Valentin Dinu

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In this paper we explore the use of biological knowledge to supplement statistical analysis in identifying genes associated with disease. It has been previously found that the 402H variant in complement factor H (CFH) is associated with risk for developing age related macular degeneration (AMD). By focusing on the single nucleotide polymorphisms (SNPs) in(More)
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)
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)
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)
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)
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)
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)
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)
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)