Abstract: The present invention relates to methods for stimulating the immune response to a tumor by implementing a two-phase vaccination strategy in which a first vaccination comprises epitopes from tumor associated antigens or epitopes which embody amino acid mutations commonly associated with the cancer that is administered before tissue diagnosis, and a second vaccination which comprises personal neoepitopes, the design of which is unique to that subject and is identified based on comparative sequencing of normal tissue and tumor tissue obtained by biopsy.

Abstract: The present invention is related to T cell epitopes and methods of their use, in particular bystander proteins, and identification of peptides which may be used to stimulate a CD8+ cytotoxic T cell response, as well as peptides which stimulate a CD4+ helper T cell response to the cells carrying the proteins.

Abstract: This invention pertains to the identification of antibody mediated epitope mimics and applications of the identification of said mimic peptides in the design of biotherapeutics and vaccines.

Abstract: This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

Abstract: This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

Abstract: The present invention relates to vaccine compositions and therapeutic interventions for treating and preventing infections and diseases caused by flaviviruses, including Zika, dengue, and Usutu virus. It also relates to compositions and methods for diagnosis and differential diagnosis of flaviviruses and co-endemic pathogens.

Abstract: This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

Abstract: This invention relates to the identification of peptidase cleavage sites in proteins and in particular to identification protease cleavage by the endopeptidases. The present invention utilizes a bioinformatic methodology for prediction of peptidase cleavage sites based on principal component analysis and based on training sets obtained by experimental protein cleavage. This invention is not limited to training sets derived from CSL approaches, nor to any other experimental determination of cleavage site.

Abstract: The present invention provides methods and systems for identifying and classifying patterns comprising the T cell exposed motifs and the frequencies of such motifs in collections of proteins that make up the human proteome, immunoglobulinome, T cell receptor repertoire or microbiome, and other proteomes of environmental of microbial origin, or subsets thereof. It further provides graphical representations that facilitate comparisons of T cell exposed motif patterns between samples or between time points. The present invention also provides methods and systems for identifying and classifying patterns in repertoires of cells including receptor bearing cells and cells of tissue samples and detecting patterns of utility in diagnosis and monitoring of health and disease.

Abstract: This invention relates to the identification of peptidase cleavage sites in proteins and in particular to identification protease cleavage by the endopeptidases. The present invention utilizes a bioinformatic methodology for prediction of peptidase cleavage sites based on principal component analysis and based on training sets obtained by experimental protein cleavage. This invention is not limited to training sets derived from CSL approaches, nor to any other experimental determination of cleavage site.

Abstract: The present invention provides a means to prepare a product from domestic animal milk, blood or eggs which comprises an array of T-cell exposed motifs similar in identity, distribution and concentration to those found in human immunoglobulin variable regions and to prepare and apply the product as an immune modulating agent for administration either as a nutritional supplement or as a pharmaceutical product.

Abstract: The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.

Abstract: This invention provides a method for maximizing the immune response to mutated tumor specific proteins, either by means of stimulation of dendritic cells or T cells in vitro followed by administration of these cells to a patient, or by means of administration of a neoantigen vaccine in which de novo peptides, or their encoding nucleic acids, have been designed to ensure an appropriate level of binding affinity to a particular cancer patient's WIC alleles. This invention further provides for modulating the immune response in an immunopathology other than cancer.

Abstract: The present invention provides a means to prepare a product from domestic animal milk, blood or eggs which comprises an array of T-cell exposed motifs similar in identity, distribution and concentration to those found in human immunoglobulin variable regions and to prepare and apply the product as an immune modulating agent for administration either as a nutritional supplement or as a pharmaceutical product.

Abstract: The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.

Abstract: This invention relates to processes for identifying peptide and polypeptide ligands for a binding partner by using principal component analysis of amino acids to derive vectors describing amino acid subsets corresponding to peptides with known binding affinities and then using this information in a neural network modeling process to derive binding prediction equations. These binding prediction equations are then used in the analysis of subsets of amino acids from a target source to identify peptides or polypeptides ligands in the target source that have affinity for a binding partner.

Abstract: This invention pertains to the identification of antibody mediated epitope mimics and applications of the identification of said mimic peptides in the design of biotherapeutics and vaccines.

Abstract: The present invention relates to vaccine compositions and therapeutic interventions for treating and preventing infections and diseases caused by flaviviruses, including Zika dengue, and Usutu virus. It also relates to compositions and methods for diagnosis and differential diagnosis of flaviviruses and co-endemic pathogens.

Abstract: The present invention provides a means to prepare a product from domestic animal milk, blood or eggs which comprises an array of T-cell exposed motifs similar in identity, distribution and concentration to those found in human immunoglobulin variable regions and to prepare and apply the product as an immune modulating agent for administration either as a nutritional supplement or as a pharmaceutical product.

Abstract: The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.