D. Topham

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Antigenic and immunogenic properties of recombinant hemagglutinin proteins from H1N1 A/Brisbane/59/07 and B/Florida/04/06 when produced in various protein expression systems.

J. Treanor, F. Santiago, Kris Lambert Emo, 2012, Vaccine.

Recombinant HA-based vaccine outperforms split and subunit vaccines in elicitation of influenza-specific CD4 T cells and CD4 T cell-dependent antibody responses in humans

J. Treanor, T. Fitzgerald, D. Topham, 2020, npj Vaccines.

Antigen-specific and non-specific CD4+ T cell recruitment and proliferation during influenza infection.

M. Castrucci, L. Bradley, D. Topham, 2005, Virology.

Immunity to Influenza Infection in Humans.

D. Topham, A. Sant, M. DeDiego, 2019, Cold Spring Harbor perspectives in medicine.

An Early CD4+ T Cell–dependent Immunoglobulin A Response to Influenza Infection in the Absence of Key Cognate T–B Interactions

P. Doherty, J. Riberdy, N. Baumgarth, 2003, The Journal of experimental medicine.

Quantifying Immune Response to Influenza Virus Infection via Multivariate Nonlinear ODE Models with Partially Observed State Variables and Time-Varying Parameters

Hulin Wu, M. Zand, Hongqi Xue, 2015, Statistics in biosciences.

Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection

E. Walsh, A. Falsey, T. Mariani, 2020, bioRxiv.

Coordinated Postnatal Trajectories of T Cells and Microbiota in Preterm and Full-term Newborns

Kristin M. Scheible, A. Falsey, S. Gill, 2019 .

Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study

E. Walsh, A. Falsey, T. Mariani, 2019, JMIR research protocols.

Newborn T Cell and Microbiota Developmental Trajectories and Their Inter-related Roles in Health and Disease

Kristin M. Scheible, A. Falsey, S. Gill, 2019 .

Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy

Kristin M. Scheible, A. Falsey, S. Gill, 2019, iScience.

Simulation and Prediction of the Adaptive Immune Response to Influenza A Virus Infection

A. Perelson, T. Mosmann, J. Holden-Wiltse, 2009, Journal of Virology.

Stat5 activation is uniquely associated with cytokine signaling in peripheral T cells.

J. Ihle, R. Moriggl, V. Sexl, 1999, Immunity.

Monoclonal Antibody Responses after Recombinant Hemagglutinin Vaccine versus Subunit Inactivated Influenza Virus Vaccine: a Comparative Study

Karlynn E. Neu, Irvin Ho, Min Huang, 2019, Journal of Virology.

Platelets Present Antigen in the Context of MHC Class I

W. Baldwin, Lesley M. Chapman, D. Topham, 2012, The Journal of Immunology.

Direct Ex Vivo Analyses of HLA-DR1 Transgenic Mice Reveal an Exceptionally Broad Pattern of Immunodominance in the Primary HLA-DR1-Restricted CD4 T-Cell Response to Influenza Virus Hemagglutinin

Francisco A. Chaves, Christopher A. Lazarski, D. Topham, 2007, Journal of Virology.

The α1β1 Integrin and TNF Receptor II Protect Airway CD8+ Effector T Cells from Apoptosis during Influenza Infection1

M. Richter, D. Topham, 2007, The Journal of Immunology.

Live attenuated H7N7 influenza vaccine primes for a vigorous antibody response to inactivated H7N7 influenza vaccine.

K. Subbarao, J. Treanor, J. Katz, 2014, Vaccine.

Some equivalence relationships of regularized regressions

Xing Qiu, A. Falsey, J. Thakar, 2018, Mathematics for Application.

Highly Efficient Hypothesis Testing Methods for Regression-type Tests with Correlated Observations and Heterogeneous Variance Structure

Xing Qiu, A. Falsey, Gautam Bandyopadhyay, 2019, bioRxiv.

Gain-of-Function Experiments on H7N9

Y. Guan, R. Webster, R. Webby, 2013, Science.

T cell and chemokine receptors differentially control CD8 T cell motility behavior in the infected airways immediately before and after virus clearance in a primary infection

Hongmei Yang, D. Topham, K. Emo, 2020, PloS one.

Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein

R. Scheuermann, E. Walsh, A. Falsey, 2020, Vaccine: X.

Activation of the aryl hydrocarbon receptor during development enhances the pulmonary CD4+ T-cell response to viral infection.

M. Pavelka, D. Topham, Bethany N Winans, 2015, American journal of physiology. Lung cellular and molecular physiology.

In situ neutrophil efferocytosis shapes T cell immunity to influenza infection

D. Topham, Minsoo Kim, Kihong Lim, 2020, Nature Immunology.

Effect of prior vaccination on carriage rates of Streptococcus pneumoniae in older adults: A longitudinal surveillance study.

A. Falsey, Hongmei Yang, J. Holden-Wiltse, 2018, Vaccine.

Neonatal gut and respiratory microbiota: coordinated development through time and space

Kristin M. Scheible, A. Falsey, S. Gill, 2018, bioRxiv.

Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates

J. Thakar, D. Topham, M. DeDiego, 2016, PloS one.

Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness

S. Bhattacharya, E. Walsh, A. Falsey, 2017, Scientific Reports.

Interferon-Induced Protein 44 Interacts with Cellular FK506-Binding Protein 5, Negatively Regulates Host Antiviral Responses, and Supports Virus Replication

D. Topham, M. DeDiego, A. Nogales, 2019, mBio.

Novel Functions of IFI44L as a Feedback Regulator of Host Antiviral Responses

D. Topham, M. DeDiego, L. Martínez-Sobrido, 2019, Journal of Virology.

Developmentally determined reduction in CD31 during gestation is associated with CD8+ T cell effector differentiation in preterm infants.

Kristin M. Scheible, T. Mariani, Hongmei Yang, 2015, Clinical immunology.

An improved method for estimating antibody titers in microneutralization assay using green fluorescent protein

Steven F. Baker, Hongmei Yang, J. Holden-Wiltse, 2016, Journal of biopharmaceutical statistics.

CD4 T Cell Epitope Specificity and Cytokine Potential Are Preserved as Cells Transition from the Lung Vasculature to Lung Tissue following Influenza Virus Infection

Jim Miller, D. Topham, A. Sant, 2018, Journal of Virology.

Role of Memory B Cells in Hemagglutinin-Specific Antibody Production Following Human Influenza A Virus Infection

D. Topham, M. Sangster, P. Nguyen, 2019, Pathogens.

Broad Hemagglutinin-Specific Memory B Cell Expansion by Seasonal Influenza Virus Infection Reflects Early-Life Imprinting and Adaptation to the Infecting Virus

Francisco A. Chaves, R. Ahmed, Hongmei Yang, 2019, Journal of Virology.

Pandemic influenza vaccines: what they have taught us about B cell immunology.

D. Topham, M. Sangster, P. Nguyen, 2018, Current opinion in immunology.

B Cell Response and Hemagglutinin Stalk-Reactive Antibody Production in Different Age Cohorts following 2009 H1N1 Influenza Virus Vaccination

K. Subbarao, N. Ilyushina, A. Henn, 2013, Clinical and Vaccine Immunology.

Stability of T cell phenotype and functional assays following heparinized umbilical cord blood collection

Kristin M. Scheible, T. Mariani, G. Pryhuber, 2012, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

Modeling the Dynamics and Migratory Pathways of Virus-Specific Antibody-Secreting Cell Populations in Primary Influenza Infection

Alan S. Perelson, Hulin Wu, Martin S. Zand, 2014, PloS one.

Statistical Estimation & Inference of Cell Counts from ELISPOT Limiting Dilution Assays

Hongmei Yang, J. Holden-Wiltse, Hulin Wu, 2013, Journal of biopharmaceutical statistics.

Squalene-Based Influenza Vaccine Adjuvants and Their Impact on the Hemagglutinin-Specific B Cell Response

D. Topham, M. Sangster, Phuong Nguyen-Contant, 2021, Pathogens.

Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season.

Seth J. Zost, S. Hensley, S. Cobey, 2019, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Kupffer cell heterogeneity: functional properties of bone marrow derived and sessile hepatic macrophages.

R. Pierce, B. John, D. Topham, 2007, Blood.

Gaps in Serologic Immunity against Contemporary Swine-Origin Influenza A Viruses among Healthy Individuals in the United States

J. Treanor, A. Bowman, T. Fitzgerald, 2021, Viruses.

Vaccination with drifted variants of avian H5 hemagglutinin protein elicits a broadened antibody response that is protective against challenge with homologous or drifted live H5 influenza virus.

J. Treanor, F. Santiago, T. Fitzgerald, 2011, Vaccine.

Immune responses to vaccinia and influenza elicited during primary versus recent or distant secondary smallpox vaccination of adults.

Hua Liang, Hulin Wu, J. Treanor, 2006, Vaccine.

Identification of a Unique Population of Tissue-Memory CD4+ T Cells in the Airways after Influenza Infection That Is Dependent on the Integrin VLA-1

D. Topham, T. Chapman, 2010, The Journal of Immunology.

Collagen Distribution and Expression of Collagen-Binding

Jonathan A. Rebhahn, D. Topham, T. Mosmann, 2007 .

PA28 and the proteasome immunosubunits play a central and independent role in the production of MHC class I‐binding peptides in vivo

P. Kloetzel, T. Chiba, D. Topham, 2011, European journal of immunology.

Discordant rearrangement of primary and anamnestic CD8+ T cell responses to influenza A viral epitopes upon exposure to bacterial superantigens: Implications for prophylactic vaccination, heterosubtypic immunity and superinfections

J. Bennink, S. Haeryfar, J. McCormick, 2020, PLoS pathogens.

Pre-existing virus-specific CD 8 + T-cells provide protection against 1 pneumovirus-induced disease in mice 2 3

D. Busch, A. Easton, D. Topham, 2013 .

Pre-existing virus-specific CD8+ T-cells provide protection against pneumovirus-induced disease in mice

D. Busch, A. Easton, D. Topham, 2012, Vaccine.

Ibuprofen and other widely used non-steroidal anti-inflammatory drugs inhibit antibody production in human cells.

D. Topham, R. Phipps, S. Bancoş, 2009, Cellular immunology.

This information is current as the Spleen Is a Major Source of Effectors during the Primary Response Indicates that T Cells + Modeling of Influenza-Specific CD 8 Zand and

A. Perelson, T. Mosmann, J. Holden-Wiltse, 2011 .

High-Af fi nity H 7 Head and Stalk Domain – Speci fi c Antibody Responses to an Inactivated In fl uenza H 7 N 7 Vaccine After Priming With Live Attenuated In fl uenza Vaccine

Steven F. Baker, K. Subbarao, Hongmei Yang, 2015 .

High-Affinity H7 Head and Stalk Domain-Specific Antibody Responses to an Inactivated Influenza H7N7 Vaccine After Priming With Live Attenuated Influenza Vaccine.

Steven F. Baker, K. Subbarao, Hongmei Yang, 2015, The Journal of infectious diseases.

Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy

Kristin M. Scheible, A. Falsey, S. Gill, 2019, iScience.

Newborn T Cell and Microbiota Developmental Trajectories and Their Inter-related Roles in Health and Disease

Kristin M. Scheible, A. Falsey, S. Gill, 2019, bioRxiv.

Formation and Expansion of Memory B Cells against Coronavirus in Acutely Infected COVID-19 Individuals

Francisco A. Chaves, M. Zand, T. Fitzgerald, 2022, Pathogens.

Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients

Michael R. Bryan, Daniel J. Steiner, D. Topham, 2020, bioRxiv.

The Bone Marrow Functions as the Central Site of Proliferation for Long-Lived NK Cells

D. Topham, C. Boog, D. Zaiss, 2012, The Journal of Immunology.

Chronic inhibition of cyclooxygenase-2 attenuates antibody responses against vaccinia infection.

J. Treanor, R. Rose, D. Topham, 2010, Vaccine.

Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies

David J. Topham, George Georgiou, Karlynn E. Neu, 2018, Cell.

Androgen receptor signaling in the lungs mitigates inflammation and improves the outcome of influenza in mice

S. Klein, S. Dhakal, D. Topham, 2020, PLoS pathogens.

Mixed Lineage Kinase 3 deficiency delays viral clearance in the lung and is associated with diminished influenza-induced cytopathic effect in infected cells.

S. Dewhurst, P. Sime, D. Topham, 2010, Virology.

Inflammation-induced effector CD 4 + T cell interstitial migration is alpha-v integrin dependent

M. Meier-Schellersheim, A. Lacy-Hulbert, D. Topham, 2013 .

Endogenous 4-1BB Ligand Plays a Critical Role in Protection from Influenza-Induced Disease1

T. Watts, T. Moraes, D. Topham, 2009, The Journal of Immunology.

Endogenous 4-1BB ligand plays a critical role in protection from influenza-induced disease

T. Watts, D. Topham, G. Lin, 2009, The Journal of Immunology.

B-Cell Responses to Intramuscular Administration of a Bivalent Virus-Like Particle Human Norovirus Vaccine

M. Estes, J. Treanor, D. Topham, 2017, Clinical and Vaccine Immunology.

Cutting Edge: CD4 T Cells Generated from Encounter with Seasonal Influenza Viruses and Vaccines Have Broad Protein Specificity and Can Directly Recognize Naturally Generated Epitopes Derived from the Live Pandemic H1N1 Virus

Francisco A. Chaves, D. Topham, Francisco Chaves, 2010, The Journal of Immunology.

Interleukin-22 (IL-22) Production by Pulmonary Natural Killer Cells and the Potential Role of IL-22 during Primary Influenza Virus Infection

D. Topham, Hailong Guo, 2010, Journal of Virology.

Tissue-Resident Memory CD8+ T Cells: From Phenotype to Function

D. Topham, Emma C. Reilly, 2018, Front. Immunol..

Quantitative analysis of the influenza virus-specific CD4+ T cell memory in the absence of B cells and Ig.

P. Doherty, R. Tripp, D. Topham, 1996, Journal of immunology.

CD4+ T Cell Effects on CD8+ T Cell Location Defined Using Bioluminescence

M. Azadniv, W. Bowers, D. Topham, 2011, PloS one.

Memory CD8 T Cells Require CD28 Costimulation

S. Jennings, D. Topham, P. Katsikis, 2007 .

Simulation and Prediction of the Adaptive Immune Response to Inﬂuenza A Virus Infection (cid:1)

A. Perelson, X. Jin, T. Mosmann, 2009 .

Early Intrahepatic Accumulation of CD8+ T Cells Provides a Source of Effectors for Nonhepatic Immune Responses1

M. Richter, D. Topham, D. Zaiss, 2007, The Journal of Immunology.

Generation of T Cell Help through a MHC Class I-Restricted TCR1

T. Schumacher, D. Topham, H. Kessels, 2006, The Journal of Immunology.

Kupffer cell-dependent hepatitis occurs during influenza infection.

R. Pierce, J. Treanor, D. Topham, 2006, The American journal of pathology.

Class I-Restricted TCR Generation of T Cell Help through a MHC Boom

T. Schumacher, D. Topham, H. Kessels, 2006 .

Prevalence and activation phenotype of Sendai virus-specific CD4+ T cells.

P. Doherty, D. Topham, C. Ewing, 1995, Virology.

The alpha1beta1 integrin and TNF receptor II protect airway CD8+ effector T cells from apoptosis during influenza infection.

M. Richter, D. Topham, 2007, Journal of immunology.

Cells, Whereas Infections Induce More IFN- IL-2-Secreting Human and Mouse CD4 T Protein Vaccines Induce Uncommitted

T. Mosmann, D. Topham, A. Divekar, 2013 .

Protein Vaccines Induce Uncommitted IL-2-Secreting Human and Mouse CD4 T Cells, Whereas Infections Induce More IFN-γ-Secreting Cells1

T. Mosmann, D. Topham, A. Divekar, 2006, The Journal of Immunology.

Whereas Infections Induce More IFN-IL-2-Secreting Human and Mouse CD 4 T Protein Vaccines Induce Uncommitted

T. Mosmann, D. Topham, A. Divekar, 2006 .

T-Cell Responses in Adults During Natural Respiratory Syncytial Virus Infection

E. Walsh, A. Falsey, Hongmei Yang, 2018, The Journal of infectious diseases.

Response and Hemagglutinin Stalk-Reactive Antibody Production in Different Age Cohorts following 2009 H 1 N 1 Influenza Virus Vaccination

N. Ilyushina, A. Henn, Hongmei Yang, 2018 .

Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants

E. Walsh, A. Falsey, T. Mariani, 2017, The Journal of infectious diseases.

Mouse lung Tissue Resident Memory ( TRM ) CD 8 T cell subsets have distinct metabolic 2 profiles from each other and from non-TRM 3 4

D. Topham, A. Geber, K. Emo, 2022 .

Association of Human Milk Antibody Induction, Persistence, and Neutralizing Capacity With SARS-CoV-2 Infection vs mRNA Vaccination.

K. Järvinen, A. Nowak‐Wegrzyn, T. Fitzgerald, 2021, JAMA pediatrics.

Formation and Maintenance of Tissue Resident Memory CD8+ T Cells after Viral Infection

D. Topham, K. Emo, Emma C. Reilly, 2019, Pathogens.

Measuring the Severity of Respiratory Illness in the First 2 Years of Life in Preterm and Term Infants

Kristin M. Scheible, A. Falsey, S. Gill, 2019, The Journal of Pediatrics.

The collagen binding alpha1beta1 integrin VLA-1 regulates CD8 T cell-mediated immune protection against heterologous influenza infection.

P. Doherty, R. Pierce, V. Koteliansky, 2004, Immunity.

A Live Attenuated Influenza Vaccine Elicits Enhanced Heterologous Protection When the Internal Genes of the Vaccine Are Matched to Those of the Challenge Virus

S. Dewhurst, D. Topham, A. Nogales, 2019, Journal of Virology.

Visualization of integrin Mac-1 in vivo.

D. Topham, Minsoo Kim, Young-Min Hyun, 2015, Journal of immunological methods.

Indirect role of T cells in development of polioencephalitis and encephalomyelitis induced by encephalomyocarditis virus

M. Shenoy, D. Topham, J. Craighead, 1991, Journal of virology.

Memory CD8+ T Cells Require CD28 Costimulation1

J. Altman, S. Jennings, D. Topham, 2007, The Journal of Immunology.

Treatment of encephalomyocarditis virus-induced central nervous system demyelination with monoclonal anti-T-cell antibodies

M. Rodriguez, D. Topham, S. Sriram, 1989, Journal of virology.

Robust mucosal-homing antibody-secreting B cell responses induced by intramuscular administration of adjuvanted bivalent human norovirus-like particle vaccine.

J. Treanor, Wilbur H. Chen, D. Topham, 2015, Vaccine.

TRM integrins CD103 and CD49a differentially support adherence and motility after resolution of influenza virus infection

Nicholas S. Reilly, Francisco A. Chaves, Patrick W. Oakes, 2020, Proceedings of the National Academy of Sciences.

The Effects of Acute Neutrophil Depletion on Resolution of Acute Influenza Infection, Establishment of Tissue Resident Memory (TRM), and Heterosubtypic Immunity

D. Topham, Emma C. Reilly, Kris Lambert-Emo, 2016, PloS one.

TGF-beta 2 decreases migration of lymphocytes in vitro and homing of cells into the central nervous system in vivo.

M. Hart, D. Topham, S. Sriram, 1995, Journal of immunology.

Bone marrow can function as a lymphoid organ during a primary immune response under conditions of disrupted lymphocyte trafficking.

P. Doherty, S. Watson, R. Tripp, 1997, Journal of immunology.

Vaccination with peptides from MHC class II beta chain hypervariable region causes allele-specific suppression of EAE

D. Topham, P. Lodge, S. Sriram, 1996, Journal of Neuroimmunology.

Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants

E. Walsh, A. Falsey, T. Mariani, 2021, BMC medical genomics.

Virus-Specific Antibody, Viral Load, and Disease Severity in Respiratory Syncytial Virus Infection

E. Walsh, A. Falsey, T. Mariani, 2018, The Journal of infectious diseases.

current as MHC Class I Platelets Present Antigen in the Context of

W. Baldwin, Lesley M. Chapman, D. Topham, 2012 .

Contrasting urban and rural lifestyles of memory CD8+ T cells.

D. Topham, I. N. Crispe, I. Crispe, 2003, Immunity.

A novel intracellular pool of LFA-1 is critical for asymmetric CD8+ T cell activation and differentiation

D. Topham, Minsoo Kim, Kihong Lim, 2017, The Journal of cell biology.

Intrahepatic Memory-T-cells dominate the immune response of naive recipients following mouse liver transplantation

D. Topham, I. N. Crispe, U. Steger, 2009 .

Multiple Distinct Forms of CD8+ T Cell Cross-Reactivity and Specificities Revealed after 2009 H1N1 Influenza A Virus Infection in Mice

D. Topham, Hailong Guo, 2012, PloS one.

In vivo administration of TNF-α prevents EMC-M virus induced viral encephalitis

M. Shenoy, D. Topham, J. Craighead, 1991 .

In vivo administration of TNF-alpha prevents EMC-M virus induced viral encephalitis.

M. Shenoy, D. Topham, J. Craighead, 1991, International immunology.

Haplotype-specific suppression of experimental allergic encephalomyelitis with anti-IA antibodies.

D. Topham, S. Sriram, L. Carroll, 1987, Journal of immunology.

Collagen distribution and expression of collagen-binding alpha1beta1 (VLA-1) and alpha2beta1 (VLA-2) integrins on CD4 and CD8 T cells during influenza infection.

Jonathan A. Rebhahn, T. Mosmann, M. Richter, 2007, Journal of immunology.

NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses

D. Topham, M. DeDiego, A. Nogales, 2016, Journal of Virology.

Broad cross-reactive IgG responses elicited by adjuvanted vaccination with recombinant influenza hemagglutinin (rHA) in ferrets and mice

O. Hyrien, M. Zand, J. Treanor, 2018, PloS one.

The Specialized Proresolving Mediator 17-HDHA Enhances the Antibody-Mediated Immune Response against Influenza Virus: A New Class of Adjuvant?

Steven F. Baker, C. Serhan, D. Topham, 2014, The Journal of Immunology.

New Class of Adjuvant ? Immune Response against Influenza Virus : A 17-HDHA Enhances the Antibody-Mediated The Specialized Proresolving Mediator

Steven F. Baker, C. Serhan, D. Topham, 2014 .

Characterization of SARS-CoV-2 RNA, Antibodies, and Neutralizing Capacity in Milk Produced by Women with COVID-19

K. Järvinen, T. Fitzgerald, D. Topham, 2021, mBio.

Assessing microstructures of the cornea with Gabor-domain optical coherence microscopy: pathway for corneal physiology and diseases.

Patrice Tankam, Cristina Canavesi, Jungeun Won, 2015, Optics letters.

T Cell-Mediated Protection against Lethal 2009 Pandemic H1N1 Influenza Virus Infection in a Mouse Model

F. Santiago, D. Topham, T. Takimoto, 2010, Journal of Virology.

The use of self-adjuvanting nanofiber vaccines to elicit high-affinity B cell responses to peptide antigens without inflammation.

Joel H Collier, Roger Sciammas, Huifang Han, 2013, Biomaterials.

Protection against Lethal Influenza with a Viral Mimic

Steven F. Baker, R. Albrecht, A. García-Sastre, 2013, Journal of Virology.

CD8+ T cells clear influenza virus by perforin or Fas-dependent processes.

P. Doherty, R. Tripp, D. Topham, 1997, Journal of immunology.

Stat5 is required for IL-2-induced cell cycle progression of peripheral T cells.

J. Ihle, R. Moriggl, G. Grosveld, 1999, Immunity.

Thymic lymphoproliferative disease after successful correction of CD40 ligand deficiency by gene transfer in mice

P. Doherty, M. Brown, D. Topham, 1998, Nature Medicine.

415. Airway Gene-Expression Classifiers for Respiratory Syncytial Virus (RSV) Disease Severity in Infants

E. Walsh, A. Falsey, T. Mariani, 2019, BMC Medical Genomics.

Neonatal gut and respiratory microbiota: coordinated development through time and space

Kristin M. Scheible, A. Falsey, S. Gill, 2018, Microbiome.

Jak2 Is Essential for Signaling through a Variety of Cytokine Receptors

J. Marine, J. Ihle, D. Stravopodis, 1998, Cell.

Host transcriptional analysis to improve the diagnosis of group A streptococcal pharyngitis

S. Bhattacharya, A. Falsey, T. Mariani, 2020, medRxiv.

Induction of CD8 T Cell Heterologous Protection by a Single Dose of Single-Cycle Infectious Influenza Virus

Steven F. Baker, D. Topham, L. Martínez-Sobrido, 2014, Journal of Virology.

Induction of CD8 T Cell Heterologous Protection by a Single Dose of Single-cycle 1

Steven F. Baker, D. Topham, L. Martínez-Sobrido, 2014 .

Collagen Distribution and Expression of Collagen-Binding α1β1 (VLA-1) and α2β1 (VLA-2) Integrins on CD4 and CD8 T Cells during Influenza Infection1

Jonathan A. Rebhahn, T. Mosmann, M. Richter, 2007, The Journal of Immunology.

during Influenza Infection (VLA-2) Integrins on CD4 and CD8 T Cells 1 b 2 a (VLA-1) and 1 b 1 a Collagen-Binding Collagen Distribution and Expression of

Jonathan A. Rebhahn, T. Mosmann, M. Richter, 2007 .

Influenza A and B Virus Intertypic Reassortment through Compatible Viral Packaging Signals

Steven F. Baker, D. Pérez, D. Topham, 2014, Journal of Virology.

Antigenicity of the 2015–2016 seasonal H1N1 human influenza virus HA and NA proteins

A. M. Clark, Hongmei Yang, M. Zand, 2017, PloS one.

Influenza A Virus Attenuation by Codon Deoptimization of the NS Gene for Vaccine Development

Steven F. Baker, S. Dewhurst, D. Topham, 2014, Journal of Virology.

Clearance of an Influenza A Virus by CD4+ T Cells Is Inefficient in the Absence of B Cells

P. Doherty, D. Topham, 1998, Journal of Virology.

Immune CD4+ T cells promote the clearance of influenza virus from major histocompatibility complex class II -/- respiratory epithelium

P. Doherty, R. Tripp, D. Topham, 1996, Journal of virology.

The K186E Amino Acid Substitution in the Canine Influenza Virus H3N8 NS1 Protein Restores Its Ability To Inhibit Host Gene Expression

C. Parrish, P. Murcia, D. Topham, 2017, Journal of Virology.

A live-attenuated influenza vaccine for H3N2 canine influenza virus.

C. Parrish, P. Murcia, D. Topham, 2017, Virology.

Temperature-Sensitive Live-Attenuated Canine Influenza Virus H3N8 Vaccine

C. Parrish, P. Murcia, D. Topham, 2016, Journal of Virology.

The TLR9 Ligand CpG Promotes the Acquisition of Plasmodium falciparum-Specific Memory B Cells in Malaria-Naive Individuals1

Peter D. Crompton, J. Treanor, I. Sanz, 2009, The Journal of Immunology.

Functional Evolution of the 2009 Pandemic H1N1 Influenza Virus NS1 and PA in Humans

D. Topham, M. DeDiego, A. Nogales, 2018, Journal of Virology.

Functional Evolution of Influenza Virus NS1 Protein in Currently Circulating Human 2009 Pandemic H1N1 Viruses

A. M. Clark, D. Topham, M. DeDiego, 2017, Journal of Virology.

Neutrophil trails guide influenza-specific CD8+ T cells in the airways

Richard J. Miller, D. Topham, Minsoo Kim, 2015, Science.

Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals.

Henry A. Utset, K. Schmader, J. Wrammert, 2019, Cell host & microbe.

The Collagen Binding α1β1 Integrin VLA-1 Regulates CD8 T Cell-Mediated Immune Protection against Heterologous Influenza Infection

P. Doherty, R. Pierce, V. Koteliansky, 2004 .

Leukocyte trafficking to the lungs and beyond: lessons from influenza for COVID-19

R. Alon, A. Zarbock, D. Topham, 2020, Nature reviews. Immunology.

SOCS3 Is Essential in the Regulation of Fetal Liver Erythropoiesis

H. Pendeville, A. Yoshimura, J. Marine, 1999, Cell.

FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis

Yun Zhang, Xing Qiu, David J. Topham, 2017, Bioinform..

Lymphoid and extralymphoid CD4 T cells that orchestrate the antiviral immune response

M. Richter, D. Topham, T. Chapman, 2006, Expert review of clinical immunology.

Individuals-Specific Memory B Cells in Malaria-Naive Plasmodium falciparum Acquisition of The TLR 9 Ligand CpG Promotes the Martin and

Peter D. Crompton, J. Treanor, I. Sanz, 2009 .

Programming of Distinct Chemokine-Dependent and -Independent Search Strategies for Th1 and Th2 Cells Optimizes Function at Inflamed Sites.

Kevin K. Chiou, Jim Miller, D. Topham, 2019, Immunity.

Leukocyte trafficking to the lungs and beyond: lessons from influenza for COVID-19

R. Alon, A. Zarbock, D. Topham, 2020, Nature Reviews Immunology.

Modulation of Innate Immune Responses by the Influenza A NS1 and PA-X Proteins

D. Topham, M. DeDiego, A. Nogales, 2018, Viruses.

Analysis of Antigen‐Specific Human Memory B Cell Populations Based on In Vitro Polyclonal Stimulation

D. Topham, M. Sangster, Phuong Nguyen-Contant, 2020, Current protocols in immunology.

Frequencies of human influenza-specific antibody secreting cells or plasmablasts post vaccination from fresh and frozen peripheral blood mononuclear cells.

Hongmei Yang, M. Zand, D. Topham, 2009, Journal of immunological methods.

Modeling of Influenza-Specific CD8+ T Cells during the Primary Response Indicates that the Spleen Is a Major Source of Effectors

Hulin Wu, Hongyu Miao, Gabrielle T Belz, 2011, The Journal of Immunology.

Short term results of vaccination with adjuvanted recombinant varicella zoster glycoprotein E during initial BTK inhibitor therapy for CLL or lymphoplasmacytic lymphoma

J. Friedberg, M. Strawderman, D. Topham, 2020, Leukemia.

S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit

Francisco A. Chaves, Hongmei Yang, D. Topham, 2020, mBio.

Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection

E. Silverman, E. Walsh, A. Falsey, 2019, Scientific Reports.

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans

Alexandra J. Lee, R. Scheuermann, A. Falsey, 2015, Journal of Virology.

Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination.

T. Mosmann, A. Henn, Hulin Wu, 2012, Vaccine.

Interplay of PA-X and NS1 Proteins in Replication and Pathogenesis of a Temperature-Sensitive 2009 Pandemic H1N1 Influenza A Virus

D. Topham, M. DeDiego, A. Nogales, 2017, Journal of Virology.

NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses

D. Topham, M. DeDiego, A. Nogales, 2016, Journal of Virology.

SOCS1 Deficiency Causes a Lymphocyte-Dependent Perinatal Lethality

A. Yoshimura, J. Marine, J. Ihle, 1999, Cell.

Rearrangement of Influenza Virus Spliced Segments for the Development of Live-Attenuated Vaccines

D. Topham, M. DeDiego, A. Nogales, 2016, Journal of Virology.

Competitive detection of influenza neutralizing antibodies using a novel bivalent fluorescence-based microneutralization assay (BiFMA).

Steven F. Baker, F. Santiago, D. Topham, 2015, Vaccine.

Packaging Signals Reassortment through Compatible Viral Influenza A and B Virus Intertypic

Steven F. Baker, D. Pérez, D. Topham, 2014 .

Establishment and Persistence of Virus‐Specific CD4+ and CD8+ T Cell Memory

P. Doherty, R. Tripp, D. Topham, 1996, Immunological reviews.

Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus

Alan S. Perelson, Hulin Wu, Martin S. Zand, 2010, Journal of Virology.

Neonatal gut and respiratory microbiota: coordinated development through time and space

Kristin M. Scheible, A. Falsey, S. Gill, 2018, Microbiome.

Host Differences in Influenza-Specific CD4 T Cell and B Cell Responses Are Modulated by Viral Strain and Route of Immunization

R. Webby, Hongmei Yang, D. Topham, 2012, PloS one.

CD8+ T cell immunity to 2009 pandemic and seasonal H1N1 influenza viruses.

Kristin M. Scheible, M. Azadniv, J. Treanor, 2011, Vaccine.

COVID-19 and human milk: SARS-CoV-2, antibodies, and neutralizing capacity

K. Järvinen, T. Fitzgerald, D. Topham, 2020, medRxiv.

CD49a Identifies Polyfunctional Memory CD8 T Cell Subsets that Persist in the Lungs After Influenza Infection

Hongmei Yang, D. Topham, Nathan Laniewski, 2021, bioRxiv.

The Role of Antigen in the Localization of Naive, Acutely Activated, and Memory CD8+ T Cells to the Lung During Influenza Pneumonia1

M. Castrucci, P. Doherty, G. Belz, 2001, The Journal of Immunology.

Both Neutralizing and Non-Neutralizing Human H7N9 Influenza Vaccine-Induced Monoclonal Antibodies Confer Protection.

Caitlin E. Mullarkey, F. Ennis, K. Subbarao, 2016, Cell host & microbe.

Perforin and Fas in murine gammaherpesvirus-specific CD8(+) T cell control and morbidity.

P. Doherty, J. Christensen, G. Belz, 2001, The Journal of general virology.

Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure

Gautam Bandyopadhyay, Yun Zhang, Xing Qiu, 2019, bioRxiv.

A systems genomics approach uncovers molecular associates of RSV severity

E. Walsh, A. Falsey, T. Mariani, 2020, PLoS Comput. Biol..

Recombinant HA-based vaccine outperforms split and subunit vaccines in elicitation of influenza-specific CD4 T cells and CD4 T cell-dependent antibody responses in humans

Hongmei Yang, J. Treanor, T. Fitzgerald, 2020, npj Vaccines.

Characterizing Emerging Canine H3 Influenza Viruses

Gavin J. D. Smith, Guohua Yang, R. Webby, 2020, PLoS pathogens.

Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility

A. Monto, S. Hensley, E. Martin, 2020, Nature Communications.

Label-free, arrayed sensing of immune response to influenza antigens.

Charles R. Mace, T. Mosmann, J. Treanor, 2011, Talanta.

Quantifying Immune Response to Influenza Virus Infection via Multivariate Nonlinear ODE Models with Partially Observed State Variables and Time-Varying Parameters

Hulin Wu, M. Zand, Hongqi Xue, 2014, Statistics in Biosciences.

Inflammation-induced interstitial migration of effector CD4+ T cells is dependent on integrin αV

Minsoo Kim, Martin Meier-Schellersheim, Bastian R Angermann, 2013, Nature Immunology.

Recombinant human activated protein C inhibits integrin-mediated neutrophil migration.

A. Ayala, J. McGrath, G. Elphick, 2009, Blood.

Antigen and G-Protein Coupled Receptor signaling differentially control CD8 T cell motility immediately before and after virus clearance in a primary infection

D. Topham, Emma C. Reilly, M. Sportiello, 2019, bioRxiv.

Live Imaging of Influenza Infection of the Trachea Reveals Dynamic Regulation of CD8+ T Cell Motility by Antigen

S. Gerber, Kris Lambert Emo, D. Topham, 2016, PLoS pathogens.

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M. Meier-Schellersheim, A. Lacy-Hulbert, D. Topham, 2013 .

Comparative Study of the Temperature Sensitive, Cold Adapted and Attenuated Mutations Present in the Master Donor Viruses of the Two Commercial Human Live Attenuated Influenza Vaccines

Baek Kim, S. Dewhurst, D. Topham, 2019, Viruses.

Exposure to a National Communication Campaign to Prevent Stunting in Indonesia

D. Topham, C. Daines, S. Torres, 2020 .

Running Title: Mathematical Modeling for Influenza A Virus Infection 1 2 Title: Simulation and Prediction of the Adaptive Immune Response to Influenza A Virus 3 Infection 4

A. Perelson, T. Mosmann, J. Holden-Wiltse, 2009 .

Consequences of viral infections for lymphocyte compartmentalization and homeostasis.

P. Doherty, J. Riberdy, D. Topham, 1997, Seminars in immunology.

Novel Functions of IFI44L as a Feedback Regulator of Host Antiviral Responses

D. Topham, M. DeDiego, L. Martínez-Sobrido, 2019, Journal of Virology.

Heterovariant cross-reactive B-cell responses induced by the 2009 pandemic influenza virus A subtype H1N1 vaccine.

K. Subbarao, C. Dekker, S. Sasaki, 2013, The Journal of infectious diseases.

Rapid Reactivation of Extralymphoid CD4 T Cells during Secondary Infection

D. Topham, T. Chapman, K. Lambert, 2011, PloS one.

Eight practices for data management to enable team data science

David J. Topham, Gloria S. Pryhuber, Andrew McDavid, 2020, Journal of Clinical and Translational Science.

T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy.

Derick R. Peterson, Kristin M. Scheible, T. Mariani, 2018, JCI insight.

B cell responses to H5 influenza HA in human subjects vaccinated with a drifted variant.

Hongmei Yang, J. Holden-Wiltse, Hulin Wu, 2010, Vaccine.

Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies

M. Piepenbrink, T. Fitzgerald, D. Topham, 2023, Microbiology spectrum.

Cutting Edge : CD 4 T Cells Generated from Encounter with Seasonal Influenza Viruses and Vaccines Have Broad Protein Specificity and Can Directly Recognize Naturally Generated Epitopes Derived from the Live Pandemic H 1 N 1 Virus

Francisco A. Chaves, D. Topham, K. Richards, 2010 .

Crowd on a Chip: Label-Free Human Monoclonal Antibody Arrays for Serotyping Influenza.

P. Wilson, Hanyuan Zhang, D. Topham, 2018, Analytical chemistry.

Interference at Influenza Hemagglutinin Antigenic-Sites Determines Antibody Levels and Specificities after Repeat Vaccination

D. Topham, C. Anderson, 2021, bioRxiv.

Fluximplied: A novel approach integrates rate limiting steps and differential expression for pathway analysis

D. Topham, Nathan Laniewski, A. Geber, 2022, bioRxiv.

Title: Mouse Memory CD8 T cell subsets defined by Tissue Resident Memory (TRM) Integrin

D. Topham, A. Geber, K. Emo, 2023 .

Airway gene expression correlates of RSV disease severity and microbiome composition in infants.

E. Walsh, A. Falsey, T. Mariani, 2020, The Journal of infectious diseases.

Insufficiency in airway interferon activation defines clinical severity to infant RSV infection

E. Walsh, A. Falsey, T. Mariani, 2019, bioRxiv.

Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection

Christopher S. Anderson, David J. Topham, Juilee Thakar, 2016, Comput. Math. Methods Medicine.

A synthetic peptide from the third hypervariable region of major histocompatibility complex class II beta chain as a vaccine for treatment of experimental autoimmune encephalomyelitis.

D. Topham, S. Sriram, B. Nag, 1994, Proceedings of the National Academy of Sciences of the United States of America.

Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain

Christopher S. Anderson, David J. Topham, Marta L. DeDiego, 2017, Scientific Reports.

Gain-of-function experiments on H7N9.

Y. Guan, R. Webster, R. Webby, 2013, Science.

Serendipity: Reflections on Being Mentored by Dr. Peter Doherty

D. Topham, 2020, Viral immunology.

The negative effect of pre-existing immunity on influenza vaccine responses transcends the impact of vaccine formulation type and vaccination history.

Francisco A. Chaves, F. Krammer, D. Topham, 2022, The Journal of infectious diseases.

Directed selection of influenza virus produces antigenic variants that match circulating human virus isolates and escape from vaccine‐mediated immune protection

Hongmei Yang, J. Holden-Wiltse, J. Treanor, 2016, Immunology.

Publisher Correction: Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain

Francisco A. Chaves, A. M. Clark, Hongmei Yang, 2018, Scientific Reports.

Susceptibility to allergic lung disease regulated by recall responses of dual-receptor memory T cells.

M. Boothby, J. Sheller, D. Mitchell, 2004, The Journal of allergy and clinical immunology.

Longitudinal analysis of the acute Sendai virus-specific CD4+ T cell response and memory.

P. Doherty, D. Topham, David J. Topham, 1998, Journal of immunology.

Memory T Cell Response and + Virus-Specific CD 4 Longitudinal Analysis of the Acute Sendai

P. Doherty, D. Topham, 1998 .

Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study (Preprint)

E. Walsh, A. Falsey, T. Mariani, 2018 .

Genetic Variation and Disease Severity of Respiratory Syncytial Viruses

R. Scheuermann, E. Walsh, T. Mariani, 2022, bioRxiv.

Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation

Harry A. Stern, Hongmei Yang, Christopher S. Anderson, 2018, BMC Bioinformatics.

Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain

Francisco A. Chaves, A. M. Clark, Hongmei Yang, 2017, Scientific Reports.

Optical Detection of Single Nanoparticles and Viruses

L. Novotny, D. Topham, L. Novotný, 2006, IEEE Journal of Selected Topics in Quantum Electronics.

Directed selection of amino acid changes in the influenza hemagglutinin and neuraminidase affecting protein antigenicity.

D. Topham, M. DeDiego, Kevin Chiem, 2018, Vaccine.

Maximum Likelihood Estimation of Titer via a Power Family of Four-Parameter Logistic Model

Hongmei Yang, J. Holden-Wiltse, J. Treanor, 2018, Journal of biopharmaceutical statistics.

Use of Host Response to Refine the Diagnosis of Group A Streptococcal Pharyngitis.

S. Bhattacharya, A. Falsey, T. Mariani, 2022, Journal of the Pediatric Infectious Diseases Society.

Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure

A. Falsey, D. Topham, Yun Zhang, 2019, BMC Bioinformatics.

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans

Alexandra J. Lee, R. Scheuermann, A. Falsey, 2015, Journal of Virology.

Inflammation-induced effector CD4+ T cell interstitial migration is alpha-v integrin dependent

M. Meier-Schellersheim, A. Lacy-Hulbert, D. Topham, 2013, Nature Immunology.

NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses

D. Topham, M. DeDiego, L. Martínez-Sobrido, 2016, Journal of Virology.

Implementing sequence-based antigenic distance calculation into immunological shape space model

T. Mariani, Hongmei Yang, D. Topham, 2020, BMC Bioinformatics.

PA28 and the proteasome immunosubunits play a central and independent role in the production of MHC class I‐binding peptides in vivo

P. Kloetzel, T. Chiba, D. Topham, 2011, European journal of immunology.

Modeling of Influenza-Specific CD8+ T Cells during the Primary Response Indicates that the Spleen Is a Major Source of Effectors

A. Perelson, T. Mosmann, J. Holden-Wiltse, 2011, The Journal of Immunology.

Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus

A. Perelson, T. Mosmann, J. Holden-Wiltse, 2010, Journal of Virology.

Statistical Estimation & Inference of Cell Counts from ELISPOT Limiting Dilution Assays

Hongmei Yang, J. Holden-Wiltse, Hulin Wu, 2013, Journal of biopharmaceutical statistics.

Association of disease severity and genetic variation during primary Respiratory Syncytial Virus infections

D. Topham, A. Corbett, M. Caserta, 2024, BMC medical genomics.

Computer Simulations of the Humoral Immune System Reveal How Imprinting Can Affect Responses to Influenza HA Stalk with Implications for the Design of Universal Vaccines

Hongmei Yang, D. Topham, M. Sangster, 2018, bioRxiv.