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Peculiar Genes Selection: A new features selection method to improve classification performances in imbalanced data sets

High-Throughput technologies provide genomic and trascriptomic data that are suitable for biomarker detection for classification purposes. However, the high dimension of the output of such technologies and the characteristics of the data sets analysed represent an issue for the classification task. Here we present a new feature selection method based on three steps to detect...

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

Biotecnologie Avanzate (CBA) , Largo Rosanna Benzi 10, I-16132 Genoa , Italy 1 Francesca Cordero, University of Torino, Italy Angelo Facchiano, CNR - Istituto di Scienze dell'Alimentazione , Avellino, Italy ... The fourteenth NETTAB workshop, NETTAB 2014, was held on October 15–17, 2014, in Torino, Italy. Workshop chairs were Francesca Cordero, University of Torino, Torsten Schwede, University of Basel, Basel

Biologic Data of Cynomolgus Monkeys Maintained under Laboratory Conditions

The cynomolgus monkey (Macaca fascicularis) is a well-known non-human primate species commonly used in non-clinical research. It is important to know basal clinical pathology parameters in order to have a reference for evaluating any potential treatment-induced effects, maintaining health status among animals and, if needed, evaluating correct substantiative therapies. In this...

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis

Background RNA-Seq provides remarkable power in the area of biomarkers discovery and disease characterization. Two crucial steps that affect RNA-Seq experiment results are Library Sample Preparation (LSP) and Bioinformatics Analysis (BA). This work describes an evaluation of the combined effect of LSP methods and BA tools in the detection of splice variants. Results Different...

A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression

Background Nowadays multidisciplinary approaches combining mathematical models with experimental assays are becoming relevant for the study of biological systems. Indeed, in cancer research multidisciplinary approaches are successfully used to understand the crucial aspects implicated in tumor growth. In particular, the Cancer Stem Cell (CSC) biology represents an area...

Chimera: a Bioconductor package for secondary analysis of fusion products

Summary: Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion and STAR. The core of Chimera is a fusion data structure...

A Mathematical-Biological Joint Effort to Investigate the Tumor-Initiating Ability of Cancer Stem Cells

The involvement of Cancer Stem Cells (CSCs) in tumor progression and tumor recurrence is one of the most studied subjects in current cancer research. The CSC hypothesis states that cancer cell populations are characterized by a hierarchical structure that affects cancer progression. Due to the complex dynamics involving CSCs and the other cancer cell subpopulations, a robust...

Differentially methylated microRNAs in prediagnostic samples of subjects who developed breast cancer in the European Prospective Investigation into Nutrition and Cancer (EPIC-Italy) cohort

) cohort Francesca Cordero Giulio Ferrero 1 Silvia Polidoro 0 Giovanni Fiorito 5 6 Gianluca Campanella 4 Carlotta Sacerdot 3 eAmalia Mattiell 8 o Giovanna Masala 7 Claudia Agnol i Graziella Frasc a

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

Background RNA-seq has the potential to discover genes created by chromosomal rearrangements. Fusion genes, also known as "chimeras", are formed by the breakage and re-joining of two different chromosomes. It is known that chimeras have been implicated in the development of cancer. Few publications in the past showed the presence of fusion events also in normal tissue, but with...

Multi-level model for the investigation of oncoantigen-driven vaccination effect

Background Cancer stem cell theory suggests that cancers are derived by a population of cells named Cancer Stem Cells (CSCs) that are involved in the growth and in the progression of tumors, and lead to a hierarchical structure characterized by differentiated cell population. This cell heterogeneity affects the choice of cancer therapies, since many current cancer treatments have...

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

Background Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. miRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. Although the...

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language

Remo Sanges 2 Francesca Cordero 1 Raffaele A. Calogero 0 Associate Editor: David Rocke 0 Department of Clinical and Biological Sciences, University of Torino , Regione Gonzole 10, 10043 Orbassano

Microarray data analysis and mining approaches

Francesca Cordero Marco Botta Raffaele A. Calogero Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics

Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

Background A new microarray platform (GeneChip® Exon 1.0 ST) has recently been developed by Affymetrix http://www.affymetrix.com. This microarray platform changes the conventional view of transcript analysis since it allows the evaluation of the expression level of a transcript by querying each exon component. The Exon 1.0 ST platform does however raise some issues regarding the...

Inflammation and breast cancer. Inflammatory component of mammary carcinogenesis in ErbB2 transgenic mice

This review addresses genes differentially expressed in the mammary gland transcriptome during the progression of mammary carcinogenesis in BALB/c mice that are transgenic for the rat neu (ERBB2, or HER-2/neu) oncogene (BALB-neuT664V-E mice). The Ingenuity knowledge database was used to characterize four functional association networks whose hub genes are directly linked to...

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international...

Apoptosis Induced by Piroxicam plus Cisplatin Combined Treatment Is Triggered by p21 in Mesothelioma

Background Malignant mesothelioma (MM) is a rare, highly aggressive tumor, associated to asbestos exposure. To date no chemotherapy regimen for MM has proven to be definitively curative, and new therapies for MM treatment need to be developed. We have previously shown in vivo that piroxicam/cisplatin combined treatment in MM, specifically acts on cell cycle regulation triggering...

Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer

Background In real-time RT quantitative PCR (qPCR) the accuracy of normalized data is highly dependent on the reliability of the reference genes (RGs). Failure to use an appropriate control gene for normalization of qPCR data may result in biased gene expression profiles, as well as low precision, so that only gross changes in expression level are declared statistically...

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention

Background Neoplastic transformation is a multistep process in which distinct gene products of specific cell regulatory pathways are involved at each stage. Identification of overexpressed genes provides an unprecedented opportunity to address the immune system against antigens typical of defined stages of neoplastic transformation. HER-2/neu/ERBB2 (Her2) oncogene is a prototype...