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BACKGROUND One of main aims of Molecular Biology is the gain of knowledge about how molecular components interact each other and to understand gene function regulations. Using microarray technology, it is possible to extract measurements of thousands of genes into a single analysis step having a picture of the cell gene expression. Several methods have been(More)
The brain tumor glioblastoma multiforme (GBM) is among the most lethal forms of human cancer. Here, we report that a small subset of GBMs (3.1%; 3 of 97 tumors examined) harbors oncogenic chromosomal translocations that fuse in-frame the tyrosine kinase coding domains of fibroblast growth factor receptor (FGFR) genes (FGFR1 or FGFR3) to the transforming(More)
Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular(More)
In recent years, techniques based on association rules discovery have been extensively used to determine change-coupling relations between artifacts that often changed together. Although association rules worked well in many cases, they fail to capture logical coupling relations between artifacts modified in subsequent change sets.
Change impact analysis aims at identifying software artifacts being affected by a change. In the past, this problem has been addressed by approaches relying on static, dynamic, and textual analysis. Recently, techniques based on historical analysis and association rules have been explored. This paper proposes a novel change impact analysis method based on(More)
The paper reports a novel approach for the problem of automatic gridding in Microarray images. Such problem often requires human intervention; therefore, the development of automated procedures is a fundamental issue for large-scale functional genomic experiments involving many microarray images. Our method uses a two-step process. First a regular(More)
Many indices have been proposed in literature for the comparison of two crisp data partitions, as resulting from two different classifications attempts, two different clustering solutions or the comparison of a predicted vs. a true labelling. Crisp partitions however cannot model ambiguity, vagueness or uncertainty in class definition and thus are not(More)
MOTIVATION Copy number alterations (CNAs) represent an important component of genetic variation and play a significant role in many human diseases. Development of array comparative genomic hybridization (aCGH) technology has made it possible to identify CNAs. Identification of recurrent CNAs represents the first fundamental step to provide a list of genomic(More)
A fundamental step of microarray image analysis is the detection of the grid structure for the accurate location of each spot, representing the state of a given gene in a particular experimental condition. This step is known as gridding and belongs to the class of deformable grid matching problems which are well known in literature. Most of the available(More)