Provided are systems and methods for rational selection of context sequences and sequence templates including a computer implemented method for obtaining a repository of attributes sets where the attributes sets are statistically associated with a sequence template representing two or more context sequences.

The invention describes how to estimate delta-Cq values from measured (raw-)Cq values gained from PCR measurements and how to calculate confidence intervals for them. This is realized by the following processing steps: A noise model, which might be constructed on some training PCR data, calculates the distribution of the true target material concentration of a single well for an observed measurement results. Said distribution is calculated for all types of measurement results including “Numeric” raw-Cq values as well as Cq being “Undetected”, which denotes that no fluorescence signal was detected during all cycles and thus corresponds to no or very few target molecules.

An information processing apparatus that selects appropriate features in polynomial time from the viewpoint of both the relevance and the redundancy of features to be selected. This information processing apparatus includes a relevance evaluator that evaluates relevance of each feature included in a set of features, a redundancy evaluator that evaluates redundancy between the features included in the set of features, and a selected feature determiner that determines selected features that optimize a submodular objective function defined using the relevance calculated by the relevance evaluator and the redundancy calculated by the redundancy evaluator.

A programmed computer functioning as a classifier operates on mass spectral data obtained from a blood-based patient sample to predict indolence or aggressiveness of prostate cancer. Methods of generating the classifier and conducting a test on a blood-based sample from a prostate cancer patient using the classifier are described.

Summarizing an aggregate contribution to a phenotypic characteristic for an individual includes: receiving information pertaining to the phenotypic characteristic of an individual; identifying, using one or more computer processors, a set of one or more markers associated with the phenotypic characteristic; obtaining a set of one or more marker measurements of the individual that corresponds to the set of one or more markers; obtaining a set of one or more statistical factors that measure associations between the set of one or more markers and the phenotypic characteristic; determining an aggregate contribution to the phenotypic characteristic of the individual based at least in part on the retrieved set of one or more statistical factors; and outputting a display characteristic to be displayed that is associated with the aggregate contribution to the phenotypic characteristic for the individual.

Systems and methods for discovery and characterization of neuroactive drugs are provided. In some aspects, a method for evaluating an effectiveness of a drug administered to a subject includes receiving neurophysiological data acquired from a subject under an administration of a drug, and analyzing the neurophysiological data to generate signatures indicative of brain states induced by the drug. The method also includes correlating the generated signatures with a database comprising information associated with a plurality of drug profiles, and determining, using the information, a molecular activity profile for the drug. The method further includes generating a report indicative of the effectiveness of the drug using the molecular activity profile.

Membrane protein expression can be predicted using statistical frameworks to provide an enhanced subset of sequences, out of an initial larger set of potentially expressing sequences, by using features derived from sequences and a model parameterized through a dataset of known expression levels. Also, membrane protein experimentation protocols can be designed using the statistical frameworks in concert known outcomes to identify which laboratory conditions are most likely to produce successful results.

Described are techniques for determining population structure from identity-by-descent (IBD) of individuals. The techniques may be used to predict that an individual belongs to zero, one or more of a number of communities identified within an IBD network. Additional data may be used to annotate the communities with birth location, surname, and ethnicity information. In turn, these data may be used to provide to an individual a prediction of membership to zero, one or more communities, accompanied by a summary of the information annotated to those communities.

The invention provides methods and formulations comprising a protein comprising solvent accessible amino acid residues susceptible to oxidation wherein N-acetyl tryptophan (NAT) is used to prevent oxidation of the protein. The invention also provides methods for making such formulations and methods of using such formulations. Methods to measure degradation of NAT in protein formulations are also provided.

A method of determining risk of diabetes is provided. In one embodiment, the method comprises: a) measuring the levels of a plurality of biomarkers in a blood samples obtained from a patient, wherein the plurality of biomarkers comprises at least five of the following biomarkers: glucose, adiponectin, CRP, IL2RA, ferritin, insulin and HbAIc; b) calculating a diabetes risk score for the patients using the levels and, optionally, patient age and/or gender. Results obtained from performing the assay on a reference population are similar or identical to those obtained using Formula I.