Publications from the Institute for Immunology and Informatics faculty at the University of Rhode Island.

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Submissions from 2016

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Dengue vaccine: the need, the challenges and progress, Alan L. Rothman and Francis A. Ennis

Submissions from 2015

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Sequential Dengue Virus Infections Detected in Active and Passive Surveillance Programs in Thailand, 1994–2010, Piraya Bhoomiboonchoo, Ananda Nisalak, Natkamol Chansatiporn, In-Kyu Yoon, Siripen Kalayanarooj, Mathuros Thipayamongkolgul, Timothy Endy, Alan L. Rothman, Sharone Green, Anon Srikiatkhachorn, Darunee Buddhari, Mammen P. Mammen, and Robert V. Gibbons

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Structure-Based Redesign of Lysostaphin Yields Potent Antistaphylococcal Enzymes that Evade Immune Cell Surveillance, Kristina Blazanovic, Hongliang Zhao, Yoonjoo Choi, Wen Li, Regina S. Salvat, Daniel C. Osipovitch, Jennifer Fields, Leonard Moise, Brett L. Berwin, Steven N. Fiering, Chris Bailey-Kellogg, and Karl E. Griswold

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C3d adjuvant effects are mediated through the activation of C3d-specific autoreactive T cells, Anne S. De Groot, Ted M. Ross, Lauren Levitz, Timothy J. Messitt, Ryan Tassone, Christine M. Boyle, Amber J. Vincelli, Leonard Moise, William Martin, and Paul M. Knopf

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An immunoinformatic approach for identification of Trypanosoma cruzi HLA-A2-restricted CD8+ T cell epitopes, Christopher S. Eickhoff, Daniel Van Aartsen, Francis E. Terry, Sheba K. Meymandi, Mahmoud M. Traina, Salvador Hernandez, William D. Martin, Leonard Moise, Anne S. De Groot, and Daniel F. Hoft

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Development and Validation of an Epitope Prediction Tool for Swine (PigMatrix) Based on the Pocket Profile Method, Andres H. Gutiérrez, William D. Martin, Chris Bailey-Kellogg, Frances Terry, Leonard Moise, and Anne S. De Groot

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Preclinical development of HIvax: human survivin Highly Immunogenic vaccines, Peter R. Hoffmann, Maddalena Panigada, Elisa Soprana, Francis Terry, Ivo Sah Bandar, Andrea Napolitano, Aaron H. Rose, Fukun W. Hoffmann, Lishomwa C. Ndhlovu, Mahdi Belcaid, Lenny Moise, Anne S. De Groot, Michele Carbone, Giovanni Gaudino, Takashi Matsui, Antonio Siccardi, and Pietro Bertino

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8th vaccine renaissance: A creative nexus for vaccine developers, Heather Johnson, Lenny Moise, Austin Menge, Sarah Beseme, and Anne S. De Groot

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Evaluation of Cardiac Involvement in Children with Dengue by Serial Echocardiographic Studies, Tawatchai Kirawittaya, In-Kyu Yoon, Sineewanlaya Wichit, Sharone Green, Francis A. Ennis, Robert V. Gibbons, Stephen J. Thomas, Alan L. Rothman, Siripen Kalayanarooj, and Anon Srikiatkhachorn

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H7N9 T-cell epitopes that mimic human sequences are less immunogenic and may induce Treg-mediated tolerance, Rui Liu, Leonard Moise, Ryan Tassone, Andres H. Gutierrez, Francis E. Terry, Kotou Sangare, Matthew T. Ardito, William D. Martin, and Anne S. De Groot

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A plasmid-based reporter system for live cell imaging of dengue infected cells, Carey L. Medin, Sierra Valois, Chinmay G. Patkar, and Alan Rothman

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T Cell Epitope Redundancy: Cross-conservation of the TCR face between Pathogens and Self and its Implications for Vaccines and Auto-immunity, Leonard Moise, Sarah Beseme, Ryan Tassone, Rui Liu, Farzana Kibria, Francis Terry, William Martin, and Anne S. De Groot

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iVax: An integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines, Leonard Moise, Andres H. Gutierrez, Farzana Kibria, Rebecca Martin, Ryan Tassone, Rui Liu, Francis Terry, William Martin, and Anne S. De Groot

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Analysis of Cell-Mediated Immune Responses in Support of Dengue Vaccine Development Efforts, Alan L. Rothman, Jeffrey R. Currier, Heather L. Friberg, and Anuja Mathew

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Time for T? Immunoinformatics addresses the challenges of vaccine design for neglected tropical and emerging infectious diseases, Francis E. Terry, Leonard Moise, Rebecca Martin, Melissa Torres, Nils Pilotte, Steven Williams, and Anne S. De Groot

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Interaction of a dengue virus NS1-derived peptide with the inhibitory receptor KIR3DL1 on natural killer cells, Elizabeth Townsley, Geraldine O'Connor, Cormac Cosgrove, Marcia Woda, Mary Co, Stephen J. Thomas, Siripen Kalayanarooj, In-Kyu Yoon, Ananda Nisalak, Anon Srikiatkhachorn, Sharone Green, Henry A. F. Stephens, Emma Gostick, David A. Price, Mary Carrington, Galit Alter, Daniel W. McVicar, Alan L. Rothman, and Anuja Mathew

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HLA class I supertype associations with clinical outcome of secondary dengue virus infections in ethnic Thais, Sasijit Vejbaesya, Rungrot Thongpradit, Siripen Kalayanarooj, Komon Luangtrakool, Panpimon Luangtrakool, Robert V. Gibbons, Duangporn Srinak, Somporn Ngammthaworn, Kusuma Apisawes, In-Kyu Yoon, Stephen J. Thomas, Richard G. Jarman, Anon Srikiakthachorn, Sharone Green, Dasnayanee Chandanayingyong, Sangshin Park, Jennifer Friedman, Alan Rothman, and Henry A.F. Stephens

Submissions from 2014

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CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production, Chris Bailey-Kellogg, Andres H. Gutiérrez, Leonard Moise, Frances Terry, William D. Martin, and Anne S. De Groot

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The Spatial Dynamics of Dengue Virus in Kamphaeng Phet, Thailand, Piraya Bhoomiboonchoo, Robert V. Gibbons, Angkana Huang, In-Kyu Yoon, Darunee Buddhari, Ananda Nisalak, Natkamol Chansatiporn, Mathuros Thipayamongkolgul, Siripen Kalanarooj, Timothy Endy, Alan Rothman, Anon Srikiatkhachorn, Sharone Green, Mammen P. Mammen, Derek A. Cummings, and Henrik Salje

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Dengue Virus Neutralizing Antibody Levels Associated with Protection from Infection in Thai Cluster Studies, Darunee Buddhari, Jared Aldstadt, Timothy P. Endy, Anon Srikiatkhachorn, Butsaya Thaisomboonsuk, Chonticha Klungthong, Ananda Nisalak, Benjawan Khuntirat, Richard G. Jarman, Stefan Fernandez, Stephen J. Thomas, Thomas W. Scott, Alan Rothman, and In-Kyu Yoon

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Tregitope: Immunomodulation Powerhouse, Leslie Cousens, Nader Najafian, William D. Martin, and Anne S. De Groot

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Tuberculosis interferon-gamma responses in the breast milk of human immunodeficiency virus infected mothers, Lisa Cranmer, Mercy Kanyugo, Barbara Lohman-Payne, Ken Tapia, and Grace John-Stewart

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Cross-conservation of T-cell epitopes: Now even more relevant to (H7N9) influenza vaccine design, Anne S. De Groot, Lenny Moise, Rui Liu, Andres H. Gutierrez, Frances Terry, Ousmane A. Koita, Ted M. Ross, and William Martin

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Immune Camouflage: Relevance to Vaccine Design and Human Immunology, Anne S. De Groot, Leonard Moise, Rui Liu, Andres H. Gutierrez, Ryan Tassone, Chris Bailey-Kellogg, and William Martin

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Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage, Lu He, Anne S. DeGroot, Andres H. Gutierrez, William D. Martin, Lenny Moise, and Chris Bailey-Kellogg

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VaxCelerate II: Rapid development of a self-assembling vaccine for Lassa fever, Pierre Leblanc, Leonard Moise, Cybelle Luza, Kanawat Chantaralawan, Lynchy Lezeau, Jianping Yuan, Mary Field, Daniel Richer, Christine Boyle, William D. Martin, Jordan B. Fishman, Eric A. Berg, David Baker, Brandon Zeigler, Dale E. Mais, William Taylor, Russell Coleman, H. Shaw Warren, Jeffrey A. Gelfand, Anne S. De Groot, Timothy Brauns, and Mark C. Poznansky

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HCV Epitope, Homologous to Multiple Human Protein Sequences, Induces a Regulatory T Cell Response in Infected Patients, Phyllis T. Losikoff, Sasmita Mishra, Francis Terry, Andres Gutierrez, Matt T. Ardito, Loren Fast, Martha Nevola, William D. Martin, Chris Bailey-Kellogg, Anne S. De Groot, and Stephen H. Gregory

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Dendritic Cell-Mediated, DNA-Based Vaccination Against Hepatitis C Induces the Multi-Epitope-Specific Response of Humanized, HLA Transgenic Mice, Sasmita Mishra, Bianca J. Lavelle, Joe Desrosiers, Matt T. Ardito, Frances Terry, William D. Martin, Anne S. De Groot, and Stephen H. Gregory

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Peptide-Pulsed Dendritic Cells Induce the Hepatitis C Viral Epitope-Specific Responses of Naïve Human T Cells, Sasmita Mishra, Phyllis T. Losikoff, Alyssa A. Self, Frances Terry, Matthew T. Ardito, Ryan Tassone, William D. Martin, Anne S. De Groot, and Stephen H. Gregory

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Smarter Vaccine Design Will Circumvent Regulatory T Cell-Mediated Evasion in Chronic HIV and HCV Infection, Leonard Moise, Frances Terry, Andres H. Gutierrez, Ryan Tassone, Phyllis Losikoff, Stephen H. Gregory, Chris Bailey-Kellogg, William D. Martin, and Anne S. De Groot

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Partial pathogen protection by tick-bite sensitization and epitope recognition in peptide-immunized HLA DR3 transgenic mice, Wendy M. C. Shattuck, Megan C. Dyer, Joe Desrosiers, Loren D. Fast, Frances E. Terry, William D. Martin, Leonard Moise, Anne S. De Groot, and Thomas N. Mather

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Preliminary Evaluation of Near Infrared Spectroscopy as a Method to Detect Plasma Leakage in Children with Dengue Hemorrhagic Fever, Babs Soller, Anon Srikiatkachorn, Fengmei Zou, Alan Rothman, In-Kyu Yoon, Robert V. Gibbons, Siripen Kalayanarooj, Stephen J. Thomas, and Sharone Green

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Distinct Activation Phenotype of a Highly Conserved Novel HLA-B57-Restricted Epitope during Dengue Virus Infection, Elizabeth Townsley, Marcia Woda, Stephen J. Thomas, Siripen Kalayanarooj, Robert V. Gibbons, Ananda Nisalak, Anon Srikiatkhachorn, Sharone Green, Henry A.F. Stephens, Alan L. Rothman, and Anuja Matthew

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Human Immune Responses to H. pylori HLA Class II Epitopes Identified by Immunoinformatic Methods, Songhua Zhang, Joseph Desrosiers, Jose R. Aponte-Pieras, Kristen DaSilva, Loren D. Fast, Frances Terry, William D. Martin, Anne S. De Groot, Leonard Moise, and Steven F. Moss

Submissions from 2013

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Application of IgG-Derived Natural Treg Epitopes (IgG Tregitopes) to Antigen-Specific Tolerance Induction in a Murine Model of Type 1 Diabetes, Leslie P. Cousens, Yan Su, Elizabeth McClaine, Xin Li, Frances Terry, Robert Smith, Jinhee Lee, William Martin, David W. Scott, and Anne S. De Groot

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Do Tregitopes have the potential to impact the current treatment landscape of autoimmune diseases?, Anne S. De Groot

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Low immunogenicity predicted for emerging avian-origin H7N9, Anne S. De Groot, Matthew Ardito, Frances Terry, Lauren Levitz, Ted Ross, Leonard Moise, and William Martin

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Tregitope Peptides: The Active Pharmaceutical Ingredient of IVIG?, Anne S. De Groot, Leslie Cousens, Federico Mingozzi, and William Martin

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Making Vaccines "On Demand", Anne S. De Groot, Leo Einck, Leonard Moise, Michael Chambers, John Ballantyne, Robert W. Malone, Matthew Ardito, and William Martin

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Beyond humanization and de-immunization: tolerization as a method for reducing the immunogenicity of biologics, Anne S. De Groot, Frances Terry, Leslie Cousens, and William Martin

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Computational Vaccinology and the ICoVax 2012 Workshop, Yongqun He, Zhiwei Cao, Anne S. De Groot, Vladimir Brusic, Christian Schönbach, and Nikolai Petrovsky

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Modulation of CD8+ T cell responses to AAV vectors with IgG-derived MHC class II epitopes, Daniel J. Hui, Etiena Banser-Tschakarjan, Yifeng Chen, Robert J. Davidson, George Buchlis, Mustafa Yazicioglu, Gary C. Pien, Jonathan D. Finn, Virginia Haurigot, Alex Tai, David W. Scott, Leslie P. Cousens, Shangzhen Zhou, Anne S. De Groot, and Federico Mingozzi

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Epitope Recognition in HLA-DR3 Transgenic Mice Immunized to TSH-R Protein or Peptides, Hidefumi Inaba, Leonard Moise, William Martin, Anne S. De Groot, Joe Desrosiers, Ryan Tassone, George Buchman, Takashi Akamizu, and Leslie J. De Groot

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Immunogenicity of Therapeutic Fusion proteins: Contributory Factors and Clinical Experience, Vibha Jawa, Leslie Cousens, and Anne S. De Groot

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T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation, Vibha Jawa, Leslie P. Cousens, Michel Awwad, Eric Wakshull, Harald Kropshofer, and Anne S. De Groot

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The two-faced T cell epitope: Examining the host-microbe interface with JanusMatrix, Leonard Moise, Andres H. Gutierrez, Chris Bailey-Kellogg, Frances Terry, Qibin Leng, Karim M. Abdel Hady, Nathan C. VerBerkmoes, Marcelo B. Sztein, Phyllis T. Losikoff, William D. Martin, Alan L. Rotham, and Anne S. De Groot

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Building Better Biotherapeutics and Vaccines by Design: EpiVax, Inc., an Immunology Company, Leonard Moise, Anthony Marcello, Ryan Tassone, Leslie Cousens, William Martin, and Anne S. De Groot

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Universal H1N1 influenza vaccine development, Leonard Moise, Frances Terry, Matthew Ardito, Ryan Tassone, Howard Latimer, Christine Boyle, William D. Martin, and Anne S. De Groot

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Telomere Length Dynamics in Human Memory T Cells Specific for Viruses Causing Acute or Latent Infections, Joel M. O'Bryan, Marcia Woda, Mary Co, Anuja Mathew, and Alan L. Rothman

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A Cross-Sectional Study to Assess HPV Knowledge and HPV Vaccine Acceptability in Mali, Danielle N. Poole, J. Kathleen Tracy, Lauren Levitz, Mali Rochas, Kotou Sangare, Shahla Yekta, Karamoko Tounkara, Ben Aboubacar, Ousmane Koita, Mark Lurie, and Anne S. De Groot

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Frequent In-Migration and Highly Focal Transmission of Dengue Viruses Among Children in Kamphaeng Phet, Thailand, Maia A. Rabaa, Chonticha Klungthong, In-Kyu Yoon, Edward C. Holmes, Piyawan Chinnawirotpisan, Butsaya Thaisomboonsuk, Anon Srikiatkhachorn, Alan L. Rothman, Darunee Tannitisupawong, Jared Aldstadt, Ananda Nisalak, Mammen P. Mammen, Robert V. Gibbons, Timothy P. Endy, Thanyalak Fansiri, Thomas W. Scott, and Richard G. Jarman

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Immunopathogenesis versus protection in dengue virus infections, Alan L. Rothman, Carey L. Medin, Heather Friberg, and Jeffery R. Currier

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Report from the field - Overview of the Sixth Annual Vaccine Renaissance Conference, Denice Spero, Lauren Levitz, and Anne S. De Groot

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Regulatory T cell epitopes (Tregitopes) in IgG induce tolerance in vivo and lack immunogenicity per se, Yan Su, Robert Rossi, Anne S. De Groot, and David W. Scott

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Characteristics of Mild Dengue Virus Infection in Thai Children, In-Kyu Yoon, Anon Srikiatkhachorn, Laura Hermann, Darunee Buddhari, Thomas W. Scott, Richard G. Jarman, Jared Aldstadt, Ananda Nisalak, Suwich Thammapalo, Piraya Bhoomiboonchoo, Mammen P. Mammen, Sharone Green, Robert V. Gibbons, Timothy P. Endy, and Alan L. Rothman

Submissions from 2012

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Further Confirmation of Broadly Conserved, Highly Immunogenic Cross-Clade HIV CTL Epitopes for Inclusion in the GAIA HIV Vaccine, A. S. De Groot, L. Moise, O. Koita, K. Sangare, L. Levitz, J. Rozenhal, Z. Koty, K. Tounkara, M. Ardito, C. M. Boyle, M. Rochas, and W. Martin

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A Decade of Partnering to Stop HIV in West Africa: GAIA VF Prevention, Education, Access to Care and Vaccine Trial Site Development in Bamako, Mali, A. De Groot, K. Tounkara, B. Aboubacar, F. Siby Diallo, F. Bougoudogo, O. Koita, O. Koita, S. Dao, S. Diallo, Y. Traoré, L. Diarra, L. Diarra, G. Diarra, Y. Koné, R. Mali, and L. Steven

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Evaluating Short-Term Patient Outcomes after HIV Care Interventions in a Low Resource Setting: Preparing for an HIV Vaccine Trial Site in Bamako, Mali, Z. Koty, A. Bicki, Y. Koné, L. Diarra, K. Tounkara, F. Siby Diallo, L. Levitz, B. Aboubacar, M. Rochas, S. Dao, and A. De Groot

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Moving H. pylori Vaccine Development Forward with Bioinformatics and Immunomics, Leonard Moise, Steven F. Moss, and Anne S. De Groot

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Knowledge/Attitude/Practices of HPV & Cervical Cancer, Willingness to Participate in Vaccine Trial in Preparation for HIV & HPV Vaccine Trials in Mali, D. Poole, K. Tracy, L. Levitz, S. Yekta, E. Kossow, T. Huang, M. Rochas, K. Sangare, K. Tounkara, B. Aboubacar, O. Koita, F. Siby Diallo, S. Sow, I. Téguété, A. Dolo, F. Bougoudogo, M. Lurie, and A. S. De Groot

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Dengue Viral RNA Levels in Peripheral Blood Mononuclear Cells are Associated with Disease Severity and Preexisting Dengue Immune Status, Anon Srikiatkhachorn, Sineewanlaya Wichit, Robert V. Gibbons, Sharone Green, Daniel H. Libraty, Timothy P. Endy, Francis A. Ennis, Siripen Kalayanarooj, and Alan L. Rothman

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A Dominant EV71-Specific CD4+ T Cell Epitope is Highly Conserved Among Human Enteroviruses, Ruicheng Wei, Chunfu Yang, Mei Zeng, Frances Terry, Kai Zhu, Chunhui Yang, Ralf Altmeyer, William Martin, Anne S. De Groot, and Qibin Leng

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Fine Scale Spatiotemporal Clustering of Dengue Virus Transmission in Children and Aedes aegypti in Rural Thai Villages, In-Kyu Yoon, Arthur Getis, Jared Aldstadt, Alan L. Rothman, Darunee Tannitisupawong, Constantianus J.M. Koenraadt, Thanyalak Fansiri, James W. Jones, Amy C. Morrison, Richard G. Jarmen, Ananda Nisalak, Mammen P. Mammen Jr., Suwich Thammapalo, Anon Srikiatkhachorn, Sharone Green, Daniel H. Libraty, Robert V. Gibbons, Timothy Endy, Chusak Pimgate, and Thomas W. Scott

Submissions from 2011

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An Integrated Genomic and Immunoinformatic Approach to H. pylori Vaccine Design, Matthew Ardito, Joanna Fueyo, Ryan Tassone, Frances Terry, Kristin DaSilva, Songhua Zhang, William Martin, Anne S. De Groot, Steven F. Moss, and Leonard Moise

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Immunogenic Consensus Sequence T Helper Epitopes for a Pan-Burkholderia Biodefense Vaccine, Anne S. De Groot, Matthew Ardito, Leonard Moise, Eric A. Gustafson, Denice Spero, Gloria Tejada, and William Martin

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A Comparison of Two Methods for T Cell Epitope Mapping: “Cell Free” In Vitro Versus Immunoinformatics, Timothy J. Messitt, Frances Terry, Leonard Moise, William Martin, and Anne S. De Groot

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Extended Interferon-Alpha Therapy Accelerates Telomere Length Loss in Human Peripheral Blood T Lymphocytes, Joel M. O'Bryan, James A. Potts, Herbert L. Bonkovsky, Anuja Mathew, and Alan L. Rothman

Submissions from 2009

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P17-26. Effective Design of T-Cell Driven Vaccines Applied to the GAIA HIV Vaccine: Advances in Vaccine Design Based on Current Preclinical Success, A. S. De Groot, L. Moise, J. Desrosiers, C. Weber, and W. Martin

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T cell epitope: Friend or Foe? Immunogenicity of biologics in context, Constanze A. Weber, Preema J. Mehta, Matthew Ardito, Leonard Moise, William Martin, and Anne S. De Groot

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P19-43. Regulatory T Cell Epitopes in a Dendritic Cell-Targeted HIV Vaccine Delivery Platform, C. Weber, C. Weber, L. Moise, H. Veelken, and W. Martin

Submissions from 2008

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Activation of natural regulatory T cells by IgG Fc-derived peptide "Tregitopes", Anne S. De Groot, Leonard Moise, Julie A. McMurry, Erik Wambre, Laurence Van Overtvelt, Philippe Moingeon, David W. Scott, and William Martin

Submissions from 2007

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Clinical validation of the "in silico" prediction of immunogenicity of a human recombinant therapeutic protein, E. Koren, Anne S. De Groot, V. Jawa, K. D. Beck, T. Boone, D. Rivera, L. Li, D. Mytych, M. Koscec, D. Weeraratne, S. Swanson, and W. Martin