Publications

A full listing of publications can be found on Google Scholar or the National Library of Medicine website.

TITLECITED BYYEAR
Evolutionary consequences of delaying intervention for monkeypoxPLF Johnson, CT Bergstrom, RR Regoes, IM Longini, ME Halloran, …The Lancet12022
Persistence of Virus-Specific Antibody after Depletion of Memory B CellsWA Langley, A Wieland, H Ahmed, MAU Rasheed, CW Davis, …Journal of Virology 96 (9), e00026-222022
The changing epidemiology of SARS-CoV-2K Koelle, MA Martin, R Antia, B Lopman, NE DeanScience 375 (6585), 1116-1121482022
Memory CD4 T cell subset organization in the female reproductive tract is regulated via the menstrual cycle through CCR5 signalingA Swaims-Kohlmeier, AN Wein, FP Hardnett, AN Sheth, ZRT Li, …bioRxiv2022
Masks Do No More Than Prevent Transmission: Theory and Data Undermine the Variolation HypothesisK Koelle, J Lin, H Zhu, R Antia, A Lowen, D WeissmanmedRxiv2022
Antibody Response to COVID-19 mRNA Vaccine in Patients With Lung Cancer After Primary Immunization and Booster: Reactivity to the SARS-CoV-2 WT Virus and Omicron Variant.RM Valanparambil, J Carlisle, SL Linderman, A Akthar, RL Millett, L Lai, …J Clin Oncol, JCO2102986-JCO210298622022
Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines (preprint)R Desikan, S Linderman, C Davis, V Zarnitsyna, H Ahmed, R Antia2022
Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccinesR Desikan, SL Linderman, CW Davis, VI Zarnitsyna, HR Ahmed, R AntiabioRxiv2022
Which ‘imperfect vaccines’ encourage the evolution of higher virulence?JJ Bull, R AntiaEvolution, Medicine, and Public Health 10 (1), 202-21312022
Humoral Responses Against SARS-CoV-2 and Variants of Concern After mRNA Vaccines in Patients With Non-Hodgkin Lymphoma and Chronic Lymphocytic Leukemia.A Chang, A Akhtar, SL Linderman, L Lai, VM Orellana-Noia, …J Clin Oncol, JCO2200088-JCO220008842022
Antibody response to SARS-CoV-2 mRNA vaccine in lung cancer patients: Reactivity to vaccine antigen and variants of concern.R Valanparambil, J Carlisle, S Linderman, A Akthar, RL Millett, L Lai, …MedRxiv92022
Influenza immunization in the context of preexisting immunitySL Linderman, AH Ellebedy, C Davis, CS Eberhardt, R Antia, R Ahmed, …Cold Spring Harbor perspectives in medicine 11 (11), a040964122021
Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccinationVI Zarnitsyna, RS Akondy, H Ahmed, DJ McGuire, VG Zarnitsyn, M Moore, …PLoS computational biology 17 (10), e100946832021
Transition to endemicity: Understanding COVID-19R Antia, ME HalloranImmunity 54 (10), 2172-2176482021
Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cellsKW Cohen, SL Linderman, Z Moodie, J Czartoski, L Lai, G Mantus, …Cell Reports Medicine 2 (7), 1003542022021
Vaccination reshapes the virus-specific T cell repertoire in unexposed adultsYG Pan, B Aiamkitsumrit, L Bartolo, Y Wang, C Lavery, A Marc, PV Holec, …Immunity 54 (6), 1245-1256. e552021
Vaccinating children against SARS-CoV-2JS Lavine, O Bjornstad, R Antiabmj 373182021
Physical ‘strength’of the multi‐protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation? The weakest link in the multi‐protein chain …R Desikan, R Antia, NM DixitBioessays 43 (4), 200015942021
Immunological characteristics govern the transition of COVID-19 to endemicityJS Lavine, ON Bjornstad, R AntiaScience 371 (6530), 741-7452602021
Directed attenuation to enhance vaccine immunityR Antia, H Ahmed, JJ BullPLoS computational biology 17 (2), e100860212021
Severity of SARS-CoV-2 reinfections in second wave determines likelihood of mild endemicityJS Lavine, ON Bjornstad, D Coombs, R AntiamedRxiv2021
Modeling Immunopathology During Persistent Viral InfectionsVI Zarnitsyna, PLF Johnson, JN Blattman, R AntiaMathematical, Computational and Experimental T Cell Immunology, 109-1202021
T cell receptor diversity and lineage relationship between virus-specific CD8 T cell subsets during chronic lymphocytic choriomeningitis virus infectionYM Chang, A Wieland, ZR Li, SJ Im, DJ McGuire, HT Kissick, R Antia, …Journal of Virology 94 (20), e00935-2092020
Adjuvanted H5N1 influenza vaccine enhances both cross-reactive memory B cell and strain-specific naive B cell responses in humansAH Ellebedy, R Nachbagauer, KJL Jackson, YN Dai, J Han, WB Alsoussi, …Proceedings of the National Academy of Sciences 117 (30), 17957-17964372020
Complexities in Predicting the Immunogenicity of Live Attenuated Influenza Vaccines ReplyL Matrajt, ME Halloran, R AntiaCLINICAL INFECTIOUS DISEASES 70 (10), 2236-22372020
Reply to Lindsey, Höschler, and de SilvaL Matrajt, ME Halloran, R AntiaClinical Infectious Diseases 70 (10), 2236-22372020
Successes and failures of the live-attenuated influenza vaccine: can we do better?L Matrajt, ME Halloran, R AntiaClinical Infectious Diseases 70 (6), 1029-1037122020
Varying inoculum dose to assess the roles of the immune response and target cell depletion by the pathogen in control of acute viral infectionsJR Moore, H Ahmed, B Manicassamy, A Garcia-Sastre, A Handel, R AntiaBulletin of Mathematical Biology 82 (3), 1-14102020
The weakest link bridging germinal center B cells and follicular dendritic cells limits antibody affinity maturationR Desikan, R Antia, NM DixitarXiv preprint arXiv:2002.026422020
Using directed attenuation to enhance vaccine immunityR Antia, H Ahmed, JJ BullbioRxiv12020
Quantifying memory CD8 T cell-mediated immune pressure on influenza A virus infection in vivoZRT Li, VI Zarnitsyna, AC Lowen, R Antia, JE KohlmeierbioRxiv2020
Clustered mutations at the murine and human IgH locus exhibit significant linkage consistent with templated mutagenesisGA Dale, DJ Wilkins, CD Bohannon, D Dilernia, E Hunter, T Bedford, …The Journal of Immunology 203 (5), 1252-126422019
A dynamical motif comprising the interactions between antigens and CD8 T cells may underlie the outcomes of viral infectionsS Baral, R Antia, NM DixitProceedings of the National Academy of Sciences 116 (35), 17393-17398262019
Incomplete influenza A virus genomes occur frequently but are readily complemented during localized viral spreadNT Jacobs, NO Onuoha, A Antia, J Steel, R Antia, AC LowenNature communications 10 (1), 1-17522019
Recombinant vector vaccine evolutionJJ Bull, SL Nuismer, R AntiaPLoS computational biology 15 (7), e1006857402019
Dependence of CD8 T cell response upon antigen load during primary infectionJR Moore, H Ahmed, D McGuire, R Akondy, R Ahmed, R AntiaBulletin of mathematical biology 81 (7), 2553-256862019
A general framework for modelling the impact of co-infections on pathogen evolutionM Bushman, R AntiaJournal of the Royal Society Interface 16 (155), 2019016552019
Quantifying the selection on influenza A virus imposed by CD8 T cellsZRT Li, VI Zarnitsyna, AC Lowen, JE Kohlmeier, R AntiaThe Journal of Immunology 202 (1 Supplement), 76.14-76.142019
Why are CD8 T cell epitopes of human influenza A virus conserved?ZRT Li, VI Zarnitsyna, AC Lowen, D Weissman, K Koelle, JE Kohlmeier, …Journal of virology 93 (6), e01534-18192019
Recombinant vector vaccines and within-host evolutionJ Bull, SL Nuismer, R AntiabioRxiv, 5450872019
Incomplete influenza A virus genomes are abundant but readily complemented during spatially structured viral spreadNT Jacobs, NO Onuoha, A Antia, R Antia, J Steel, AC LowenbioRxiv, 52906582019
Immune priming and long-term persistence of memory B cells after inactivated poliovirus vaccine in macaque models: support for at least 2 dosesSK Bhaumik, RR Kulkarni, WC Weldon, ELV Silveira, H Ahmed, …Clinical Infectious Diseases 67 (suppl_1), S66-S7772018
Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine designA Handel, Y Li, B McKay, KA Pawelek, V Zarnitsyna, R AntiaPLoS computational biology 14 (10), e1006505322018
Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?VI Zarnitsyna, AC Lowen, D Weissman, K Koelle, JE Kohlmeier, R Antia2018
Within-host competition can delay evolution of drug resistance in malariaM Bushman, R Antia, V Udhayakumar, JC de RoodePLoS biology 16 (8), e2005712352018
Heterogeneity and longevity of antibody memory to viruses and vaccinesA Antia, H Ahmed, A Handel, NE Carlson, IJ Amanna, R Antia, M SlifkaPLoS biology 16 (8), e20066011022018
Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaksVI Zarnitsyna, I Bulusheva, A Handel, IM Longini, ME Halloran, R AntiaPLoS One 13 (6), e019967482018
High dimensional random walks can appear low dimensional: Application to influenza H3N2 evolutionJ Moore, H Ahmed, R AntiaJournal of theoretical biology 447, 56-6452018
What controls the acute viral infection following yellow fever vaccination?J Moore, H Ahmed, J Jia, R Akondy, R Ahmed, R AntiaBulletin of mathematical biology 80 (1), 46-63102018
Effector CD8 T cells dedifferentiate into long-lived memory cellsB Youngblood, JS Hale, HT Kissick, E Ahn, X Xu, A Wieland, K Araki, …Nature 552 (7685), 404-4093492017
WITHIN-HOST DYNAMICS AND SPREAD OF DRUG RESISTANCE IN PLASMODIUM FALCIPARUM MALARIAM Bushman, J de Roode, R AntiaAMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE 95 (5), 116-1162017
Mathematical analysis of a mouse experiment suggests little role for resource depletion in controlling influenza infection within hostH Ahmed, J Moore, B Manicassamy, A Garcia-Sastre, A Handel, R AntiaarXiv preprint arXiv:1705.0256592017
Differential localization of distinct CD4 T cell subsets in the female genital tract during the menstrual cycle is regulated by CCR5A Kohlmeier, S McMaster, ZR Li, J Radzio-Basu, LB Haddad, AN Sheth, …The Journal of Immunology 198 (1 Supplement), 149.20-149.202017
Quantifying the relative impact of influenza virus mutations on viral fitness and escape from cellular immunityZRT Li, VI Zarnitsyna, AC Lowen, JE Kohlmeier, R AntiaThe Journal of Immunology 198 (1 Supplement), 203.6-203.62017
Gene conversion contributes significantly to IgHV somatic hypermutation in mice and humansGA Dale, CD Bohannon, DJ Wilkins, D Dilernia, E Hunter, T Bedford, …The Journal of Immunology 198 (1 Supplement), 195.7-195.72017
Eradicating infectious disease using weakly transmissible vaccinesSL Nuismer, BM Althouse, R May, JJ Bull, SP Stromberg, R AntiaProceedings of the Royal Society B: Biological Sciences 283 (1841), 20161903262016
The role of gene conversion in the diversification of murine IgM plasma cellsG Dale, C Bohannon, R Antia, J JacobEUROPEAN JOURNAL OF IMMUNOLOGY 46, 63-642016
Multi-epitope models explain how pre-existing antibodies affect the generation of broadly protective responses to influenzaVI Zarnitsyna, J Lavine, A Ellebedy, R Ahmed, R AntiaPLoS pathogens 12 (6), e1005692702016
Mathematical model reveals the role of memory CD8 T cell populations in recall responses to influenzaVI Zarnitsyna, A Handel, SR McMaster, SL Hayward, JE Kohlmeier, …Frontiers in immunology 7, 165362016
Masking of antigenic epitopes by antibodies shapes the humoral immune response to influenzaVI Zarnitsyna, AH Ellebedy, C Davis, J Jacob, R Ahmed, R AntiaThe Journal of Immunology 196 (1 Supplement), 80.6-80.612016
Understanding heterogeneous CTL responses to the yellow fever vaccine using mathematical models.JR Moore, R Antia, R Akondy, J Jia, R AhmedThe Journal of Immunology 196 (1 Supplement), 80.4-80.42016
Inflammatory monocytes mediate competition between genetically diverse malaria parasites during mixed-strain Plasmodium infections.NT Jacobs, J Barra, R Antia, TJ LambThe Journal of Immunology 196 (1 Supplement), 134.6-134.62016
Masking of antigenic epitopes by antibodies shapes the humoral immune response to influenzaVI Zarnitsyna, AH Ellebedy, C Davis, J Jacob, R Ahmed, R AntiaPhilosophical Transactions of the Royal Society B: Biological Sciences 370 …562015
Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccinationRS Akondy, PLF Johnson, HI Nakaya, S Edupuganti, MJ Mulligan, …Proceedings of the National Academy of Sciences 112 (10), 3050-30551032015
A population biological approach to understanding the maintenance and loss of the T‐cell repertoire during agingPLF Johnson, JJ Goronzy, R AntiaImmunology 142 (2), 167-175362014
DNA origami: single cell analysis of T cell receptors without single cell sorting.(LYM7P. 719)L Schoettle, X Wei, M Garcia-Neurer, V Zarnitsyna, R Antia, H Yan, …The Journal of Immunology 192 (1 Supplement), 193.7-193.72014
How sticky should a virus be? The impact of virus binding and release on transmission fitness using influenza as an exampleA Handel, V Akin, SS Pilyugin, V Zarnitsyna, R AntiaJournal of the Royal Society Interface 11 (92), 20131083342014
How sticky should a virus be? The impact of virus binding andA Handel, V Akin, SS Pilyugin, V Zarnitsyna, R Antia2014
Estimating the diversity, completeness, and cross-reactivity of the T cell repertoireVI Zarnitsyna, BD Evavold, LN Schoettle, JN Blattman, R AntiaFrontiers in immunology 4, 4851722013
Population-expression models of immune responseSP Stromberg, R Antia, I NemenmanPhysical Biology 10 (3), 03501052013
A quantitative explanation of vaccination for disease (P4315)M McAfee, P Johnson, R Antia, J BlattmanThe Journal of Immunology 190 (1 Supplement), 123.21-123.212013
Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with agePLF Johnson, AJ Yates, JJ Goronzy, R AntiaProceedings of the National Academy of Sciences 109 (52), 21432-21437882012
Defensive complexity and the phylogenetic conservation of immune controlE Chastain, R Antia, CT BergstromarXiv preprint arXiv:1211.287872012
On the role of CD8 T cells in the control of persistent infectionsSP Stromberg, R AntiaBiophysical journal 103 (8), 1802-1810102012
How do antigenically varying pathogens avoid cross-reactive responses to invariant antigens?PLF Johnson, BF Kochin, R Ahmed, R AntiaProceedings of the Royal Society B: Biological Sciences 279 (1739), 2777-2785212012
How to minimize the attack rate during multiple influenza outbreaks in a heterogeneous populationICH Fung, R Antia, A HandelPloS one 7 (6), e36573172012
The global spread of drug-resistant influenzaDL Chao, JD Bloom, BF Kochin, R Antia, IM Longini JrJournal of The Royal Society Interface 9 (69), 648-656532012
Defensive complexity in antagonistic coevolutionE Chastain, R Antia, CT BergstromarXiv 120312012
Vaccination by delayed treatment of infectionSP Stromberg, R AntiaVaccine 29 (52), 9624-963192011
Virus replication strategies and the critical CTL numbers required for the control of infectionAJ Yates, M Van Baalen, R AntiaPLoS computational biology 7 (11), e1002274132011
Vaccination alters the balance between protective immunity, exhaustion, escape, and death in chronic infectionsPLF Johnson, BF Kochin, MS McAfee, IM Stromnes, RR Regoes, …Journal of virology 85 (11), 5565-5570512011
Parasite evolution and life history theoryBF Kochin, JJ Bull, R AntiaPLoS biology 8 (10), e1000524482010
On the control of acute rodent malaria infections by innate immunityBF Kochin, AJ Yates, JC De Roode, R AntiaPLoS One 5 (5), e10444262010
Towards a quantitative understanding of the within-host dynamics of influenza A infectionsA Handel, IM Longini Jr, R AntiaJournal of the Royal Society Interface 7 (42), 35-471582010
Homeostatic turnover of virus-specific memory CD8 T cells occurs stochastically and is independent of CD4 T cell help.AR Choo DK, Murali-Krishna K, Anita RJournal of Immunology 185, 3436-3444.622010
Intervention strategies for an influenza pandemic taking into account secondary bacterial infectionsA Handel, IM Longini Jr, R AntiaEpidemics 1 (3), 185-195222009
Vezys et al. replyV Vezys, A Yates, KA Casey, G Lanier, R Ahmed, R Antia, D MasopustNature 459 (7247), E4-E412009
Quantifying the development of the peripheral naive CD4+ T-cell pool in humansI Bains, R Antia, R Callard, AJ YatesBlood, The Journal of the American Society of Hematology 113 (22), 5480-54871452009
Sharing the burden: antigen transport and firebreaks in immune responsesA Handel, A Yates, SS Pilyugin, R AntiaJournal of the Royal Society interface 6 (34), 447-454122009
Antiviral resistance and the control of pandemic influenza: the roles of stochasticity, evolution and model detailsA Handel, IM Longini Jr, R AntiaJournal of theoretical biology 256 (1), 117-125592009
Philip Lee Falk Johnson Biology-Psychology Bldg# 144, Room 1210B Pulendran, R Antia, R Ahmed, MMJV MLUniversity of California, Berkeley 20042009
Memory CD8 T-cell compartment grows in size with immunological experienceV Vezys, A Yates, KA Casey, G Lanier, R Ahmed, R Antia, D MasopustNature 457 (7226), 196-1992552009
A simple mathematical model helps to explain the immunodominance of CD8 T cells in influenza A virus infectionsA Handel, R AntiaJournal of virology 82 (16), 7768-7772342008
The dynamics of acute malaria infections. I. Effect of the parasite’s red blood cell preferenceR Antia, A Yates, JC de RoodeProceedings of the Royal Society B: Biological Sciences 275 (1641), 1449-1458832008
Correction: Understanding the Slow Depletion ofA Yates, J Stark, N Klein, R Antia, R Callard2008
Correction: Understanding the Slow Depletion of Memory CD4+ T Cells in HIV InfectionA Yates, J Stark, N Klein, R Antia, R CallardPLoS Medicine 5 (1), e1142008
Emergence of new infectious diseasesM Woolhouse, R AntiaEvolution in health and disease (eds SC Stearns & JK Koella), 215-228262008
Revisiting estimates of CTL killing rates in vivoA Yates, F Graw, DL Barber, R Ahmed, RR Regoes, R AntiaPloS one 2 (12), e1301522007
Neuraminidase inhibitor resistance in influenza: assessing the danger of its generation and spreadA Handel, IM Longini Jr, R AntiaPLoS Computational Biology 3 (12), e2401562007
463 Gap junction-mediated antigen transport in immune responsesC Jolly, QJ Sattentau, AS De Groot, DW Scott, M Terabe, JA Berzofsky, …Immunology 28 (11), 463-5102007
Gap junction-mediated antigen transport in immune responsesA Handel, A Yates, SS Pilyugin, R AntiaTRENDS in Immunology 28 (11), 463-466312007
AIBSnewsR Antia, C BustamanteBioScience 57 (7), 634-6362007
Mathematical models of cytotoxic T‐lymphocyte killingRR Regoes, A Yates, R AntiaImmunology and Cell Biology 85 (4), 274-279472007
Understanding the Slow Depletion of Memory CD4+ T Cells in HIV InfectionA Yates, J Stark, N Klein, R Antia, R CallardPLoS medicine 4 (5), e177922007
What is the best control strategy for multiple infectious disease outbreaks?A Handel, IM Longini Jr, R AntiaProceedings of the Royal Society B: Biological Sciences 274 (1611), 833-8371002007
Estimation of the rate of killing by cytotoxic T lymphocytes in vivoRR Regoes, DL Barber, R Ahmed, R AntiaProceedings of the National Academy of Sciences 104 (5), 1599-1603792007
Home/All Titles/BioScience/Jul 2007/pg (s) 634-636E Green, E Holmes, R Antia, C Bustamante, DC Wallace, S Tishkoff, …2007
How do pathogen evolution and host heterogeneity interact in disease emergence?A Yates, R Antia, RR RegoesProceedings of the Royal Society B: Biological Sciences 273 (1605), 3075-3083862006
Quantifying cell turnover using USE data (vol 298, pg 183, 2005)VV Ganusov, SS Pilyugin, RJ de Boer, K Murali-Krishna, R Ahmed, …JOURNAL OF IMMUNOLOGICAL METHODS 317 (1-2), 186-1872006
The role of compensatory mutations in the emergence of drug resistanceA Handel, RR Regoes, R AntiaPLoS computational biology 2 (10), e1371322006
Correction: how does cross-reactive stimulation affect the longevity of CD8+ T cell memory?VV Ganusov, SS Pilyugin, R Ahmed, R AntiaPLoS Computational Biology 2 (7), e972006
How does cross-reactive stimulation affect the longevity of CD8+ T cell memory?VV Ganusov, SS Pilyugin, R Ahmed, R AntiaPLoS Computational Biology 2 (6), e5582006
Imperfect vaccines and the evolution of pathogens causing acute infections in vertebratesVV Ganusov, R AntiaEvolution 60 (5), 957-969352006
Erratum to” Quantifying cell turnover using CFSE data”[J. Immunol. Methods (298)(2005) 183VV Ganusov, SS Pilyugin, RJ de Boer, K Murali-Krishna, R Ahmed, …Journal of Immunological Methods 317 (1-2), 186-1872006
RNA interference as an intracellular immune systemCT Bergstrom, R AntiaTrends in Ecology & Evolution 1 (21), 22-282006
Ecology and evolutionC Rutte, M Taborsky, MWG Brinkhof, CT Bergstrom, R Antia, JM Ranz, …Ecology 21 (1), 1-542006
How do adaptive immune systems control pathogens while avoiding autoimmunity?CT Bergstrom, R AntiaTrends in ecology & evolution 21 (1), 22-28502006
Pathology during acute infections: contributions of intracellular pathogens and the CTL responseVV Ganusov, R AntiaBiology letters 1 (2), 239-24262005
Ecology and EvolutionC Perrings, K Dehnen-Schmutz, J Touza, M Williamson, D Simberloff, …Ecology 20 (5), 211-2702005
Emerging pathogens: the epidemiology and evolution of species jumpsMEJ Woolhouse, DT Haydon, R AntiaTrends in ecology & evolution 20 (5), 238-2447472005
Optimal replication of poliovirus within cellsRR Regoes, S Crotty, R Antia, MM TanakaThe American Naturalist 165 (3), 364-373352005
Quantifying cell turnover using CFSE dataVV Ganusov, SS Pilyugin, RJ de Boer, K Murali-Krishna, R Ahmed, …Journal of immunological methods 298 (1-2), 183-200952005
The role of models in understanding CD8+ T-cell memoryR Antia, VV Ganusov, R AhmedNature Reviews Immunology 5 (2), 101-1112322005
Epidemic thresholds and R0, the basic reproduction numberMEJ Woolhouse, DT Haydon, R AntiaTrends in Ecology & Evolution 5 (20), 238-2442005
On RNA interference as template immunityCT Bergstrom, R AntiaIndian Academy of Sciences22005
NATUREVIEWGED Oldroyd, JA Downie, R Antia, J Koella, RL Chisholm, RA Firtel, …Nature2004
Parasitic turncoatR Antia, J KoellaNature 429 (6991), 511-51362004
Roles of target cells and virus-specific cellular immunity in primary simian immunodeficiency virus infectionRR Regoes, R Antia, DA Garber, G Silvestri, MB Feinberg, SI StapransJournal of virology 78 (9), 4866-4875562004
NATUREVIEWA Ciechanover, R Antia, VV Ganusov, R Ahmed, GR Weller, VL Brandt, …Nature Reviews Immunology2004
Effect of human leukocyte antigen heterozygosity on infectious disease outcome: the need for allele-specific measuresM Lipsitch, CT Bergstrom, R AntiaBMC Medical Genetics 4 (1), 1-9512003
Epidemiological models for the spread of anti-malarial resistanceJC Koella, R AntiaMalaria Journal 2 (1), 1-112412003
The role of evolution in the emergence of infectious diseasesR Antia, RR Regoes, JC Koella, CT BergstromNature 426 (6967), 658-6615252003
The rescaling method for quantifying the turnover of cell populationsSS Pilyugin, VV Ganusov, K Murali-Krishna, R Ahmed, R AntiaJournal of Theoretical Biology 225 (2), 275-283572003
Mathematical models of RNA silencing: unidirectional amplification limits accidental self-directed reactionsCT Bergstrom, E McKittrick, R AntiaProceedings of the National Academy of Sciences 100 (20), 11511-11516652003
Trade-offs and the evolution of virulence of microparasites: do details matter?VV Ganusov, R AntiaTheoretical population biology 64 (2), 211-220712003
Models of CD8+ responses: 1. What is the antigen-independent proliferation programR Antia, CT Bergstrom, SS Pilyugin, SM Kaech, R AhmedJournal of theoretical biology 221 (4), 585-5981762003
Lineage relationship and protective immunity of memory CD8 T cell subsetsEJ Wherry, V Teichgräber, TC Becker, D Masopust, SM Kaech, R Antia, …Nature immunology 4 (3), 225-23421652003
Interleukin 15 is required for proliferative renewal of virus-specific memory CD8 T cellsTC Becker, EJ Wherry, D Boone, K Murali-Krishna, R Antia, A Ma, …The Journal of experimental medicine 195 (12), 1541-15488562002
Estimating the precursor frequency of naive antigen-specific CD8 T cellsJN Blattman, R Antia, DJD Sourdive, X Wang, SM Kaech, …The Journal of experimental medicine 195 (5), 657-6647592002
Within‐host population dynamics and the evolution of microparasites in a heterogeneous host populationVV Ganusov, CT Bergstrom, R AntiaEvolution 56 (2), 213-2231412002
Recruitment Times, Proliferation, and Apoptosis Rates during the CD8+ T-Cell Response to Lymphocytic Choriomeningitis VirusRJ De Boer, M Oprea, R Antia, K Murali-Krishna, R Ahmed, AS PerelsonJournal of virology 75 (22), 10663-106692252001
Why we don’t get sick: the within-host population dynamics of bacterial infectionsBR Levin, R AntiaScience 292 (5519), 1112-11151012001
The Peacock, the Sparrow, and the Evolution of HumanCT Bergstrom, R Antia, S Számadó, M Lachmann2001
The peacock, the sparrow, and the evolution of human languageCT Bergstrom, R Antia, S Számadó, M LachmannSanta Fe Institute Working Papers22001
Effects of antiviral usage on transmission dynamics of herpes simplex virus type 1 and on antiviral resistance: predictions of mathematical modelsM Lipsitch, TH Bacon, JJ Leary, R Antia, BR LevinAntimicrobial agents and chemotherapy 44 (10), 2824-2835252000
Modeling immune responses with handling timeSS Pilyugin, R AntiaBulletin of mathematical biology 62 (5), 869-890662000
The role of target cell availability and immune control in primary SIV replicationL Perry, R Antia, G Silvestri, M Feinberg, S StapransFASEB JOURNAL 14 (6), A938-A9382000
What can evolutionary biology contribute to understanding virulenceAF Read, P Aaby, R Antia, D Ebert, PW Ewald, S Gupta, EC Holmes, …Evolution in health and disease, 205-215341999
Models of immune memory: on the role of cross-reactive stimulation, competition, and homeostasis in maintaining immune memoryR Antia, SS Pilyugin, R AhmedProceedings of the National Academy of Sciences 95 (25), 14926-149311021998
The population genetics of antibiotic resistance II: Analytic theory for sustained populations of bacteria in a community of hostsFM Stewart, R Antia, BR Levin, M Lipsitch, JE MittlerTheoretical population biology 53 (2), 152-165831998
Humoral immunity due to long-lived plasma cellsMK Slifka, R Antia, JK Whitmire, R AhmedImmunity 8 (3), 363-37213711998
Resistance to antimicrobial chemotherapy: a prescription for research and actionBR Levin, R Antia, E Berllner, P Bloland, S Bonhoeffer, M Cohen, …The American journal of the medical sciences 315 (2), 87-94391998
Theoretical Population Biology TB1383P Amarasekare, R Antia, BJ Bentz, A Bergman, FB Christiansen, …Theoretical Population Biology 53, 2851998
Mathematical models of parasite responses to host immune defencesR Antia, M LipsitchParasitology 115 (7), 155-167731997
Modeling T-cell proliferation: an investigation of the consequences of the Hayflick limitS Pilyugin, J Mittler, R AntiaJournal of theoretical biology 186 (1), 117-129331997
Mathematical models of parasite responses to host immune defensesCL Blankespoor, R Antia, PW Pappas, M Lipsitch, T EisnerPARASITOLOGY-CAMBRIDGE- 115 (1), S155-S1681997
The population genetics of antibiotic resistanceBR Levin, M Lipsitch, V Perrot, S Schrag, R Antia, L Simonsen, …Clinical infectious diseases 24 (Supplement_1), S9-S163981997
Antigenic variation and the within-host dynamics of parasites (vol 93, pg 985, 1996)R Antia, MA Nowak, RM AndersonPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF …1996
Recent developments in theories of pathogenesis of AIDSR Antia, ME HalloranTrends in Microbiology 4 (7), 282-285151996
T-cell homeostasis, competition, and drift: AIDS as HIV-accelerated senescence of the immune repertoireJE Mittler, BR Levin, R AntiaJAIDS Journal of Acquired Immune Deficiency Syndromes 12 (3), 233-248331996
Models of the within-host dynamics of persistent mycobacterial infectionsR Antia, JC Koella, V PerrotProceedings of the Royal Society of London. Series B: Biological Sciences …741996
Antigenic variation and the within-host dynamics of parasites.R Antia, MA Nowak, RM AndersonProceedings of the National Academy of Sciences 93 (3), 985-9891091996
Population dynamics of HIV pathogenesisJ Mittler, R Antia, B LevinTrends in Ecology & Evolution 10 (6), 224-22781995
Optimal pattern of replication and transmission for parasites with two stages in their life cycleJC Koella, R AntiaTheoretical Population Biology 47 (3), 277-291561995
Within-host population dynamics and the evolution and maintenance of microparasite virulenceR Antia, BR Levin, RM MayThe American Naturalist 144 (3), 457-4723261994
A model of non-specific immunityR Antia, JC KoellaJournal of theoretical biology 168 (2), 141-150541994
Population biology of virus-host interactionsGP Garnett, R AntiaThe evolutionary biology of viruses, 51-73271994
Parasite evolution in response to immunological defensesR Antia, JC Koella, BR Levin, GP GarnettOxford surveys in evolutionary biology 9 (1), 383-38381993
Binding of perforin to membranes is sensitive to lipid spacing and not headgroupR Antia, RA Schlegel, P WilliamsonImmunology letters 32 (2), 153-157401992
The organization of lipids in membranes and the binding of perforin to membranes.R Antia11992
A quantitative model suggests immune memory involves the colocalization of B and Th cellsR Antia, B Levin, P WilliamsonJournal of theoretical biology 153 (3), 371-38481991
AIDS as a population-dynamic-evolutionary processBR Levin, R Antia, L SimonsenTrends in Ecology & Evolution 6 (8), 237-23911991
Mechanism of killing by virus-induced cytotoxic T lymphocytes elicited in vivoRM Welsh, WK Nishioka, R Antia, PL DundonJournal of virology 64 (8), 3726-3733351990
Maintenance of membrane phospholipid asymmetry Lipid‐cytoskeletal interactions or lipid pump?P Williamson, R Antia, RA SchlegelFEBS letters 219 (2), 316-320771987
Vaccine models predict rules for updating vaccines against evolving pathogens such as SARS-CoV-2 and influenza in the context of pre-existing immunityR Desikan, SL Linderman, CW Davis, VI Zarnitsyna, HR Ahmed, R AntiaFrontiers in Immunology, 5872
Immunological characteristics govern the changing severity of COVID-19 during the transition to endemicityJS Lavine, ON Bjornstad, R Antia
This content has been downloaded from IOPscience. Please scroll down to see the full text.M Thomas, R Schwartz, SP Stromberg, R Antia, I Nemenman, HW Engl, …
The dynamics of acute malaria infections. I. Effect of theR Antia, A Yates, JC de Roode
Sharing the burden: antigen transport and firebreaks inA Handel, A Yates, SS Pilyugin, R Antia
Supplementary Information forS Baral, R Antia, NM Dixit
PLOS Pathogens would like to thank all those who reviewed on behalf of the journal in 2014: Pierre Abad Derek Abbott Kristina AbelE Abel-Santos, L Abi-Rached, M Abreu, H Ackerman, M Ackerman, …
Supplementary Material for “On the role of CD8 T cells in the control of persistent infections,” bySP Stromberg, R Antia
A. Personal statementR Antiamemory 5, 101-111
A Novel SIRC Model for Horizontal and Vertical LCMV TransmissionSA Holechek, J McKay, CA Bruce, LM Nieves, VP Guzman, C Contreras, …
Cognitive Ethology, edited by CA Ristau 196 Bell, MA, Review of Evolutionary Palaeobiology ofJ Fowler, L Cohen, T Alerstam, JA Allen, R Knill, ER Alvarez-Buylla, …
Linda JS AllenR Antia, SM Baer, C Blomberg, S Bonhoeffer, R Butera, M Chaplain, …
Co-Chief EditorsLJS Allen, R Antia, SM Baer, C Blomberg, R Butera, M Chaplain, J Chave, …
EPIDEMICSR Antia, RJ de Boer, D Burke, J Edmunds, GP Garnett, WM Getz, …
Neil FergusonR Antia, PY Boelle, RJ de Boer, S Bonhoeffer, D Burke, J Edmunds, …
Homeostatic turnover of virus-specific memory CD8 T cells occurs stochastically and is independent of CD4 T cell helpAR Choo DK, Murali-Krishna K, Anita Rjournal of immunology 185, 3436-44.62*
Population-Expression DynamicsSP Stromberg, R Antia, I Nemenman
Resistance to Antimicrobial Chemotherapy: A Prescription for Research and ActionL BR, R ANTIA, E BERLINER, P BLOLAND, S BONHOEFFER, M COHEN