The identification of early and stage-specific biomarkers for Alzheimer's disease (AD) is critical, as the development disease-modification therapies may depend on discovery validation such markers. reliable depends new diagnostic algorithms to computationally exploit information in large biological datasets. To identify potential from mRNA expression profile data, we used Logic Mining method unbiased analysis a microarray dataset anti-NGF AD11 transgenic mouse model. gene brain regions was...

Alzheimer's Disease (AD) is a neurodegenaritive disorder characterized by progressive dementia, for which actually no cure known. An early detection of patients affected AD can be obtained analyzing their electroencephalography (EEG) signals, show reduction the complexity, perturbation synchrony, and slowing down rhythms. In this work, we apply procedure that exploits feature extraction classification techniques to EEG whose aim distinguish patient from ones Mild Cognitive Impairment (MCI)...

Abstract BLOG (Barcoding with LOG ic) is a diagnostic and character‐based DNA Barcode analysis method. Its aim to classify specimens species based on sequences supervised machine learning approach, using classification rules that compactly characterize in terms of locations key nucleotides. The 2.0 software, its fundamental modules, online/offline user interfaces recent improvements are described. These affect both methodology software design, lead the availability different releases website...

A digraph is upward planar if it has a drawing such that all the edges are monotone with respect to vertical direction. Testing planarity and constructing drawings important for displaying hierarchical network structures, which frequently arise in software engineering, project management, visual languages. In this paper we investigate testing of single-source digraphs; provide new combinatorial characterization give an optimal algorithm testing. Our tests whether n vertices O(n) sequential...

Abstract Background According to many field experts, specimens classification based on morphological keys needs be supported with automated techniques the analysis of DNA fragments. The most successful results in this area are those obtained from a particular fragment mitochondrial DNA, gene cytochrome c oxidase I (COI) (the "barcode"). Since 2004 Consortium for Barcode Life (CBOL) promotes collection barcode and development methods analyze several tasks, among which identification rules...

Increasing evidence points to a key role played by epithelial-mesenchymal transition (EMT) in cancer progression and drug resistance. In this study, we used wet silico approaches investigate whether EMT phenotypes are associated resistance target therapy non-small cell lung model system harboring activating mutations of the epidermal growth factor receptor. The combination different analysis techniques allowed us describe intermediate/hybrid complete respectively HCC827- HCC4006-derived...

Alzheimer's Disease (AD) and its preliminary stage - Mild Cognitive Impairment (MCI) are the most widespread neurodegenerative disorders, their investigation remains an open challenge. ElectroEncephalography (EEG) appears as a non-invasive repeatable technique to diagnose brain abnormalities. Despite technical advances, analysis of EEG spectra is usually carried out by experts that must manually perform laborious interpretations. Computational methods may lead quantitative these signals...

We describe a branch-and-bound algorithm for computing an orthogonal grid drawing with the minimum number of bends biconnected planar graph. Such is based on efficient enumeration schema embeddings graph and several new methods lower bounds bends. experiment such large test suite compare results state art. The experiments show feasibility approach also its limitations. Further, how minimizing has positive effects other quality measures effectiveness drawing. present method dealing vertices...

Systems Biology holds that complex cellular functions are generated as system-level properties endowed with robustness, each involving large networks of molecular determinants, generally identified by "omics" analyses. In this paper we describe four basic cancer cell properties, can easily be investigated in vitro: enhanced proliferation, evasion from apoptosis, genomic instability, inability to undergo oncogene-induced senescence. Focusing our analysis on a K-ras dependent transformation...

Abstract Motivation: Nowadays, knowledge extraction methods from Next Generation Sequencing data are highly requested. In this work, we focus on RNA-seq gene expression analysis and specifically case–control studies with rule-based supervised classification algorithms that build a model able to discriminate cases controls. State of the art compute single contains few features (genes). On contrary, our goal is elicit higher amount by computing many models, therefore identify most genes...

Recent advances in large datasets analysis offer new insights to modern biology allowing system-level investigation of pathologies. Here we describe a novel computational method that exploits the ever-growing amount "omics" data shed light on Alzheimer's and Parkinson's diseases. Neurological disorders exhibit huge number molecular alterations due complex interplay between genetic environmental factors. Classical reductionist approaches are focused few elements, providing narrow overview...

In this paper we give a model for dynamic graph algorithms, based on performing queries and updates an implicit representation of the drawing. We present algorithms drawing planar graphs that use variety standards (such as polyline, straight-line, orthogonal, grid, upward, visibility drawings), address aesthetic criteria are important readability, such display planarity, symmetry, reachability. Also, provide techniques especially tailored subclasses trees series-parallel digraphs. Our have...

Upward and dominance drawings of acyclic digraphs find important applications in the display hierarchical structures such as PERT diagrams, subroutine-call charts, is-a relationships. The combinatorial model underlying is often a series-parallel digraph. In this paper problem constructing upward investigated. We show that area requirement crucially depends on choice planar embedding. Also, we present efficient sequential parallel algorithms for drawing digraphs. Our results while have rather...

The wide spread of electronic data collection in medical environments leads to an exponential growth clinical extracted from heterogeneous patient samples. Collecting, managing, integrating and analyzing these are essential activities order shed light on diseases related therapies. major issues analysis the incompleteness (missing values), different adopted measure scales, integration disparate procedures. Therefore, main challenges managing data, discovering patients interactions, sources....

A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites generally based on geometry often combined with physico-chemical properties site since conformation, size chemical composition surface are all for interaction a specific ligand. Several matching strategies have been designed protein-ligand protein-protein interfaces but cannot be considered solved.In this paper we propose new method local structural alignment surfaces continuous global...

Microarray Logic Analyzer (MALA) is a clustering and classification software, particularly engineered for microarray gene expression analysis. The aims of MALA are to cluster the profiles in order reduce amount data be analyzed classify experiments. To fulfil this objective uses machine learning process based methodology, that relies on 1) Discretization, 2) Gene clustering, 3) Feature selection, 4) Formulas computation,5) Classification. In paper we describe software design, different...

Next Generation Sequencing (NGS) machines extract from a biological sample large number of short DNA fragments (reads). These reads are then used for several applications, e.g., sequence reconstruction, assembly, gene expression profiling, mutation analysis. We propose method to evaluate the similarity between reads. This does not rely on alignment and it is based distance frequencies their substrings fixed dimensions (k-mers). compare this alignment-free with measures derived two methods:...

Experimental co-expression data and protein-protein interaction networks are frequently used to analyze the interactions among genes or proteins. Recent studies have investigated methods integrate these two sources of information. We propose a new method obtained through DNA microarray analysis (MA) (PPI) network data, apply it Arabidopsis thaliana. The proposed identifies small subsets highly interacting Based on basis co-localization mRNA developmental expression, we show that groups...

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification species emerged as one the main applications DNA has addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- character-based methods.We propose a supervised method based on genetic algorithm identify...