Topological Structures in the Space of Treatment-Naïve Patients with Chronic Lymphocytic Leukemia.

Patients are complex and heterogeneous; clinical data sets are complicated by noise, missing data, and the presence of mixed-type data. Using such data sets requires understanding the high-dimensional "space of patients", composed of all measurements that define all relevant phenotypes. The current state-of-the-art merely defines spatial groupings of patients using cluster analyses.

Maximally informative next experiments for nonlinear models.

Mathematical modeling is a powerful tool in systems biology; we focus here on improving the reliability of model predictions by reducing the uncertainty in model dynamics through experimental design. Model-based experimental design is a process by which experiments can be systematically chosen to reduce dynamic uncertainty in a given model. We discuss the Maximally Informative Next Experiment (MINE) method for group-wise selection of points in an experimental design and present a convergence result for MINE with nonlinear models.

A Computational Study of the Effects of Syk Activity on B Cell Receptor Signaling Dynamics.

The kinase Syk is intricately involved in early signaling events in B cells and is required for proper response when antigens bind to B cell receptors (BCRs). Experiments using an analog-sensitive version of Syk (Syk-AQL) have better elucidated its role, but have not completely characterized its behavior. We present a computational model for BCR signaling, using dynamical systems, which incorporates both wild-type Syk and Syk-AQL.