Models

Controlling testing volume for respiratory viruses using machine learning and text mining.

Viral testing for pediatric inpatients with respiratory symptoms is common, with considerable associated charges. In an attempt to reduce testing volumes, we studied whether data available at the time of admission could aid in identifying children …

Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors.

BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole-exome sequencing of drug-resistant BRAF(V600K) melanoma …

Adjusting for background mutation frequency biases improves the identification of cancer driver genes.

A common goal of tumor sequencing projects is finding genes whose mutations are selected for during tumor development. This is accomplished by choosing genes that have more non-synonymous mutations than expected from an estimated background mutation …

Modeling the neurovascular niche: unbiased transcriptome analysis of the murine subventricular zone in response to hypoxic insult.

Premature infants often experience chronic hypoxia, resulting in cognitive & motor neurodevelopmental handicaps. These sometimes devastating handicaps are thought to be caused by compromised neural precursor cell (NPC) repair/recovery resulting in …

Type II p21-activated kinases (PAKs) are regulated by an autoinhibitory pseudosubstrate.

The type II p21-activated kinases (PAKs) are key effectors of RHO-family GTPases involved in cell motility, survival, and proliferation. Using a structure-guided approach, we discovered that type II PAKs are regulated by an N-terminal autoinhibitory …

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma.

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like CtextgreaterT somatic mutations …

Finding and accessing diagrams in biomedical publications.

Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published …

Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.

A major challenge in human genetics is identifying the molecular basis of common heritable disorders. In contrast to rare single-gene diseases, multifactorial disorders are thought to arise from the combined effect of multiple gene variants, such …

Probabilistic inference of molecular networks from noisy data sources.

Information on molecular networks, such as networks of interacting proteins, comes from diverse sources that contain remarkable differences in distribution and quantity of errors. Here, we introduce a probabilistic model useful for predicting protein …

Probabilistic inference of molecular networks from noisy data sources.

Information on molecular networks, such as networks of interacting proteins, comes from diverse sources that contain remarkable differences in distribution and quantity of errors. Here, we introduce a probabilistic model useful for predicting protein …