Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

Dynamics of strongly degenerate electron-hole plasmas and excitons in single InP nanowires.

Low-temperature time-resolved photoluminescence spectroscopy is used to probe the dynamics of photoexcited carriers in single InP nanowires. At early times after pulsed excitation, the photoluminescence line shape displays a characteristic broadening, consistent with emission from a degenerate, high-density electron-hole plasma. As the electron-hole plasma cools and the carrier density decreases, the emission rapidly converges toward a relatively narrow band consistent with free exciton emission from the InP nanowire. The free excitons in these single InP nanowires exhibit recombination lifetimes closely approaching that measured in a high-quality epilayer, suggesting that in these InP nanowires, electrons and holes are relatively insensitive to surface states. This results in higher quantum efficiencies than other single-nanowire systems as well as significant state-filling and band gap renormalization, which is observed at high electron-hole carrier densities.