Abstract: The invention provides for isolated nucleic acid sequences of newly discovered micro RNAs that have been identified to exist in normal Human B cells and/or in tumor-related Human B cells, using an integrated bioinformatics method and pipeline described herein.

Abstract: The present subject matter relates to systems and methods for predicting molecular interactions within biological networks based on structural and non-structural indicators. Such molecules include but are not limited to proteins, nucleic acids and small molecules. In some embodiments, the present subject matter is directed to methods for predicting protein-protein interactions comprising obtaining a pair of query proteins, using sequence alignment to identify structural representatives for each of the pair of query proteins, and using structural alignment to determine sets of close and remote structural neighbors for each of the structural representatives. The method can include analyzing the close and remote structural neighbors to identify a reported complex, and using the reported complex to define a template for creating a model for interaction of the pair of query proteins.

Abstract: The invention provides for methods for treating nervous system cancers in a subject. The invention further provides methods for treating nervous system tumor cell invasion, migration, proliferation, and angiogenesis associated with nervous system tumors.

Abstract: A method of processing semiotic data includes receiving semiotic data including at least one data set P, selecting a function h, and for at least one of each data set P to be collected, computing h(P), destroying data set P, and storing h(P) in a database, wherein data set P cannot be extracted from h(P). The method further includes selecting a private key/public key (K, k) once for all cases, one of destroying the private key K and sending the private key K to a trusted party, and choosing function h as the public encryption function corresponding to k.

Abstract: Disclosed herein is a systems biology approach to prediction of phenotypically relevant genes such as oncogenes and perturbation targets. Interactions from a comprehensive cellular network such as the B Cell Interactome (BCI) can be used to identify those that become affected, or dysregulated, by a phenotype (e.g, disease, tumor and cancer) or perturbation (e.g., drug treatment) based on correlation changes between expression profiles of gene pairs in the interactions upon removal or addition of samples showing the phenotype or perturbation. Genes can be ranked based on the affected interactions involving the genes to predict phenotypically relevant genes and/or perturbation targets.

Abstract: Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.

Abstract: The systems and methods provide a dynamic process for obtaining and managing informed consent documentation. In general, the dynamic informed consent process (DICP) makes use of an intermediary organization, e.g., a trusted intermediary, which: (a) provides ICFs which have been dynamically generated for a specified trial or medical procedure and based on particular state or federal requirements, if any; and (b) archives copies of signed ICFs. In certain preferred embodiments, there may also be a procedure to provide training materials, such as audio or video presentations, to be viewed by prospective participants. In certain preferred embodiments, the process also includes contacting subjects who have signed ICFs in the event that there is a change of circumstance which the subject may deem material to whether s/he would continue to consent, or whether the participant needs to provide a different type of consent to participate in particular event or trial.

Abstract: The systems and methods provide a dynamic process for obtaining and managing informed consent documentation. In general, the dynamic informed consent process (DICP) makes use of an intermediary organization, e.g., a trusted intermediary, which: (a) provides ICFs which have been dynamically generated for a specified trial or medical procedure and based on particular state or federal requirements, if any; and (b) archives copies of signed ICFs. In certain preferred embodiments, there may also be a procedure to provide training materials, such as audio or video presentations, to be viewed by prospective participants. In certain preferred embodiments, the process also includes contacting subjects who have signed ICFs in the event that there is a change of circumstance which the subject may deem material to whether s/he would continue to consent, or whether the participant needs to provide a different type of consent to participate in particular event or trial.

Abstract: The invention provides for isolated nucleic acid sequences of newly discovered micro RNAs that have been identified to exist in normal Human B cells and/or in tumor-related Human B cells, using an integrated bioinformatics method and pipeline described herein.

Abstract: A method (as well as system and signal-bearing medium) of processing biometric data, includes receiving biometric data including a data set P, selecting a secure hash function h, and for each data set P to be collected, computing h(P), destroying the data set P, and storing h(P) in a database, wherein data set P cannot be extracted from h(P).

Abstract: A method of processing semiotic data includes receiving semiotic data including at least one data set P, selecting a function h, and for at least one of each data set P to be collected, computing h(P), destroying data set P, and storing h(P) in a database, wherein data set P cannot be extracted from h(P). The method further includes selecting a private key/public key (K, k) once for all cases, one of destroying the private key K and sending the private key K to a trusted party, and choosing function h as the public encryption function corresponding to k.

Abstract: Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.

Abstract: Systems, methods, and apparatus for searching for a combination of compounds of therapeutic interest are provided. Cell-based assays are performed, each cell-based assay exposing a different sample of cells to a different compound in a plurality of compounds. From the cell-based assays, a subset of the tested compounds is selected. For each respective compound in the subset, a molecular abundance profile from cells exposed to the respective compound is measured. Targets of transcription factors and post-translational modulators of transcription factor activity are inferred from the molecular abundance profile data using information theoretic measures. This data is used to construct an interaction network. Variances in edges in the interaction network are used to determine the drug activity profile of compounds in the subset of compounds. The drug activity profiles are used to form a filter set of compound combinations from the subset of compounds.

Abstract: The systems and methods provide a dynamic process for obtaining and managing informed consent documentation. In general, the dynamic informed consent process (DICP) makes use of an intermediary organization, e.g., a trusted intermediary, which: (a) provides ICFs which have been dynamically generated for a specified trial or medical procedure and based on particular state or federal requirements, if any; and (b) archives copies of signed ICFs. In certain preferred embodiments, there may also be a procedure to provide training materials, such as audio or video presentations, to be viewed by prospective participants. In certain preferred embodiments, the process also includes contacting subjects who have signed ICFs in the event that there is a change of circumstance which the subject may deem material to whether s/he would continue to consent, or whether the participant needs to provide a different type of consent to participate in particular event or trial.

Abstract: A pattern discovery-based method for identifying genetic associations in mapping complex traits. In one embodiment, this invention describes the applicable study designs, the pattern discovery algorithm on phenotypic/genotypic data, and methods to evaluate statistical significance of identified patterns. Patterns identified through the proposed methods act as signatures or profiles that can be used to locate genes or genomic regions responsible for the traits of interests in the genome. This invention has been successfully applied to two independent datasets collected from actual genetic studies and has produced significant results.

Abstract: A system and method for maintaining an individual's privacy such that only he could authorize the use of his genotype data. The systems and methods described herein discuss the use of a system that may act as a personal electronic safe to allow any individual to store his or her medical records, including genotype data and associated tissue sample management data, on a personal computer or on a remote site linked to the Internet. The safe, in one practice, allows one's own medical information to be used solely for the purposes authorized by the individual, or an agent or guardian of that individual. This includes the management of the individual's own health records as well as the use of stored information for medical purposes. This safe's encryption mechanisms and certificates may allow only designated parties to access the data.

Abstract: Methods for indexing and storing genetic data include assigning a virtual private identity (VPI) to participants in a clinical study. The VPI may comprise a random number, or some other type of identifier that lacks any information that may be employed, in and of itself, to determine identity information. The system may then create an encrypted and secure database that contains the pairing between patient identity information and the assigned VPI. Information collected from the patient may be stored into data tables of a database where the VPI is employed as an index into the tables that store the patient data. The data stored in association with a respective VPI may be encrypted with an encryption key generated from the VPI. The encryption key may be stored in a Key Table and the Key Table may be encrypted with a Master Key.

Abstract: The systems and methods provide a dynamic process for obtaining and managing informed consent documentation. In general, the dynamic informed consent process (DICP) makes use of an intermediary organization, e.g., a trusted intermediary, which: (a) provides ICFs which have been dynamically generated for a specified trial or medical procedure and based on particular state or federal requirements, if any; and (b) archives copies of signed ICFs. In certain preferred embodiments, there may also be a procedure to provide training materials, such as audio or video presentations, to be viewed by prospective participants. In certain preferred embodiments, the process also includes contacting subjects who have signed ICFs in the event that there is a change of circumstance which the subject may deem material to whether s/he would continue to consent, or whether the participant needs to provide a different type of consent to participate in particular event or trial.

Abstract: Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.

Abstract: The invention provides automatic acquisition and recognition of complex visual shapes within images. During an acquisition phase, models are derived from interest points acquired from a target shape. The models are stored in and can be retrieved from a lookup table via high dimension indices. When an image is inputted, triplets of interest points in the image are used to compute local shape descriptors, which descrb the geometry of local shapes in the image. In turn, triplets of local shape descriptors are used to compute high dimension indices. These indices arm used for accessing the lookup table having the models The models are used for the automatic recognition of target shapes.