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: 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: 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: 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: Identification of autoantibodies associated with Crohn's disease useful in diagnosis and management using an innovative protein array technology, namely nucleic acid programmable protein arrays (NAPPA) and applications relating thereto. Overall, reactivity of IgG autoantibodies was stronger than that of IgA autoantibodies; however, IgA autoantibodies showed greater differential reactivity between cases and controls. Four IgA autoantibodies against SNRPB, PRPH, PTTG1 and SNAI1 were newly identified with sensitivities above 15% at 95% specificity, among which anti-SNRPB-IgA had the highest sensitivity of 24.0%. Autoantibodies associated with specific disease subtypes were also found.

Abstract: Provided herein are affinity reagents having affinity for particular target, each reagent having a unique DNA barcode, and methods for using the same to measure the abundance of targets in a sample. In particular, methods are provided in which unique barcodes linked to affinity reagents are contacted to a sample to bind antigens if present in said sample. In cases in which the affinity reagents are antibodies and the targets are antigens, antibodies that are bound to their target antigens can be separated from unbound antibodies and the DNA barcode associated with the affinity reagent is amplified, such as with a PCR reaction. In some cases, amplified barcode DNA is subjected to DNA sequencing as a measure of the levels of the target protein in the sample.

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: Provided herein are affinity reagents having affinity for particular target, each reagent having a unique DNA barcode, and methods for using the same to measure the abundance of targets in a sample. In particular, methods are provided in which unique barcodes linked to affinity reagents are contacted to a sample to bind antigens if present in said sample. In cases in which the affinity reagents are antibodies and the targets are antigens, antibodies that are bound to their target antigens can be separated from unbound antibodies and the DNA barcode associated with the affinity reagent is amplified, such as with a PCR reaction. In some cases, amplified barcode DNA is subjected to DNA sequencing as a measure of the levels of the target protein in the sample.

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: Compositions and methods relating to a panel of antigen biomarkers for the early detection of ovarian cancer. The compositions and methods encompass antigen biomarkers coupled to a substrate, with the biomarkers being selected from the group consisting of one or more of ICAM3, CTAG2, p53, STYXL1, PVR, POMC, NUDT11, TRIM39, UHMK1, KSR1, and NXF3.

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

Abstract: Embodiments of the present disclosure relate generally to detection and diagnosis of tuberculosis (TB) infections. More particularly, the present disclosure provides novel immunogenic biomarkers associated with TB infections for the diagnosis and treatment of TB. Novel TB biomarkers can enhance the diagnosis and treatment of TB by providing greater accuracy and efficiency, especially for point-of-care technologies.

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 Bacteriodes 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: Provided herein are qPCR-based methods for quantitatively detecting and differentiating between live and dead pathogenic bacteria such as carbapenem-resistant Enterobacteriaceae (CRE). Also provided herein are simple, fast, and reliable genomic DNA extraction methods with improved efficiency.

Abstract: Methods for screening of affinity reagents for many target proteins of interest simultaneously. Arrayed targets (e.g., peptide, protein, RNA, cell, etc.) are used in affinity selection experiments to reduce the amount of target needed and to improve the throughput of discovering recombinant affinity reagents to a large collection of targets.

Abstract: An immune-proteomic screening of AAb responses using protein arrays has identified two panels of Aab (antigen/antibody complexes) that can potentially differentiate lung adenocarcinoma from smoker controls as well as CT positive benign lung disease. The resulting biomarkers appear to have high specificity so that high risk subjects with a positive CT screen and a positive serum test should get more invasive test such as needle biopsy for a timely cancer diagnosis, among other advantages.

Abstract: Provided herein are methods of classifying antigens and epitopes as being recognized by an individual's cellular immune response. More particularly, provided herein are methods for unbiased determination of which antigens are recognized by a population of T cells.

Abstract: Biomolecule arrays on a substrate are described which contain a plurality of biomolecules, such as coding nucleic acids and/or isolated polypeptides, at a plurality of discrete, isolated, locations. The arrays can be used, for example, in high throughput genomics and proteomics for specific uses including, but not limited molecular diagnostics for early detection, diagnosis, treatment, prognosis, monitoring clinical response, and protein crystallography.

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: Identification of autoantibodies associated with Crohn's disease useful in diagnosis and management using an innovative protein array technology, namely nucleic acid programmable protein arrays (NAPPA) and applications relating thereto. Overall, reactivity of IgG autoantibodies was stronger than that of IgA autoantibodies; however, IgA autoantibodies showed greater differential reactivity between cases and controls. Four IgA autoantibodies against SNRPB, PRPH, PTTG1 and SNAI1 were newly identified with sensitivities above 15% at 95% specificity, among which anti-SNRPB-IgA had the highest sensitivity of 24.0%. Autoantibodies associated with specific disease subtypes were also found.