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Random Forest has become a standard data analysis tool in computational biology. However, extensions to existing implementations are often necessary to handle the complexity of biological datasets and their associated research questions. The growing size of these datasets requires high performance implementations. We describe CloudForest, a Random Forest package written in Go, which is particularly well suited for large, heterogeneous, genetic and biomedical datasets. CloudForest includes several extensions, such as dealing with unbalanced classes and missing values. Its flexible design enables users to easily implement additional extensions. CloudForest achieves fast running times by effective use of the CPU cache, optimizing for different classes of features and efficiently multi-threading. https://github.com/ilyalab/CloudForest.

Horne, J. K., Sawada, K., Abe, K., Kreisberg, R. B., Barbee, D. H., and Sadayasu, K. 2009. Swimbladders under pressure: anatomical and acoustic responses by walleye pollock. – ICES Journal of Marine Science, 66: 1162–1168.Pressure influences echo intensities from fish through changes in swimbladder volumes and surface areas. Volume reduction is expected to correspond to Boyle’s law (volume α pressure−1), but the effects of deforming the dorsal-aspect surface area of the swimbladder on the target strength (TS) of a physoclist have not been quantified at geometric scattering frequencies. Dorsal and lateral radiographs of three juvenile walleye pollock (Theragra chalcogramma) in a pressure chamber were used to image swimbladders from ambient to a maximum of 4.9 × 105 Pa (i.e. 5 atm). Radiographs from an additional 16 0-group, 21 juvenile, and 28 adult fish were used to compare swimbladder sizes and shapes across life-history stages. The directional elliptical eccentricity, which describes the relative compression in dorsal and lateral planes, was formulated to define swimbladder shapes and their variation. As pressure increased, dorsal-aspect surface areas of the swimbladder decreased at a constant rate. Swimbladder-volume reductions were similar among individuals, but less than those predicted by Boyle’s law. Compression was greatest in the dorsal–ventral plane and asymmetric anterior to posterior. The Kirchhoff-ray mode backscatter model predicted that TS at 38 and 120 kHz decreased by ∼4 dB as pressure increased from ambient to 4.9 × 105 Pa. [ABSTRACT FROM PUBLISHER]

Breast cancer is one of the most common cancers with greater than 1,300,000 cases and 450,000 deaths each year worldwide. Clinically, this heterogeneous disease is categorized into three basic therapeutic [...], We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at >10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer.