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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.


Immune Priming and Long-term Persistence of Memory B Cells After Inactivated Poliovirus Vaccine in Macaque Models: Support for at least 2 Doses.

Bhaumik SK, Kulkarni RR, Weldon WC, Silveira ELV, Ahmed H, Gunisetty S, Chandele A, Antia R, Verma H, Sutter R, Pallansch MA, Oberste MS, Villinger F, Orenstein W, Murali-Krishna K.

Clin Infect Dis. 2018 Oct 30;67(suppl_1):S66-S77. doi: 10.1093/cid/ciy634.


Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design.

Handel A, Li Y, McKay B, Pawelek KA, Zarnitsyna V, Antia R.

PLoS Comput Biol. 2018 Oct 1;14(10):e1006505. doi: 10.1371/journal.pcbi.1006505. eCollection 2018 Oct.


Hepatitis E Virus infection seroprevalence and the associated risk factors in animals raised in Ibadan, Nigeria.

Antia RE, Adekola AA, Jubril AJ, Ohore OG, Emikpe BO.

J Immunoassay Immunochem. 2018;39(5):509-520. doi: 10.1080/15321819.2018.1514507. Epub 2018 Sep 13.


Within-host competition can delay evolution of drug resistance in malaria.

Bushman M, Antia R, Udhayakumar V, de Roode JC.

PLoS Biol. 2018 Aug 21;16(8):e2005712. doi: 10.1371/journal.pbio.2005712. eCollection 2018 Aug.


Heterogeneity and longevity of antibody memory to viruses and vaccines.

Antia A, Ahmed H, Handel A, Carlson NE, Amanna IJ, Antia R, Slifka M.

PLoS Biol. 2018 Aug 10;16(8):e2006601. doi: 10.1371/journal.pbio.2006601. eCollection 2018 Aug.


Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaks.

Zarnitsyna VI, Bulusheva I, Handel A, Longini IM, Halloran ME, Antia R.

PLoS One. 2018 Jun 26;13(6):e0199674. doi: 10.1371/journal.pone.0199674. eCollection 2018.


Adaptation of the agyrophil technique for nucleolar organizer regions to canine peripheral blood smears.

Ogunsola J, Antia R.

Open Vet J. 2018;8(2):182-185. doi: 10.4314/ovj.v8i2.11. Epub 2018 May 25.


High dimensional random walks can appear low dimensional: Application to influenza H3N2 evolution.

Moore J, Ahmed H, Antia R.

J Theor Biol. 2018 Jun 14;447:56-64. doi: 10.1016/j.jtbi.2018.03.022. Epub 2018 Mar 21.


Effector CD8 T cells dedifferentiate into long-lived memory cells.

Youngblood B, Hale JS, Kissick HT, Ahn E, Xu X, Wieland A, Araki K, West EE, Ghoneim HE, Fan Y, Dogra P, Davis CW, Konieczny BT, Antia R, Cheng X, Ahmed R.

Nature. 2017 Dec 21;552(7685):404-409. doi: 10.1038/nature25144. Epub 2017 Dec 13.


What Controls the Acute Viral Infection Following Yellow Fever Vaccination?

Moore J, Ahmed H, Jia J, Akondy R, Ahmed R, Antia R.

Bull Math Biol. 2018 Jan;80(1):46-63. doi: 10.1007/s11538-017-0365-3. Epub 2017 Nov 6.


Prevalence and renal pathology of pathogenic <i>Leptospira</i> spp. in wildlife in Abeokuta, Ogun State, Nigeria.

Ajayi OL, Antia RE, Ojo OE, Awoyomi OJ, Oyinlola LA, Ojebiyi OG.

Onderstepoort J Vet Res. 2017 Mar 24;84(1):e1-e9. doi: 10.4102/ojvr.v84i1.1210.


Eradicating infectious disease using weakly transmissible vaccines.

Nuismer SL, Althouse BM, May R, Bull JJ, Stromberg SP, Antia R.

Proc Biol Sci. 2016 Oct 26;283(1841). pii: 20161903.


Multi-epitope Models Explain How Pre-existing Antibodies Affect the Generation of Broadly Protective Responses to Influenza.

Zarnitsyna VI, Lavine J, Ellebedy A, Ahmed R, Antia R.

PLoS Pathog. 2016 Jun 23;12(6):e1005692. doi: 10.1371/journal.ppat.1005692. eCollection 2016 Jun.


Mathematical Model Reveals the Role of Memory CD8 T Cell Populations in Recall Responses to Influenza.

Zarnitsyna VI, Handel A, McMaster SR, Hayward SL, Kohlmeier JE, Antia R.

Front Immunol. 2016 May 9;7:165. doi: 10.3389/fimmu.2016.00165. eCollection 2016.


Masking of antigenic epitopes by antibodies shapes the humoral immune response to influenza.

Zarnitsyna VI, Ellebedy AH, Davis C, Jacob J, Ahmed R, Antia R.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140248. doi: 10.1098/rstb.2014.0248.


Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccination.

Akondy RS, Johnson PL, Nakaya HI, Edupuganti S, Mulligan MJ, Lawson B, Miller JD, Pulendran B, Antia R, Ahmed R.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3050-5. doi: 10.1073/pnas.1500475112. Epub 2015 Feb 23.


Baseline Haematology and Erythrocyte Morphological Changes of Apparently Normal Dogs Raised in Ibadan, Oyo State.

Adekola AA, Jagun AT, Emikpe BO, Antia RE.

Niger J Physiol Sci. 2015 Dec 20;30(1-2):111-8.


How sticky should a virus be? The impact of virus binding and release on transmission fitness using influenza as an example.

Handel A, Akin V, Pilyugin SS, Zarnitsyna V, Antia R.

J R Soc Interface. 2014 Jan 15;11(92):20131083. doi: 10.1098/rsif.2013.1083. Print 2014 Mar 6.


Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire.

Zarnitsyna VI, Evavold BD, Schoettle LN, Blattman JN, Antia R.

Front Immunol. 2013 Dec 26;4:485. doi: 10.3389/fimmu.2013.00485. Review.


A population biological approach to understanding the maintenance and loss of the T-cell repertoire during aging.

Johnson PL, Goronzy JJ, Antia R.

Immunology. 2014 Jun;142(2):167-75. doi: 10.1111/imm.12244. Review.


Population-expression models of immune response.

Stromberg SP, Antia R, Nemenman I.

Phys Biol. 2013 Jun;10(3):035010. doi: 10.1088/1478-3975/10/3/035010. Epub 2013 Jun 4.


Rhabdomyosarcoma in a terrestrial tortoise (Geochelone nigra) in Nigeria: a case report.

Eyarefe OD, Antia RE, Oguntoye CO, Abiola OO, Alaka OO, Ogunsola JO.

J S Afr Vet Assoc. 2012 Nov 30;83(1):300. doi: 10.4102/jsava.v83i1.300.


Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age.

Johnson PL, Yates AJ, Goronzy JJ, Antia R.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21432-7. doi: 10.1073/pnas.1209283110. Epub 2012 Dec 10.


On the role of CD8 T cells in the control of persistent infections.

Stromberg SP, Antia R.

Biophys J. 2012 Oct 17;103(8):1802-10. doi: 10.1016/j.bpj.2012.07.059. Epub 2012 Oct 16.


How to minimize the attack rate during multiple influenza outbreaks in a heterogeneous population.

Fung IC, Antia R, Handel A.

PLoS One. 2012;7(6):e36573. doi: 10.1371/journal.pone.0036573. Epub 2012 Jun 11.


How do antigenically varying pathogens avoid cross-reactive responses to invariant antigens?

Johnson PL, Kochin BF, Ahmed R, Antia R.

Proc Biol Sci. 2012 Jul 22;279(1739):2777-85. doi: 10.1098/rspb.2012.0005. Epub 2012 Mar 21.


Virus replication strategies and the critical CTL numbers required for the control of infection.

Yates AJ, Van Baalen M, Antia R.

PLoS Comput Biol. 2011 Nov;7(11):e1002274. doi: 10.1371/journal.pcbi.1002274. Epub 2011 Nov 17.


Vaccination by delayed treatment of infection.

Stromberg SP, Antia R.

Vaccine. 2011 Dec 6;29(52):9624-31. doi: 10.1016/j.vaccine.2011.10.047. Epub 2011 Oct 30.


The global spread of drug-resistant influenza.

Chao DL, Bloom JD, Kochin BF, Antia R, Longini IM Jr.

J R Soc Interface. 2012 Apr 7;9(69):648-56. doi: 10.1098/rsif.2011.0427. Epub 2011 Aug 24.


Vaccination alters the balance between protective immunity, exhaustion, escape, and death in chronic infections.

Johnson PL, Kochin BF, McAfee MS, Stromnes IM, Regoes RR, Ahmed R, Blattman JN, Antia R.

J Virol. 2011 Jun;85(11):5565-70. doi: 10.1128/JVI.00166-11. Epub 2011 Mar 16.


Parasite evolution and life history theory.

Kochin BF, Bull JJ, Antia R.

PLoS Biol. 2010 Oct 19;8(10):e1000524. doi: 10.1371/journal.pbio.1000524. No abstract available.


On the control of acute rodent malaria infections by innate immunity.

Kochin BF, Yates AJ, de Roode JC, Antia R.

PLoS One. 2010 May 6;5(5):e10444. doi: 10.1371/journal.pone.0010444.


Intervention strategies for an influenza pandemic taking into account secondary bacterial infections.

Handel A, Longini IM Jr, Antia R.

Epidemics. 2009 Sep;1(3):185-95. doi: 10.1016/j.epidem.2009.09.001.


Towards a quantitative understanding of the within-host dynamics of influenza A infections.

Handel A, Longini IM Jr, Antia R.

J R Soc Interface. 2010 Jan 6;7(42):35-47. doi: 10.1098/rsif.2009.0067. Epub 2009 May 27.


Quantifying the development of the peripheral naive CD4+ T-cell pool in humans.

Bains I, Antia R, Callard R, Yates AJ.

Blood. 2009 May 28;113(22):5480-7. doi: 10.1182/blood-2008-10-184184. Epub 2009 Jan 28.


Memory CD8 T-cell compartment grows in size with immunological experience.

Vezys V, Yates A, Casey KA, Lanier G, Ahmed R, Antia R, Masopust D.

Nature. 2009 Jan 8;457(7226):196-9. doi: 10.1038/nature07486. Epub 2008 Nov 12.


Antiviral resistance and the control of pandemic influenza: the roles of stochasticity, evolution and model details.

Handel A, Longini IM Jr, Antia R.

J Theor Biol. 2009 Jan 7;256(1):117-25. doi: 10.1016/j.jtbi.2008.09.021. Epub 2008 Oct 8.


Sharing the burden: antigen transport and firebreaks in immune responses.

Handel A, Yates A, Pilyugin SS, Antia R.

J R Soc Interface. 2009 May 6;6(34):447-54. doi: 10.1098/rsif.2008.0258. Epub 2008 Aug 15.


A simple mathematical model helps to explain the immunodominance of CD8 T cells in influenza A virus infections.

Handel A, Antia R.

J Virol. 2008 Aug;82(16):7768-72. doi: 10.1128/JVI.00653-08. Epub 2008 Jun 11.


Oviductal volvulus in a Nera black chicken (Gallus gallus domesticus) in Nigeria.

Ajayi OL, Antia RE, Omotainse SO.

Avian Pathol. 2008 Apr;37(2):139-40. doi: 10.1080/03079450801895324.


The dynamics of acute malaria infections. I. Effect of the parasite's red blood cell preference.

Antia R, Yates A, de Roode JC.

Proc Biol Sci. 2008 Jun 22;275(1641):1449-58. doi: 10.1098/rspb.2008.0198.


Revisiting estimates of CTL killing rates in vivo.

Yates A, Graw F, Barber DL, Ahmed R, Regoes RR, Antia R.

PLoS One. 2007 Dec 12;2(12):e1301.


Gap junction-mediated antigen transport in immune responses.

Handel A, Yates A, Pilyugin SS, Antia R.

Trends Immunol. 2007 Nov;28(11):463-6. Epub 2007 Oct 24.


Understanding the slow depletion of memory CD4+ T cells in HIV infection.

Yates A, Stark J, Klein N, Antia R, Callard R.

PLoS Med. 2007 May;4(5):e177. Erratum in: PLoS Med. 2008 Jan;5(1):e11.


Mathematical models of cytotoxic T-lymphocyte killing.

Regoes RR, Yates A, Antia R.

Immunol Cell Biol. 2007 Jun;85(4):274-9. Epub 2007 Apr 10. Review.


What is the best control strategy for multiple infectious disease outbreaks?

Handel A, Longini IM Jr, Antia R.

Proc Biol Sci. 2007 Mar 22;274(1611):833-7.


Estimation of the rate of killing by cytotoxic T lymphocytes in vivo.

Regoes RR, Barber DL, Ahmed R, Antia R.

Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1599-603. Epub 2007 Jan 22.


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