Abstract: Compositions and methods are provided for the identification of peptide sequences that are presented to T cells in an MHC context.

Abstract: Peptides and vaccine compositions comprising peptides based upon EGFRvIII and lacking a glycine at the splice junction are disclosed. The vaccines can induce immune responses against EGFRvIII. Methods of inhibiting formation or growth of EGFvIII tumors, methods of inducing regression of EGFvIII tumors, methods of immunizing against EGFvIII tumors and methods of treating a subjects who have EGFvIII tumors are disclosed.

Abstract: The present invention relates to a novel form of human EGFR found in certain tumors and conditions. The protein is termed here mLEEK, and the cDNA that encodes it has also been isolated. The mLEEK protein is capable of efficiently inducing the transcription of multiple genes resulting in various physiologic processes. Antibodies directed against the protein can be used for improving the diagnosis of diseases or for the treatment of diseases. The protein itself can be directly used or blocked for therapeutic purposes. Nucleic acid based probes or PCR primers specific for the mLEEK sequence can be used for diagnostic purposes. Inhibitory nucleic acid based molecules, such as antisense, siRNA, or shRNA, may be used for therapeutic purposes. The mLEEK sequence is essentially formed by the skipping of exons 2 through 22 in the EGF receptor gene leading to a fusion of exon 1 to exon 23. Other mutants are disclosed, which include the fusion of exon 1 to exon 24 and the fusion of exons 1 to exon 28.

Abstract: A computer-implemented method can include receiving, at a computing device including one or more processors, an input from a user. The input can include one or more characters in a first writing system. The method can further include segmenting the input to obtain one or more segmentations, where each segmentation can include at least one segment including at least one character in the first writing system. A fuzzy model can be applied to the segmentations to obtain potential formal representations for the segmentations. Each of the potential formal representations can be in the first writing system and represent text in a second writing system. A plurality of character candidates can be determined based on the potential formal representations. Each of the plurality of character candidates can be a possible appropriate representation of the user input in the second writing system.

Abstract: Peptides and vaccine compositions comprising peptides based upon EGFRvIII and lacking a glycine at the splice junction are disclosed. The vaccines can induce immune responses against EGFRvIII. Methods of inhibiting formation or growth of EGFvIII tumors, methods of inducing regression of EGFvIII tumors, methods of immunizing against EGFvIII tumors and methods of treating a subjects who have EGFvIII tumors are disclosed.

Abstract: A set of markers for cancer stem cells are provided. The cells can be prospectively isolated or identified from primary tumor samples, and possess the unique properties of cancer stem cells in functional assays for tumor initiation, cancer stem cell self-renewal and differentiation. In addition, cancer stem cells can be used as a predictor for disease progression. The CSC have the phenotype of being positive for expression of CD133, and for EGFRvIII. In another embodiment of the invention, compositions are provided of a bispecific reagent that recognizes CD133 and EGFRvIII, including bispecific antibodies, which are optionally conjugated to a detectable marker, chemotherapeutic agent are radionuclide for imaging or therapy.

Abstract: Peptides or antibodies derived from alternative splice forms of proteins associated with a disease or physiologic condition are used as therapeutic or prophylactic agents. Peptides and antibodies derived from alternative splice forms of the vascular endothelial growth factor (VEGF) family of proteins are particularly useful in preventing or delaying the onset of tumors and inducing tumor regression.

Abstract: A set of markers for cancer stem cells are provided. The cells can be prospectively isolated or identified from primary tumor samples, and possess the unique properties of cancer stem cells in functional assays for tumor initiation, cancer stem cell self-renewal and differentiation. In addition, cancer stem cells can be used as a predictor for disease progression. The CSC have the phenotype of being positive for expression of CD133, and for EGFRvIII. In another embodiment of the invention, compositions are provided of a bispecific reagent that recognizes CD133 and EGFRvIII, including bispecific antibodies, which are optionally conjugated to a detectable marker, chemotherapeutic agent are radionuclide for imaging or therapy.

Abstract: Alternatively spliced RNA, along with their normally-spliced counterparts, can be rapidly identified by hybridizing cDNA from normal tissue to cDNA from an abnormal or test tissue. The two cDNA populations are separately tagged prior to hybridization, which allows isolation of double-stranded cDNA containing both normal and alternatively spliced molecules. Within this population, pairing of cDNA molecules representing an alternatively spliced mRNA with cDNA molecules representing the counterpart normally spliced mRNA will form double-stranded cDNA with single-stranded mismatched regions. The mismatched double-stranded cDNA are isolated with reagents that bind single-stranded nucleic acids. The strands of each mismatched double-stranded cDNA are then coupled and analyzed, simultaneously identifying both normal and alternatively spliced molecules.

Abstract: The present invention relates to a novel form of human EGFR found in certain tumors and conditions. The protein is termed here mLEEK, and the cDNA that encodes it has also been isolated. The mLEEK protein is capable of efficiently inducing the transcription of multiple genes resulting in various physiologic processes. Antibodies directed against the protein can be used for improving the diagnosis of diseases or for the treatment of diseases. The protein itself can be directly used or blocked for therapeutic purposes. Nucleic acid based probes or PCR primers specific for the mLEEK sequence can be used for diagnostic purposes. Inhibitory nucleic acid based molecules, such as antisense, siRNA, or shRNA, may be used for therapeutic purposes. The mLEEK sequence is essentially formed by the skipping of exons 2 through 22 in the EGF receptor gene leading to a fusion of exon 1 to exon 23. Other mutants are disclosed, which include the fusion of exon 1 to exon 24 and the fusion of exons 1 to exon 28.

Abstract: Alternatively spliced RNA, along with their normally-spliced counterparts, can be rapidly identified by hybridizing cDNA from normal tissue to cDNA from an abnormal or test tissue. The two cDNA populations are separately tagged prior to hybridization, which allows isolation of double-stranded cDNA containing both normal and alternatively spliced molecules. Within this population, pairing of cDNA molecules representing an alternatively spliced mRNA with cDNA molecules representing the counterpart normally spliced mRNA will form double-stranded cDNA with single-stranded mismatched regions. The mismatched double-stranded cDNA are isolated with reagents that bind single-stranded nucleic acids. The strands of each mismatched double-stranded cDNA are then coupled and analyzed, simultaneously identifying both normal and alternatively spliced molecules.

Abstract: Peptides or antibodies derived from alternative splice forms of proteins associated with a disease or physiologic condition are used as therapeutic or prophylactic agents. Peptides and antibodies derived from alternative splice forms of the vascular endothelial growth factor (VEGF) family of proteins are particularly useful in preventing or delaying the onset of tumors and inducing tumor regression.

Abstract: The present invention generally relates a method of detecting type III mutant EGF receptor (EGFRvIII) in biological samples, a method of detecting cancers and other diseases in biological samples, and to a method of assessing treatment and selecting therapy for cancer patients.

Abstract: Vaccines comprising peptides from a fusion junction present in a mutant human EGF receptor and methods of using these vaccines in the inhibition of tumor formation and enhancement of tumor regression are provided. Cell lines which overexpress a Type III mutant EGF receptor and methods of producing these cell lines are also provided. In addition, antibodies raised against peptides expressed by these cell lines are provided. Further, antisense oligonucleotides targeted to a mutant EGF receptor which decreases expression of a mutant EGF receptor are disclosed.

Abstract: A substantially pure protein, Gab1, that binds to Grb2 is disclosed. Isolated nucleic acid molecules that encode Gab1 is disclosed. Pharmaceutical compositions comprising a pharmaceutically acceptable carrier in combination with nucleic acid molecules are disclosed. Fragments of nucleic acid molecules that encode Gab1 having at least 10 nucleotides and oligonucleotide molecule comprising a nucleotide sequence complimentary to a nucleotide sequence of at least 10 nucleotides are disclosed. Recombinant expression vectors that comprise the nucleic acid molecule that encode Gab1, and host cells that comprise such recombinant vectors are disclosed. Antibodies that bind to an epitope on Gab1 are disclosed. Methods of identifying inhibitors, activators and substrates of Gab1 are disclosed. Antisense compounds and methods of using the same are disclosed.

Abstract: A substantially pure protein, Gab1, that binds to Grb2 is disclosed. Isolated nucleic acid molecules that encode Gab1 is disclosed. Pharmaceutical compositions comprising a pharmaceutically acceptable carrier in combination with nucleic acid molecules are disclosed. Fragments of nucleic acid molecules that encode Gab1 having at least 10 nucleotides and oligonucleotide molecule comprising a nucleotide sequence complimentary to a nucleotide sequence of at least 10 nucleotides are disclosed. Recombinant expression vectors that comprise the nucleic acid molecule that encode Gab1, and host cells that comprise such recombinant vectors are disclosed. Antibodies that bind to an epitope on Gab1 are disclosed. Methods of identifying inhibitors, activators and substrates of Gab1 are disclosed. Antisense compounds and methods of using the same are disclosed.