Valentin Dinu

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PURPOSE To introduce the goals of EAV database modeling, to describe the situations where entity-attribute-value (EAV) modeling is a useful alternative to conventional relational methods of database modeling, and to describe the fine points of implementation in production systems. METHODS We analyze the following circumstances: (1) data are sparse and(More)
Entity-Attribute-Value (EAV) data, as present in repositories of clinical patient data, must be transformed (pivoted) into one-column-per-parameter format before it can be used by a variety of analytical programs. Pivoting approaches have not been described in depth in the literature, and existing descriptions are dated. We describe and benchmark three(More)
Genome-wide association studies can help identify multi-gene contributions to disease. As the number of high-density genomic markers tested increases, however, so does the number of loci associated with disease by chance. Performing a brute-force test for the interaction of four or more high-density genomic loci is unfeasible given the current computational(More)
The discovery of genetic associations is an important factor in the understanding of human illness to derive disease pathways. Identifying multiple interacting genetic mutations associated with disease remains challenging in studying the etiology of complex diseases. And although recently new single nucleotide polymorphisms (SNPs) at genes implicated in(More)
BACKGROUND Immunosignaturing is a new peptide microarray based technology for profiling of humoral immune responses. Despite new challenges, immunosignaturing gives us the opportunity to explore new and fundamentally different research questions. In addition to classifying samples based on disease status, the complex patterns and latent factors underlying(More)
From microarrays and next generation sequencing to clinical records, the amount of biomedical data is growing at an exponential rate. Handling and analyzing these large amounts of data demands that computing power and methodologies keep pace. The goal of this paper is to illustrate how high performance computing methods in SAS can be easily implemented(More)
Glioblastoma is the most aggressive primary central nervous tumor and carries a very poor prognosis. Invasion precludes effective treatment and virtually assures tumor recurrence. In the current study, we applied analytical and bioinformatics approaches to identify a set of microRNAs (miRs) from several different human glioblastoma cell lines that exhibit(More)
MOTIVATION The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly(More)
MOTIVATION Modern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization. RESULTS We have created the AMASS database, which maps 1D sequence annotation databases to 3D(More)
Centralized silos of genomic data are architecturally easier to initially design, develop and deploy than distributed models. However, as interoperability pains in EHR/EMR, HIE and other collaboration-centric life sciences domains have taught us, the core challenge of networking genomics systems is not in the construction of individual silos, but the(More)