275(1631):123-32.


Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans.

Koelle K, Cobey S, Grenfell B, Pascual M.

Science. 2006 Dec 22;314(5807):1898-903.


Serotype cycles in cholera dynamics.

Koelle K, Pascual M, Yunus M.

Proc Biol Sci. 2006 Nov 22;273(1603):2879-86.


Hyperinfectivity in cholera: a new mechanism for an old epidemiological model?

Pascual M, Koelle K, Dobson AP.

PLoS Med. 2006 Jun;3(6):e280. Epub 2006 Jun 27. No abstract available.


Refractory periods and climate forcing in cholera dynamics.

Koelle K, Rodó X, Pascual M, Yunus M, Mostafa G.

Nature. 2005 Aug 4;436(7051):696-700.


Pathogen adaptation to seasonal forcing and climate change.

Koelle K, Pascual M, Yunus M.

Proc Biol Sci. 2005 May 7;272(1566):971-7.


The effects of host contact network structure on pathogen diversity and strain structure.

Buckee CO, Koelle K, Mustard MJ, Gupta S.

Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10839-44. Epub 2004 Jul 9.


Live attenuated HIV vaccines: predicting the tradeoff between efficacy and safety.

Blower SM, Koelle K, Kirschner DE, Mills J.

Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3618-23.


Antibiotic resistance--to treat...

Blower S, Koelle K, Lietman T.

Nat Med. 1999 Apr;5(4):358. No abstract available.


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