Abstract: Methods for obtaining structural data from RNA in a sample, and RNA probes for performing the same, are provided. Methods of reversibly modifying RNA is a sample, in vitro or in vivo, and reversible probes for performing the same, are provided. The RNA probes may be SHAPE probes that include aryl or heteroaryl acyl imidazoles. The RNA probes may be reversible probes that include an aryl or heteroaryl ring substituted with a hydroxyl-reactive group and an azido-containing group. Also provided are methods of comparing in vitro and in vivo RNA structural data. Also provided are methods of diagnosing a cellular proliferative disease condition, e.g., by probing HOTAIR RNA. Aspects of the invention further include compositions, e.g., probes and kits, etc., that find use in methods of the invention.

Abstract: A method for constructing an association map between imaging features and biological data is described. The method comprises combining one or more image features relating to a clinical subject with biological data and using an algorithm to make predictions based on the features and data.

Abstract: A method of sample analysis is provided. In certain cases, the method comprises: a) cross-linking the contents of a cell using a heat stable crosslinking agent to produce cross-linked ribonucleotide complexes; b) fragmenting the cross-linked ribonucleotide complexes to produce complexes comprising protein, RNA fragments and, optionally, genomic DNA fragments; c) contacting the complexes with a plurality of non-overlapping oligonucleotides comprise an affinity tag and that are complementary to a specific target RNA of the cell under high stringency conditions that include high temperature; d) isolating complexes that contain the oligonucleotides using the affinity tag to produce isolated complexes; e) enzymatically releasing the protein, RNA fragments and/or the genomic DNA fragments from the isolated complexes to produce a released component, without reversing the crosslinking; and f) analyzing the released component.

Abstract: Methods for obtaining structural data from RNA in a sample, and RNA probes for performing the same, are provided. Methods of reversibly modifying RNA is a sample, in vitro or in vivo, and reversible probes for performing the same, are provided. The RNA probes may be SHAPE probes that include aryl or heteroaryl acyl imidazoles. The RNA probes may be reversible probes that include an aryl or heteroaryl ring substituted with a hydroxyl-reactive group and an azido-containing group. Also provided are methods of comparing in vitro and in vivo RNA structural data. Also provided are methods of diagnosing a cellular proliferative disease condition, e.g., by probing HOTAIR RNA. Aspects of the invention further include compositions, e.g., probes and kits, etc., that find use in methods of the invention.

Abstract: Compositions and methods of modulating an immune response by controlling levels of interferon-gamma (IFN-?) production by leukocytes are disclosed. Adjustment of IFN-? levels is achieved by increasing or decreasing the activity of NeST (nettoie Salmonella pas Theiler's [cleanup Salmonella not Theiler's]), a long non-coding RNA that induces expression of IFN-?. In particular, the invention relates to the use of NeST and inhibitors of NeST to modulate levels of IFN-? for treatment of inflammatory conditions, autoimmune diseases, infectious diseases, immunodeficiency, and cancer.

Abstract: A method of sample analysis is provided. In certain cases, the method comprises: a) cross-linking the contents of a cell using a heat stable crosslinking agent to produce cross-linked ribonucleotide complexes; b) fragmenting the cross-linked ribonucleotide complexes to produce complexes comprising protein, RNA fragments and, optionally, genomic DNA fragments; c) contacting the complexes with a plurality of non-overlapping oligonucleotides comprise an affinity tag and that are complementary to a specific target RNA of the cell under high stringency conditions that include high temperature; d) isolating complexes that contain the oligonucleotides using the affinity tag to produce isolated complexes; e) enzymatically releasing the protein, RNA fragments and/or the genomic DNA fragments from the isolated complexes to produce a released component, without reversing the crosslinking; and f) analyzing the released component.

Abstract: Methods are provided for classification of cancers by the expression of a set of genes referred to as the core serum response (CSR), or a subset thereof. The expression pattern of the CSR in normal tissues correlates with that seen in quiescent fibroblasts cultured in the absence of serum, while cancer tissues can be classified as having a quiescent or induced CSR signature. Patients with the induced CSR signature have a higher probability of metastasis. Classification according to CSR signature allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like.

Abstract: The present invention relates to compositions and methods for treating, characterizing, and diagnosing autoimmune diseases or other inflammatory diseases. In particular, the present invention provides gene expression profiles as well as novel TKI Responsive Signature(s) useful for the diagnosis, characterization, prognosis and treatment of autoimmune disease or other inflammatory diseases.

Abstract: A method for constructing an association map between imaging features and biological data is described. The method comprises combining one or more image features relating to a clinical subject with biological data and using an algorithm to make predictions based on the features and data.