Abstract: Systems and methods for predictive network modeling are disclosed. The systems and methods disclosed compute a top-down causal model and a bottom-up predictive model and utilize those models to determine the conditional independence among multiple variables and causality among equivalent variable structures. Before or during modeling, the data is passed through Markov Chain Monte Carlo sampling.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of analytical reactions in which protein synthesis is occurring. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance, inhibit, or otherwise affect such reactions including, but not limited to, affecting the reaction rate, processivity, fidelity, duration, and the like.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of analytical reactions in which protein synthesis is occurring. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance, inhibit, or otherwise affect such reactions including, but not limited to, affecting the reaction rate, processivity, fidelity, duration, and the like.

Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.

Abstract: Methods, computer program products and systems for identifying cellular constituents in a secondary tissue that serve as surrogate markers for a target gene expressed in a primary tissue of a species are provided. A classifier is constructed using cellular constituent abundances of cellular constituents in a first plurality of cellular constituents measured in the secondary tissue in a population. This population comprises a first and second subgroup. The classifier is based on a second plurality of cellular constituents that comprises all or a portion of the first plurality of cellular constituents. Abundance levels of each cellular constituent in the second plurality of cellular constituents varies between the first and second subgroup. All or portion of the population is classified into a plurality of subtypes using the classifier. Then, one or more cellular constituents that can discriminate members of the population between a first subtype and a second subtype in the plurality of subtypes are identified.

Abstract: A method for confirming the association of a query QTL or a query gene in the genome of a second species with a clinical trait T exhibited by the second species. A first QTL or a first gene in a first species that is linked to a trait T? is found. The trait T? is indicative of trait T. A region of the genome of the first species that comprises the first QTL or the first gene is mapped to a particular region of the genome of the second species. A query QTL or a query gene in the second species that is potentially associated with the trait T is found. The potential association of the query QTL or the query gene with the clinical trait T is confirmed when the query QTL or the query gene is in the particular region of the genome of the second species.

Abstract: Methods, computer program products, and systems are provided for associating a cellular constituent with a trait T exhibited by a species. A cellular constituent i that has at least one abundance quantitative trait locus (eQTL) coincident with a respective clinical quantitative trait locus (cQTL) for the trait of interest T is identified. For each eQTL, a determination is made as to whether (i) the genetic variation of the eQTL and (ii) the variation of the trait of interest T across the plurality of organisms are correlated conditional on an abundance pattern of the cellular constituent i across the plurality of organisms. When the genetic variation of (i) one of the eQTL and (ii) the variation of the trait of interest T across the plurality of organisms are uncorrelated conditional on the abundance pattern of the cellular constituent i, the cellular constituent i is considered causal for, and is therefore associated with, the trait of interest T.

Abstract: Methods for determining whether a molecule affects a disorder are provided. A cell from an organism is contacted with the molecule, or the molecule is expressed within the cell. A determination is made as to whether the RNA or protein expression in the cell of at least one open reading frame is changed relative to the expression of the reading frame in the absence of the molecule. Each such open reading frame is regulated by a promoter native to SEQ ID NOS: 5-9, 11-12, 14, 16, 18, 20-21, 23, 25, 27, 29, 31, 33 or homologs of the foregoing. A determination is made as to whether the molecule affects the disorder when the RNA or protein expression of the at least one reading frame is changed. Alternatively, a determination is made that the molecule does not affect the disorder when the RNA or protein expression of the at least one reading frame is unchanged.

Abstract: A method for identifying a quantitative trait loci for a complex trait that is exhibited by a plurality of organisms in a population. The population is divided into a plurality of sub-populations using a classification scheme. Depending on what is known about the population, either a supervised or unsupervised classification is used. The classification scheme is derived from a plurality of cellular constituent measurements obtained from each organism in the population. For each sub-population in the plurality of sub-populations, a quantitative genetic analysis is performed on the sub-population in order to identify one or more quantitative trait loci for the complex trait.

Abstract: A method for associating a gene G in the genome of a species with a clinical trait T exhibited by one or more organisms in a plurality of organisms of the species. An expression quantitative trait loci (eQTL) is identified for the gene G using a first quantitative trait loci (QTL) analysis. The first QTL analysis uses a plurality of expression statistics for gene G as a quantitative trait. Each expression statistic in the plurality of expression statistics represents an expression value for gene G in an organism in the plurality of organisms. A clinical quantitative trait loci (cQTL) that is linked to the clinical trait T is identified using a second QTL analysis. The second QTL analysis uses a plurality of phenotypic values as a quantitative trait. Each phenotypic value in the plurality of phenotypic values represents a phenotypic value for the clinical trait T in an organism in the plurality of organisms.