Robust identification of target genes and outliers in triple-negative breast cancer data.

Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal.

Comparing Reverse Complementary Genomic Words Based on Their Distance Distributions and Frequencies.

In this work, we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks.

Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.

The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple.

On the calculation of a robust S-estimator of a covariance matrix.

An S-estimator of multivariate location and scale minimizes the determinant of the covariance matrix, subject to a constraint on the magnitudes of the corresponding Mahalanobis distances. The relationship between S-estimators and w-estimators of multivariate location and scale can be used to calculate robust estimates of covariance matrices. Elemental subsets of observations are generated to derive initial estimates of means and covariances, and the w-estimator equations are then iterated until convergence to obtain the S-estimates.

The two-factorial symptom structure of post-traumatic stress disorder: depression-avoidance and arousal-anxiety.

Unlabelled: The first part of this study showed that the DSM-III-R symptom structure of post-traumatic stress disorder (PTSD), i.e. criteria B (reexperience), C (avoidance-numbing), and D (arousal), and, consequently the diagnosis of PTSD, could not be validated in fire and car-accident victims.