Vaccine Publications

Selected EpiVax Vaccine Publications (Chronological)

  • Liu R, Moise L, Tassone R, Gutierrez AH, Terry FE, Sangare K, Ardito MT, Martin WD, De Groot AS. H7N9 T-cell epitopes that mimic human sequences are less immunogenic and may induce Treg-mediated tolerance. Hum Vaccin Immunother. 2015;11(9):2241-52. PMID: 26090577
  • Hoffmann PR, Panigada M, Soprana E, Terry F, Bandar IS, Napolitano A, Rose AH, Hoffmann FW, Ndhlovu LC, Belcaid M, Moise L, De Groot AS, Carbone M, Gaudino G, Matsui T, Siccardi A, Bertino P. Preclinical development of HIvax: human survivin Highly Immunogenic vaccines. Hum Vaccin Immunother.  2015;11(7):1585-95. PMID: 26042612
  • Tomimaru Y, Mishra S, Safran H, Charpentier KP, Martin W, De Groot AS, Gregory SH, Wands JR. Aspartate-β-hydroxylase induces epitope-specific T cell responses in hepatocellular carcinoma. Vaccine. 2015;33(10):1256-66. PMCID: PMC4331251
  • Eickhoff CS, Van Aartsen D, Terry FE, Meymandi SK, Traina MM, Hernandez S, Martin WD, Moise L, De Groot AS, Hoft DF. An immunoinformatic approach for identification of Trypanosoma cruzi HLA-A2-restricted CD8+ T cell epitopes. Hum Vaccin Immunother. 2015;11(9):2322-8. PMID: 26107442
  • Moise L, Terry F, Gutierrez AH, Tassone R, Losikoff P, Gregory SH, Martin WD, De Groot AS. Smarter vaccine design will circumvent immunoregulatory evasion in chronic HIV and HCV infection. In: Why vaccines to HIV, HCV and Malaria have so far failed – challenges to developing vaccines against immunoregulating pathogens. Frontiers in Microbiology. 2014. Editor (Gowans).
  • Leonard Moise, Frances Terry, Andres H. Gutierrez, Ryan Tassone, Phyllis Losikoff, Stephen H. Gregory, Chris Bailey-Kellogg, William D. Martin, Anne S. De Groot. Time for T? Immunoinformatics addresses the challenges of vaccine design for neglected tropical and emerging infectious diseases. Expert Review of Vaccines. Resubmitted 3 Aug 2014. Full Text
  • Abdel-Hady KM, Gutierrez AH, Terry F, Desrosiers J, De Groot AS, Azzazy HM. Identification and retrospective validation of T-cell epitopes in the hepatitis C virus genotype 4 proteome: An accelerated approach toward epitope-driven vaccine development. Hum Vaccin Immunother. 2014 Jun 24;10(8). [Epub ahead of print] Full Text
  • Zhang S, Desrosiers J, Aponte-Pieras JR, DaSilva K, Fast LD, Terry F, Martin WD, De Groot AS, Moise L, Moss SF.Human immune responses to H. pylori HLA Class II epitopes identified by immunoinformatic methods. PlosOne. 2014 Apr 16. Full Text
  • Mishra S, Losikoff PT, Self AA, Terry F, Ardito MT, Tassone R, Martin WD, De Groot AS, Gregory SH. Peptide-pulsed dendritic cells induce the hepatitis C viral epitope-specific responses of naïve human T cells. Vaccine. 2014 May 30;32(26):3285-92. doi: 10.1016/j.vaccine.2014.03.083. Epub 2014 Apr 8.
  • Lu He, Anne S De Groot, Andres H Gutierrez, William D Martin, Lenny Moise and Chris Bailey-Kellogg. Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. BMC Bioinformatics 2014, 15 (Suppl 4): S1 doi:10.1186/1471-2105-15-S4-S1.
  • De Groot AS, Moise L, Liu R, Gutierrez AH, Terry F, Koita OA, Ross TM, Martin W. Cross-conservation of T-cell epitopes: now even more relevant to (H7N9) influenza vaccine design. Hum Vaccin Immunother. 2014 Feb Full Text
  • Leonard Moise, Ryan Tassone, Howard Latimer, Frances Terry, Lauren Levitz, John P. Haran, Ted M. Ross, Christine Boyle, William D. Martin, Anne S. De Groot. Immunization with Cross-conserved H1N1 Influenza CD4+ T Cell Epitopes Lowers Viral Burden in HLA DR3 Transgenic Mice. Hum Vaccin Immunother. 2013 Sep 17;9(10).
  • Review. De Groot AS, Einck L., Moise L, Chambers M., Ballantyne J., Malone RW, Ardito M, Martin W. Making Vaccines “On Demand”: A Potential Solution for Emerging Pathogens and Biodefense? Human Vaccines and Immunotherapy. Sep 2013.
  • Wei R, Xu L, Zhang N, Zhu K, Yang J, Yang C, Deng C, Zhu Z, De Groot AS, Altmeyer R, Zeng M, Leng Q. Elevated antigen-specific Th2 type response is associated with the poor prognosis of hand, foot and mouth disease. Virus Res. 2013 Jul 22. doi:pii: S0168-1702(13)00231-1. 10.1016/j.virusres.2013.07.009.
  • Proceedings. Spero D, Levitz L, De Groot AS. Report from the field: Overview of the Sixth Annual Vaccine Renaissance Conference. Hum Vaccin Immunother. 2013 Jul;9(7):1555-7. doi: 10.4161/hv.24833. Epub 2013 May 31.
  • Moise L, Gutierrez AH, Bailey-Kellogg C, Terry F, Leng Q, Abdel Hady KM, Verberkmoes N, Sztein MB, Losikoff P, Martin WD, Rothman A, De Groot AS. The two-faced T cell epitope: Examining the host-microbe interface with JanusMatrix. Hum Vaccin Immunother. 2013 Apr 12;9(7). PubMed PMID 23584251.
  • Moise L, Terry F, Ardito M, Tassone R, Latimer H, Boyle C, Martin WD. Universal H1N1 influenza vaccine development: Identification of consensus class II hemagglutinin and neuraminidase epitopes derived from strains circulating between 1980 and 2011. Human Vaccines & Immunotherapeutics 2013; 9:1598 – 1607; PMID: 23846304; http://dx.doi.org/10.4161/hv.25598
  • Proceedings. He Y, Cao Z, De Groot AS, Brusic V, Schönbach C, Petrovsky N. Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinformatics. 2013;14 Suppl 4:I1.doi: 10.1186/1471-2105-14-S4-I1. Epub 2013 Mar 8. PubMed PMID: 23514034; PubMed Central PMCID: PMC3599086.
  • Review. Moise L., Marcello, A, Tassone, R., Cousens, L., Martin, W., De Groot, A.S., Building Better Biotherapeutics and Vaccines by Design: EpiVax, Inc., an Immunology Company. Rhode Island Medical Journal, February 2013. rimed.org/rimedicaljournal/2013-02/2013-02-19-bio-epivax.pdf
  • Levitz L, Koita OA, Sangare K, Ardito MT, Boyle CM, Rozehnal J, Tounkara K, Dao SM, Koné Y, Koty Z, Buus S, Moise L, Martin WD, De Groot AS. Conservation of HIV-1 T cell epitopes across time and clades: Validation of immunogenic HLA-A2 epitopes selected for the GAIA HIV vaccine. Vaccine. 2012 Dec 14;30(52):7547-60. PMCID: PMC3522424
  • De Groot AS, Levitz L, Ardito MT, Skowron G, Mayer KH, Buus S, Boyle CM, Martin WD. Further progress on defining highly conserved immunogenic epitopes for a global HIV vaccine: HLA-A3-restricted GAIA vaccine epitopes. Hum Vaccin Immunother. 2012 Jul;8(7):987-1000.
  • Schanen, Brian C. , De Groot AS, Moise L, Ardito M, McClaine E,, Martin, WB, Vaughan Wittman, William L. Warren, and Donald R. Drake III* Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4+ T cells against  the swine-origin H1N1 influenza virus. Vaccine 2011: Feb 21. [Epub ahead of print]
  • Moss SF, Moise L, Lee DS, Kim W, Zhang S, Lee, J, Rogers AB, Martin W, De Groot AS. HelicoVax: Epitope-based therapeutic H. pylori vaccination in a mouse model of gastric cancer. Vaccine. 2011.  Mar 3;29(11):2085-91.
  • Moise L, Buller RM, Schriewer J, Lee J, Frey S, Weiner DB, Martin W, De Groot AS. VennVax, a DNA-prime, peptide-boost multi-T-cell epitope poxvirus vaccine, induces protective immunity against vaccinia infection by T cell response alone. Vaccine. 2011. Jan 10;29(3):501-11. Epub 2010 Nov 4.
  • Cohen T., Moise, L. Ardito M., Martin W.D., De Groot AS. A method for individualizing the prediction of immunogenicity of protein vaccines and biologic therapeutics: iTEM (individualized T Cell Epitope Measure). J Biomed Biotechnol. 2010. pii: 961752. Epub 2010 Jul 18. doi: 10.1155/2010/961752.
  • Gregory SH, Mott S, Phung J, Lee J, Moise L, McMurry JA, Martin W, De Groot AS. Epitope-based vaccination against pneumonic tularemia. Vaccine. 2009 Aug 27;27(39):5299-306. Epub 2009 Jul 17
  • Moise L., McMurry JA, Buus S., Frey S., Martin WD and De Groot AS. In Silico-Accelerated Identification of Conserved and Immunogenic Variola/Vaccinia T-Cell Epitopes. http://dx.doi.org/10.1016/j.vaccine.2009.06.018 Vaccine, 2009 Oct 30;27(46):6471-9. Epub 2009 Jun 24.
  • De Groot AS. Rivera DS, McMurry JA, Buus S, Martin W, Identification of Immunogenic HLA-B7 “Achilles’ heel” Epitopes Within Highly Conserved Regions of HIV. Vaccine, 2008 26, 3059—3071.
  • Knopf PM, Rivera DS, Hai SH, McMurry J, Martin W, De Groot ASNovel function of complement C3d as an autologous helper T-cell target. Immunol Cell Biol. 2008 Mar;86(3):221-5.
  • Moise L, McMurry JA, Pappo J, Lee DS, Moss SF, Martin WD, De Groot ASIdentification of genome-derived vaccine candidates conserved between human and mouse-adapted strains of H. pylori. Hum Vaccin. 2008 May-Jun;4(3):219-23. Epub 2010 May 8.
  • De Groot AS, L. Moise, W. Martin, F. Guirakhoo, and T. Monath. Analysis of ChimeriVax Japanese Encephalitis(JE) virus Sequence for T cell epitopes and comparison to circulating wild type JE Virus strains. Nov. 2007. Vaccine 25 (2007) 8077–8084.
  • McMurry JA, Gregory SH, Moise L, Rivera D, Buus S, De Groot AS. Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans: Identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine. Vaccine. 2007 Apr 20;25(16):3179-91.
  • McMurry JA, S. Kimball, J. Lee, D. Rivera, W. Martin, D.B. Weiner, M. Kutzler, D.R. Sherman, H. Kornfeld, De Groot AS. Epitope-Driven TB Vaccine Development : A streamlined approach using immunoinformatics, ELISpot assays, and HLA transgenic mice. Current Molecular Medicine, Curr Mol Med. 2007 Jun;7(4):351-68.
  • Koita, OA, D. Dabitao, I. Mahamadou, M. Tall, A. S. Dao, A. Tounkara, H. Guiteye, C. Noumsi, O. Thiero, M. Kone, D. Rivera, J. A. McMurry, W. Martin, De Groot AS. Confirmation of Immunogenic Consensus Sequence HIV-1 T-cell Epitopes in Bamako, Mali and Providence, Rhode Island. Human Vaccines  2006 June; 2(3), 119-128.
  • Otero M, Calarota SA, Dai A, De Groot AS, Boyer JD, Weiner DB.      Efficacy of novel plasmid DNA encoding vaccinia antigens in improving current smallpox vaccination strategy. Vaccine. 2005 Aug 30.
  • De Groot AS, McMurry J, Marcon L, Franco J, Rivera D, Kutzler M, Weiner D, Martin B.        Developing an epitope-driven tuberculosis (TB) vaccine. Vaccine. 2005 Mar 18; 23(17-18):2121-31.
  • De Groot AS, Marcon L, Bishop EA, Rivera D, Kutzler M, Weiner DB, Martin W. HIV vaccine development by computer assisted design: the GAIA vaccine. Vaccine. 2005 Mar 18; 23 [7-18):2136-48.
  • McMurry, J, Sbai H, Gennaro ML, Carter EJ, Martin W, De Groot AS.  Analyzing Mycobacterium tuberculosis proteomes for candidate vaccine epitopes. Tuberculosis (Edinb). 2005; 85(1-2):95-105.
  • De Groot AS, Bishop EA, Khan B, Lally M, Marcon L, Franco J, Mayer KH, Carpenter CC, Martin W. Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine. Methods. 2004 Dec; 34(4):476-87 Bioinformatics in Vaccine Design.
  • Dong Y, Demaria S, Sun X, Santori FR, Jesdale BM, De Groot AS, Rom WN, Bushkin Y. HLA-A2-restricted CD8+-cytotoxic-T-cell responses to novel epitopes in Mycobacterium tuberculosis superoxide dismutase, alanine dehydrogenase, and glutamine synthetase. Infect Immun. 2004 Apr; 72(4):2412-5.
  • De Groot A,S. Hakima Sbai, Bill Jesdale, W. Martin, C. Saint Aubin, H. Sbai, A. Bosma, Judy Lieberman, G.A. Skowron, Fadi Mansourati, Ken Mayer. Mapping Cross-clade HIV-1 Vaccine Epitopes Using a Bioinformatics Approach. Vaccine 21 (2003) 4486–4504. http://www.sciencedirect.com/science/journal/0264410X.
  • Lopes AR, Jaye A, Dorrell L, Sabally S, Alabi A, Jones NA, Flower DR, De Groot AS, Newton P, Lascar RM, Williams I, Whittle H, Bertoletti A, Borrow P, Maini MK. Greater CD8+ TCR heterogeneity and functional flexibility in HIV-2 compared to HIV-1 infection. J Immunol. 2003 Jul 1; 171(1):307-16.
  • A.S. De Groot, Vishvanath Nene, Nagendra R. Hedge, S. Srikumaran, James Rayner and William Martin. T Cell Epitope Identification for Bovine Vaccines: An Epitope Mapping Method for BoLA A-11. International Journal for Parasitology (Thematic Issue on Vaccines, David Brake Editor, (Vol 33/5-6 pp 641-653). 2003.
  • W. Martin, A. Bosma, H. Sbai and A.S. De Groot. The use of bioinformatics for identifying class I restricted T cell epitopesMethods (Epitope Mapping Issue). Bill Kwok, editor, Methods 29 (2003) 289–298.
  • A.S. De Groot, H. Sbai, C. Saint Aubin, J.A. McMurry, William MartinImmuno-informatics: Mining the genome for Vaccine Components. Immunology and Cell Biology. Immunology and Cell Biology (2002) 80, 255–269.
  • H. Sbai, A. Mehta, A.S. De Groot. Use of T cell epitopes for vaccine development. Current Drug Targets – Infectious Disorders, 2001, 1, 283-293.
  • A.S. De Groot, Andrew  Bosma, N. Chinai, J. Frost, Bill M. Jesdale, Michael A. Gonzalez, W. Martin, Caitlin Saint-Aubin. From genome to vaccine: In silico predictions, ex vivo verification.  Vaccine 2001 Aug 14; 19(31):4385-95.
  • A.S. De Groot, Saint Aubin, CS, Rayner, J, Martin, W. Rapid Determination of HLA B*07- ligands from the West Nile Virus genome. Emerging Infectious Diseases, Vol. 7, No. 4, July–August 2001: 706-713.
  • A.S. De Groot, H. Sbai, C. Saint-Aubin, W. Martin, A. Bosma, G. Skowron, K. H. Mayer  Designing HIV-1 vaccines to reflect viral diversity and the global context of HIV/AIDSAIDScience 1(2) June 22, 2001.
  • Bond KB, Sriwanthana B, Hodge TW, De Groot AS, Mastro TD, Young NL, Promadej N, Altman JD, Limpakarnjanarat K, McNicholl JM. An HLA-directed molecular and bioinformatics approach identifies new HLA-A11 HIV-1 subtype E cytotoxic T lymphocyte epitopes in HIV-1 infected Thais. AIDS Research and Human Retroviruses 2001; 17(8):703-18.
  • Xia Jin, DF Nixon, CGP Roberts, Nixon DF, J Safrit, LQ Zhang, YX Huang, N Bhardwaj, B Jesdale, A.S. De Groot, RA Koup, Identification of subdominant cytotoxic T lymphocyte epitopes encoded by autologous  HIV type 1 sequences, using dendritic cell stimulation and computer-driven algorithm. AIDS Res Hu Retroviruses Vol 16, No.1, pp. 67-76, January 2000.
  • Schafer JA, Jesdale BM, George JA, Kouttab NM, A.S. De Groot, Prediction of well-conserved HIV-1 ligands using a Matrix-based Algorithm, EpiMatrix, Vaccine, 1998, Vol. 16, No. 19, pp. 1880-1884.
  • Nguyen, KB, Suri, PK, Shah, AM, Goldberg, M, De Groot, AS, and Knopf, PM. Differential immune responses against a Schistosoma mansoni candidate vaccine antigen in three murine strains. Vaccines 97, 1997, 213-217.
  • Jesdale BM, Deocampo G, Meisell J, Mullen L, Beall J, Marinello M, A.S. De Groot, Matrix-based prediction of MHC-binding peptides: the EpiMatrix algorithm, reagent for HIV research, Vaccines 97, pp. 57-64, Cold Spring Harbor Laboratory Press 1997.
  • De Groot AS, Jesdale BM, Szu E, Schafer JR, Chicz RM, Deocampo G. An interactive Web site providing major histocompatibility ligand predictions: application to HIV researchAIDS Res Hum Retroviruses. 1997 May 1; 13(7):529-31.
  • Roberts CGP, Meister GE, Jesdale BM, Lieberman J, Berzofsky JA, A.S. De Groot, Prediction of HIV peptide epitopes by a novel algorithmAIDS Research and Human Retroviruses, 1996, Vol. 12, No. 7, pp. 593-610.
  • A.S. De Groot, Carter EJ, Roberts CGP, Edelson BT, Jesdale BM, Meister GE, Houghten RA, Montoya J, Romulo RC, Berzofsky JA, and Ramirez BDLL, A novel algorithm for the efficient identification of T cell epitopes: prediction and testing of candidate TB vaccine peptides in genetically diverse populations, Vaccines  96, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 127-134.
  • A.S. De Groot, Jesdale BM, Meister GE, Muni N, Roberts CGP, Prediction of T Cell Epitopes for HIV vaccine development by computer-driven algorithm, in HIV Molecular Immunology Database 1995, Bette Korber, Gerald Meyers eds., Los Alamos National Laboratories, New Mexico, pp. iv17-iv28.
  • De Groot AS,  Ardito M. McClaine E.  Moise, L. Martin W. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-09 Conventional Influenza Vaccine. Vaccine. 2009 Sep 25;27(42):5740-7. PMID: 19660593.
  • Meister GE, Roberts CGP, Berzofsky JA, A.S. De Groot, Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequencesVaccine  1995, Vol. 13, No. 6, pp. 581-591.

Also, see Dr. Annie De Groot’s PubMed List HERE and full Curriculum Vitae HERE.

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