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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.
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)
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)
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)
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)
BACKGROUND Recently, supervised learning methods have been exploited to reconstruct gene regulatory networks from gene expression data. The reconstruction of a network is modeled as a binary classification problem for each pair of genes. A statistical classifier is trained to recognize the relationships between the activation profiles of gene pairs. This(More)