DNA copy number profiles correlate with outcome in colorectal cancer patients treated with fluoropyrimidine/antifolate-based regimens.

For decades 5-fluorouracil (5-FU) has remained the treatment of choice in the adjuvant and palliative setting of colorectal cancer (CRC). The combinations of 5-FU or its oral prodrug capecitabine with irinotecan/oxaliplatin and the novel agents bevacizumab/cetuximab increased responses. However, the overall prognosis is poor, and predictive biomarkers of cytotoxic drugs activity are missing.

CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.

Summary: CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).

Accurate confidence aware clustering of array CGH tumor profiles.

Motivation: Chromosomal aberrations tend to be characteristic for given (sub)types of cancer. Such aberrations can be detected with array comparative genomic hybridization (aCGH). Clustering aCGH tumor profiles aids in identifying chromosomal regions of interest and provides useful diagnostic information on the cancer type.

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations.

Background: Array comparative genomic hybridization (aCGH) is a popular technique for detection of genomic copy number imbalances. These play a critical role in the onset of various types of cancer. In the analysis of aCGH data, normalization is deemed a critical pre-processing step.

Modeling the effects of binary mixtures on survival in time.

In general, effects of mixtures are difficult to describe, and most of the models in use are descriptive in nature and lack a strong mechanistic basis. The aim of this experiment was to develop a process-based model for the interpretation of mixture toxicity measurements, with effects of binary mixtures on survival as a starting point. The survival of Folsomia candida was monitored daily for 21 d during the exposure to six binary mixtures of cadmium, copper, lead, and zinc in a loamy sand soil.