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We demonstrate a genome-wide method for the integration of many studies of gene expression of phenotypically similar disease processes, a method of multiplex meta-analysis. We use immune dysfunction as an example disease process.

We describe a novel, crowdsourcing method for generating a knowledge base of problem-medication pairs that takes advantage of manually asserted links between medications and problems.

Patient discharge summaries provide detailed medical information about hospitalized patients and are a rich resource of data for clinical record text mining. The textual expressions of this information are highly variable. In order to acquire a precise understanding of the patient, it is important to uncover the relationship between all instances in the text. In natural language processing (NLP), this task falls under the category of coreference resolution.

Pharmacogenomics evaluations of variability in drug metabolic processes may be useful for making individual drug response predictions. We present an approach to deriving 'phenotype scores' based on existing pharmacogenomics knowledge and a patient's genomics data. Pharmacogenomics plays an important role in the bioactivation of tamoxifen, a prodrug administered to patients for breast cancer treatment. Tamoxifen is therefore considered a model for many drugs requiring bioactivation. We investigate whether this knowledge-based [...]

To evaluate non-response rates to follow-up online surveys using a prospective cohort of parents raising at least one child with an autism spectrum disorder. A secondary objective was to investigate predictors of non-response over time.

Because breast tissue composition partially predicts breast cancer risk, classification of mammography reports by breast tissue composition is important from both a scientific and clinical perspective. A method is presented for using the unstructured text of mammography reports to classify them into BI-RADS breast tissue composition categories. An algorithm that uses regular expressions to automatically determine BI-RADS breast tissue composition classes for unstructured mammography reports was developed. The algorithm assigns [...]

Thousands of complex-disease single-nucleotide polymorphisms (SNPs) have been discovered in genome-wide association studies (GWAS). However, these intragenic SNPs have not been collectively mined to unveil the genetic architecture between complex clinical traits. The authors hypothesize that biological annotations of host genes of trait-associated SNPs may reveal the biomolecular modularity across complex-disease traits and offer insights for drug repositioning.

The performance of a classification system depends on the context in which it will be used, including the prevalence of the classes and the relative costs of different types of errors. Metrics such as accuracy are limited to the context in which the experiment was originally carried out, and metrics such as sensitivity, specificity, and receiver operating characteristic area--while independent of prevalence--do not provide a clear picture of the performance [...]

Computerized drug alerts for psychotropic drugs are expected to reduce fall-related injuries in older adults. However, physicians over-ride most alerts because they believe the benefit of the drugs exceeds the risk.

Accurate clinical problem lists are critical for patient care, clinical decision support, population reporting, quality improvement, and research. However, problem lists are often incomplete or out of date.