Abstract: Methods and compositions for multiplexed protein-protein interaction profiling (e.g., immunoprofiling), based on nucleic acid tagging of polypeptides (e.g., by RNA display) are described. In some embodiments the described compositions and methods utilize a library of prey polypeptide targets linked to prey RNAs encoding them, and a population of bait polypeptides, e.g., a mixture of antibodies, that bind to one or more of the prey polypeptide targets and are used to isolate and identify the bound prey polypeptide targets by amplification of their associated prey RNAs and sequencing of the corresponding cDNAs. In other embodiments the prey polypeptide targets are linked to DNA Bar Codes, which serve as unique identifiers of the tagged polypeptide.

Abstract: Methods and compositions for multiplexed protein-protein interaction profiling (e.g., immunoprofiling), based on nucleic acid tagging of polypeptides (e.g., by RNA display) are described. In some embodiments the described compositions and methods utilize a library of prey polypeptide targets linked to prey RNAs encoding them, and a population of bait polypeptides, e.g., a mixture of antibodies, that bind to one or more of the prey polypeptide targets and are used to isolate and identify the bound prey polypeptide targets by amplification of their associated prey RNAs and sequencing of the corresponding cDNAs. In other embodiments the prey polypeptide targets are linked to DNA Bar Codes, which serve as unique identifiers of the tagged polypeptide.

Abstract: The present invention provides reagents and methods for breast cancer detection.

Abstract: Disclosed herein are methods of treating diseases that exhibit over-activation of the ERBB4 pathway, such as breast cancer and lung cancer. The method comprises administering to a subject having a disease that exhibits over-activation of the ERBB4 pathway and a gene expression profile consistent with an ERBB4-sensitive profile a therapeutically effective amount of an ERBB4 inhibitor, wherein the disease is effectively treated. Gene expression profiles of ERBB4-sensitive cells and microarrays suitable for protein-tyrosine kinases are also provided.

Abstract: The present invention provides reagents and methods for breast cancer detection.

Abstract: Cancer patients make antibodies to tumor-derived proteins that are potential biomarkers for early detection. Twenty-eight antigens have been identified as potential biomarkers for the early detection of basal-like breast cancer (Tables 1, 2). Also, a 13-AAb classifier has been developed that differentiate patients with BLBC from healthy controls with 33% sensitivity at 98% specificity (Table 3).

Abstract: The present disclosure provides for characterization of normal flora and identifying biomarkers in the gut of healthy, neurotypical subjects. Aspect of the disclosure provide for the characterization of the gut microbiome in ADS subjects, characterized by reduced richness and significant loss of the ‘Prevotella-like enterotype’ compared to neurotypical subjects. The relative abundance of genera Prevotella, Coprococcus, Prevotellaceae and Veillonellaceae are significantly lower in autistic children than in neurotypical children. Further, Prevotella, is one of the three main classifiers for the human enterotypes, along with Bacteroides and Ruminococcus. These three core genera are among main contributors in the principle component analysis. ‘Prevotella-like enterotype’ was absent in the autistic group, while neurotypical samples showed an even distribution among the three enterotypes.

Abstract: The present disclosure provides for characterization of normal flora and identifying biomarkers in the gut of healthy, neruotypical subjects. Aspect of the disclosure provide for the characterization of the gut microbiome in ADS subjects, characterized by reduced richness and significant loss of the ‘Prevotella-like enterotype’ compared to neurotypical subjects. The relative abundance of genera Prevotella, Coprococcus, Prevotellaceae and Veillonellaceae are significantly lower in autistic children than in neurotypical children. Further, Prevotella, is one of the three main classifiers for the human enterotypes, along with Bacteroides and Ruminococcus. These three core genera are among main contributors in the principle component analysis. ‘Prevotella-like enterotype’ was absent in the autistic group, while neurotypical samples showed an even distribution among the three enterotypes.

Abstract: Methods for making and using a programmable bead composition that in some embodiments includes a magnetic bead coupled to an antibody with DMTMM and an antigen coupled to the antibody, with the antigen having been expressed from a human cell lysate (FIG. 1). An ELISA method with the composition includes contacting a fluid sample from a patient with the magnetic programmable bead composition, the composition comprising a plurality of magnetic beads coupled to an antibody with MM and being bound to an antigen expressed from a human call lysate, and adding a detection antibody under conditions and for a time to measure the detection antibody.

Abstract: A method and related microfluidic chip and kit for high throughput detection of proteins of interest contained in a sample is disclosed. The method comprises of specifically labeling fusion proteins in a complex sample with fusion tag specific fluorophores that specifically bind the fusion tags coupled to the proteins of interest, and subjecting the sample to automated capillary electrophoresis, wherein the presence of the proteins of interest in the sample is detected by fluorescence signals associated with the fusion tag specific fluorophores.

Abstract: Nucleic acid-guided ordered protein assembly (NOPA) arrays and methods for their generation and related applications are disclosed herein.

Abstract: Provided herein are methods for the rapid detection of HPV types, such as HPV 16- and HPV18-specific antibodies, in patient samples that contain antibodies. For example, patients with head and neck cancers have detectable antibodies to multiple early genes derived from HPV. These antibodies also are useful as biomarkers for HPV-associated malignancies and premalignant states, for diagnosis and prognosis, and for methods of assessing treatment and cancer-recurrence prediction.

Abstract: A method and related microfluidic chip and kit for high throughput detection of proteins of interest contained in a sample is disclosed. The method comprises of specifically labeling fusion proteins in a complex sample with fusion tag specific fluorophores that specifically bind the fusion tags coupled to the proteins of interest, and subjecting the sample to automated capillary electrophoresis, wherein the presence of the proteins of interest in the sample is detected by fluorescence signals associated with the fusion tag specific fluorophores.

Abstract: The disclosure provides for methods and apparatuses relating to technology for monitoring chemical and/or biological reactions. Some methods provided herein relate to utilization of NAPPA technology to create large protein arrays suitable for use in combination with various ISFET arrays to enable massive parallel assays of kinase activity and inhibition. Some devices provided herein relate to CMOS chips which utilize the NAPPA array technology to build protein inventories of interest upon an ISFET architecture. Further devices provided herein are capable, inter alia, of processing the arrays created by the combination of NAPPA technology and ISFET architecture.

Abstract: Type 1 diabetes (T1D) patients make antibodies to self-proteins that are potential biomarkers for early detection and risk prediction. We have identified seventeen antigens as biomarkers for early diagnosis and risk prediction of T1D, including the antigens MLH1, MTIF3, PPIL2, NUP50, TOX4, FIGN, C9orf142, ZNF280D, HES1, QRFPR, CTRC, SNX6, SYTL4, ELA2A, IGRP, PAX6, and HMGN3.

Abstract: Methods and compositions for multiplexed protein-protein interaction profiling (e.g., immunoprofiling), based on nucleic acid tagging of polypeptides (e.g., by RNA display) are described. In some embodiments the described compositions and methods utilize a library of prey polypeptide targets linked to prey RNAs encoding them, and a population of bait polypeptides, e.g., a mixture of antibodies, that bind to one or more of the prey polypeptide targets and are used to isolate and identify the bound prey polypeptide targets by amplification of their associated prey RNAs and sequencing of the corresponding cDNAs. In other embodiments the prey polypeptide targets are linked to DNA Bar Codes, which serve as unique identifiers of the tagged polypeptide.

Abstract: Disclosed herein are compositions and methods for accurately estimating the absorbed dose of radiation indicated by a subject based on the expression pattern of a panel of radiation-modulated (RM) genes at various time points following exposure of the subject to ionizing radiation.

Abstract: Described herein are biosensor microarrays comprising detector polypeptide monolayers substantially free of contaminants. Also provided are methods for generation of such biosensor microarrays by capture of polypeptides by arrays comprising capture moieties and associated sensors.

Abstract: Methods for identifying antigens as potential biomarkers for the early detection of ovarian cancer, as well as kits for utilizing said antigens as biomarkers and in personalized medicine/therapeutics assessment. Protein microarrays displaying full-length candidate antigens were developed and sequentially screening to select candidate autoantibody biomarkers to limit the false discovery rate inherent to large-scale proteomic screening.

Abstract: The present disclosure provides for characterization of normal flora and identifying biomarkers in the gut of healthy, neruotypical subjects. Aspect of the disclosure provide for the characterization of the gut microbiome in ADS subjects, characterized by reduced richness and significant loss of the ‘Prevotella-like enterotype’ compared to neurotypical subjects. The relative abundance of genera Prevotella, Coprococcus, Prevotellaceae and Veillonellaceae are significantly lower in autistic children than in neurotypical children. Further, Prevotella, is one of the three main classifiers for the human enterotypes, along with Bacteroides and Ruminococcus. These three core genera are among main contributors in the principle component analysis. ‘Prevotella-like enterotype’ was absent in the autistic group, while neurotypical samples showed an even distribution among the three enterotypes.