Categorical meta-analysis of Osteopontin as a clinical cancer marker.

Although extensive literature exists on cancer biomarkers few have found entry into clinical use. In particular, the cancer metastasis gene Osteopontin has been investigated extensively but it has not yet been applied to routine diagnostics. Here, we conduct a meta-analysis of data from the published literature and from RNA microarrays deposited in Oncomine.

Ab initio stochastic optimization of conformational and many-body degrees of freedom.

Moderate to large size molecules in solution have complex energy surfaces due to intramolecular (conformational) and intermolecular (many-body) interactions. The first principles Monte Carlo (FPMC) method, previously shown to effectively locate minimum-energy structures for systems with only many-body complexity, has been extended to address conformational flexibility by adding three new Monte Carlo move types. The primary advantage of the FPMC method is the ability to efficiently locate minimum energy structures of molecules with conformational flexibility in the presence of explicit solvent molecules using highly accurate quantum chemical calculations.

Many-body optimization using an ab initio monte carlo method.

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems.